From c09422ac2f3d395ff058723c7d3fedce329f548f Mon Sep 17 00:00:00 2001
From: Piotr Gawron <piotr.gawron@uni.lu>
Date: Fri, 16 Nov 2018 18:15:01 +0100
Subject: [PATCH] export to sbml includes default compartment, and import
ingornes this compartment
---
.../model/sbml/SbmlBioEntityExporter.java | 2 +-
.../model/sbml/SbmlCompartmentExporter.java | 39 --------
.../model/sbml/SbmlElementParser.java | 6 +-
.../converter/model/sbml/SbmlExporter.java | 1 +
.../converter/model/sbml/SbmlParser.java | 2 +
.../compartment/SbmlCompartmentExporter.java | 96 +++++++++++++++++++
.../SbmlCompartmentParser.java | 12 ++-
.../sbml/reaction/SbmlReactionParser.java | 2 +-
.../sbml/species/SbmlSpeciesExporter.java | 8 +-
.../model/sbml/species/SbmlSpeciesParser.java | 2 +-
.../model/sbml/SbmlExporterTest.java | 2 +
.../reaction/SbmlReactionExportArrowType.java | 1 +
.../reaction/SbmlReactionExporterTest.java | 2 +-
.../sbml/species/SbmlSpeciesExporterTest.java | 2 +-
14 files changed, 123 insertions(+), 54 deletions(-)
delete mode 100644 converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlCompartmentExporter.java
create mode 100644 converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/compartment/SbmlCompartmentExporter.java
rename converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/{ => compartment}/SbmlCompartmentParser.java (84%)
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 be31323ace..58f4824698 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
@@ -38,7 +38,7 @@ public abstract class SbmlBioEntityExporter<T extends BioEntity, S extends org.s
private Map<String, S> sbmlElementByElementId = new HashMap<>();
Map<String, AbstractReferenceGlyph> sbmlGlyphByElementId = new HashMap<>();
- private Map<String, S> sbmlElementByElementNameAndCompartmentName = new HashMap<>();
+ protected Map<String, S> sbmlElementByElementNameAndCompartmentName = new HashMap<>();
private int idCounter = 0;
diff --git a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlCompartmentExporter.java b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlCompartmentExporter.java
deleted file mode 100644
index 2399328b4f..0000000000
--- a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlCompartmentExporter.java
+++ /dev/null
@@ -1,39 +0,0 @@
-package lcsb.mapviewer.converter.model.sbml;
-
-import java.util.List;
-
-import org.apache.log4j.Logger;
-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.compartment.Compartment;
-
-public class SbmlCompartmentExporter extends SbmlElementExporter<Compartment, org.sbml.jsbml.Compartment> {
- Logger logger = Logger.getLogger(SbmlCompartmentExporter.class);
-
- public SbmlCompartmentExporter(Layout layout, lcsb.mapviewer.model.map.model.Model minervaModel) {
- super(layout, minervaModel);
- }
-
- @Override
- public org.sbml.jsbml.Compartment createSbmlElement(Compartment element) throws InconsistentModelException {
- return getSbmlModel().createCompartment("comp_" + (getNextId()));
- }
-
- @Override
- protected List<Compartment> getElementList() {
- return getMinervaModel().getCompartments();
- }
-
- @Override
- protected AbstractReferenceGlyph createElementGlyph(String sbmlCompartmentId, String glyphId) {
- return getLayout().createCompartmentGlyph(glyphId, sbmlCompartmentId);
- }
-
- @Override
- protected String getSbmlIdKey(Compartment element) {
- return element.getName();
- }
-
-}
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 8f630430f0..fd13c6671c 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
@@ -33,8 +33,10 @@ public abstract class SbmlElementParser<T extends org.sbml.jsbml.Symbol> extends
List<Element> result = new ArrayList<>();
for (T sbmlElement : getSbmlElementList(sbmlModel)) {
Element element = parse(sbmlElement, sbmlModel);
- result.add(element);
- elementBySbmlId.put(element.getElementId(), element);
+ if (element != null) {
+ result.add(element);
+ elementBySbmlId.put(element.getElementId(), element);
+ }
}
return result;
}
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 c3461c3d7d..4b2b94f06f 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
@@ -18,6 +18,7 @@ import org.sbml.jsbml.ext.render.RenderLayoutPlugin;
import lcsb.mapviewer.common.Configuration;
import lcsb.mapviewer.common.exception.InvalidStateException;
+import lcsb.mapviewer.converter.model.sbml.compartment.SbmlCompartmentExporter;
import lcsb.mapviewer.converter.model.sbml.reaction.SbmlReactionExporter;
import lcsb.mapviewer.converter.model.sbml.species.SbmlSpeciesExporter;
import lcsb.mapviewer.converter.model.sbml.units.SbmlUnitExporter;
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 2b97fc6adf..2696dc1037 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
@@ -29,12 +29,14 @@ import lcsb.mapviewer.converter.ConverterException;
import lcsb.mapviewer.converter.ConverterParams;
import lcsb.mapviewer.converter.IConverter;
import lcsb.mapviewer.converter.InvalidInputDataExecption;
+import lcsb.mapviewer.converter.model.sbml.compartment.SbmlCompartmentParser;
import lcsb.mapviewer.converter.model.sbml.reaction.SbmlReactionParser;
import lcsb.mapviewer.converter.model.sbml.species.SbmlSpeciesParser;
import lcsb.mapviewer.converter.model.sbml.units.SbmlUnitsParser;
import lcsb.mapviewer.model.map.BioEntity;
import lcsb.mapviewer.model.map.InconsistentModelException;
import lcsb.mapviewer.model.map.MiriamData;
+import lcsb.mapviewer.model.map.compartment.Compartment;
import lcsb.mapviewer.model.map.model.Model;
import lcsb.mapviewer.model.map.model.ModelFullIndexed;
import lcsb.mapviewer.model.map.modifier.Modulation;
diff --git a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/compartment/SbmlCompartmentExporter.java b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/compartment/SbmlCompartmentExporter.java
new file mode 100644
index 0000000000..a2c9440808
--- /dev/null
+++ b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/compartment/SbmlCompartmentExporter.java
@@ -0,0 +1,96 @@
+package lcsb.mapviewer.converter.model.sbml.compartment;
+
+import java.util.ArrayList;
+import java.util.List;
+
+import org.apache.log4j.Logger;
+import org.sbml.jsbml.ext.layout.AbstractReferenceGlyph;
+import org.sbml.jsbml.ext.layout.BoundingBox;
+import org.sbml.jsbml.ext.layout.CompartmentGlyph;
+import org.sbml.jsbml.ext.layout.Dimensions;
+import org.sbml.jsbml.ext.layout.Layout;
+import org.sbml.jsbml.ext.layout.Point;
+
+import lcsb.mapviewer.converter.model.sbml.SbmlElementExporter;
+import lcsb.mapviewer.model.map.InconsistentModelException;
+import lcsb.mapviewer.model.map.compartment.Compartment;
+
+public class SbmlCompartmentExporter extends SbmlElementExporter<Compartment, org.sbml.jsbml.Compartment> {
+ Logger logger = Logger.getLogger(SbmlCompartmentExporter.class);
+
+ public SbmlCompartmentExporter(Layout layout, lcsb.mapviewer.model.map.model.Model minervaModel) {
+ super(layout, minervaModel);
+ }
+
+ @Override
+ public org.sbml.jsbml.Compartment createSbmlElement(Compartment element) throws InconsistentModelException {
+ if (element == null || element.getElementId().equals("default")) {
+ return getSbmlModel().createCompartment("default");
+ }
+ return getSbmlModel().createCompartment("comp_" + (getNextId()));
+ }
+
+ @Override
+ protected List<Compartment> getElementList() {
+ List<Compartment> result = new ArrayList<>();
+ result.addAll(getMinervaModel().getCompartments());
+ boolean defaultFound = false;
+ for (Compartment compartment : result) {
+ if (compartment.getElementId().equals("default")) {
+ defaultFound = true;
+ }
+ }
+ if (!defaultFound) {
+ Compartment defaultCompartment = new Compartment("default");
+ result.add(defaultCompartment);
+ }
+ return result;
+ }
+
+ @Override
+ protected AbstractReferenceGlyph createElementGlyph(String sbmlCompartmentId, String glyphId) {
+ if (sbmlCompartmentId.equals("default")) {
+ glyphId = "default_compartment";
+ }
+ CompartmentGlyph result = getLayout().createCompartmentGlyph(glyphId, sbmlCompartmentId);
+ return result;
+ }
+
+ @Override
+ protected String getSbmlIdKey(Compartment compartment) {
+ if (compartment == null || compartment.getElementId().equals("default")) {
+ return "default";
+ }
+ return compartment.getName();
+ }
+
+ @Override
+ protected void assignLayoutToGlyph(Compartment element, AbstractReferenceGlyph speciesGlyph) {
+ if (element.getElementId().equals("default")) {
+ BoundingBox boundingBox = new BoundingBox();
+
+ boundingBox.setPosition(new Point(element.getX(), element.getY()));
+ Dimensions dimensions = new Dimensions();
+
+ if (getMinervaModel().getWidth() != null) {
+ dimensions.setWidth(getMinervaModel().getWidth());
+ dimensions.setHeight(getMinervaModel().getHeight());
+ }
+ boundingBox.setDimensions(dimensions);
+ speciesGlyph.setBoundingBox(boundingBox);
+ } else {
+ super.assignLayoutToGlyph(element, speciesGlyph);
+ }
+ }
+
+ @Override
+ public org.sbml.jsbml.Compartment getSbmlElement(Compartment element) throws InconsistentModelException {
+ String mapKey = getSbmlIdKey(element);
+ if (element == null && sbmlElementByElementNameAndCompartmentName.get(mapKey) == null) {
+ org.sbml.jsbml.Compartment sbmlElement = createSbmlElement(element);
+ sbmlElementByElementNameAndCompartmentName.put(mapKey, sbmlElement);
+ }
+ return super.getSbmlElement(element);
+ }
+
+}
diff --git a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlCompartmentParser.java b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/compartment/SbmlCompartmentParser.java
similarity index 84%
rename from converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlCompartmentParser.java
rename to converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/compartment/SbmlCompartmentParser.java
index 1853edcf89..7fe2925b57 100644
--- a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlCompartmentParser.java
+++ b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/compartment/SbmlCompartmentParser.java
@@ -1,4 +1,4 @@
-package lcsb.mapviewer.converter.model.sbml;
+package lcsb.mapviewer.converter.model.sbml.compartment;
import java.util.ArrayList;
import java.util.List;
@@ -13,6 +13,7 @@ import org.sbml.jsbml.ext.layout.Layout;
import lcsb.mapviewer.commands.layout.ApplySimpleLayoutModelCommand;
import lcsb.mapviewer.common.Pair;
import lcsb.mapviewer.converter.InvalidInputDataExecption;
+import lcsb.mapviewer.converter.model.sbml.SbmlElementParser;
import lcsb.mapviewer.model.map.compartment.Compartment;
import lcsb.mapviewer.model.map.compartment.SquareCompartment;
import lcsb.mapviewer.model.map.species.Element;
@@ -27,6 +28,9 @@ public class SbmlCompartmentParser extends SbmlElementParser<org.sbml.jsbml.Comp
@Override
protected Compartment parse(org.sbml.jsbml.Compartment compartment, Model sbmlModel)
throws InvalidInputDataExecption {
+ if (compartment.getId().equals("default")) {
+ return null;
+ }
Compartment result = new SquareCompartment(compartment.getId());
assignBioEntityData(compartment, result);
return result;
@@ -38,7 +42,7 @@ public class SbmlCompartmentParser extends SbmlElementParser<org.sbml.jsbml.Comp
}
@Override
- protected List<Element> mergeLayout(List<? extends Element> elements, Layout sbmlLayout, Model sbmlModel)
+ public List<Element> mergeLayout(List<? extends Element> elements, Layout sbmlLayout, Model sbmlModel)
throws InvalidInputDataExecption {
List<Element> result = super.mergeLayout(elements, sbmlLayout, sbmlModel);
@@ -64,7 +68,9 @@ public class SbmlCompartmentParser extends SbmlElementParser<org.sbml.jsbml.Comp
protected List<Pair<String, AbstractReferenceGlyph>> getGlyphs(Layout sbmlLayout) {
List<Pair<String, AbstractReferenceGlyph>> result = new ArrayList<>();
for (CompartmentGlyph glyph : sbmlLayout.getListOfCompartmentGlyphs()) {
- result.add(new Pair<String, AbstractReferenceGlyph>(glyph.getCompartment(), glyph));
+ if (!glyph.getCompartment().equals("default")) {
+ result.add(new Pair<>(glyph.getCompartment(), glyph));
+ }
}
return result;
}
diff --git a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/reaction/SbmlReactionParser.java b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/reaction/SbmlReactionParser.java
index 0b001e485d..e3614d5bb4 100644
--- a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/reaction/SbmlReactionParser.java
+++ b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/reaction/SbmlReactionParser.java
@@ -35,8 +35,8 @@ import lcsb.mapviewer.common.exception.InvalidXmlSchemaException;
import lcsb.mapviewer.converter.InvalidInputDataExecption;
import lcsb.mapviewer.converter.model.celldesigner.types.ModifierType;
import lcsb.mapviewer.converter.model.sbml.SbmlBioEntityParser;
-import lcsb.mapviewer.converter.model.sbml.SbmlCompartmentParser;
import lcsb.mapviewer.converter.model.sbml.SbmlParameterParser;
+import lcsb.mapviewer.converter.model.sbml.compartment.SbmlCompartmentParser;
import lcsb.mapviewer.converter.model.sbml.species.SbmlSpeciesParser;
import lcsb.mapviewer.model.graphics.ArrowType;
import lcsb.mapviewer.model.graphics.ArrowTypeData;
diff --git a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/species/SbmlSpeciesExporter.java b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/species/SbmlSpeciesExporter.java
index dba417b273..5679f8aabd 100644
--- a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/species/SbmlSpeciesExporter.java
+++ b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/species/SbmlSpeciesExporter.java
@@ -7,8 +7,8 @@ import org.sbml.jsbml.ext.layout.AbstractReferenceGlyph;
import org.sbml.jsbml.ext.layout.Layout;
import org.sbml.jsbml.ext.render.LocalStyle;
-import lcsb.mapviewer.converter.model.sbml.SbmlCompartmentExporter;
import lcsb.mapviewer.converter.model.sbml.SbmlElementExporter;
+import lcsb.mapviewer.converter.model.sbml.compartment.SbmlCompartmentExporter;
import lcsb.mapviewer.model.map.InconsistentModelException;
import lcsb.mapviewer.model.map.species.Species;
@@ -26,9 +26,7 @@ public class SbmlSpeciesExporter extends SbmlElementExporter<Species, org.sbml.j
public org.sbml.jsbml.Species createSbmlElement(Species element) throws InconsistentModelException {
org.sbml.jsbml.Species result = getSbmlModel().createSpecies("species_" + (getNextId()));
result.setSBOTerm(SBOTermSpeciesType.getTermByType(element.getClass()));
- if (element.getCompartment() != null) {
- result.setCompartment(compartmentExporter.getSbmlElement(element.getCompartment()));
- }
+ result.setCompartment(compartmentExporter.getSbmlElement(element.getCompartment()));
if (element.getInitialAmount() != null) {
result.setInitialAmount(element.getInitialAmount());
}
@@ -56,7 +54,7 @@ public class SbmlSpeciesExporter extends SbmlElementExporter<Species, org.sbml.j
if (element.getComplex() != null) {
complexName = element.getComplex().getName();
}
- return element.getClass().getSimpleName() + "\n" + element.getName() + "\n" + compartmentName+ "\n" + complexName;
+ return element.getClass().getSimpleName() + "\n" + element.getName() + "\n" + compartmentName + "\n" + complexName;
}
protected LocalStyle createStyle(Species element) {
diff --git a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/species/SbmlSpeciesParser.java b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/species/SbmlSpeciesParser.java
index c17c23765e..baf83327bb 100644
--- a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/species/SbmlSpeciesParser.java
+++ b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/species/SbmlSpeciesParser.java
@@ -71,7 +71,7 @@ public class SbmlSpeciesParser extends SbmlElementParser<org.sbml.jsbml.Species>
if (compartment == null && layout != null) {
List<Compartment> compartments = new ArrayList<>();
for (CompartmentGlyph glyph : layout.getListOfCompartmentGlyphs()) {
- if (glyph.getCompartment().equals(compartmentId)) {
+ if (glyph.getCompartment().equals(compartmentId) && !glyph.getCompartment().equals("default")) {
compartments.add(minervaModel.getElementByElementId(glyph.getId()));
}
}
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 75a368f66c..5dfe01e510 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
@@ -184,6 +184,8 @@ public class SbmlExporterTest {
private Model createModelWithReaction() {
Model model = new ModelFullIndexed(null);
+ model.setWidth(1000);
+ model.setHeight(1000);
GenericProtein p1 = new GenericProtein("s1");
p1.setWidth(100);
p1.setHeight(20);
diff --git a/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/reaction/SbmlReactionExportArrowType.java b/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/reaction/SbmlReactionExportArrowType.java
index 99be077087..bcc59d335e 100644
--- a/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/reaction/SbmlReactionExportArrowType.java
+++ b/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/reaction/SbmlReactionExportArrowType.java
@@ -93,6 +93,7 @@ public class SbmlReactionExportArrowType {
model.addElement(ion3);
Reaction reaction = (Reaction) clazz.getConstructor().newInstance();
+ reaction.setIdReaction("reactionId");
reaction.addReactant(createReactant(ion));
Product product = createProduct(ion2);
reaction.addProduct(product);
diff --git a/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/reaction/SbmlReactionExporterTest.java b/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/reaction/SbmlReactionExporterTest.java
index 472737e3dd..b41612ed3e 100644
--- a/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/reaction/SbmlReactionExporterTest.java
+++ b/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/reaction/SbmlReactionExporterTest.java
@@ -10,7 +10,7 @@ import org.sbml.jsbml.ext.layout.Layout;
import org.sbml.jsbml.ext.layout.LayoutModelPlugin;
import lcsb.mapviewer.converter.model.sbml.SbmlBioEntityExporter;
-import lcsb.mapviewer.converter.model.sbml.SbmlCompartmentExporter;
+import lcsb.mapviewer.converter.model.sbml.compartment.SbmlCompartmentExporter;
import lcsb.mapviewer.converter.model.sbml.species.SbmlSpeciesExporter;
import lcsb.mapviewer.model.map.InconsistentModelException;
import lcsb.mapviewer.model.map.kinetics.SbmlKinetics;
diff --git a/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/species/SbmlSpeciesExporterTest.java b/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/species/SbmlSpeciesExporterTest.java
index a3ed722dd9..0a5a2db97f 100644
--- a/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/species/SbmlSpeciesExporterTest.java
+++ b/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/species/SbmlSpeciesExporterTest.java
@@ -7,8 +7,8 @@ import org.junit.Test;
import org.sbml.jsbml.SBMLDocument;
import org.sbml.jsbml.ext.layout.Layout;
-import lcsb.mapviewer.converter.model.sbml.SbmlCompartmentExporter;
import lcsb.mapviewer.converter.model.sbml.SbmlExporter;
+import lcsb.mapviewer.converter.model.sbml.compartment.SbmlCompartmentExporter;
import lcsb.mapviewer.model.map.InconsistentModelException;
import lcsb.mapviewer.model.map.compartment.Compartment;
import lcsb.mapviewer.model.map.model.Model;
--
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