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 be31323ace489bad052aa2171c8e6c23b4ffdfd4..190a2bb028a68693626e4e0b417a5ce4fbd42246 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;
@@ -150,16 +150,7 @@ public abstract class SbmlBioEntityExporter<T extends BioEntity, S extends org.s
protected ColorDefinition getColorDefinition(Color color) {
RenderLayoutPlugin renderPlugin = getRenderPlugin();
- LocalRenderInformation renderInformation = null;
- for (LocalRenderInformation lri : renderPlugin.getListOfLocalRenderInformation()) {
- if (lri.getId().equals("minerva_definitions")) {
- renderInformation = lri;
- }
- }
- if (renderInformation == null) {
- renderInformation = new LocalRenderInformation("minerva_definitions");
- renderPlugin.addLocalRenderInformation(renderInformation);
- }
+ LocalRenderInformation renderInformation = getRenderInformation(renderPlugin);
for (ColorDefinition cd : renderInformation.getListOfColorDefinitions()) {
if (cd.getValue().equals(color)) {
@@ -168,11 +159,24 @@ public abstract class SbmlBioEntityExporter<T extends BioEntity, S extends org.s
}
ColorDefinition colorDefinition = new ColorDefinition("color_" + colorToString(color), color);
-
renderInformation.addColorDefinition(colorDefinition);
return colorDefinition;
}
+ protected LocalRenderInformation getRenderInformation(RenderLayoutPlugin renderPlugin) {
+ LocalRenderInformation renderInformation = null;
+ for (LocalRenderInformation lri : renderPlugin.getListOfLocalRenderInformation()) {
+ if (lri.getId().equals("minerva_definitions")) {
+ renderInformation = lri;
+ }
+ }
+ if (renderInformation == null) {
+ renderInformation = new LocalRenderInformation("minerva_definitions");
+ renderPlugin.addLocalRenderInformation(renderInformation);
+ }
+ return renderInformation;
+ }
+
protected void assignStyleToGlyph(AbstractReferenceGlyph speciesGlyph, LocalStyle style) {
RenderGraphicalObjectPlugin rgop = new RenderGraphicalObjectPlugin(speciesGlyph);
rgop.setObjectRole(style.getRoleList().get(0));
@@ -181,12 +185,11 @@ public abstract class SbmlBioEntityExporter<T extends BioEntity, S extends org.s
}
protected LocalStyle createStyle(T element) {
- LocalRenderInformation renderInformation = new LocalRenderInformation();
+ LocalRenderInformation renderInformation = getRenderInformation(getRenderPlugin());
LocalStyle style = new LocalStyle();
style.getRoleList().add("style_" + element.getElementId());
style.setGroup(new RenderGroup());
renderInformation.addLocalStyle(style);
- getRenderPlugin().addLocalRenderInformation(renderInformation);
return style;
}
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 2399328b4f428b9a98936151c20777765a2117a6..0000000000000000000000000000000000000000
--- 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 8f630430f001d5675aaabb8b031cf18d5035623f..fd13c6671c7220751eaeaf06d8b701c1083967be 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 3d860fecee9bbe994a4011e7674ffc9c333979fd..25fa73c370852f74c3251b892851a98950cb2359 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
@@ -1,5 +1,7 @@
package lcsb.mapviewer.converter.model.sbml;
+import java.io.UnsupportedEncodingException;
+
import javax.xml.stream.XMLStreamException;
import org.apache.commons.io.output.ByteArrayOutputStream;
@@ -14,6 +16,9 @@ import org.sbml.jsbml.ext.layout.LayoutModelPlugin;
import org.sbml.jsbml.ext.render.GlobalRenderInformation;
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;
@@ -25,35 +30,40 @@ public class SbmlExporter {
public String toXml(lcsb.mapviewer.model.map.model.Model model)
throws SBMLException, XMLStreamException, InconsistentModelException {
- SBMLDocument doc = new SBMLDocument(3, 1);
- Model result = doc.createModel(model.getIdModel());
- result.setName(model.getName());
- Layout layout = createSbmlLayout(model, result);
+ try {
+ SBMLDocument doc = new SBMLDocument(3, 2);
+ Model result = doc.createModel(model.getIdModel());
+ result.setName(model.getName());
+ Layout layout = createSbmlLayout(model, result);
- 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,
- compartmentExporter);
- SbmlUnitExporter unitExporter = new SbmlUnitExporter(model);
- SbmlParameterExporter parameterExporter = new SbmlParameterExporter(model);
- SbmlFunctionExporter functionExporter = new SbmlFunctionExporter(model);
+ 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,
+ compartmentExporter);
+ SbmlUnitExporter unitExporter = new SbmlUnitExporter(model);
+ SbmlParameterExporter parameterExporter = new SbmlParameterExporter(model);
+ SbmlFunctionExporter functionExporter = new SbmlFunctionExporter(model);
- compartmentExporter.exportElements(result);
- speciesExporter.exportElements(result);
- reactionExporter.exportElements(result);
- unitExporter.exportUnits(result);
- parameterExporter.exportParameter(result);
- functionExporter.exportFunction(result);
+ compartmentExporter.exportElements(result);
+ speciesExporter.exportElements(result);
+ reactionExporter.exportElements(result);
+ unitExporter.exportUnits(result);
+ parameterExporter.exportParameter(result);
+ functionExporter.exportFunction(result);
- ByteArrayOutputStream stream = new ByteArrayOutputStream();
- SBMLWriter.write(doc, stream, "minerva", "1.0");
- return stream.toString();
+ ByteArrayOutputStream stream = new ByteArrayOutputStream();
+ SBMLWriter.write(doc, stream, "minerva", Configuration.getSystemVersion(null));
+ return stream.toString("UTF-8");
+ } catch (UnsupportedEncodingException e) {
+ throw new InvalidStateException(e);
+ }
}
public Layout createSbmlLayout(lcsb.mapviewer.model.map.model.Model model, Model result) {
LayoutModelPlugin layoutPlugin = new LayoutModelPlugin(result);
Layout layout = new Layout();
+ layout.setId("minerva_layout");
Dimensions dimensions = new Dimensions();
if (model.getHeight() != null) {
dimensions.setHeight(model.getHeight());
@@ -68,7 +78,7 @@ public class SbmlExporter {
layout.setDimensions(dimensions);
layoutPlugin.add(layout);
result.addExtension("layout", layoutPlugin);
-
+
createSbmlRenderPlugin(layout, result);
return layout;
}
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 2b97fc6adfaf3290c49edee6f5527386218b81bd..2696dc103750d1e660b955e74782e2b711bd99cd 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 0000000000000000000000000000000000000000..d47b472dc0d2920154d1d807a1cd8aa43a5ec53f
--- /dev/null
+++ b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/compartment/SbmlCompartmentExporter.java
@@ -0,0 +1,101 @@
+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 {
+ org.sbml.jsbml.Compartment result;
+ if (element == null || element.getElementId().equals("default")) {
+ result = getSbmlModel().createCompartment("default");
+ } else {
+ result = getSbmlModel().createCompartment("comp_" + (getNextId()));
+ }
+ //for now we don't have this information - needed for validation
+ result.setConstant(false);
+ return result;
+ }
+
+ @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 1853edcf89e597da59a2304fe944df56474bbe1d..7fe2925b571841f96f5baa348b556e42127f4000 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/SbmlReactionExporter.java b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/reaction/SbmlReactionExporter.java
index 5594f48fabb34e57ac59942acbf55576d0723715..441ee02e450c67864debaa1f489399fd54f78157 100644
--- a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/reaction/SbmlReactionExporter.java
+++ b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/reaction/SbmlReactionExporter.java
@@ -77,11 +77,13 @@ public class SbmlReactionExporter extends SbmlBioEntityExporter<Reaction, org.sb
for (Product product : reaction.getProducts()) {
Species sbmlSymbol = speciesExporter.getSbmlElementByElementId(product.getElement().getElementId());
SpeciesReference speciesReference = result.createProduct(sbmlSymbol);
+ speciesReference.setConstant(false);
speciesReferenceByReactionNode.put(product, speciesReference);
}
for (Reactant reactant : reaction.getReactants()) {
Species sbmlSymbol = speciesExporter.getSbmlElementByElementId(reactant.getElement().getElementId());
SpeciesReference speciesReference = result.createReactant(sbmlSymbol);
+ speciesReference.setConstant(false);
speciesReferenceByReactionNode.put(reactant, speciesReference);
}
for (Modifier modifier : reaction.getModifiers()) {
@@ -261,13 +263,12 @@ public class SbmlReactionExporter extends SbmlBioEntityExporter<Reaction, org.sb
}
private LocalStyle createStyleForModifier(Modifier modifier) {
- LocalRenderInformation renderInformation = new LocalRenderInformation();
+ LocalRenderInformation renderInformation = getRenderInformation(getRenderPlugin());
LocalStyle style = new LocalStyle();
style.getRoleList()
.add("style_" + modifier.getReaction().getElementId() + "_modifier_" + modifier.getElement().getElementId());
style.setGroup(new RenderGroup());
renderInformation.addLocalStyle(style);
- getRenderPlugin().addLocalRenderInformation(renderInformation);
style.getGroup().setStroke(modifier.getLine().getType().name());
return style;
}
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 0b001e485d9d1fc40bc7c96b5451b80da3ec81bb..e3614d5bb4eda32a71b24d0b6229cdde783a253e 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 dba417b2738f687400dc32e25ea076b234e8eb52..806ba53900fdce13be552be6f00f72c7a04b770c 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;
@@ -26,12 +26,19 @@ 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());
}
+ if (element.hasOnlySubstanceUnits() != null) {
+ result.setHasOnlySubstanceUnits(element.hasOnlySubstanceUnits());
+ }
+ if (element.getBoundaryCondition() != null) {
+ result.setBoundaryCondition(element.getBoundaryCondition());
+ }
+ if (element.getConstant() != null) {
+ result.setConstant(element.getConstant());
+ }
return result;
}
@@ -56,7 +63,7 @@ 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 c17c23765e6b96ef4e29f3a242395b22d58f82b5..7e9d35443eb4bd1f50e548bff33a8726f25a04a3 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
@@ -37,6 +37,15 @@ public class SbmlSpeciesParser extends SbmlElementParser<org.sbml.jsbml.Species>
if (!Double.isNaN(species.getInitialAmount())) {
result.setInitialAmount(species.getInitialAmount());
}
+ if (species.isSetHasOnlySubstanceUnits()) {
+ result.setOnlySubstanceUnits(species.hasOnlySubstanceUnits());
+ }
+ if (species.isSetBoundaryCondition()) {
+ result.setBoundaryCondition(species.getBoundaryCondition());
+ }
+ if (species.isSetConstant()) {
+ result.setConstant(species.getConstant());
+ }
assignBioEntityData(species, result);
if (layout == null) {
assignCompartment(result, species.getCompartment());
@@ -71,7 +80,7 @@ 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 75a368f66c5e5c02a882a3a552a22c7b35c67f71..2a71a99c922b843070be949031bb9c62f553153b 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
@@ -68,7 +68,6 @@ public class SbmlExporterTest {
private Model getModelAfterSerializing(Model originalModel) throws Exception {
String xml = exporter.toXml(originalModel);
- logger.debug(xml);
ByteArrayInputStream stream = new ByteArrayInputStream(xml.getBytes("UTF-8"));
Model result = parser.createModel(new ConverterParams().inputStream(stream));
// showImage(originalModel);
@@ -184,6 +183,8 @@ 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 99be07708747cd4e6001d377039ecedb064867dd..d630040e5a232218753722f4afd2a09723271eeb 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
@@ -68,31 +68,17 @@ public class SbmlReactionExportArrowType {
Model model = new ModelFullIndexed(null);
model.setWidth(1000);
model.setHeight(1000);
- Ion ion = new Ion("x1");
- ion.setName("ion 1");
- ion.setWidth(100);
- ion.setHeight(100);
- ion.setX(200);
- ion.setY(50);
+ Ion ion = createIon(1);
model.addElement(ion);
- Ion ion2 = new Ion("x2");
- ion2.setName("ion 1");
- ion2.setWidth(100);
- ion2.setHeight(100);
- ion2.setX(200);
- ion2.setY(250);
+ Ion ion2 = createIon(2);
model.addElement(ion2);
- Ion ion3 = new Ion("x3");
- ion3.setName("ion 1");
- ion3.setWidth(100);
- ion3.setHeight(100);
- ion3.setX(400);
- ion3.setY(450);
+ Ion ion3 = createIon(3);
model.addElement(ion3);
Reaction reaction = (Reaction) clazz.getConstructor().newInstance();
+ reaction.setIdReaction("reactionId");
reaction.addReactant(createReactant(ion));
Product product = createProduct(ion2);
reaction.addProduct(product);
@@ -133,6 +119,20 @@ public class SbmlReactionExportArrowType {
return modelAfterSerialization;
}
+ private static Ion createIon(int id) {
+ Ion ion = new Ion("x" + id);
+ ion.setName("ion " + id);
+ ion.setWidth(100);
+ ion.setHeight(100);
+ ion.setX(200 * (id % 2 + 1));
+ ion.setY(50 * (id / 2 + 1));
+ ion.setOnlySubstanceUnits(true);
+ ion.setConstant(true);
+ ion.setInitialAmount(2.0);
+ ion.setBoundaryCondition(true);
+ return ion;
+ }
+
private static Reactant createReactant(Ion ion) {
Reactant result = new Reactant(ion);
Point2D point = ion.getCenter();
@@ -164,7 +164,7 @@ public class SbmlReactionExportArrowType {
Reaction originalReaction = modelToBeTested.getReactions().iterator().next();
Reaction afterSerializationReaction = modelAfterSerialization.getReactions().iterator().next();
-
+
afterSerializationReaction.setIdReaction(originalReaction.getIdReaction());
assertEquals(0, reactionComparator.compare(originalReaction, afterSerializationReaction));
} catch (Exception e) {
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 472737e3dd47a1c5d0c837a68da664a05bea1255..b41612ed3ec30e12d23dbfba3fb338e177e67970 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 a3ed722dd9f0e8e8ac8a43b54718feb80bac05f5..0a5a2db97f858a34d10b2be982b7b44ab6efd84b 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;
diff --git a/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/species/SbmlSpeciesParserTest.java b/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/species/SbmlSpeciesParserTest.java
index 99fd30b620d0a1e04ad903aaab9975a434516b1d..320f64b88aaef466070471fa289582caa970680d 100644
--- a/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/species/SbmlSpeciesParserTest.java
+++ b/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/species/SbmlSpeciesParserTest.java
@@ -152,4 +152,10 @@ public class SbmlSpeciesParserTest {
Species element = model.getElementByElementId("s1");
assertEquals((Double)1.0, element.getInitialAmount());
}
+ @Test
+ public void testParseHasOnlySubstanceUnits() throws Exception {
+ Model model = parser.createModel(new ConverterParams().filename("testFiles/small/has_only_substance_units.xml"));
+ Species element = model.getElementByElementId("s1");
+ assertTrue(element.hasOnlySubstanceUnits());
+ }
}
diff --git a/converter-sbml/testFiles/small/has_only_substance_units.xml b/converter-sbml/testFiles/small/has_only_substance_units.xml
new file mode 100644
index 0000000000000000000000000000000000000000..311e9322fa3558a7cf9f003310cf54ac13869473
--- /dev/null
+++ b/converter-sbml/testFiles/small/has_only_substance_units.xml
@@ -0,0 +1,26 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml xmlns="http://www.sbml.org/sbml/level2/version4" level="2" version="4">
+ <model id="TestGEN">
+ <annotation/>
+ <listOfCompartments>
+ <compartment constant="true" id="cell" name="cell" sboTerm="SBO:0000290" size="1">
+ <annotation>
+ <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqmodel="http://biomodels.net/model-qualifiers/" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+ <rdf:Description rdf:about="#">
+ <bqbiol:isVersionOf>
+ <rdf:Bag>
+ <rdf:li rdf:resource="urn:miriam:obo.go:GO:0005623"/>
+ </rdf:Bag>
+ </bqbiol:isVersionOf>
+ </rdf:Description>
+ </rdf:RDF>
+ </annotation>
+ </compartment>
+ </listOfCompartments>
+ <listOfSpecies>
+ <species boundaryCondition="false" compartment="cell" hasOnlySubstanceUnits="true" id="s1" name="nm1" sboTerm="SBO:0000247" initialAmount="1">
+ <annotation/>
+ </species>
+ </listOfSpecies>
+ </model>
+</sbml>
\ No newline at end of file