Improve exporting for mcq-cli / local

tzok · Oct 16, 2018 · 647fb8a · 647fb8a
1 parent 0e38d8e
commit 647fb8a
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Showing 7 changed files with 267 additions and 101 deletions.
diff --git a/mcq-cli/colorbars.R b/mcq-cli/colorbars.R
@@ -0,0 +1,29 @@
+#! /usr/bin/env Rscript
+library(lattice)
+library(RColorBrewer)
+
+args = commandArgs(trailingOnly=TRUE)
+if (length(args)==0) {
+  stop("At least one argument must be supplied (input file)\n")
+}
+
+c <- read.csv(file=args[1], header=FALSE)
+residues <- c[1,]
+dotbrackets <- c[2,]
+c <- c[3:nrow(c),1:ncol(c)]
+models <- c[,1]
+c <- c[1:nrow(c),2:ncol(c)]
+c <- t(c)
+m <- as.matrix(c)
+mode(m) <- 'numeric'
+
+residues <- unlist(residues)
+dotbrackets <- unlist(dotbrackets)
+models <- unlist(models)
+
+m <- ifelse(m > 60, 60, m)
+p <- colorRampPalette(brewer.pal(9, 'YlOrRd'))
+
+pdf('colorbars.pdf', width=11)
+levelplot(m, col.regions=p, xlab='', ylab='', scales=list(x=list(at=0:nrow(m), labels=dotbrackets), y=list(at=1:ncol(m), labels=models)))
+dev.off()
diff --git a/mcq-cli/src/main/java/pl/poznan/put/mcq/cli/Global.java b/mcq-cli/src/main/java/pl/poznan/put/mcq/cli/Global.java
@@ -27,7 +27,7 @@
 import pl.poznan.put.interfaces.Exportable;
 import pl.poznan.put.interfaces.Visualizable;
 import pl.poznan.put.matching.StructureSelection;
-import pl.poznan.put.rna.torsion.RNATorsionAngleType;
+import pl.poznan.put.torsion.MasterTorsionAngleType;
 import pl.poznan.put.types.DistanceMatrix;
 import pl.poznan.put.utility.ExecHelper;
 import pl.poznan.put.utility.svg.Format;
@@ -50,7 +50,7 @@ public static void main(final String[] args) throws ParseException {
     final CommandLineParser parser = new DefaultParser();
     final CommandLine commandLine = parser.parse(Global.OPTIONS, args);
     final List<StructureSelection> models = Helper.selectModels(commandLine);
-    final List<RNATorsionAngleType> angles = Helper.parseAngles(commandLine);
+    final List<MasterTorsionAngleType> angles = Helper.parseAngles(commandLine);
     final MCQ mcq = new MCQ(angles);
 
     final long size = models.size();
@@ -94,7 +94,7 @@ public void complete(final GlobalMatrix matrix) {
         Listener.exportResults(directory, matrix);
         Listener.exportDrawing(directory, partitionalClustering);
         Listener.exportClustering(directory, partitionalClustering);
-        System.out.println("Results available in file: " + directory);
+        System.out.println("Results available in: " + directory);
       } catch (final IOException e) {
         System.err.println("Failed to store results");
         e.printStackTrace(System.err);

diff --git a/mcq-cli/src/main/java/pl/poznan/put/mcq/cli/Helper.java b/mcq-cli/src/main/java/pl/poznan/put/mcq/cli/Helper.java
@@ -27,6 +27,7 @@
 import pl.poznan.put.pdb.analysis.PdbModel;
 import pl.poznan.put.rna.torsion.RNATorsionAngleType;
 import pl.poznan.put.structure.tertiary.StructureManager;
+import pl.poznan.put.torsion.MasterTorsionAngleType;
 
 @Slf4j
 public final class Helper {
@@ -186,9 +187,9 @@ private static String modelName(final File modelFile, final PdbModel model) {
     return StringUtils.isNotBlank(idCode) ? idCode : modelFile.getName();
   }
 
-  public static List<RNATorsionAngleType> parseAngles(final CommandLine commandLine) {
+  public static List<MasterTorsionAngleType> parseAngles(final CommandLine commandLine) {
     if (commandLine.hasOption(Helper.OPTION_ANGLES.getOpt())) {
-      final List<RNATorsionAngleType> angles = new ArrayList<>();
+      final List<MasterTorsionAngleType> angles = new ArrayList<>();
 
       for (final String angleName : commandLine.getOptionValues(Helper.OPTION_ANGLES.getOpt())) {
         angles.add(RNATorsionAngleType.valueOf(angleName));
@@ -197,9 +198,8 @@ public static List<RNATorsionAngleType> parseAngles(final CommandLine commandLin
       return angles;
     }
 
-    return Arrays.stream(RNATorsionAngleType.mainAngles())
-        .map(t -> (RNATorsionAngleType) t)
-        .collect(Collectors.toList());
+    // do not use Arrays.asList because it creates unmodifiable list and this one is modified further
+    return Arrays.stream(RNATorsionAngleType.mainAngles()).collect(Collectors.toList());
   }
 
   public static boolean isHelpRequested(final String[] args) throws ParseException {

diff --git a/mcq-cli/src/main/java/pl/poznan/put/mcq/cli/Local.java b/mcq-cli/src/main/java/pl/poznan/put/mcq/cli/Local.java
@@ -5,8 +5,9 @@
 import java.io.IOException;
 import java.io.OutputStream;
 import java.util.List;
-import javax.swing.table.DefaultTableModel;
-import javax.swing.table.TableModel;
+import java.util.stream.Collectors;
+import java.util.stream.IntStream;
+import java.util.stream.Stream;
 import org.apache.commons.cli.CommandLine;
 import org.apache.commons.cli.CommandLineParser;
 import org.apache.commons.cli.DefaultParser;
@@ -15,105 +16,152 @@
 import org.apache.commons.io.FileUtils;
 import org.w3c.dom.svg.SVGDocument;
 import pl.poznan.put.comparison.MCQ;
-import pl.poznan.put.comparison.local.MCQLocalResult;
+import pl.poznan.put.comparison.exception.IncomparableStructuresException;
+import pl.poznan.put.comparison.local.LocalComparator;
+import pl.poznan.put.comparison.local.ModelsComparisonResult;
+import pl.poznan.put.comparison.local.SelectedAngle;
 import pl.poznan.put.comparison.mapping.AngleDeltaMapper;
+import pl.poznan.put.comparison.mapping.ComparisonMapper;
+import pl.poznan.put.comparison.mapping.RangeDifferenceMapper;
+import pl.poznan.put.interfaces.Exportable;
 import pl.poznan.put.matching.FragmentMatch;
-import pl.poznan.put.matching.ResidueComparison;
-import pl.poznan.put.matching.SelectionMatch;
 import pl.poznan.put.matching.StructureSelection;
-import pl.poznan.put.pdb.PdbParsingException;
+import pl.poznan.put.pdb.analysis.PdbCompactFragment;
 import pl.poznan.put.rna.torsion.RNATorsionAngleType;
 import pl.poznan.put.svg.SecondaryStructureVisualizer;
-import pl.poznan.put.torsion.TorsionAngleDelta;
+import pl.poznan.put.torsion.MasterTorsionAngleType;
 import pl.poznan.put.utility.ExecHelper;
-import pl.poznan.put.utility.TabularExporter;
 import pl.poznan.put.utility.svg.Format;
 import pl.poznan.put.utility.svg.SVGHelper;
 
-@SuppressWarnings({"UseOfSystemOutOrSystemErr", "MethodWithTooExceptionsDeclared"})
+@SuppressWarnings({"CallToSystemExit", "UseOfSystemOutOrSystemErr"})
 public final class Local {
   private static final Options OPTIONS =
       new Options()
           .addOption(Helper.OPTION_TARGET)
-          .addOption(Helper.OPTION_MODEL)
+          .addOption(Helper.OPTION_MODELS)
           .addOption(Helper.OPTION_SELECTION_TARGET)
           .addOption(Helper.OPTION_SELECTION_MODEL)
           .addOption(Helper.OPTION_ANGLES);
 
   public static void main(final String[] args)
-      throws ParseException, IOException, PdbParsingException {
+      throws ParseException, IncomparableStructuresException {
     if (Helper.isHelpRequested(args)) {
       Helper.printHelp("local", Local.OPTIONS);
       return;
     }
 
     final CommandLineParser parser = new DefaultParser();
     final CommandLine commandLine = parser.parse(Local.OPTIONS, args);
-    final StructureSelection s1 = Helper.selectTarget(commandLine);
-    final StructureSelection s2 = Helper.selectModel(commandLine);
+    final StructureSelection target = Helper.selectTarget(commandLine);
+    final List<StructureSelection> models = Helper.selectModels(commandLine);
+
+    // check for gaps
+    Stream.concat(Stream.of(target), models.stream())
+        .parallel()
+        .filter(selection -> selection.getCompactFragments().size() != 1)
+        .peek(
+            selection ->
+                System.err.println("The following structure contains gaps: " + selection.getName()))
+        .findAny()
+        .ifPresent(selection -> System.exit(1));
+
+    // check for size
+    final int expectedSize = target.getResidues().size();
+    models
+        .parallelStream()
+        .filter(selection -> selection.getResidues().size() != expectedSize)
+        .peek(
+            selection ->
+                System.err.printf(
+                    "The following structure has different size (%d) than the target (%d)%n",
+                    selection.getResidues().size(), expectedSize))
+        .findAny()
+        .ifPresent(selection -> System.exit(1));
+
+    final PdbCompactFragment targetFragment = target.getCompactFragments().get(0);
+    final List<PdbCompactFragment> modelFragments =
+        models
+            .stream()
+            .map(selection -> selection.getCompactFragments().get(0))
+            .collect(Collectors.toList());
+
+    // rename
+    targetFragment.setName(target.getName());
+    IntStream.range(0, models.size())
+        .forEach(i -> modelFragments.get(i).setName(models.get(i).getName()));
+
+    final List<MasterTorsionAngleType> angleTypes = Helper.parseAngles(commandLine);
+    angleTypes.add(RNATorsionAngleType.getAverageOverMainAngles());
+
+    final LocalComparator mcq = new MCQ(angleTypes);
+    final ModelsComparisonResult comparisonResult =
+        mcq.compareModels(targetFragment, modelFragments);
+    final File directory = Local.exportResults(comparisonResult);
+    System.out.println("Results are available in: " + directory);
+  }
 
-    final List<RNATorsionAngleType> angleTypes = Helper.parseAngles(commandLine);
-    final MCQ mcq = new MCQ(angleTypes);
-    final MCQLocalResult result = (MCQLocalResult) mcq.comparePair(s1, s2);
+  private static File exportResults(final ModelsComparisonResult comparisonResult) {
+    try {
+      final File directory = ExecHelper.createRandomDirectory();
+      Local.exportTable(directory, comparisonResult);
+      comparisonResult
+          .getFragmentMatches()
+          .parallelStream()
+          .forEach(fragmentMatch -> Local.exportModelResults(directory, fragmentMatch));
+      return directory;
+    } catch (final IOException e) {
+      throw new IllegalArgumentException("Failed to export results", e);
+    }
+  }
 
-    final File directory = ExecHelper.createRandomDirectory();
-    final File csvFile = new File(directory, "results.csv");
+  private static void exportModelResults(
+      final File parentDirectory, final FragmentMatch fragmentMatch) {
+    try {
+      final String name = fragmentMatch.getModelFragment().getName();
+      final File directory = new File(parentDirectory, name);
+      FileUtils.forceMkdir(directory);
+
+      Local.exportSecondaryStructureImage(
+          fragmentMatch, directory, "delta.svg", AngleDeltaMapper.getInstance());
+      Local.exportSecondaryStructureImage(
+          fragmentMatch, directory, "range.svg", RangeDifferenceMapper.getInstance());
+      Local.exportDifferences(fragmentMatch, directory);
+    } catch (final IOException e) {
+      throw new IllegalArgumentException("Failed to export results", e);
+    }
+  }
 
-    try (final OutputStream stream = new FileOutputStream(csvFile)) {
-      result.export(stream);
+  private static void exportDifferences(final Exportable fragmentMatch, final File directory)
+      throws IOException {
+    final File file = new File(directory, "differences.csv");
+    try (final OutputStream stream = new FileOutputStream(file)) {
+      fragmentMatch.export(stream);
     }
+  }
 
-    final SelectionMatch selectionMatch = result.getSelectionMatch();
-    final List<FragmentMatch> fragmentMatches = selectionMatch.getFragmentMatches();
-
-    for (int i = 0, fragmentMatchesSize = fragmentMatches.size(); i < fragmentMatchesSize; i++) {
-      final FragmentMatch fragmentMatch = fragmentMatches.get(i);
-
-      // FIXME: creating charts is now a domain of mcq4structures
-      //      final File chartFile = new File(directory, String.format("chart-%02d.svg", i));
-      //      final SVGDocument chartSvg = fragmentMatch.visualize(1052, 744);
-      //      FileUtils.writeByteArrayToFile(chartFile, SVGHelper.export(chartSvg, Format.SVG));
-
-      final File secondaryFile = new File(directory, String.format("secondary-%02d.svg", i));
-      final SVGDocument secondarySvg =
-          SecondaryStructureVisualizer.visualize(fragmentMatch, AngleDeltaMapper.getInstance());
-      FileUtils.writeByteArrayToFile(secondaryFile, SVGHelper.export(secondarySvg, Format.SVG));
-
-      for (final RNATorsionAngleType angleType : angleTypes) {
-        final File angleRangesFile =
-            new File(directory, String.format("angle-%s-%02d.csv", angleType.getExportName(), i));
-        final List<ResidueComparison> residueComparisons = fragmentMatch.getResidueComparisons();
-        final Object[][] data = new Object[fragmentMatch.getResidueCount()][];
-
-        for (int j = 0, size = residueComparisons.size(); j < size; j++) {
-          final ResidueComparison residueComparison = residueComparisons.get(j);
-          final TorsionAngleDelta angleDelta = residueComparison.getAngleDelta(angleType);
-
-          data[j] = new Object[8];
-          data[j][0] = residueComparison.getTarget();
-          data[j][1] = angleDelta.getTarget().getDegrees();
-          data[j][2] = angleType.getRange(angleDelta.getTarget()).getDisplayName();
-          data[j][3] = residueComparison.getModel();
-          data[j][4] = angleDelta.getModel().getDegrees();
-          data[j][5] = angleType.getRange(angleDelta.getModel()).getDisplayName();
-          data[j][6] = angleDelta.getDelta().getDegrees();
-          data[j][7] = angleDelta.getRangeDifference();
-        }
-
-        final String[] columns = {
-          "Target Residue", "Target Value", "Target Range",
-          "Model Residue", "Model Value", "Model Range",
-          "Value Difference", "Range Difference"
-        };
-        final TableModel tableModel = new DefaultTableModel(data, columns);
-
-        try (final OutputStream stream = new FileOutputStream(angleRangesFile)) {
-          TabularExporter.export(tableModel, stream);
-        }
-      }
+  private static void exportSecondaryStructureImage(
+      final FragmentMatch fragmentMatch,
+      final File directory,
+      final String filename,
+      final ComparisonMapper deltaMapper)
+      throws IOException {
+    final SVGDocument svg = SecondaryStructureVisualizer.visualize(fragmentMatch, deltaMapper);
+    final File file = new File(directory, filename);
+
+    try (final OutputStream stream = new FileOutputStream(file)) {
+      stream.write(SVGHelper.export(svg, Format.SVG));
     }
+  }
 
-    System.out.println("Results are available in: " + directory);
+  private static void exportTable(
+      final File directory, final ModelsComparisonResult comparisonResult) throws IOException {
+    final File file = new File(directory, "table.csv");
+    try (final OutputStream stream = new FileOutputStream(file)) {
+      final SelectedAngle selectedAngle =
+          comparisonResult.selectAngle(RNATorsionAngleType.getAverageOverMainAngles());
+      selectedAngle.export(stream);
+    }
   }
 
   private Local() {

diff --git a/mcq-core/src/main/java/pl/poznan/put/comparison/MCQ.java b/mcq-core/src/main/java/pl/poznan/put/comparison/MCQ.java
@@ -180,7 +180,7 @@ public final ModelsComparisonResult compareModels(
       if ((fragment.getMoleculeType() != target.getMoleculeType())
           || (fragment.getResidues().size() != target.getResidues().size())) {
         throw new IncomparableStructuresException(
-            "All models must be of the same type and size as the " + "reference structure");
+            "All models must be of the same type and size as the reference structure");
       }
     }