Finish tag 0.10

.gitignore

@@ -18,4 +18,5 @@ met4j-core/src/main/java/fr/inra/toulouse/metexplore/met4j_core/Test\.java
 /met4j-toolbox/src/main/java/fr/inrae/toulouse/metexplore/met4j_toolbox/sandbox/
 
 
-dependency-reduced-pom.xml
\ No newline at end of file
+dependency-reduced-pom.xml
+/met4j.sif

.gitlab-ci.yml

-image: maven:3.6-adoptopenjdk-14
+
+
+stages:
+  - build
+  - test
+  - deploy
+  - build-containers
+
+.template_docker:
+  stage: build-containers
+  image: docker:latest
+  services:
+    - docker:dind
 
 variables:
   MAVEN_CLI_OPTS: "-s .m2/settings.xml --batch-mode"
@@ -9,19 +21,20 @@ cache:
     - .m2/repository/
 
 build:
+  image: maven:3.6-adoptopenjdk-14
   stage: build
   script:
     - mvn compile
 
 test:
+  image: maven:3.6-adoptopenjdk-14
   stage: test
   script:
     - mvn clean test
     - cat coverage/target/site/jacoco-aggregate/index.html | grep -o '<tfoot>.*</tfoot>'
 
-
-
 deploySnapshot:
+  image: maven:3.6-adoptopenjdk-14
   stage: deploy
   script:
     - mvn $MAVEN_CLI_OPTS deploy -Dmaven.test.skip=true
@@ -29,6 +42,7 @@ deploySnapshot:
     - develop
 
 deployCentral:
+  image: maven:3.6-adoptopenjdk-14
   stage: deploy
   before_script:
     - 'which ssh-agent || ( apt-get update -qy && apt-get install openssh-client -qqy )'
@@ -49,3 +63,47 @@ deployCentral:
     - mvn $MAVEN_CLI_OPTS release:perform -Darguments=-Dgpg.passphrase=${GPG_PASSPHRASE} -DlocalCheckout=true
   only:
     - master
+
+buildSingularity:
+  stage: build-containers
+  image:
+    name: quay.io/singularity/singularity:v3.4.0
+    entrypoint: [ "" ]
+  script:
+    - singularity build met4j-toolbox.sif met4j.singularity
+    - singularity push --docker-username "${CI_REGISTRY_USER}" --docker-password "${CI_REGISTRY_PASSWORD}" met4j-toolbox.sif oras://"$CI_REGISTRY_IMAGE"/met4j-singularity:"$CI_COMMIT_TAG"
+  rules:
+    - if: $CI_COMMIT_BRANCH == $CI_DEFAULT_BRANCH
+      when: manual
+    - if: $CI_COMMIT_BRANCH != $CI_DEFAULT_BRANCH
+      when: manual
+
+buildDockerProdGitlab:
+  extends: .template_docker
+  before_script:
+    - docker login -u $CI_REGISTRY_USER -p $CI_REGISTRY_PASSWORD $CI_REGISTRY
+  script:
+    - docker build -t "$CI_REGISTRY/metexplore/met4j/met4j-docker:latest" .
+    - docker push "$CI_REGISTRY/metexplore/met4j/met4j-docker:latest"
+  rules:
+    - if: $CI_COMMIT_BRANCH == $CI_DEFAULT_BRANCH
+      when: manual
+    - if: $CI_COMMIT_BRANCH != $CI_DEFAULT_BRANCH
+      when: manual
+
+buildDockerProdDockerhub:
+  extends: .template_docker
+  before_script:
+    - docker login -u "$DOCKERHUB_USER" -p "$DOCKERHUB_PASSWORD" $DOCKERHUB_REGISTRY
+  script:
+    - docker build --pull -t "$DOCKERHUB_IMAGE:latest" .
+    - docker push "$DOCKERHUB_IMAGE:latest"
+  rules:
+    - if: $CI_COMMIT_BRANCH == $CI_DEFAULT_BRANCH
+      when: manual
+    - if: $CI_COMMIT_BRANCH != $CI_DEFAULT_BRANCH
+      when: manual
+
+
+
+

CHANGELOG.md

@@ -4,6 +4,18 @@ All notable changes to this project will be documented in this file.
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+## 0.10.0
+
+### Features
+
+[met4j-toolbox] New app: networkAnalysis.CompoundNet: Advanced compound graph building
+
+[met4j-toolbox] New app: attributes.ExtractPathways: SBML sub network creation from a list of pathways
+
+[met4j-toolbox] New app: attributes.ExtractSbmlAnnot: Extract sbml annotations 
+
+[met4j-toolbox] App improvements: networkAnalysis.SideCompoundsScan: Handle multiple compartments
+
 ## 0.9.1
 
 ### Fixed

Dockerfile

+FROM debian:stable-slim
+
+RUN export DEBIAN_FRONTEND=noninteractive
+
+RUN apt-get update \
+&& apt-get upgrade -y \
+&& apt-get install -y openjdk-11-jre git maven \
+&& apt-get clean \
+&& apt-get purge
+
+RUN mkdir -p /opt && cd /opt \
+&& git clone https://forgemia.inra.fr/metexplore/met4j.git \
+&& cd met4j \
+&& mvn install \
+&& cd met4j-toolbox \
+&& mvn package
+
+RUN mkdir -p /opt/bin \
+&& cd /opt/met4j/met4j-toolbox \
+&& cp target/met4j*.jar /opt/bin/met4j.jar \
+&& cd /opt \
+&& rm -rf met4j ~/.m2  \
+&& apt-get remove -y git && apt-get autoremove -y
+
+COPY ./docker_files/met4j.sh /opt/bin
+
+ENTRYPOINT ["/opt/bin/met4j.sh"]
+

README.md

@@ -62,7 +62,7 @@ mv ./target/*-jar-with-dependencies.jar ../../../
 ## Usage
 
 Documentation for the library modules can be found in each module's own README.  
-Detailed code examples can be found at [https://forgemia.inra.fr/metexplore/tutorialmet4j](https://cecill.info/licences/Licence_CeCILL_V2.1-en.html).  
+Detailed code examples can be found at [here](https://forgemia.inra.fr/metexplore/tutorialmet4j).  
 
 The toolbox can be launched using
 ```
@@ -74,6 +74,14 @@ which will list all the contained applications that can be called using
 java -cp met4j-toolbox-0.8.0-jar-with-dependencies.jar <App full name> -h
 ```
 
+### With singularity
+
+You need at least [singularity](https://sylabs.io/guides/3.5/user-guide/quick_start.html) v3.5.
+
+```console
+singularity pull met4j-toolbox.sif oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:latest
+```
+
 ## Contributing
 Pull requests are welcome **on the gitlab repo** ([https://forgemia.inra.fr/metexplore/met4j](https://forgemia.inra.fr/metexplore/met4j)). For major changes, please open an issue first to discuss what you would like to change.  
 

coverage/pom.xml

@@ -44,7 +44,7 @@
     <parent>
         <groupId>fr.inrae.toulouse.metexplore</groupId>
         <artifactId>met4j</artifactId>
-        <version>0.9.1-SNAPSHOT</version>
+        <version>0.10.0-SNAPSHOT</version>
         <relativePath>../pom.xml</relativePath>
     </parent>
 

docker_files/met4j.sh

+#!bin/bash
+#
+# Copyright INRAE (2022)
+#
+# contact-metexplore@inrae.fr
+#
+# This software is a computer program whose purpose is to [describe
+# functionalities and technical features of your software].
+#
+# This software is governed by the CeCILL license under French law and
+# abiding by the rules of distribution of free software.  You can  use,
+# modify and/ or redistribute the software under the terms of the CeCILL
+# license as circulated by CEA, CNRS and INRIA at the following URL
+# "https://cecill.info/licences/Licence_CeCILL_V2.1-en.html".
+#
+# As a counterpart to the access to the source code and  rights to copy,
+# modify and redistribute granted by the license, users are provided only
+# with a limited warranty  and the software's author,  the holder of the
+# economic rights,  and the successive licensors  have only  limited
+# liability.
+#
+# In this respect, the user's attention is drawn to the risks associated
+# with loading,  using,  modifying and/or developing or reproducing the
+# software by the user in light of its specific status of free software,
+# that may mean  that it is complicated to manipulate,  and  that  also
+# therefore means  that it is reserved for developers  and  experienced
+# professionals having in-depth computer knowledge. Users are therefore
+# encouraged to load and test the software's suitability as regards their
+# requirements in conditions enabling the security of their systems and/or
+# data to be ensured and,  more generally, to use and operate it in the
+# same conditions as regards security.
+#
+# The fact that you are presently reading this means that you have had
+# knowledge of the CeCILL license and that you accept its terms.
+#
+#
+
+
+path_jar=/opt/bin/met4j.jar
+# path_jar=../met4j-toolbox/target/met4j-toolbox-0.9.1-SNAPSHOT.jar
+
+if [ $# -lt 1 ]
+    then
+        echo "display Help"
+        exec java -jar $path_jar
+    else
+        echo "Lauch met4j-toolbox"
+	      exec java -Dlog4j.configuration= -cp $path_jar fr.inrae.toulouse.metexplore.met4j_toolbox."$@"
+fi
\ No newline at end of file

met4j-chemUtils/pom.xml

@@ -5,7 +5,7 @@
   <parent>
     <groupId>fr.inrae.toulouse.metexplore</groupId>
     <artifactId>met4j</artifactId>
-    <version>0.9.1-SNAPSHOT</version>
+    <version>0.10.0-SNAPSHOT</version>
   </parent>
 
     <properties>
@@ -35,7 +35,7 @@
         <dependency>
             <groupId>fr.inrae.toulouse.metexplore</groupId>
             <artifactId>met4j-core</artifactId>
-            <version>0.9.1-SNAPSHOT</version>
+            <version>0.10.0-SNAPSHOT</version>
         </dependency>
         <!-- https://mvnrepository.com/artifact/org.mockito/mockito-all -->
         <dependency>

met4j-core/pom.xml

@@ -5,7 +5,7 @@
   <parent>
     <groupId>fr.inrae.toulouse.metexplore</groupId>
     <artifactId>met4j</artifactId>
-    <version>0.9.1-SNAPSHOT</version>
+    <version>0.10.0-SNAPSHOT</version>
   </parent>
 
     <scm>

met4j-graph/pom.xml

@@ -5,7 +5,7 @@
     <parent>
         <groupId>fr.inrae.toulouse.metexplore</groupId>
         <artifactId>met4j</artifactId>
-        <version>0.9.1-SNAPSHOT</version>
+        <version>0.10.0-SNAPSHOT</version>
     </parent>
 
     <artifactId>met4j-graph</artifactId>
@@ -40,7 +40,7 @@
         <dependency>
             <groupId>fr.inrae.toulouse.metexplore</groupId>
             <artifactId>met4j-core</artifactId>
-            <version>0.9.1-SNAPSHOT</version>
+            <version>0.10.0-SNAPSHOT</version>
         </dependency>
         <dependency>
             <groupId>org.apache.commons</groupId>
@@ -50,12 +50,12 @@
         <dependency>
             <groupId>fr.inrae.toulouse.metexplore</groupId>
             <artifactId>met4j-mathUtils</artifactId>
-            <version>0.9.1-SNAPSHOT</version>
+            <version>0.10.0-SNAPSHOT</version>
         </dependency>
         <dependency>
             <groupId>fr.inrae.toulouse.metexplore</groupId>
             <artifactId>met4j-chemUtils</artifactId>
-            <version>0.9.1-SNAPSHOT</version>
+            <version>0.10.0-SNAPSHOT</version>
         </dependency>
     </dependencies>
 

met4j-graph/src/main/java/fr/inrae/toulouse/metexplore/met4j_graph/computation/connect/weighting/AtomMappingWeightPolicy.java

@@ -4,11 +4,13 @@ import fr.inrae.toulouse.metexplore.met4j_core.biodata.BioMetabolite;
 import fr.inrae.toulouse.metexplore.met4j_graph.core.WeightingPolicy;
 import fr.inrae.toulouse.metexplore.met4j_graph.core.compound.CompoundGraph;
 import fr.inrae.toulouse.metexplore.met4j_graph.core.compound.ReactionEdge;
+import org.apache.commons.lang3.StringUtils;
 
 import java.util.ArrayList;
 import java.util.Collection;
 import java.util.HashMap;
 import java.util.Map;
+import java.util.function.Function;
 import java.util.regex.Matcher;
 import java.util.regex.Pattern;
 import java.util.stream.Collectors;
@@ -101,6 +103,23 @@ public class AtomMappingWeightPolicy extends WeightingPolicy<BioMetabolite, Reac
                 .sep("\t"));
     }
 
+    public AtomMappingWeightPolicy fromConservedCarbonIndexes(String GSAMoutputFile){
+        String sep =",";
+        return this.fromNumberOfConservedCarbons(new WeightsFromFile(GSAMoutputFile, false)
+                .weightCol(8)
+                .edgeLabelCol(6)
+                .sourceCol(0)
+                .targetCol(3)
+                .processWeigthCol(new Function<String, Double>() {
+                    @Override
+                    public Double apply(String s) {
+                        return Double.valueOf(s.split(sep).length);
+                    }
+                })
+                .sep("\t"))
+                ;
+    }
+
     @Override
     public void setWeight(CompoundGraph compoundGraph) {
         if(conservedCarbons==null) throw new IllegalArgumentException("an atom mapping must be provided");
@@ -110,7 +129,8 @@ public class AtomMappingWeightPolicy extends WeightingPolicy<BioMetabolite, Reac
         for(ReactionEdge e : compoundGraph.edgeSet()){
             Integer cc = null;
             if(importer !=null){
-                cc=(int) compoundGraph.getEdgeWeight(e);
+                Double w = compoundGraph.getEdgeWeight(e);
+                if(!Double.isNaN(w)) cc= Integer.valueOf((int) compoundGraph.getEdgeWeight(e));
             }else{
                 Map<BioMetabolite,Integer> mapping = conservedCarbons.get(e.getV1());
                 if(mapping!=null) cc = conservedCarbons.get(e.getV1()).get(e.getV2());

met4j-graph/src/main/java/fr/inrae/toulouse/metexplore/met4j_graph/computation/connect/weighting/WeightsFromFile.java

@@ -42,6 +42,7 @@ import java.util.Arrays;
 import java.util.Collections;
 import java.util.HashSet;
 import java.util.Set;
+import java.util.function.Function;
 
 import fr.inrae.toulouse.metexplore.met4j_graph.core.BioGraph;
 import fr.inrae.toulouse.metexplore.met4j_graph.core.Edge;
@@ -71,7 +72,12 @@ public class WeightsFromFile<V extends BioEntity, E extends Edge<V>,G extends Bi
 	private int weightCol = 3;
 	private boolean skipHeader = false;
 	private boolean missingAsNaN = true;
+	private Function<String,Double> process = Double::parseDouble;
 
+	public WeightsFromFile<V,E,G> processWeigthCol(Function<String,Double> process) {
+		this.process = process;
+		return this;
+	}
 	public WeightsFromFile<V,E,G> removeEdgeNotInFile() {
 		this.removeEdgeNotInFile = true;
 		return this;
@@ -151,7 +157,7 @@ public class WeightsFromFile<V extends BioEntity, E extends Edge<V>,G extends Bi
 					if(e!=null){
 						if(!seenEdges.contains(e)){
 							try{
-								double w = Double.parseDouble(lineParts[weightCol]);
+								double w = process.apply(lineParts[weightCol]);
 								if(!Double.isNaN(w)){
 									g.setEdgeWeight(e, w);
 									seenEdges.add(e);

met4j-graph/src/test/java/fr/inrae/toulouse/metexplore/met4j_graph/TestWeightingPolicy.java

@@ -416,6 +416,94 @@ public class TestWeightingPolicy {
 
 	}
 
+	/**
+	 * Test the weights Import
+	 */
+	@Test
+	public void testWeightsFromFileImportIII() {
+		Path tmpPath = null;
+		try {
+			tmpPath = Files.createTempFile("test_edgeWeightmport", ".tmp");
+		} catch (IOException e1) {
+			e1.printStackTrace();
+			Assert.fail("Creation of the temporary directory");
+		}
+		String filePath = "EdgeWeightTestFileII.tab";
+		try {
+			filePath = TestUtils.copyProjectResource(filePath, tmpPath.toFile());
+		} catch (IOException e) {
+			e.printStackTrace();
+			fail("problem while reading edge weight file");
+		}
+
+		double abWeight,bcWeight,adWeight,efWeight,bxWeight,ebWeight,deWeight,fcWeight,ycWeight;
+		abWeight=0.2;
+		bcWeight=0.4;
+		adWeight=0.6;
+		efWeight=0.8;
+		bxWeight=1.0;
+		ebWeight=1.2;
+		deWeight=1.4;
+		fcWeight=1.6;
+		ycWeight=1.8;
+
+		WeightsFromFile<BioMetabolite,ReactionEdge,CompoundGraph> wp =
+				new WeightsFromFile<BioMetabolite,ReactionEdge,CompoundGraph>(filePath)
+						.sep(",")
+						.sourceCol(0)
+						.targetCol(1)
+						.edgeLabelCol(2)
+						.weightCol(4)
+						.processWeigthCol(s -> {return Double.parseDouble(s)*2;});
+		wp.setWeight(g);
+
+		assertEquals("wrong weight after import", abWeight, g.getEdgeWeight(ab),Double.MIN_VALUE);
+		assertEquals("wrong weight after import", adWeight, g.getEdgeWeight(ad),Double.MIN_VALUE);
+		assertEquals("wrong weight after import", bcWeight, g.getEdgeWeight(bc),Double.MIN_VALUE);
+		assertEquals("wrong weight after import", bxWeight, g.getEdgeWeight(bx),Double.MIN_VALUE);
+		assertEquals("wrong weight after import", deWeight, g.getEdgeWeight(de),Double.MIN_VALUE);
+		assertEquals("wrong weight after import", ebWeight, g.getEdgeWeight(eb),Double.MIN_VALUE);
+		assertEquals("wrong weight after import", efWeight, g.getEdgeWeight(ef),Double.MIN_VALUE);
+		assertEquals("wrong weight after import", fcWeight, g.getEdgeWeight(fc),Double.MIN_VALUE);
+		assertEquals("wrong weight after import", ycWeight, g.getEdgeWeight(yc),Double.MIN_VALUE);
+
+	}
+
+	@Test
+	public void testAtomMappingWeightPolicy() {
+		Path tmpPath = null;
+		try {
+			tmpPath = Files.createTempFile("test_edgeWeightmport", ".tmp");
+		} catch (IOException e1) {
+			e1.printStackTrace();
+			Assert.fail("Creation of the temporary directory");
+		}
+		String filePath = "AAMTestFile.tab";
+		try {
+			filePath = TestUtils.copyProjectResource(filePath, tmpPath.toFile());
+		} catch (IOException e) {
+			e.printStackTrace();
+			fail("problem while reading edge weight file");
+		}
+
+		int CCnb1 =21;
+		int CCnb5 =5;
+		int CCnb6 =1;
+
+
+
+		AtomMappingWeightPolicy wp1 = new AtomMappingWeightPolicy().fromConservedCarbonIndexes(filePath);
+		wp1.setWeight(g);
+		assertEquals("wrong weight for AAM weight", CCnb1, g.getEdgeWeight(ad),Double.MIN_VALUE);
+		assertTrue("wrong weight for AAM weight", Double.isNaN(g.getEdgeWeight(ab)));
+		assertTrue("wrong weight for AAM weight", Double.isNaN(g.getEdgeWeight(bc)));
+		assertTrue("wrong weight for AAM weight", Double.isNaN(g.getEdgeWeight(bx)));
+		assertEquals("wrong weight for AAM weight", CCnb5, g.getEdgeWeight(eb),Double.MIN_VALUE);
+		assertEquals("wrong weight for AAM weight", CCnb6, g.getEdgeWeight(ef),Double.MIN_VALUE);
+		assertTrue("wrong weight for AAM weight", Double.isNaN(g.getEdgeWeight(yc)));
+
+	}
+
 	@Test
 	public void testAtomMappingWeightPolicyI() {
 

met4j-graph/src/test/resources/AAMTestFile.tab

+a	60.021129368	4-2	d	60.021129368	4-2	abd	0.0	2,4,5,6,7,9,10,12,13,23,24,26,28,30,31,33,35,37,43,45,47
+e	60.021129368	35-33	b	139.98745989	35-33	efb	79.96633052199999	50,52,53,57,59
+e	169.998024574	49-47-46	f	265.959269716	49-47-46	efb	95.961245142	54
\ No newline at end of file

met4j-io/pom.xml

@@ -6,7 +6,7 @@
     <parent>
         <groupId>fr.inrae.toulouse.metexplore</groupId>
         <artifactId>met4j</artifactId>
-        <version>0.9.1-SNAPSHOT</version>
+        <version>0.10.0-SNAPSHOT</version>
     </parent>
 
     <artifactId>met4j-io</artifactId>
@@ -25,7 +25,7 @@
         <dependency>
             <groupId>fr.inrae.toulouse.metexplore</groupId>
             <artifactId>met4j-core</artifactId>
-            <version>0.9.1-SNAPSHOT</version>
+            <version>0.10.0-SNAPSHOT</version>
         </dependency>
         <dependency>
             <groupId>org.sbml.jsbml</groupId>

met4j-io/src/main/java/fr/inrae/toulouse/metexplore/met4j_io/annotations/GenericAttributes.java

@@ -55,27 +55,49 @@ import fr.inrae.toulouse.metexplore.met4j_io.jsbml.attributes.Notes;
  */
 public class GenericAttributes {
 
-    /** Constant <code>SBML_UNIT_DEFINITIONS="unit_definitions"</code> */
+    /**
+     * Constant <code>SBML_UNIT_DEFINITIONS="unit_definitions"</code>
+     */
     public static final String SBML_UNIT_DEFINITIONS = "unit_definitions";
-    /** Constant <code>SBML_NOTES="notes"</code> */
+    /**
+     * Constant <code>SBML_NOTES="notes"</code>
+     */
     public static final String SBML_NOTES = "notes";
-    /** Constant <code>PMIDS="pmids"</code> */
+    /**
+     * Constant <code>PMIDS="pmids"</code>
+     */
     public static final String PMIDS = "pmids";
-    /** Constant <code>COMMENT="comment"</code> */
+    /**
+     * Constant <code>COMMENT="comment"</code>
+     */
     public static final String COMMENT = "comment";
-    /** Constant <code>SBO_TERM="sbo_term"</code> */
+    /**
+     * Constant <code>SBO_TERM="sbo_term"</code>
+     */
     public static final String SBO_TERM = "sbo_term";
-    /** Constant <code>CONSTANT="constant"</code> */
+    /**
+     * Constant <code>CONSTANT="constant"</code>
+     */
     public static final String CONSTANT = "constant";
-    /** Constant <code>SBML_ANNOTATION="annotation"</code> */
+    /**
+     * Constant <code>SBML_ANNOTATION="annotation"</code>
+     */
     public static final String SBML_ANNOTATION = "annotation";
-    /** Constant <code>GENERIC="generic"</code> */
+    /**
+     * Constant <code>GENERIC="generic"</code>
+     */
     public static final String GENERIC = "generic";
-    /** Constant <code>TYPE="type"</code> */
+    /**
+     * Constant <code>TYPE="type"</code>
+     */
     public static final String TYPE = "type";
-    /** Constant <code>ANNOTATOR_COMMENTS="annotator_comments"</code> */
+    /**
+     * Constant <code>ANNOTATOR_COMMENTS="annotator_comments"</code>
+     */
     public static final String ANNOTATOR_COMMENTS = "annotator_comments";
-    /** Constant <code>AUTHORS="AUTHORS"</code> */
+    /**
+     * Constant <code>AUTHORS="AUTHORS"</code>
+     */
     public static final String AUTHORS = "AUTHORS";
 
 
@@ -103,7 +125,7 @@ public class GenericAttributes {
     /**
      * Set constant condition
      *
-     * @param e a {@link fr.inrae.toulouse.metexplore.met4j_core.biodata.BioEntity} object.
+     * @param e    a {@link fr.inrae.toulouse.metexplore.met4j_core.biodata.BioEntity} object.
      * @param flag a {@link java.lang.Boolean} object.
      */
     public static void setConstant(BioEntity e, Boolean flag) {
@@ -131,7 +153,7 @@ public class GenericAttributes {
     /**
      * set notes
      *
-     * @param e a {@link fr.inrae.toulouse.metexplore.met4j_core.biodata.BioEntity} object.
+     * @param e     a {@link fr.inrae.toulouse.metexplore.met4j_core.biodata.BioEntity} object.
      * @param notes a {@link fr.inrae.toulouse.metexplore.met4j_io.jsbml.attributes.Notes} object.
      */
     public static void setNotes(BioEntity e, Notes notes) {
@@ -145,7 +167,7 @@ public class GenericAttributes {
      * <p>
      * TODO : see if it useful since there is BioRef...
      *
-     * @param e a {@link fr.inrae.toulouse.metexplore.met4j_core.biodata.BioEntity} object.
+     * @param e     a {@link fr.inrae.toulouse.metexplore.met4j_core.biodata.BioEntity} object.
      * @param pmids a {@link java.util.Set} object.
      */
     public static void setPmids(BioEntity e, Set<Integer> pmids) {
@@ -157,7 +179,7 @@ public class GenericAttributes {
     /**
      * add pmid
      *
-     * @param e a {@link fr.inrae.toulouse.metexplore.met4j_core.biodata.BioEntity} object.
+     * @param e    a {@link fr.inrae.toulouse.metexplore.met4j_core.biodata.BioEntity} object.
      * @param pmid a {@link java.lang.Integer} object.
      */
     public static void addPmid(BioEntity e, Integer pmid) {
@@ -196,7 +218,7 @@ public class GenericAttributes {
     /**
      * set comment
      *
-     * @param e a {@link fr.inrae.toulouse.metexplore.met4j_core.biodata.BioEntity} object.
+     * @param e       a {@link fr.inrae.toulouse.metexplore.met4j_core.biodata.BioEntity} object.
      * @param comment a {@link java.lang.String} object.
      */
     public static void setComment(BioEntity e, String comment) {
@@ -206,13 +228,14 @@ public class GenericAttributes {
     /**
      * set Sbo term
      *