From 836994f33cf56b82fdae8a0623ecb8adeb17693e Mon Sep 17 00:00:00 2001
From: Piotr Gawron <piotr.gawron@uni.lu>
Date: Thu, 21 Dec 2017 16:16:38 +0100
Subject: [PATCH] export of sbml reaction without layout
---
.../model/sbml/SbmlBioEntityExporter.java | 84 +++++++++++++++++++
.../model/sbml/SbmlElementExporter.java | 71 +---------------
.../model/sbml/SbmlElementParser.java | 20 +++--
.../converter/model/sbml/SbmlExporter.java | 2 +
.../converter/model/sbml/SbmlParser.java | 2 +-
.../model/sbml/SbmlReactionExporter.java | 63 ++++++++++++++
.../model/sbml/SbmlReactionParser.java | 12 ++-
.../model/sbml/SbmlSpeciesParser.java | 2 +-
.../model/sbml/SbmlExporterTest.java | 17 +---
.../layout/ApplySimpleLayoutModelCommand.java | 2 -
.../lcsb/mapviewer/model/map/BioEntity.java | 2 +
.../model/map/reaction/Reaction.java | 5 ++
12 files changed, 187 insertions(+), 95 deletions(-)
create mode 100644 converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlBioEntityExporter.java
create mode 100644 converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlReactionExporter.java
diff --git a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlBioEntityExporter.java b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlBioEntityExporter.java
new file mode 100644
index 0000000000..1a18c6ef25
--- /dev/null
+++ b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlBioEntityExporter.java
@@ -0,0 +1,84 @@
+package lcsb.mapviewer.converter.model.sbml;
+
+import java.util.Collection;
+import java.util.HashMap;
+import java.util.Map;
+
+import javax.xml.stream.XMLStreamException;
+
+import org.apache.log4j.Logger;
+import org.sbml.jsbml.Model;
+import org.sbml.jsbml.ext.layout.AbstractReferenceGlyph;
+import org.sbml.jsbml.ext.layout.Layout;
+
+import lcsb.mapviewer.common.exception.InvalidStateException;
+import lcsb.mapviewer.model.map.BioEntity;
+import lcsb.mapviewer.model.map.InconsistentModelException;
+
+public abstract class SbmlBioEntityExporter<T extends BioEntity, S extends org.sbml.jsbml.AbstractNamedSBase> {
+ Logger logger = Logger.getLogger(SbmlBioEntityExporter.class);
+
+ Layout layout;
+
+ lcsb.mapviewer.model.map.model.Model minervaModel;
+ Model sbmlModel;
+
+ Map<String, S> sbmlElementByElementId = new HashMap<>();
+ Map<String, AbstractReferenceGlyph> sbmlGlyphByElementId = new HashMap<>();
+
+ private Map<String, S> sbmlElementByElementNameAndCompartmentName = new HashMap<>();
+
+ public SbmlBioEntityExporter(Layout sbmlLayout, lcsb.mapviewer.model.map.model.Model minervaModel) {
+ this.layout = sbmlLayout;
+ this.minervaModel = minervaModel;
+ }
+
+ public void exportElements(Model model) throws InconsistentModelException {
+ sbmlModel = model;
+ Collection<T> speciesList = getElementList();
+ for (T species : speciesList) {
+ S sbmlCompartment = getSbmlElement(species, null);
+
+ if (sbmlElementByElementId.get(species.getElementId()) != null) {
+ throw new InconsistentModelException("More than one species with id: " + species.getElementId());
+ }
+ sbmlElementByElementId.put(species.getElementId(), sbmlCompartment);
+ }
+ for (T species : speciesList) {
+ AbstractReferenceGlyph compartmentGlyph = createGlyph(species);
+ sbmlGlyphByElementId.put(species.getElementId(), compartmentGlyph);
+ }
+ }
+
+ protected abstract Collection<T> getElementList();
+
+ public abstract S createSbmlElement(T element) throws InconsistentModelException;
+
+ protected S getSbmlElement(T element, String compartmentName) throws InconsistentModelException {
+ String mapKey = element.getName() + "\n" + compartmentName;
+ if (sbmlElementByElementNameAndCompartmentName.get(mapKey) == null) {
+ S sbmlElement = createSbmlElement(element);
+ sbmlElement.setName(element.getName());
+ try {
+ sbmlElement.setNotes(element.getNotes());
+ } catch (XMLStreamException e) {
+ throw new InvalidStateException(e);
+ }
+ sbmlElementByElementNameAndCompartmentName.put(mapKey, sbmlElement);
+ }
+ return sbmlElementByElementNameAndCompartmentName.get(mapKey);
+ }
+
+ protected abstract void assignLayoutToGlyph(T element, AbstractReferenceGlyph compartmentGlyph);
+
+ protected AbstractReferenceGlyph createGlyph(T element) {
+ String sbmlCompartmentId = sbmlElementByElementId.get(element.getElementId()).getId();
+ String glyphId = element.getElementId();
+ AbstractReferenceGlyph compartmentGlyph = createElementGlyph(sbmlCompartmentId, glyphId);
+ assignLayoutToGlyph(element, compartmentGlyph);
+ return compartmentGlyph;
+ }
+
+ protected abstract AbstractReferenceGlyph createElementGlyph(String sbmlCompartmentId, String glyphId);
+
+}
diff --git a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlElementExporter.java b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlElementExporter.java
index de56245f1f..d0aebc087f 100644
--- a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlElementExporter.java
+++ b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlElementExporter.java
@@ -1,75 +1,20 @@
package lcsb.mapviewer.converter.model.sbml;
-import java.util.HashMap;
-import java.util.List;
-import java.util.Map;
-
-import javax.xml.stream.XMLStreamException;
-
import org.apache.log4j.Logger;
-import org.sbml.jsbml.Model;
import org.sbml.jsbml.ext.layout.AbstractReferenceGlyph;
import org.sbml.jsbml.ext.layout.BoundingBox;
import org.sbml.jsbml.ext.layout.Dimensions;
import org.sbml.jsbml.ext.layout.Layout;
import org.sbml.jsbml.ext.layout.Point;
-import lcsb.mapviewer.common.exception.InvalidStateException;
-import lcsb.mapviewer.model.map.InconsistentModelException;
import lcsb.mapviewer.model.map.species.Element;
-public abstract class SbmlElementExporter<T extends Element, S extends org.sbml.jsbml.Symbol> {
+public abstract class SbmlElementExporter<T extends Element, S extends org.sbml.jsbml.Symbol>
+ extends SbmlBioEntityExporter<T, S> {
Logger logger = Logger.getLogger(SbmlElementExporter.class);
- Layout layout;
-
- lcsb.mapviewer.model.map.model.Model minervaModel;
- Model sbmlModel;
-
- Map<String, S> sbmlElementByElementId = new HashMap<>();
- Map<String, AbstractReferenceGlyph> sbmlGlyphByElementId = new HashMap<>();
-
- private Map<String, S> sbmlElementByElementNameAndCompartmentName = new HashMap<>();
-
public SbmlElementExporter(Layout sbmlLayout, lcsb.mapviewer.model.map.model.Model minervaModel) {
- this.layout = sbmlLayout;
- this.minervaModel = minervaModel;
- }
-
- public void exportElements(Model model) throws InconsistentModelException {
- sbmlModel = model;
- List<T> speciesList = getElementList();
- for (T species : speciesList) {
- S sbmlCompartment = getSbmlElement(species, null);
-
- if (sbmlElementByElementId.get(species.getElementId()) != null) {
- throw new InconsistentModelException("More than one species with id: " + species.getElementId());
- }
- sbmlElementByElementId.put(species.getElementId(), sbmlCompartment);
- }
- for (T species : speciesList) {
- AbstractReferenceGlyph compartmentGlyph = createCompartmentGlyph(species);
- sbmlGlyphByElementId.put(species.getElementId(), compartmentGlyph);
- }
- }
-
- protected abstract List<T> getElementList();
-
- public abstract S createSbmlElement(T element) throws InconsistentModelException;
-
- protected S getSbmlElement(T element, String compartmentName) throws InconsistentModelException {
- String mapKey = element.getName() + "\n" + compartmentName;
- if (sbmlElementByElementNameAndCompartmentName.get(mapKey) == null) {
- S sbmlElement = createSbmlElement(element);
- sbmlElement.setName(element.getName());
- try {
- sbmlElement.setNotes(element.getNotes());
- } catch (XMLStreamException e) {
- throw new InvalidStateException(e);
- }
- sbmlElementByElementNameAndCompartmentName.put(mapKey, sbmlElement);
- }
- return sbmlElementByElementNameAndCompartmentName.get(mapKey);
+ super(sbmlLayout, minervaModel);
}
protected void assignLayoutToGlyph(T element, AbstractReferenceGlyph compartmentGlyph) {
@@ -84,14 +29,4 @@ public abstract class SbmlElementExporter<T extends Element, S extends org.sbml.
compartmentGlyph.setBoundingBox(boundingBox);
}
- protected AbstractReferenceGlyph createCompartmentGlyph(T compartment) {
- String sbmlCompartmentId = sbmlElementByElementId.get(compartment.getElementId()).getId();
- String glyphId = compartment.getElementId();
- AbstractReferenceGlyph compartmentGlyph = createElementGlyph(sbmlCompartmentId, glyphId);
- assignLayoutToGlyph(compartment, compartmentGlyph);
- return compartmentGlyph;
- }
-
- protected abstract AbstractReferenceGlyph createElementGlyph(String sbmlCompartmentId, String glyphId);
-
}
diff --git a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlElementParser.java b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlElementParser.java
index f97d872d5f..5250fc675f 100644
--- a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlElementParser.java
+++ b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlElementParser.java
@@ -35,28 +35,32 @@ public abstract class SbmlElementParser<T extends org.sbml.jsbml.Symbol> {
public List<Element> parseList(Model sbmlModel) throws InvalidInputDataExecption {
List<Element> result = new ArrayList<>();
for (T sbmlElement : getSbmlElementList(sbmlModel)) {
- result.add(parse(sbmlElement, sbmlModel));
+ Element element = parse(sbmlElement, sbmlModel);
+ result.add(element);
+ elementBySbmlId.put(element.getElementId(), element);
}
return result;
}
protected abstract ListOf<T> getSbmlElementList(Model sbmlModel);
+ Map<String, Element> elementBySbmlId = new HashMap<>();
+
+ public Element getAnyElementBySbmlElementId(String id) {
+ return elementBySbmlId.get(id);
+ }
+
protected List<Element> mergeLayout(List<? extends Element> elements, Layout sbmlLayout, Model sbmlModel)
throws InvalidInputDataExecption {
Set<String> used = new HashSet<>();
- Map<String, Element> elementById = new HashMap<>();
List<Element> result = new ArrayList<>();
for (Element species : elements) {
- if (elementById.get(species.getElementId()) != null) {
- throw new InvalidInputDataExecption("Duplicated element id: " + species.getElementId());
- }
- elementById.put(species.getElementId(), species);
+ elementBySbmlId.put(species.getElementId(), species);
}
for (Pair<String, AbstractReferenceGlyph> idGlyphPair : getGlyphs(sbmlLayout)) {
String id = idGlyphPair.getLeft();
- Element source = elementById.get(id);
+ Element source = elementBySbmlId.get(id);
if (source == null) {
throw new InvalidInputDataExecption("Layout contains invalid Species id: " + idGlyphPair.getLeft());
}
@@ -70,6 +74,8 @@ public abstract class SbmlElementParser<T extends org.sbml.jsbml.Symbol> {
elementWithLayout.setHeight(glyph.getBoundingBox().getDimensions().getHeight());
minervaModel.addElement(elementWithLayout);
result.add(elementWithLayout);
+ elementBySbmlId.put(id, elementWithLayout);
+ elementBySbmlId.put(elementWithLayout.getElementId(), elementWithLayout);
}
for (Element element : elements) {
if (!used.contains(element.getElementId())) {
diff --git a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlExporter.java b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlExporter.java
index 2ce062a880..0a54f2fa59 100644
--- a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlExporter.java
+++ b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlExporter.java
@@ -22,8 +22,10 @@ public class SbmlExporter {
SbmlCompartmentExporter compartmentExporter = new SbmlCompartmentExporter(layout, model);
SbmlSpeciesExporter speciesExporter = new SbmlSpeciesExporter(layout, model, compartmentExporter);
+ SbmlReactionExporter reactionExporter = new SbmlReactionExporter(layout, model, speciesExporter);
compartmentExporter.exportElements(result);
speciesExporter.exportElements(result);
+ reactionExporter.exportElements(result);
// // Create some sample content in the SBML model.
// Species specOne = result.createSpecies("test_spec1", compartment);
diff --git a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlParser.java b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlParser.java
index 2847e01973..733826af7b 100644
--- a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlParser.java
+++ b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlParser.java
@@ -62,7 +62,7 @@ public class SbmlParser implements IConverter {
SbmlCompartmentParser compartmentParser = new SbmlCompartmentParser(layout, model);
SbmlSpeciesParser speciesParser = new SbmlSpeciesParser(layout, model);
- SbmlReactionParser reactionParser = new SbmlReactionParser(layout, model);
+ SbmlReactionParser reactionParser = new SbmlReactionParser(layout, model, speciesParser);
Set<MiriamData> annotations = compartmentParser.parseAnnotation(sbmlModel.getAnnotation());
if (annotations.size() > 0) {
diff --git a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlReactionExporter.java b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlReactionExporter.java
new file mode 100644
index 0000000000..092a3b7679
--- /dev/null
+++ b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlReactionExporter.java
@@ -0,0 +1,63 @@
+package lcsb.mapviewer.converter.model.sbml;
+
+import java.util.Collection;
+
+import org.apache.log4j.Logger;
+import org.sbml.jsbml.Species;
+import org.sbml.jsbml.ext.layout.AbstractReferenceGlyph;
+import org.sbml.jsbml.ext.layout.Layout;
+
+import lcsb.mapviewer.model.map.InconsistentModelException;
+import lcsb.mapviewer.model.map.reaction.Modifier;
+import lcsb.mapviewer.model.map.reaction.Product;
+import lcsb.mapviewer.model.map.reaction.Reactant;
+import lcsb.mapviewer.model.map.reaction.Reaction;
+
+public class SbmlReactionExporter extends SbmlBioEntityExporter<Reaction, org.sbml.jsbml.Reaction> {
+ Logger logger = Logger.getLogger(SbmlReactionExporter.class);
+ private int idCounter = 0;
+ private SbmlSpeciesExporter speciesExporter;
+
+ public SbmlReactionExporter(Layout layout, lcsb.mapviewer.model.map.model.Model minervaModel,
+ SbmlSpeciesExporter speciesExporter) {
+ super(layout, minervaModel);
+ this.speciesExporter = speciesExporter;
+ }
+
+ @Override
+ public org.sbml.jsbml.Reaction createSbmlElement(Reaction reaction) throws InconsistentModelException {
+ org.sbml.jsbml.Reaction result = sbmlModel.createReaction("reaction_" + (idCounter++));
+ for (Product product : reaction.getProducts()) {
+ Species sbmlSymbol = speciesExporter.sbmlElementByElementId.get(product.getElement().getElementId());
+ result.createProduct(sbmlSymbol);
+ }
+ for (Reactant reactant : reaction.getReactants()) {
+ Species sbmlSymbol = speciesExporter.sbmlElementByElementId.get(reactant.getElement().getElementId());
+ result.createReactant(sbmlSymbol);
+ }
+ for (Modifier modifier : reaction.getModifiers()) {
+ Species sbmlSymbol = speciesExporter.sbmlElementByElementId.get(modifier.getElement().getElementId());
+ result.createModifier(sbmlSymbol);
+ }
+ return result;
+ }
+
+ @Override
+ protected AbstractReferenceGlyph createElementGlyph(String sbmlElementId, String glyphId) {
+// AbstractReferenceGlyph speciesGlyph = layout.createReactionGlyph(glyphId, sbmlElementId);
+// return speciesGlyph;
+ return null;
+ }
+
+ @Override
+ protected Collection<Reaction> getElementList() {
+ return minervaModel.getReactions();
+ }
+
+ @Override
+ protected void assignLayoutToGlyph(Reaction element, AbstractReferenceGlyph compartmentGlyph) {
+ // TODO Auto-generated method stub
+
+ }
+
+}
diff --git a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlReactionParser.java b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlReactionParser.java
index f96d4e2f7b..33b08697c0 100644
--- a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlReactionParser.java
+++ b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlReactionParser.java
@@ -55,9 +55,13 @@ public class SbmlReactionParser {
lcsb.mapviewer.model.map.model.Model minervaModel;
ElementUtils eu = new ElementUtils();
- public SbmlReactionParser(Layout sbmlLayout, lcsb.mapviewer.model.map.model.Model minervaModel) {
+ SbmlSpeciesParser speciesParser;
+
+ public SbmlReactionParser(Layout sbmlLayout, lcsb.mapviewer.model.map.model.Model minervaModel,
+ SbmlSpeciesParser speciesParser) {
this.layout = sbmlLayout;
this.minervaModel = minervaModel;
+ this.speciesParser = speciesParser;
}
public List<Reaction> parseList(Model sbmlModel) throws InvalidInputDataExecption {
@@ -224,7 +228,11 @@ public class SbmlReactionParser {
Set<Reaction> elementsToRemove = new HashSet<>();
for (Reaction reaction : reactions) {
if (!used.contains(reaction)) {
- logger.warn("Layout doesn't contain information about Reaction: " + reaction.getIdReaction());
+ for (ReactionNode node : reaction.getReactionNodes()) {
+ // we might have different elements here, the reason is that single SBML species
+ // can be split into two or more (due to layout)
+ node.setElement(speciesParser.getAnyElementBySbmlElementId(node.getElement().getElementId()));
+ }
} else {
elementsToRemove.add(reaction);
}
diff --git a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlSpeciesParser.java b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlSpeciesParser.java
index 648d7002ba..7b0900458d 100644
--- a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlSpeciesParser.java
+++ b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlSpeciesParser.java
@@ -91,7 +91,7 @@ public class SbmlSpeciesParser extends SbmlElementParser<org.sbml.jsbml.Species>
compartment = compartment2;
}
}
-
+
}
if (compartment != null) {
compartment.addElement(element);
diff --git a/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/SbmlExporterTest.java b/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/SbmlExporterTest.java
index a5a7554748..a6cda5f298 100644
--- a/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/SbmlExporterTest.java
+++ b/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/SbmlExporterTest.java
@@ -21,6 +21,7 @@ import lcsb.mapviewer.model.map.compartment.Compartment;
import lcsb.mapviewer.model.map.model.Model;
import lcsb.mapviewer.model.map.reaction.Reaction;
import lcsb.mapviewer.model.map.reaction.ReactionNode;
+import lcsb.mapviewer.model.map.species.Element;
import lcsb.mapviewer.model.map.species.Species;
public class SbmlExporterTest {
@@ -51,7 +52,8 @@ public class SbmlExporterTest {
String xml = exporter.toXml(originalModel);
ByteArrayInputStream stream = new ByteArrayInputStream(xml.getBytes("UTF-8"));
Model result = parser.createModel(new ConverterParams().inputStream(stream));
-
+// showImage(originalModel);
+// showImage(result);
return result;
}
@@ -118,17 +120,4 @@ public class SbmlExporterTest {
assertEquals(2, reaction.getOperators().size());
}
- @Test
- public void testReactionWithoutLayout() throws Exception {
- Model model = getModelAfterSerializing("testFiles/layoutExample/Complete_Example_level2.xml");
- assertNotNull(model);
- assertEquals(1, model.getReactions().size());
- Reaction reaction = model.getReactions().iterator().next();
- for (ReactionNode node : reaction.getReactionNodes()) {
- assertNotNull(node.getLine());
- assertTrue(node.getLine().length() > 0);
- }
- assertEquals(2, reaction.getOperators().size());
- }
-
}
diff --git a/model-command/src/main/java/lcsb/mapviewer/commands/layout/ApplySimpleLayoutModelCommand.java b/model-command/src/main/java/lcsb/mapviewer/commands/layout/ApplySimpleLayoutModelCommand.java
index 83cfd8e86b..041820ea04 100644
--- a/model-command/src/main/java/lcsb/mapviewer/commands/layout/ApplySimpleLayoutModelCommand.java
+++ b/model-command/src/main/java/lcsb/mapviewer/commands/layout/ApplySimpleLayoutModelCommand.java
@@ -114,8 +114,6 @@ public class ApplySimpleLayoutModelCommand extends ApplyLayoutModelCommand {
protected void modifyElementLocation(Collection<Element> elements, Compartment parent, Point2D minPoint,
Dimension2D dimension) {
- logger.debug(minPoint);
- logger.debug(dimension);
Set<Compartment> compartments = new HashSet<>();
Set<Species> elementToAlign = new HashSet<>();
Map<Compartment, Set<Element>> elementsByStaticCompartment = new HashMap<>();
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/BioEntity.java b/model/src/main/java/lcsb/mapviewer/model/map/BioEntity.java
index 70319d5914..068af61908 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/BioEntity.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/BioEntity.java
@@ -173,4 +173,6 @@ public interface BioEntity extends Serializable {
*/
Model getModel();
+ String getElementId();
+
}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/reaction/Reaction.java b/model/src/main/java/lcsb/mapviewer/model/map/reaction/Reaction.java
index 5d04e7781c..d1139cf5a6 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/reaction/Reaction.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/reaction/Reaction.java
@@ -621,6 +621,11 @@ public class Reaction implements BioEntity {
return idReaction;
}
+ @Override
+ public String getElementId() {
+ return getIdReaction();
+ }
+
/**
* @param idReaction
* the idReaction to set
--
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