Merge branch 'release/1.6'

README.md

@@ -3,6 +3,15 @@
 Mean of Circular Quantities (MCQ) is a dissimilarity measure useful in comparison of 3D protein and/or RNA structures. It calculates an average difference between corresponding torsion angle values (rotations around bonds). More information can be found in:
 > Zok, T., Popenda, M., & Szachniuk, M. (2014). MCQ4Structures to compute similarity of molecule structures. Central European Journal of Operations Research, 22(3), 457–473. https://doi.org/10.1007/s10100-013-0296-5
 
+## Installation
+
+```sh
+git clone https://github.com/RNA-Puzzles/mcq-parent
+cd mcq-parent
+git submodule update --init
+mvn install
+```
+
 ## Contents
 
 This project consists of a few subprojets:
@@ -21,4 +30,4 @@ This project consists of a few subprojets:
 
 - Use `pl.poznan.put.clustering.hierarchical.Clusterer` to construct dendrograms from a distance matrix (with `COMPLETE`, `SINGLE` or `AVERAGE` linkage option)
 - Use `pl.poznan.put.clustering.partitional.KMedoids` to perform partitional clustering based on distance matrix
-- Use `pl.poznan.put.clustering.partitional.KScanner#parallelScan` to find optimum number of clusters with respect to silhouette score
+- Use `pl.poznan.put.clustering.partitional.KScanner#parallelScan` to find optimum number of clusters with respect to silhouette score

pom.xml

@@ -4,7 +4,7 @@
 
   <groupId>pl.poznan.put</groupId>
   <artifactId>mcq-parent</artifactId>
-  <version>1.5.1</version>
+  <version>1.6</version>
   <packaging>pom</packaging>
 
   <modules>
@@ -21,7 +21,6 @@
   <properties>
     <batik.version>1.10</batik.version>
     <biojava.version>5.2.0</biojava.version>
-    <jackson.version>2.9.8</jackson.version>
     <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
     <slf4j.version>1.7.25</slf4j.version>
   </properties>
@@ -34,12 +33,6 @@
         <version>1.2.3</version>
       </dependency>
 
-      <dependency>
-        <groupId>com.fasterxml.jackson.core</groupId>
-        <artifactId>jackson-databind</artifactId>
-        <version>${jackson.version}</version>
-      </dependency>
-
       <dependency>
         <groupId>commons-cli</groupId>
         <artifactId>commons-cli</artifactId>
@@ -133,6 +126,10 @@
             <artifactId>log4j-slf4j-impl</artifactId>
             <groupId>org.apache.logging.log4j</groupId>
           </exclusion>
+          <exclusion>
+            <artifactId>jackson-databind</artifactId>
+            <groupId>com.fasterxml.jackson.core</groupId>
+          </exclusion>
         </exclusions>
       </dependency>
 
@@ -193,7 +190,7 @@
       <dependency>
         <groupId>pl.poznan.put</groupId>
         <artifactId>BioCommons</artifactId>
-        <version>2.2.1</version>
+        <version>2.3.2</version>
       </dependency>
 
       <dependency>
@@ -205,7 +202,7 @@
       <dependency>
         <groupId>pl.poznan.put</groupId>
         <artifactId>TzokCommons</artifactId>
-        <version>1.5.1</version>
+        <version>1.6</version>
       </dependency>
 
       <dependency>