From a9a8ca36b8f192b5a26a8adf234c78fdf24720a9 Mon Sep 17 00:00:00 2001
From: lcottret <ludovic.cottret@inrae.fr>
Date: Thu, 31 Oct 2024 11:16:13 +0100
Subject: [PATCH] fix protein/gene names in sbml reading
---
.../jsbml/reader/plugin/FBCParser.java | 715 +++++++++---------
.../met4j_io/jsbml/reader/SbmlDocMock.java | 8 +-
.../jsbml/reader/plugin/FBCParserTest.java | 34 +-
3 files changed, 385 insertions(+), 372 deletions(-)
diff --git a/met4j-io/src/main/java/fr/inrae/toulouse/metexplore/met4j_io/jsbml/reader/plugin/FBCParser.java b/met4j-io/src/main/java/fr/inrae/toulouse/metexplore/met4j_io/jsbml/reader/plugin/FBCParser.java
index 91985cfb7..f31e44f40 100644
--- a/met4j-io/src/main/java/fr/inrae/toulouse/metexplore/met4j_io/jsbml/reader/plugin/FBCParser.java
+++ b/met4j-io/src/main/java/fr/inrae/toulouse/metexplore/met4j_io/jsbml/reader/plugin/FBCParser.java
@@ -37,12 +37,12 @@
package fr.inrae.toulouse.metexplore.met4j_io.jsbml.reader.plugin;
import fr.inrae.toulouse.metexplore.met4j_core.biodata.*;
+import fr.inrae.toulouse.metexplore.met4j_core.utils.StringUtils;
import fr.inrae.toulouse.metexplore.met4j_io.annotations.network.NetworkAttributes;
import fr.inrae.toulouse.metexplore.met4j_io.annotations.reaction.Flux;
import fr.inrae.toulouse.metexplore.met4j_io.annotations.reaction.ReactionAttributes;
import fr.inrae.toulouse.metexplore.met4j_io.jsbml.dataTags.PrimaryDataTag;
import fr.inrae.toulouse.metexplore.met4j_io.jsbml.errors.GeneSetException;
-import fr.inrae.toulouse.metexplore.met4j_io.jsbml.errors.JSBMLPackageReaderException;
import fr.inrae.toulouse.metexplore.met4j_io.jsbml.fbc.*;
import fr.inrae.toulouse.metexplore.met4j_io.jsbml.reader.Met4jSbmlReaderException;
import fr.inrae.toulouse.metexplore.met4j_io.jsbml.reader.plugin.tags.ReaderSBML3Compatible;
@@ -52,18 +52,7 @@ import org.sbml.jsbml.Model;
import org.sbml.jsbml.Parameter;
import org.sbml.jsbml.Reaction;
import org.sbml.jsbml.Species;
-import org.sbml.jsbml.ext.fbc.And;
-import org.sbml.jsbml.ext.fbc.Association;
-import org.sbml.jsbml.ext.fbc.FBCModelPlugin;
-import org.sbml.jsbml.ext.fbc.FBCReactionPlugin;
-import org.sbml.jsbml.ext.fbc.FBCSpeciesPlugin;
-import org.sbml.jsbml.ext.fbc.FluxObjective;
-import org.sbml.jsbml.ext.fbc.GeneProduct;
-import org.sbml.jsbml.ext.fbc.GeneProductRef;
-import org.sbml.jsbml.ext.fbc.Objective;
-import org.sbml.jsbml.ext.fbc.Or;
-
-import fr.inrae.toulouse.metexplore.met4j_core.utils.StringUtils;
+import org.sbml.jsbml.ext.fbc.*;
import java.util.ArrayList;
@@ -74,230 +63,229 @@ import java.util.ArrayList;
*/
public class FBCParser implements PackageParser, PrimaryDataTag, ReaderSBML3Compatible {
- /**
- * The sbml namespace of the FBC version 2 package
- */
- private String PackageNamespace = "http://www.sbml.org/sbml/level3/version1/fbc/version2";
+ /**
+ * The Flux Network created by this parser
+ *
+ * @see FluxNetwork
+ */
+ public FluxNetwork flxNet;
+ /**
+ * The SBML fbc model plugin
+ */
+ public FBCModelPlugin fbcModel;
+ /**
+ * Indicates if the genes are parsed or not
+ */
+ public Boolean parseGenes = true;
+ /**
+ * The sbml namespace of the FBC version 2 package
+ */
+ private String PackageNamespace = "http://www.sbml.org/sbml/level3/version1/fbc/version2";
+
+ public FBCParser(Boolean parseGenes) {
+
+ this.parseGenes = parseGenes;
+ }
- /**
- * The Flux Network created by this parser
- *
- * @see FluxNetwork
- */
- public FluxNetwork flxNet;
+ public FBCParser() {
+
+ this.parseGenes = true;
+ }
- /**
- * The SBML fbc model plugin
- */
- public FBCModelPlugin fbcModel;
+ /**
+ * {@inheritDoc}
+ */
+ @Override
+ public String getAssociatedPackageName() {
+ return "fbc";
+ }
- /**
- * Indicates if the genes are parsed or not
- */
- public Boolean parseGenes = true;
+ /**
+ * {@inheritDoc}
+ */
+ @Override
+ public boolean isPackageUseableOnModel(Model model) {
+ return model.isPackageURIEnabled(PackageNamespace);
+ }
- /** {@inheritDoc} */
- @Override
- public String getAssociatedPackageName() {
- return "fbc";
- }
+ /**
+ * {@inheritDoc}
+ * <p>
+ * Parse the new object introduced by the SBML FBC version 2 package and
+ * some of the objects introduced by the FBC version 1 package:
+ * <ul>
+ * <li>The list of flux bounds, (introduced in fbc v1 but now present in the
+ * list of Global Parameters)
+ * <li>The list of flux Objectives (introduced in fbc v1)
+ * <li>The list of Gene Product (introduced in fbc v2)
+ * <li>The additional attributes present in the Species elements (introduced
+ * in fbc v1)
+ * <li>The additional attributes present in the Reaction elements
+ * (introduced in fbc v2) including the GeneAssociation Objects
+ * </ul>
+ */
+ public void parseModel(Model model, BioNetwork bionetwork) throws Met4jSbmlReaderException {
+
+ this.setFlxNet(new FluxNetwork(bionetwork));
+ this.setFbcModel((FBCModelPlugin) model.getPlugin("fbc"));
+ System.err.println("Starting " + this.getAssociatedPackageName() + " version "
+ + this.getFbcModel().getPackageVersion() + " plugin...");
+
+ this.setStrictFromFbcModel();
+
+ this.parseParameters();
+
+ if (parseGenes) {
+ this.parseListOfGeneProducts();
+ }
+ try {
+ this.parseFluxReactions();
+ } catch (GeneSetException | Met4jSbmlReaderException e) {
+ e.printStackTrace();
+ throw new Met4jSbmlReaderException(e.getMessage());
+ }
+
+ /**
+ * Same Methods as FBC1 parser.
+ */
+ this.parseFluxSpecies();
+ this.parseListOfFluxObjectives();
- /** {@inheritDoc} */
- @Override
- public boolean isPackageUseableOnModel(Model model) {
- return model.isPackageURIEnabled(PackageNamespace);
- }
+ }
+ /**
+ * Get FBC data only present in the SBML Model object, ie the fbc:strict
+ * attribute
+ *
+ * @see FluxNetwork#setFbcStrict(boolean)
+ */
+ private void setStrictFromFbcModel() {
- public FBCParser(Boolean parseGenes) {
+ this.getFlxNet().setFbcStrict(this.getFbcModel().isSetStrict() ? this.getFbcModel().getStrict() : false);
+ }
- this.parseGenes = parseGenes;
+ /**
+ * Retrieves the list of global parameters of this model. This list includes
+ * all the possible flux bounds values of the reactions in this model.
+ */
+ private void parseParameters() {
+
+ if (this.getFbcModel().getParent().getListOfParameters().size() > 0) {
+ BioUnitDefinitionCollection udList = NetworkAttributes.getUnitDefinitions(this.flxNet.getUnderlyingBionet());
+ if (udList == null) {
+ System.err.println("[Warning] No unit definition in the SBML file, default one selected");
+ udList = new BioUnitDefinitionCollection();
+ this.flxNet.getUnderlyingBionet().setAttribute(NetworkAttributes.UNIT_DEFINITIONS, udList);
+ }
+
+ for (Parameter gParam : this.getFbcModel().getParent().getListOfParameters()) {
+ Flux bioParam = new Flux(gParam.getId());
+ bioParam.setConstant(gParam.getConstant());
+ bioParam.value = gParam.getValue();
+
+ String unit = gParam.getUnits();
+
+ if (unit != "") {
+ BioUnitDefinition unitDefinition = udList.get(gParam.getUnits());
+ if (unitDefinition == null) {
+ System.err.println("[Warning] Unit definition " + gParam.getUnits() + " not defined in the SBML : we add it");
+ unitDefinition = new BioUnitDefinition(gParam.getUnits(), gParam.getUnits());
+ udList.add(unitDefinition);
+ }
+ bioParam.unitDefinition = unitDefinition;
+ }
+
+ this.flxNet.addFluxBound(bioParam);
+ }
+ }
}
- public FBCParser() {
-
- this.parseGenes = true;
- }
-
- /**
- * {@inheritDoc}
- *
- * Parse the new object introduced by the SBML FBC version 2 package and
- * some of the objects introduced by the FBC version 1 package:
- * <ul>
- * <li>The list of flux bounds, (introduced in fbc v1 but now present in the
- * list of Global Parameters)
- * <li>The list of flux Objectives (introduced in fbc v1)
- * <li>The list of Gene Product (introduced in fbc v2)
- * <li>The additional attributes present in the Species elements (introduced
- * in fbc v1)
- * <li>The additional attributes present in the Reaction elements
- * (introduced in fbc v2) including the GeneAssociation Objects
- * </ul>
- */
- public void parseModel(Model model, BioNetwork bionetwork) throws Met4jSbmlReaderException {
-
- this.setFlxNet(new FluxNetwork(bionetwork));
- this.setFbcModel((FBCModelPlugin) model.getPlugin("fbc"));
- System.err.println("Starting " + this.getAssociatedPackageName() + " version "
- + this.getFbcModel().getPackageVersion() + " plugin...");
-
- this.setStrictFromFbcModel();
-
- this.parseParameters();
-
- if(parseGenes) {
- this.parseListOfGeneProducts();
- }
- try {
- this.parseFluxReactions();
- } catch (GeneSetException | Met4jSbmlReaderException e) {
- e.printStackTrace();
- throw new Met4jSbmlReaderException(e.getMessage());
- }
-
- /**
- * Same Methods as FBC1 parser.
- */
- this.parseFluxSpecies();
- this.parseListOfFluxObjectives();
-
- }
-
- /**
- * Get FBC data only present in the SBML Model object, ie the fbc:strict
- * attribute
- *
- * @see FluxNetwork#setFbcStrict(boolean)
- */
- private void setStrictFromFbcModel() {
-
- this.getFlxNet().setFbcStrict(this.getFbcModel().isSetStrict() ? this.getFbcModel().getStrict() : false);
- }
-
- /**
- * Retrieves the list of global parameters of this model. This list includes
- * all the possible flux bounds values of the reactions in this model.
- */
- private void parseParameters() {
-
- if(this.getFbcModel().getParent().getListOfParameters().size() > 0) {
- BioUnitDefinitionCollection udList = NetworkAttributes.getUnitDefinitions(this.flxNet.getUnderlyingBionet());
- if(udList == null) {
- System.err.println("[Warning] No unit definition in the SBML file, default one selected");
- udList = new BioUnitDefinitionCollection();
- this.flxNet.getUnderlyingBionet().setAttribute(NetworkAttributes.UNIT_DEFINITIONS, udList);
- }
-
- for (Parameter gParam : this.getFbcModel().getParent().getListOfParameters()) {
- Flux bioParam = new Flux(gParam.getId());
- bioParam.setConstant(gParam.getConstant());
- bioParam.value = gParam.getValue();
-
- String unit = gParam.getUnits();
-
- if (unit != "") {
- BioUnitDefinition unitDefinition = udList.get(gParam.getUnits());
- if(unitDefinition == null) {
- System.err.println("[Warning] Unit definition "+gParam.getUnits()+" not defined in the SBML : we add it");
- unitDefinition = new BioUnitDefinition(gParam.getUnits(), gParam.getUnits());
- udList.add(unitDefinition);
- }
- bioParam.unitDefinition = unitDefinition;
- }
-
- this.flxNet.addFluxBound(bioParam);
- }
- }
- }
-
- /**
- * Parse the list of GeneProduct to create the corresponding genes. Only
- * introduced in package fbc version 2
- */
- private void parseListOfGeneProducts() {
- for (GeneProduct geneProd : this.getFbcModel().getListOfGeneProducts()) {
- String geneId = geneProd.getId();
- String geneName = geneProd.getName() != null ? geneProd.getName() :
- (geneProd.getLabel() != null ? geneProd.getLabel() : geneProd.getId());
-
- BioGene gene = new BioGene(geneId, geneName);
-
- this.getFlxNet().getUnderlyingBionet().add(gene);
-
- BioProtein protein = new BioProtein(geneId, geneName);
-
- this.getFlxNet().getUnderlyingBionet().add(protein);
-
- this.getFlxNet().getUnderlyingBionet().affectGeneProduct(protein, gene);
-
-
- }
- }
-
- /**
- * Parse the list of reaction and uses the data provided by the fbc package
- * to fill the missing data for the reactions presents in the bionetwork.
- * Example are:
- * <ul>
- * <li>fbc:upperbound
- * <li>fbc:lowerbound
- * <li>fbc:GeneProductAssociation
- * </ul>
- */
- private void parseFluxReactions() throws Met4jSbmlReaderException, GeneSetException {
-
- for (Reaction rxn : this.getFbcModel().getParent().getListOfReactions()) {
-
- BioReaction reaction = this.flxNet.getUnderlyingBionet().getReaction(rxn.getId());
-
- FBCReactionPlugin rxnPlugin = (FBCReactionPlugin) rxn.getPlugin("fbc");
- FluxReaction flxReaction = new FluxReaction(reaction);
+ /**
+ * Parse the list of GeneProduct to create the corresponding genes. Only
+ * introduced in package fbc version 2
+ */
+ private void parseListOfGeneProducts() {
+ for (GeneProduct geneProd : this.getFbcModel().getListOfGeneProducts()) {
+ String geneId = geneProd.getId();
+ String geneName = ! StringUtils.isVoid(geneProd.getName()) ? geneProd.getName() :
+ (! StringUtils.isVoid(geneProd.getLabel()) ? geneProd.getLabel() : geneProd.getId());
+
+ BioGene gene = new BioGene(geneId, geneName);
- GeneAssociation geneAssociation = new GeneAssociation();
+ this.getFlxNet().getUnderlyingBionet().add(gene);
- // System.err.println(rxn.getId());
- if (parseGenes && rxnPlugin.isSetGeneProductAssociation()) {
- geneAssociation = this.computeGeneAssocations(rxnPlugin.getGeneProductAssociation().getAssociation());
- }
- // System.err.println("out of recursion");
- flxReaction.setReactionGeneAssociation(geneAssociation);
- flxReaction.convertGeneAssociationstoComplexes(flxNet.getUnderlyingBionet());
+ BioProtein protein = new BioProtein(geneId, geneName);
- ReactionAttributes.setLowerBound(reaction,
- this.flxNet.getListOfFluxBounds().get(rxnPlugin.getLowerFluxBound()));
+ this.getFlxNet().getUnderlyingBionet().add(protein);
- ReactionAttributes.setUpperBound(reaction,
- this.flxNet.getListOfFluxBounds().get(rxnPlugin.getUpperFluxBound()));
+ this.getFlxNet().getUnderlyingBionet().affectGeneProduct(protein, gene);
- this.flxNet.getListOfFluxReactions().put(flxReaction.getId(), flxReaction);
- }
+ }
+ }
+
+ /**
+ * Parse the list of reaction and uses the data provided by the fbc package
+ * to fill the missing data for the reactions presents in the bionetwork.
+ * Example are:
+ * <ul>
+ * <li>fbc:upperbound
+ * <li>fbc:lowerbound
+ * <li>fbc:GeneProductAssociation
+ * </ul>
+ */
+ private void parseFluxReactions() throws Met4jSbmlReaderException, GeneSetException {
- }
+ for (Reaction rxn : this.getFbcModel().getParent().getListOfReactions()) {
- /**
- * Recursively parse Association blocks to retrieve all possible combination
- * of Gene associations
- *
- * @param block
- * the current Association block
- * @return an ArrayList of {@link GeneSet}
- */
- private GeneAssociation computeGeneAssocations(Association block) throws GeneSetException, Met4jSbmlReaderException {
+ BioReaction reaction = this.flxNet.getUnderlyingBionet().getReaction(rxn.getId());
- GeneAssociation geneAssociation = new GeneAssociation();
+ FBCReactionPlugin rxnPlugin = (FBCReactionPlugin) rxn.getPlugin("fbc");
+ FluxReaction flxReaction = new FluxReaction(reaction);
- if (block != null) {
+ GeneAssociation geneAssociation = new GeneAssociation();
- if (block.getClass().getSimpleName().equals("And")) {
- And andBlock = (And) block;
+ // System.err.println(rxn.getId());
+ if (parseGenes && rxnPlugin.isSetGeneProductAssociation()) {
+ geneAssociation = this.computeGeneAssocations(rxnPlugin.getGeneProductAssociation().getAssociation());
+ }
+ // System.err.println("out of recursion");
+ flxReaction.setReactionGeneAssociation(geneAssociation);
+ flxReaction.convertGeneAssociationstoComplexes(flxNet.getUnderlyingBionet());
- ArrayList<GeneAssociation> geneAssociations = new ArrayList<GeneAssociation>();
+ ReactionAttributes.setLowerBound(reaction,
+ this.flxNet.getListOfFluxBounds().get(rxnPlugin.getLowerFluxBound()));
- for (Association andEl : andBlock.getListOfAssociations()) {
+ ReactionAttributes.setUpperBound(reaction,
+ this.flxNet.getListOfFluxBounds().get(rxnPlugin.getUpperFluxBound()));
- geneAssociations.add(this.computeGeneAssocations(andEl));
+ this.flxNet.getListOfFluxReactions().put(flxReaction.getId(), flxReaction);
+
+ }
+
+ }
+
+ /**
+ * Recursively parse Association blocks to retrieve all possible combination
+ * of Gene associations
+ *
+ * @param block the current Association block
+ * @return an ArrayList of {@link GeneSet}
+ */
+ private GeneAssociation computeGeneAssocations(Association block) throws GeneSetException, Met4jSbmlReaderException {
+
+ GeneAssociation geneAssociation = new GeneAssociation();
+
+ if (block != null) {
+
+ if (block.getClass().getSimpleName().equals("And")) {
+ And andBlock = (And) block;
+
+ ArrayList<GeneAssociation> geneAssociations = new ArrayList<GeneAssociation>();
+
+ for (Association andEl : andBlock.getListOfAssociations()) {
+
+ geneAssociations.add(this.computeGeneAssocations(andEl));
// for (GeneSet x : this.computeGeneAssocations(andEl)) {
//
@@ -312,172 +300,169 @@ public class FBCParser implements PackageParser, PrimaryDataTag, ReaderSBML3Comp
//
// }
- }
+ }
+
+ // Cross the geneAssociations
+ geneAssociation = GeneAssociations.merge(geneAssociations.stream().toArray(GeneAssociation[]::new));
+
+ } else if (block.getClass().getSimpleName().equals("Or")) {
+ Or orBlock = (Or) block;
+
+ for (Association orEl : orBlock.getListOfAssociations()) {
+ geneAssociation.addAll(this.computeGeneAssocations(orEl));
+ }
+
+ } else {
+
+ // The association is composed of a GeneProductRef.
- // Cross the geneAssociations
- geneAssociation = GeneAssociations.merge(geneAssociations.stream().toArray(GeneAssociation[]::new));
+ GeneProductRef geneRef = (GeneProductRef) block;
+ GeneSet geneSet = new GeneSet();
- } else if (block.getClass().getSimpleName().equals("Or")) {
- Or orBlock = (Or) block;
+ geneSet.setId(geneRef.getId());
- for (Association orEl : orBlock.getListOfAssociations()) {
- geneAssociation.addAll(this.computeGeneAssocations(orEl));
- }
+ BioGene g = this.flxNet.getUnderlyingBionet().getGene(geneRef.getGeneProduct());
- } else {
-
- // The association is composed of a GeneProductRef.
+ if (g == null) {
+ throw new Met4jSbmlReaderException("Gene " + geneRef.getGeneProduct() + " not present in the list of genes");
+ }
- GeneProductRef geneRef = (GeneProductRef) block;
- GeneSet geneSet = new GeneSet();
+ geneSet.add(g.getId());
- geneSet.setId(geneRef.getId());
+ geneAssociation.add(geneSet);
+ }
+ }
- BioGene g = this.flxNet.getUnderlyingBionet().getGene(geneRef.getGeneProduct());
+ return geneAssociation;
+ }
+
+ /**
+ * Parse the list of species and uses the data provided by the fbc package
+ * to fill the missing data for the metabolites presents in the bionetwork.
+ * Example are:
+ * <ul>
+ * <li>fbc:charge
+ * <li>fbc:chemicalformula
+ * </ul>
+ */
+ private void parseFluxSpecies() {
+ for (Species specie : this.getFbcModel().getParent().getListOfSpecies()) {
+ FBCSpeciesPlugin speciePlugin = (FBCSpeciesPlugin) specie.getPlugin("fbc");
+
+ BioNetwork net = this.flxNet.getUnderlyingBionet();
+
+ BioMetabolite metabolite = net.getMetabolite(specie.getId());
+
+ if (speciePlugin.isSetCharge())
+ metabolite.setCharge(speciePlugin.getCharge());
+ if (speciePlugin.isSetChemicalFormula())
+ metabolite.setChemicalFormula(speciePlugin.getChemicalFormula());
+ }
+
+ }
+
+ /**
+ * Parse the list of Flux objective of this FBC model
+ *
+ * @see BioObjective
+ */
+ private void parseListOfFluxObjectives() {
+
+
+ BioObjectiveCollection objectives = new BioObjectiveCollection();
+
+ for (Objective fbcObj : this.getFbcModel().getListOfObjectives()) {
+
+ BioObjective objective = new BioObjective(fbcObj.getId(), fbcObj.getName());
+
+ String type = "maximize";
+
+ if (fbcObj.getType() != null) {
+ type = fbcObj.getType().toString();
+ }
+
+ objective.setType(fbcObj.getType().toString());
+
+ objective.active = this.getFbcModel().getActiveObjective().equals(fbcObj.getId()) ? true : false;
+
+ for (FluxObjective fbcFluxObj : fbcObj.getListOfFluxObjectives()) {
+
+ String id, name;
+
+ BioReaction r = this.flxNet.getUnderlyingBionet().getReaction(fbcFluxObj.getReaction());
- if(g== null) {
- throw new Met4jSbmlReaderException("Gene "+geneRef.getGeneProduct() + " not present in the list of genes");
- }
+ if (r != null) {
- geneSet.add(g.getId());
+ if (!StringUtils.isVoid(fbcFluxObj.getId())) {
+ id = fbcFluxObj.getId();
+ } else {
+ id = fbcFluxObj.getReaction();
+ }
- geneAssociation.add(geneSet);
- }
- }
+ if (!StringUtils.isVoid(fbcFluxObj.getName())) {
+ name = fbcFluxObj.getName();
+ } else {
+ name = id;
+ }
- return geneAssociation;
- }
+ ReactionObjective biodataFluxObj = new ReactionObjective(id, name);
- /**
- * Parse the list of species and uses the data provided by the fbc package
- * to fill the missing data for the metabolites presents in the bionetwork.
- * Example are:
- * <ul>
- * <li>fbc:charge
- * <li>fbc:chemicalformula
- * </ul>
- */
- private void parseFluxSpecies() {
- for (Species specie : this.getFbcModel().getParent().getListOfSpecies()) {
- FBCSpeciesPlugin speciePlugin = (FBCSpeciesPlugin) specie.getPlugin("fbc");
+ biodataFluxObj.setCoefficient(fbcFluxObj.getCoefficient());
- BioNetwork net = this.flxNet.getUnderlyingBionet();
+ biodataFluxObj.setFlxReaction(new FluxReaction(r));
- BioMetabolite metabolite = net.getMetabolite(specie.getId());
+ objective.getListOfReactionObjectives().add(biodataFluxObj);
+ }
+ }
- if (speciePlugin.isSetCharge())
- metabolite.setCharge(speciePlugin.getCharge());
- if (speciePlugin.isSetChemicalFormula())
- metabolite.setChemicalFormula(speciePlugin.getChemicalFormula());
- }
-
- }
-
- /**
- * Parse the list of Flux objective of this FBC model
- *
- * @see BioObjective
- */
- private void parseListOfFluxObjectives() {
-
-
- BioObjectiveCollection objectives = new BioObjectiveCollection();
-
- for (Objective fbcObj : this.getFbcModel().getListOfObjectives()) {
-
- BioObjective objective = new BioObjective(fbcObj.getId(), fbcObj.getName());
-
- String type = "maximize";
-
- if(fbcObj.getType() != null)
- {
- type = fbcObj.getType().toString();
- }
-
- objective.setType(fbcObj.getType().toString());
-
- objective.active = this.getFbcModel().getActiveObjective().equals(fbcObj.getId()) ? true : false;
-
- for (FluxObjective fbcFluxObj : fbcObj.getListOfFluxObjectives()) {
-
- String id, name;
-
- BioReaction r = this.flxNet.getUnderlyingBionet().getReaction(fbcFluxObj.getReaction());
-
- if(r != null) {
-
- if (!StringUtils.isVoid(fbcFluxObj.getId())) {
- id = fbcFluxObj.getId();
- } else {
- id = fbcFluxObj.getReaction();
- }
-
- if (!StringUtils.isVoid(fbcFluxObj.getName())) {
- name = fbcFluxObj.getName();
- } else {
- name = id;
- }
-
- ReactionObjective biodataFluxObj = new ReactionObjective(id, name);
-
- biodataFluxObj.setCoefficient(fbcFluxObj.getCoefficient());
-
- biodataFluxObj.setFlxReaction(new FluxReaction(r));
-
- objective.getListOfReactionObjectives().add(biodataFluxObj);
- }
- }
-
- objectives.add(objective);
-
- // TODO : est ce qu'on s'en sert encore ?
- this.flxNet.getListOfObjectives().put(objective.getId(), objective);
-
- }
-
- NetworkAttributes.setObjectives(this.flxNet.getUnderlyingBionet(), objectives);
-
-
- this.flxNet.setActiveObjective(this.getFbcModel().getActiveObjective());
-
- }
-
- /**
- * <p>Getter for the field <code>flxNet</code>.</p>
- *
- * @return the flxNet
- */
- public FluxNetwork getFlxNet() {
- return flxNet;
- }
-
- /**
- * <p>Setter for the field <code>flxNet</code>.</p>
- *
- * @param flxNet
- * the flxNet to set
- */
- public void setFlxNet(FluxNetwork flxNet) {
- this.flxNet = flxNet;
- }
-
- /**
- * <p>Getter for the field <code>fbcModel</code>.</p>
- *
- * @return the fbcModel
- */
- public FBCModelPlugin getFbcModel() {
- return fbcModel;
- }
-
- /**
- * <p>Setter for the field <code>fbcModel</code>.</p>
- *
- * @param fbcModel
- * the fbcModel to set
- */
- public void setFbcModel(FBCModelPlugin fbcModel) {
- this.fbcModel = fbcModel;
- }
+ objectives.add(objective);
+
+ // TODO : est ce qu'on s'en sert encore ?
+ this.flxNet.getListOfObjectives().put(objective.getId(), objective);
+
+ }
+
+ NetworkAttributes.setObjectives(this.flxNet.getUnderlyingBionet(), objectives);
+
+
+ this.flxNet.setActiveObjective(this.getFbcModel().getActiveObjective());
+
+ }
+
+ /**
+ * <p>Getter for the field <code>flxNet</code>.</p>
+ *
+ * @return the flxNet
+ */
+ public FluxNetwork getFlxNet() {
+ return flxNet;
+ }
+
+ /**
+ * <p>Setter for the field <code>flxNet</code>.</p>
+ *
+ * @param flxNet the flxNet to set
+ */
+ public void setFlxNet(FluxNetwork flxNet) {
+ this.flxNet = flxNet;
+ }
+
+ /**
+ * <p>Getter for the field <code>fbcModel</code>.</p>
+ *
+ * @return the fbcModel
+ */
+ public FBCModelPlugin getFbcModel() {
+ return fbcModel;
+ }
+
+ /**
+ * <p>Setter for the field <code>fbcModel</code>.</p>
+ *
+ * @param fbcModel the fbcModel to set
+ */
+ public void setFbcModel(FBCModelPlugin fbcModel) {
+ this.fbcModel = fbcModel;
+ }
}
diff --git a/met4j-io/src/test/java/fr/inrae/toulouse/metexplore/met4j_io/jsbml/reader/SbmlDocMock.java b/met4j-io/src/test/java/fr/inrae/toulouse/metexplore/met4j_io/jsbml/reader/SbmlDocMock.java
index f60f41a35..1d07fe1a1 100644
--- a/met4j-io/src/test/java/fr/inrae/toulouse/metexplore/met4j_io/jsbml/reader/SbmlDocMock.java
+++ b/met4j-io/src/test/java/fr/inrae/toulouse/metexplore/met4j_io/jsbml/reader/SbmlDocMock.java
@@ -91,15 +91,15 @@ public class SbmlDocMock {
FBCModelPlugin fbcModel = (FBCModelPlugin) model.getPlugin("http://www.sbml.org/sbml/level3/version1/fbc/version2");
GeneProduct gene1 = fbcModel.createGeneProduct();
gene1.setId("g1");
- gene1.setName("g1");
- gene1.setLabel("g1");
+ gene1.setName("G1_name");
+ gene1.setLabel("G1_label");
fbcModel.addGeneProduct(gene1);
GeneProduct gene2 = fbcModel.createGeneProduct();
gene2.setId("g2");
- gene2.setName("g2");
- gene2.setLabel("g2");
+ gene2.setName("G2_name");
+ gene2.setLabel("G2_label");
fbcModel.addGeneProduct(gene2);
diff --git a/met4j-io/src/test/java/fr/inrae/toulouse/metexplore/met4j_io/jsbml/reader/plugin/FBCParserTest.java b/met4j-io/src/test/java/fr/inrae/toulouse/metexplore/met4j_io/jsbml/reader/plugin/FBCParserTest.java
index bc6947c41..38ad03a01 100644
--- a/met4j-io/src/test/java/fr/inrae/toulouse/metexplore/met4j_io/jsbml/reader/plugin/FBCParserTest.java
+++ b/met4j-io/src/test/java/fr/inrae/toulouse/metexplore/met4j_io/jsbml/reader/plugin/FBCParserTest.java
@@ -45,6 +45,7 @@ import java.util.stream.Collectors;
import javax.xml.stream.XMLStreamException;
+import fr.inrae.toulouse.metexplore.met4j_core.biodata.BioGene;
import fr.inrae.toulouse.metexplore.met4j_io.annotations.reaction.ReactionAttributes;
import fr.inrae.toulouse.metexplore.met4j_io.jsbml.reader.Met4jSbmlReaderException;
import org.junit.Before;
@@ -242,9 +243,20 @@ public class FBCParserTest {
rxn2Plugin = (FBCReactionPlugin) rSbml2.getPlugin("fbc");
rxn3Plugin = (FBCReactionPlugin) rSbml3.getPlugin("fbc");
- plugin.addGeneProduct(new GeneProduct("g1"));
- plugin.addGeneProduct(new GeneProduct("g2"));
- plugin.addGeneProduct(new GeneProduct("g3"));
+ GeneProduct g1 = new GeneProduct("g1");
+ g1.setLabel("g1Label");
+ g1.setName("g1Name");
+
+ GeneProduct g2 = new GeneProduct("g2");
+ g2.setLabel("g2Label");
+ // G2 Does not have name
+
+ GeneProduct g3 = new GeneProduct("g3");
+ // G3 does not have neither name or label
+
+ plugin.addGeneProduct(g1);
+ plugin.addGeneProduct(g2);
+ plugin.addGeneProduct(g3);
GeneProductRef p1 = new GeneProductRef("g1ref");
p1.setGeneProduct("g1");
@@ -280,6 +292,22 @@ public class FBCParserTest {
parser.parseModel(model, network);
+ BioGene bioGene1 = network.getGenesView().get("g1");
+ assertNotNull(bioGene1);
+ assertEquals("g1", bioGene1.getId());
+ assertEquals("g1Name", bioGene1.getName());
+
+ BioGene bioGene2 = network.getGenesView().get("g2");
+ assertNotNull(bioGene2);
+ assertEquals("g2", bioGene2.getId());
+ assertEquals("g2Label", bioGene2.getName());
+
+ BioGene bioGene3 = network.getGenesView().get("g3");
+ assertNotNull(bioGene3);
+ assertEquals("g3", bioGene3.getId());
+ assertEquals("g3", bioGene3.getName());
+
+
String ga1 = BioReactionUtils.getGPR(network, r1, false);
assertEquals("g1", ga1);
--
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