From db9da5829f0c823b3e6788c774210f429ed375e0 Mon Sep 17 00:00:00 2001
From: Piotr Gawron <piotr.gawron@uni.lu>
Date: Mon, 5 Feb 2018 10:06:45 +0100
Subject: [PATCH] simple export of reaction kinetics
---
.../java/lcsb/mapviewer/common/XmlParser.java | 2 +-
.../reaction/KineticsXmlParser.java | 6 +-
.../reaction/ReactionFromXml.java | 40 ++++++++---
.../model/sbml/SbmlBioEntityExporter.java | 3 +-
.../model/sbml/SbmlElementParser.java | 1 +
.../converter/model/sbml/SbmlExporter.java | 5 +-
.../converter/model/sbml/SbmlParser.java | 1 +
.../model/sbml/SbmlReactionExporter.java | 68 ++++++++++++++++++-
.../model/sbml/SbmlReactionParser.java | 1 +
.../model/sbml/SbmlSpeciesParser.java | 5 +-
.../model/sbml/SbmlUnitExporter.java | 30 ++++++++
.../model/sbml/GenericSbmlParserTest.java | 8 +--
.../sbml/GenericSbmlToXmlParserTest.java | 2 +-
.../model/map/InconsistentModelException.java | 30 ++++----
.../model/map/compartment/Compartment.java | 6 ++
.../map/reaction/ReactionComparator.java | 2 +
16 files changed, 172 insertions(+), 38 deletions(-)
create mode 100644 converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlUnitExporter.java
diff --git a/commons/src/main/java/lcsb/mapviewer/common/XmlParser.java b/commons/src/main/java/lcsb/mapviewer/common/XmlParser.java
index d7ac52a290..66be945a96 100644
--- a/commons/src/main/java/lcsb/mapviewer/common/XmlParser.java
+++ b/commons/src/main/java/lcsb/mapviewer/common/XmlParser.java
@@ -8,6 +8,7 @@ import java.io.InputStream;
import java.io.StringReader;
import java.io.StringWriter;
import java.util.ArrayList;
+import java.util.Collection;
import java.util.List;
import javax.xml.parsers.DocumentBuilder;
@@ -374,5 +375,4 @@ public class XmlParser {
}
return result;
}
-
}
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/reaction/KineticsXmlParser.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/reaction/KineticsXmlParser.java
index b1ae5738ed..e77e87b9d8 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/reaction/KineticsXmlParser.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/reaction/KineticsXmlParser.java
@@ -63,7 +63,11 @@ public class KineticsXmlParser extends XmlParser {
elementsUsedInKinetics.add(element);
}
result.addArguments(elementsUsedInKinetics);
- result.setDefinition(super.nodeToString(mathNode, true));
+
+ String definition = super.nodeToString(mathNode, true);
+ definition = definition.replace(" xmlns=\"http://www.sbml.org/sbml/level2/version4\"", "");
+ definition = definition.replace("<math>", "<math xmlns=\"http://www.w3.org/1998/Math/MathML\">");
+ result.setDefinition(definition);
return result;
}
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/reaction/ReactionFromXml.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/reaction/ReactionFromXml.java
index c0a3ef113e..cbf7f44399 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/reaction/ReactionFromXml.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/reaction/ReactionFromXml.java
@@ -225,20 +225,40 @@ public class ReactionFromXml extends XmlParser {
for (Node node : elementNodes) {
String speciesId = super.getNodeAttr("species", node);
String aliasId = super.getNodeAttr("alias", node);
- Element element = model.getElementByElementId(aliasId);
- result.put(speciesId, element);
-
- Compartment compartment = element.getCompartment();
- if (compartment != null) {
- // in kinetics we can have reference to compartment (so we need to find SBML
- // compartment id)
- String compartmentId = elements.getElementByElementId(compartment.getElementId()).getElementId();
- result.put(compartmentId, compartment);
- }
+ addElementMapping(model, result, speciesId, aliasId);
+ }
+
+ for (Node node : super.getAllNotNecessirellyDirectChild("celldesigner:reactantLink", annotationNode)) {
+ String speciesId = super.getNodeAttr("reactant", node);
+ String aliasId = super.getNodeAttr("alias", node);
+ addElementMapping(model, result, speciesId, aliasId);
+ }
+
+ for (Node node : super.getAllNotNecessirellyDirectChild("celldesigner:productLink", annotationNode)) {
+ String speciesId = super.getNodeAttr("product", node);
+ String aliasId = super.getNodeAttr("alias", node);
+ addElementMapping(model, result, speciesId, aliasId);
}
+
return result;
}
+ private void addElementMapping(Model model, Map<String, Element> result, String speciesId, String aliasId) {
+ Element element = model.getElementByElementId(aliasId);
+ result.put(speciesId, element);
+ addCompartmentMapping(result, element);
+ }
+
+ private void addCompartmentMapping(Map<String, Element> result, Element element) {
+ Compartment compartment = element.getCompartment();
+ if (compartment != null) {
+ // in kinetics we can have reference to compartment (so we need to find SBML
+ // compartment id)
+ String compartmentId = elements.getElementByElementId(compartment.getElementId()).getElementId();
+ result.put(compartmentId, compartment);
+ }
+ }
+
/**
* Parses reaction annotation node and update reaction.
*
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
index 97f1c528a8..b864632fea 100644
--- 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
@@ -11,11 +11,12 @@ import org.sbml.jsbml.Model;
import org.sbml.jsbml.ext.layout.AbstractReferenceGlyph;
import org.sbml.jsbml.ext.layout.Layout;
+import lcsb.mapviewer.common.XmlParser;
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> {
+public abstract class SbmlBioEntityExporter<T extends BioEntity, S extends org.sbml.jsbml.AbstractNamedSBase> extends XmlParser {
Logger logger = Logger.getLogger(SbmlBioEntityExporter.class);
Layout layout;
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 5987e77f0c..7cd9676e7a 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
@@ -15,6 +15,7 @@ import org.sbml.jsbml.ext.layout.Layout;
import lcsb.mapviewer.common.Pair;
import lcsb.mapviewer.converter.InvalidInputDataExecption;
+import lcsb.mapviewer.model.map.compartment.Compartment;
import lcsb.mapviewer.model.map.species.Element;
public abstract class SbmlElementParser<T extends org.sbml.jsbml.Symbol> extends SbmlBioEntityParser {
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 cc105d8a04..1b159bd344 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
@@ -25,10 +25,13 @@ public class SbmlExporter {
SbmlCompartmentExporter compartmentExporter = new SbmlCompartmentExporter(layout, model);
SbmlBioEntityExporter<Species, org.sbml.jsbml.Species> speciesExporter = new SbmlSpeciesExporter(layout, model,
compartmentExporter);
- SbmlReactionExporter reactionExporter = new SbmlReactionExporter(layout, model, speciesExporter);
+ SbmlReactionExporter reactionExporter = new SbmlReactionExporter(layout, model, speciesExporter, compartmentExporter);
+ SbmlUnitExporter unitExporter = new SbmlUnitExporter(model);
compartmentExporter.exportElements(result);
speciesExporter.exportElements(result);
reactionExporter.exportElements(result);
+ unitExporter.exportUnits(result);
+
ByteArrayOutputStream stream = new ByteArrayOutputStream();
SBMLWriter.write(doc, stream, "minerva", "1.0");
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 5d17c13bd7..07429d9d30 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
@@ -226,6 +226,7 @@ public class SbmlParser implements IConverter {
throws ConverterException, InconsistentModelException, IOException {
File file = new File(filePath);
String exportedString = toXml(model);
+ logger.debug(exportedString);
FileWriter fileWriter = new FileWriter(file);
fileWriter.write(exportedString);
fileWriter.flush();
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
index a563670114..02ec6cbdf8 100644
--- 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
@@ -7,6 +7,9 @@ import java.util.List;
import java.util.Map;
import org.apache.log4j.Logger;
+import org.sbml.jsbml.ASTNode;
+import org.sbml.jsbml.KineticLaw;
+import org.sbml.jsbml.LocalParameter;
import org.sbml.jsbml.SimpleSpeciesReference;
import org.sbml.jsbml.Species;
import org.sbml.jsbml.SpeciesReference;
@@ -18,26 +21,35 @@ import org.sbml.jsbml.ext.layout.Point;
import org.sbml.jsbml.ext.layout.ReactionGlyph;
import org.sbml.jsbml.ext.layout.SpeciesReferenceGlyph;
import org.sbml.jsbml.ext.layout.SpeciesReferenceRole;
+import org.sbml.jsbml.text.parser.ParseException;
+import org.w3c.dom.Node;
import lcsb.mapviewer.common.Configuration;
+import lcsb.mapviewer.common.exception.InvalidXmlSchemaException;
import lcsb.mapviewer.model.map.InconsistentModelException;
+import lcsb.mapviewer.model.map.compartment.Compartment;
+import lcsb.mapviewer.model.map.kinetics.SbmlKinetics;
+import lcsb.mapviewer.model.map.kinetics.SbmlParameter;
import lcsb.mapviewer.model.map.modifier.Inhibition;
-import lcsb.mapviewer.model.map.modifier.Modulation;
import lcsb.mapviewer.model.map.modifier.Trigger;
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;
import lcsb.mapviewer.model.map.reaction.ReactionNode;
+import lcsb.mapviewer.model.map.species.Element;
public class SbmlReactionExporter extends SbmlBioEntityExporter<Reaction, org.sbml.jsbml.Reaction> {
Logger logger = Logger.getLogger(SbmlReactionExporter.class);
private SbmlBioEntityExporter<lcsb.mapviewer.model.map.species.Species, Species> speciesExporter;
+ private SbmlBioEntityExporter<Compartment, org.sbml.jsbml.Compartment> compartmentExporter;
public SbmlReactionExporter(Layout layout, lcsb.mapviewer.model.map.model.Model minervaModel,
- SbmlBioEntityExporter<lcsb.mapviewer.model.map.species.Species, Species> speciesExporter) {
+ SbmlBioEntityExporter<lcsb.mapviewer.model.map.species.Species, Species> speciesExporter,
+ SbmlBioEntityExporter<lcsb.mapviewer.model.map.compartment.Compartment, org.sbml.jsbml.Compartment> compartmentExporter) {
super(layout, minervaModel);
this.speciesExporter = speciesExporter;
+ this.compartmentExporter = compartmentExporter;
}
Map<ReactionNode, SimpleSpeciesReference> speciesReferenceByReactionNode = new HashMap<>();
@@ -66,9 +78,61 @@ public class SbmlReactionExporter extends SbmlBioEntityExporter<Reaction, org.sb
SimpleSpeciesReference speciesReference = result.createModifier(sbmlSymbol);
speciesReferenceByReactionNode.put(modifier, speciesReference);
}
+ if (reaction.getKinetics() != null) {
+ result.setKineticLaw(createKineticLaw(reaction));
+ }
return result;
}
+ private KineticLaw createKineticLaw(Reaction reaction) throws InconsistentModelException {
+ SbmlKinetics kinetics = reaction.getKinetics();
+ KineticLaw result = new KineticLaw();
+ for (SbmlParameter minervaParameter : kinetics.getParameters()) {
+ if (minervaModel.getParameterById(minervaParameter.getElementId()) == null) {
+ LocalParameter parameter = new LocalParameter();
+ parameter.setId(minervaParameter.getElementId());
+ parameter.setName(minervaParameter.getName());
+ parameter.setValue(minervaParameter.getValue());
+ parameter.setUnits(minervaParameter.getUnits().getUnitId());
+ result.addLocalParameter(parameter);
+ }
+ }
+
+ try {
+ Node node = super.getXmlDocumentFromString(kinetics.getDefinition());
+ for (Node ciNode : super.getAllNotNecessirellyDirectChild("ci", node)) {
+ String id = super.getNodeValue(ciNode).trim();
+ Element element = minervaModel.getElementByElementId(id);
+ if (element != null) {
+ String sbmlId = null;
+ Species species= speciesExporter.sbmlElementByElementId.get(id);
+ if (species !=null) {
+ sbmlId = species.getId();
+ } else {
+ sbmlId = compartmentExporter.sbmlElementByElementId.get(id).getId();
+ }
+
+ logger.debug(id);
+ logger.debug(element.getElementId());
+ logger.debug(speciesExporter);
+ logger.debug(speciesExporter.sbmlElementByElementId);
+ logger.debug(speciesExporter.sbmlElementByElementId.get(element.getElementId()));
+ ciNode.setTextContent(sbmlId);
+ }
+ }
+ String definition = super.nodeToString(node);
+ definition = definition.replace(" xmlns=\"http://www.sbml.org/sbml/level2/version4\"", "");
+ definition = definition.replace("<math>", "<math xmlns=\"http://www.w3.org/1998/Math/MathML\">");
+ logger.debug(definition);
+ result.setMath(ASTNode.parseMathML(definition));
+ logger.debug(result.getMathMLString());
+ return result;
+ } catch (InvalidXmlSchemaException e) {
+ throw new InconsistentModelException(e);
+ }
+
+ }
+
private String getReactionId(Reaction reaction) {
int separatorIndex = reaction.getElementId().indexOf("__");
if (separatorIndex > 0) {
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 0f91b7a80c..cceec32e95 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
@@ -305,6 +305,7 @@ public class SbmlReactionParser extends SbmlBioEntityParser {
elementsUsedInKinetics.add(element);
}
result.addArguments(elementsUsedInKinetics);
+ result.setDefinition(super.nodeToString(node));
} catch (InvalidXmlSchemaException e) {
throw new InvalidInputDataExecption(e);
}
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 15b76f37b1..1a9826c4e3 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
@@ -40,6 +40,9 @@ public class SbmlSpeciesParser extends SbmlElementParser<org.sbml.jsbml.Species>
try {
Species result = clazz.getConstructor(String.class).newInstance(species.getId());
assignBioEntityData(species, result);
+ if (layout == null) {
+ assignCompartment(result, species.getCompartment());
+ }
return result;
} catch (SecurityException | NoSuchMethodException | InstantiationException | IllegalAccessException
| IllegalArgumentException | InvocationTargetException e) {
@@ -67,7 +70,7 @@ public class SbmlSpeciesParser extends SbmlElementParser<org.sbml.jsbml.Species>
private void assignCompartment(Element element, String compartmentId) {
Compartment compartment = minervaModel.getElementByElementId(compartmentId);
- if (compartment == null) {
+ if (compartment == null && layout != null) {
List<Compartment> compartments = new ArrayList<>();
for (CompartmentGlyph glyph : layout.getListOfCompartmentGlyphs()) {
if (glyph.getCompartment().equals(compartmentId)) {
diff --git a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlUnitExporter.java b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlUnitExporter.java
new file mode 100644
index 0000000000..27e2fa310d
--- /dev/null
+++ b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlUnitExporter.java
@@ -0,0 +1,30 @@
+package lcsb.mapviewer.converter.model.sbml;
+
+import org.apache.log4j.Logger;
+import org.sbml.jsbml.UnitDefinition;
+
+import lcsb.mapviewer.model.map.kinetics.SbmlUnit;
+import lcsb.mapviewer.model.map.model.Model;
+
+public class SbmlUnitExporter {
+ Logger logger = Logger.getLogger(SbmlUnitExporter.class);
+ private Model minervaModel;
+
+ public SbmlUnitExporter(lcsb.mapviewer.model.map.model.Model minervaModel) {
+ this.minervaModel = minervaModel;
+ }
+
+ public void exportUnits(org.sbml.jsbml.Model result) {
+ for (SbmlUnit unit : minervaModel.getUnits()) {
+ result.addUnitDefinition(createUnitDefinition(unit));
+ }
+ }
+
+ private UnitDefinition createUnitDefinition(SbmlUnit unit) {
+ UnitDefinition result = new UnitDefinition();
+ result.setId(unit.getUnitId());
+ result.setName(unit.getName());
+ return result;
+ }
+
+}
diff --git a/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/GenericSbmlParserTest.java b/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/GenericSbmlParserTest.java
index 9266510347..026f607a24 100644
--- a/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/GenericSbmlParserTest.java
+++ b/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/GenericSbmlParserTest.java
@@ -7,7 +7,6 @@ import java.io.ByteArrayInputStream;
import java.io.File;
import java.io.IOException;
import java.io.InputStream;
-import java.io.PrintWriter;
import java.nio.file.Files;
import java.nio.file.Path;
import java.nio.file.Paths;
@@ -60,7 +59,7 @@ public class GenericSbmlParserTest {
@Test
public void createModelTest() throws Exception {
try {
- String dir = Files.createTempDirectory("sbgn-temp-images-dir").toFile().getAbsolutePath();
+ String dir = Files.createTempDirectory("sbml-temp-images-dir").toFile().getAbsolutePath();
IConverter converter = new SbmlParser();
@@ -80,11 +79,6 @@ public class GenericSbmlParserTest {
CellDesignerXmlParser cellDesignerXmlParser = new CellDesignerXmlParser();
String xmlString = cellDesignerXmlParser.toXml(model);
- String cellDesignerFilePath = pathWithouExtension.concat("_CD.xml");
- PrintWriter out = new PrintWriter(cellDesignerFilePath);
- out.print(xmlString);
- out.close();
-
InputStream is = new ByteArrayInputStream(xmlString.getBytes("UTF-8"));
Model model2 = cellDesignerXmlParser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
diff --git a/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/GenericSbmlToXmlParserTest.java b/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/GenericSbmlToXmlParserTest.java
index 65211af194..7fbdd583ff 100644
--- a/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/GenericSbmlToXmlParserTest.java
+++ b/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/GenericSbmlToXmlParserTest.java
@@ -59,7 +59,7 @@ public class GenericSbmlToXmlParserTest {
+ filePath.getFileName().toString().substring(0, filePath.getFileName().toString().indexOf(".xml"));
String xmlFilePath = pathWithouExtension.concat(".xml");
converter.exportModelToFile(model, xmlFilePath);
-
+
Model model2 = converter.createModel(new ConverterParams().filename(xmlFilePath));
model2.setName(null);
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/InconsistentModelException.java b/model/src/main/java/lcsb/mapviewer/model/map/InconsistentModelException.java
index 2b339c01e9..a823e1bf11 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/InconsistentModelException.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/InconsistentModelException.java
@@ -7,18 +7,22 @@ package lcsb.mapviewer.model.map;
*
*/
public class InconsistentModelException extends Exception {
- /**
- *
- */
- private static final long serialVersionUID = 1L;
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
- /**
- * Default constructor with a message passed in the argument.
- *
- * @param message
- * text message of this exception
- */
- public InconsistentModelException(String message) {
- super(message);
- }
+ /**
+ * Default constructor with a message passed in the argument.
+ *
+ * @param message
+ * text message of this exception
+ */
+ public InconsistentModelException(String message) {
+ super(message);
+ }
+
+ public InconsistentModelException(Exception e) {
+ super(e);
+ }
}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/compartment/Compartment.java b/model/src/main/java/lcsb/mapviewer/model/map/compartment/Compartment.java
index b06a1b5dd4..bfba815afd 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/compartment/Compartment.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/compartment/Compartment.java
@@ -395,4 +395,10 @@ public class Compartment extends Element {
return "Compartment";
}
+ public void removeElements(Set<Element> elements) {
+ for (Element element : elements) {
+ removeElement(element);
+ }
+ }
+
}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/reaction/ReactionComparator.java b/model/src/main/java/lcsb/mapviewer/model/map/reaction/ReactionComparator.java
index eb812a44ed..856ed07348 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/reaction/ReactionComparator.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/reaction/ReactionComparator.java
@@ -177,6 +177,8 @@ public class ReactionComparator extends Comparator<Reaction> {
SbmlKineticsComparator kineticsComparator = new SbmlKineticsComparator();
if (kineticsComparator.compare(arg0.getKinetics(), arg1.getKinetics()) != 0) {
logger.debug("Kinetics different");
+ logger.debug(arg0.getKinetics());
+ logger.debug(arg1.getKinetics());
return kineticsComparator.compare(arg0.getKinetics(), arg1.getKinetics());
}
return 0;
--
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