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 9897735de5cfc5ffaa43123b20eeb70f84616ef8..3e8819a342f1f91c004c230e26bdf9967e09cbb3 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
@@ -20,8 +20,6 @@ import org.sbml.jsbml.ext.layout.Layout;
import org.sbml.jsbml.ext.layout.LayoutModelPlugin;
import org.sbml.jsbml.ext.multi.MultiModelPlugin;
import org.sbml.jsbml.ext.multi.MultiSpeciesType;
-import org.sbml.jsbml.ext.multi.PossibleSpeciesFeatureValue;
-import org.sbml.jsbml.ext.multi.SpeciesFeatureType;
import org.sbml.jsbml.ext.render.GlobalRenderInformation;
import org.sbml.jsbml.ext.render.RenderLayoutPlugin;
@@ -29,23 +27,16 @@ 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.SBOTermSpeciesType;
import lcsb.mapviewer.converter.model.sbml.species.SbmlSpeciesExporter;
import lcsb.mapviewer.converter.model.sbml.units.SbmlUnitExporter;
import lcsb.mapviewer.model.map.InconsistentModelException;
-import lcsb.mapviewer.model.map.species.Complex;
-import lcsb.mapviewer.model.map.species.Element;
-import lcsb.mapviewer.model.map.species.Protein;
import lcsb.mapviewer.model.map.species.Species;
-import lcsb.mapviewer.modelutils.map.ElementUtils;
public class SbmlExporter {
@SuppressWarnings("unused")
private static Logger logger = Logger.getLogger(SbmlExporter.class);
- private int idCounter = 0;
-
/**
* Set of SBML extensions that should be used during export.
*/
@@ -94,10 +85,8 @@ public class SbmlExporter {
createSbmlLayout(model, result);
}
- MultiModelPlugin multiPlugin = null;
if (usedExtensions.contains(SbmlExtension.MULTI)) {
- multiPlugin = createSbmlMultiPlugin(result);
- assignModelDataToTypes(multiPlugin, model);
+ createSbmlMultiPlugin(result);
}
SbmlCompartmentExporter compartmentExporter = new SbmlCompartmentExporter(result, model, usedExtensions);
@@ -119,40 +108,6 @@ public class SbmlExporter {
return doc;
}
- private void assignModelDataToTypes(MultiModelPlugin multiPlugin, lcsb.mapviewer.model.map.model.Model model) {
- for (Species species : model.getSpeciesList()) {
- MultiSpeciesType speciesType = speciesTypeByClass.get(species.getClass());
- addStructuralStateToPossibleValues(speciesType, species);
- if (species instanceof Species) {
- addPositionToCompartmentToPossibleValues(speciesType, ((Species) species));
- }
- }
-
- }
-
- private void addStructuralStateToPossibleValues(MultiSpeciesType speciesType, Species species) {
- String structuralState = null;
- if (species instanceof Protein) {
- structuralState = ((Protein) species).getStructuralState();
- } else if (species instanceof Complex) {
- structuralState = ((Complex) species).getStructuralState();
- }
- if (structuralState != null) {
- SpeciesFeatureType feature = speciesType.getListOfSpeciesFeatureTypes()
- .get(MultiPackageNamingUtils.getStructuralStateFeatureId(species));
- addPosibleValueToFeature(feature, structuralState);
- }
-
- }
-
- private void addPositionToCompartmentToPossibleValues(MultiSpeciesType speciesType, Species species) {
- if (species.getPositionToCompartment() != null) {
- SpeciesFeatureType feature = speciesType.getListOfSpeciesFeatureTypes()
- .get(MultiPackageNamingUtils.getPositionToCompartmentFeatureId(species));
- addPosibleValueToFeature(feature, species.getPositionToCompartment().name());
- }
- }
-
/**
* Create SBML layout for the given model.
*
@@ -192,58 +147,9 @@ public class SbmlExporter {
protected MultiModelPlugin createSbmlMultiPlugin(Model result) {
MultiModelPlugin multiPlugin = new MultiModelPlugin(result);
result.addExtension("multi", multiPlugin);
- for (Class<? extends Element> clazz : new ElementUtils().getAvailableElementSubclasses()) {
- if (Species.class.isAssignableFrom(clazz)) {
- createSpeciesTypeForClass(multiPlugin, clazz);
- }
- }
return multiPlugin;
}
- @SuppressWarnings("unchecked")
- private void createSpeciesTypeForClass(MultiModelPlugin multiPlugin, Class<? extends Element> clazz) {
- MultiSpeciesType speciesType = new MultiSpeciesType();
- speciesType.setName(clazz.getSimpleName());
- speciesType.setId(MultiPackageNamingUtils.getSpeciesTypeId(clazz));
- if (Protein.class.isAssignableFrom(clazz) || Complex.class.isAssignableFrom(clazz)) {
- createStructuralStateFeature(clazz, speciesType);
- }
- createPositionToCompartmentFeature(clazz, speciesType);
- multiPlugin.getListOfSpeciesTypes().add(speciesType);
- speciesTypeByClass.put(clazz, speciesType);
- speciesType.setSBOTerm(SBOTermSpeciesType.getTermByType((Class<? extends Species>) clazz));
- }
-
- private void createStructuralStateFeature(Class<? extends Element> clazz, MultiSpeciesType speciesType) {
- SpeciesFeatureType feature = new SpeciesFeatureType();
- feature.setName("Structural state");
- feature.setId(MultiPackageNamingUtils.getStructuralStateFeatureId(clazz));
- addPosibleValueToFeature(feature, "");
- speciesType.getListOfSpeciesFeatureTypes().add(feature);
- }
-
- private void createPositionToCompartmentFeature(Class<? extends Element> clazz, MultiSpeciesType speciesType) {
- SpeciesFeatureType feature = new SpeciesFeatureType();
- feature.setName("Position to compartment");
- feature.setId(MultiPackageNamingUtils.getPositionToCompartmentFeatureId(clazz));
- addPosibleValueToFeature(feature, "undefined");
- speciesType.getListOfSpeciesFeatureTypes().add(feature);
- }
-
- private void addPosibleValueToFeature(SpeciesFeatureType feature, String value) {
- boolean alreadyExists = false;
- for (PossibleSpeciesFeatureValue existingValue : feature.getListOfPossibleSpeciesFeatureValues()) {
- if (existingValue.getName().equals(value)) {
- alreadyExists = true;
- }
- }
- if (!alreadyExists) {
- PossibleSpeciesFeatureValue featureEmptyValue = new PossibleSpeciesFeatureValue();
- featureEmptyValue.setId(feature.getId() + "_" + (idCounter++));
- featureEmptyValue.setName(value);
- feature.getListOfPossibleSpeciesFeatureValues().add(featureEmptyValue);
- }
- }
/**
* Creates SBML render plugin for SBML model.
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 04e566a37f31ae43e4bef280bc642d2ac2cc6d77..eb1b3053c6da1e9d591440e0dc0659d53af24a72 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
@@ -6,6 +6,7 @@ import java.util.List;
import org.apache.log4j.Logger;
import org.sbml.jsbml.Model;
import org.sbml.jsbml.ext.layout.AbstractReferenceGlyph;
+import org.sbml.jsbml.ext.multi.MultiModelPlugin;
import org.sbml.jsbml.ext.multi.MultiSpeciesPlugin;
import org.sbml.jsbml.ext.multi.MultiSpeciesType;
import org.sbml.jsbml.ext.multi.PossibleSpeciesFeatureValue;
@@ -14,19 +15,20 @@ import org.sbml.jsbml.ext.multi.SpeciesFeatureType;
import org.sbml.jsbml.ext.multi.SpeciesFeatureValue;
import org.sbml.jsbml.ext.render.LocalStyle;
-import lcsb.mapviewer.common.exception.InvalidStateException;
import lcsb.mapviewer.converter.model.sbml.MultiPackageNamingUtils;
import lcsb.mapviewer.converter.model.sbml.SbmlElementExporter;
import lcsb.mapviewer.converter.model.sbml.SbmlExtension;
import lcsb.mapviewer.converter.model.sbml.compartment.SbmlCompartmentExporter;
import lcsb.mapviewer.model.map.InconsistentModelException;
import lcsb.mapviewer.model.map.species.Complex;
+import lcsb.mapviewer.model.map.species.Element;
import lcsb.mapviewer.model.map.species.Protein;
import lcsb.mapviewer.model.map.species.Species;
-import lcsb.mapviewer.modelutils.map.ElementUtils;
public class SbmlSpeciesExporter extends SbmlElementExporter<Species, org.sbml.jsbml.Species> {
+ private static int idCounter = 0;
+
/**
* Default class logger.
*/
@@ -84,18 +86,9 @@ public class SbmlSpeciesExporter extends SbmlElementExporter<Species, org.sbml.j
structuralState = ((Complex) element).getStructuralState();
}
if (structuralState != null) {
- SpeciesFeatureType structuralStateFeature = speciesType
- .getSpeciesFeatureType(MultiPackageNamingUtils.getStructuralStateFeatureId(element));
- PossibleSpeciesFeatureValue structuralStateFeatureValue = null;
- for (PossibleSpeciesFeatureValue value : structuralStateFeature.getListOfPossibleSpeciesFeatureValues()) {
- if (value.getName().equals(structuralState)) {
- structuralStateFeatureValue = value;
- }
- }
- if (structuralStateFeatureValue == null) {
- throw new InvalidStateException(
- new ElementUtils().getElementTag(element) + "Cannot find structural state value for: " + structuralState);
- }
+ SpeciesFeatureType structuralStateFeature = getStructuralStateFeature(element.getClass(), speciesType);
+ PossibleSpeciesFeatureValue structuralStateFeatureValue = getPosibleFeatureIdByName(structuralState,
+ structuralStateFeature);
SpeciesFeature feature = multiExtension.createSpeciesFeature();
feature.setSpeciesFeatureType(structuralStateFeature.getId());
@@ -105,25 +98,29 @@ public class SbmlSpeciesExporter extends SbmlElementExporter<Species, org.sbml.j
}
}
- private void assignPostionToCompartmentToMulti(Species element, MultiSpeciesPlugin multiExtension,
- MultiSpeciesType speciesType) {
- String positionToCompartmentName = "undefined";
- if (element.getPositionToCompartment() != null) {
- positionToCompartmentName = element.getPositionToCompartment().name();
- }
- SpeciesFeatureType structuralStateFeature = speciesType
- .getSpeciesFeatureType(MultiPackageNamingUtils.getPositionToCompartmentFeatureId(element));
+ private PossibleSpeciesFeatureValue getPosibleFeatureIdByName(String featureValueName,
+ SpeciesFeatureType speciesFeature) {
PossibleSpeciesFeatureValue structuralStateFeatureValue = null;
- for (PossibleSpeciesFeatureValue value : structuralStateFeature.getListOfPossibleSpeciesFeatureValues()) {
- if (value.getName().equals(positionToCompartmentName)) {
+ for (PossibleSpeciesFeatureValue value : speciesFeature.getListOfPossibleSpeciesFeatureValues()) {
+ if (value.getName().equals(featureValueName)) {
structuralStateFeatureValue = value;
}
}
if (structuralStateFeatureValue == null) {
- throw new InvalidStateException(
- new ElementUtils().getElementTag(element) + "Cannot find position to compartment value for: "
- + positionToCompartmentName);
+ structuralStateFeatureValue = addPosibleValueToFeature(speciesFeature, featureValueName);
}
+ return structuralStateFeatureValue;
+ }
+
+ private void assignPostionToCompartmentToMulti(Species element, MultiSpeciesPlugin multiExtension,
+ MultiSpeciesType speciesType) {
+ String positionToCompartmentName = "undefined";
+ if (element.getPositionToCompartment() != null) {
+ positionToCompartmentName = element.getPositionToCompartment().name();
+ }
+ SpeciesFeatureType structuralStateFeature = getPositionToCompartmentFeature(element.getClass(), speciesType);
+ PossibleSpeciesFeatureValue structuralStateFeatureValue = getPosibleFeatureIdByName(positionToCompartmentName,
+ structuralStateFeature);
SpeciesFeature feature = multiExtension.createSpeciesFeature();
feature.setSpeciesFeatureType(structuralStateFeature.getId());
@@ -133,8 +130,10 @@ public class SbmlSpeciesExporter extends SbmlElementExporter<Species, org.sbml.j
}
private MultiSpeciesType getMultiSpeciesType(Species element) {
- MultiSpeciesType speciesType = getMultiPlugin()
- .getSpeciesType(MultiPackageNamingUtils.getSpeciesTypeId(element));
+ MultiSpeciesType speciesType = getMultiPlugin().getSpeciesType(MultiPackageNamingUtils.getSpeciesTypeId(element));
+ if (speciesType == null) {
+ speciesType = createSpeciesTypeForClass(getMultiPlugin(), element.getClass());
+ }
return speciesType;
}
@@ -170,7 +169,8 @@ public class SbmlSpeciesExporter extends SbmlElementExporter<Species, org.sbml.j
}
multiDistinguisher = structuralState;
}
- String result =element.getClass().getSimpleName() + "\n" + element.getName() + "\n" + compartmentName + "\n" + complexName
+ String result = element.getClass().getSimpleName() + "\n" + element.getName() + "\n" + compartmentName + "\n"
+ + complexName
+ "\n" + multiDistinguisher;
return result;
}
@@ -181,4 +181,65 @@ public class SbmlSpeciesExporter extends SbmlElementExporter<Species, org.sbml.j
return style;
}
+ @SuppressWarnings("unchecked")
+ private MultiSpeciesType createSpeciesTypeForClass(MultiModelPlugin multiPlugin, Class<? extends Element> clazz) {
+ MultiSpeciesType speciesType = new MultiSpeciesType();
+ speciesType.setName(clazz.getSimpleName());
+ speciesType.setId(MultiPackageNamingUtils.getSpeciesTypeId(clazz));
+ multiPlugin.getListOfSpeciesTypes().add(speciesType);
+ speciesType.setSBOTerm(SBOTermSpeciesType.getTermByType((Class<? extends Species>) clazz));
+ return speciesType;
+ }
+
+ private SpeciesFeatureType getStructuralStateFeature(Class<? extends Element> clazz, MultiSpeciesType speciesType) {
+ SpeciesFeatureType feature = speciesType
+ .getSpeciesFeatureType(MultiPackageNamingUtils.getStructuralStateFeatureId(clazz));
+ if (feature == null) {
+ feature = new SpeciesFeatureType();
+ feature.setName("Structural state");
+ feature.setId(MultiPackageNamingUtils.getStructuralStateFeatureId(clazz));
+ addPosibleValueToFeature(feature, "");
+ speciesType.getListOfSpeciesFeatureTypes().add(feature);
+ }
+ return feature;
+ }
+
+ private SpeciesFeatureType getPositionToCompartmentFeature(Class<? extends Element> clazz,
+ MultiSpeciesType speciesType) {
+ SpeciesFeatureType feature = speciesType
+ .getSpeciesFeatureType(MultiPackageNamingUtils.getPositionToCompartmentFeatureId(clazz));
+ if (feature == null) {
+ feature = new SpeciesFeatureType();
+ feature.setName("Position to compartment");
+ feature.setId(MultiPackageNamingUtils.getPositionToCompartmentFeatureId(clazz));
+ addPosibleValueToFeature(feature, "undefined");
+ speciesType.getListOfSpeciesFeatureTypes().add(feature);
+ }
+ return feature;
+ }
+
+ private PossibleSpeciesFeatureValue addPosibleValueToFeature(SpeciesFeatureType feature, String value) {
+ PossibleSpeciesFeatureValue result = null;
+ for (PossibleSpeciesFeatureValue existingValue : feature.getListOfPossibleSpeciesFeatureValues()) {
+ if (existingValue.getName().equals(value)) {
+ result = existingValue;
+ }
+ }
+ if (result == null) {
+ result = new PossibleSpeciesFeatureValue();
+ result.setId(feature.getId() + "_" + (idCounter++));
+ result.setName(value);
+ feature.getListOfPossibleSpeciesFeatureValues().add(result);
+ }
+ return result;
+ }
+
+ private void addPositionToCompartmentToPossibleValues(MultiSpeciesType speciesType, Species species) {
+ if (species.getPositionToCompartment() != null) {
+ SpeciesFeatureType feature = speciesType.getListOfSpeciesFeatureTypes()
+ .get(MultiPackageNamingUtils.getPositionToCompartmentFeatureId(species));
+ addPosibleValueToFeature(feature, species.getPositionToCompartment().name());
+ }
+ }
+
}
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 cffe83e9340a9cbbbf15bd7a40d84a99147e78e9..5181a0ff31165f12502c278e49534c43a73b1f49 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
@@ -13,7 +13,6 @@ import java.io.File;
import java.lang.reflect.Modifier;
import java.nio.file.Files;
import java.util.Arrays;
-import java.util.HashSet;
import java.util.Set;
import org.apache.log4j.Logger;
@@ -43,13 +42,9 @@ 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.reaction.type.StateTransitionReaction;
-import lcsb.mapviewer.model.map.species.Complex;
import lcsb.mapviewer.model.map.species.Element;
import lcsb.mapviewer.model.map.species.GenericProtein;
-import lcsb.mapviewer.model.map.species.IonChannelProtein;
-import lcsb.mapviewer.model.map.species.ReceptorProtein;
import lcsb.mapviewer.model.map.species.Species;
-import lcsb.mapviewer.model.map.species.TruncatedProtein;
import lcsb.mapviewer.model.map.species.field.ModificationState;
import lcsb.mapviewer.model.map.species.field.PositionToCompartment;
import lcsb.mapviewer.model.map.species.field.Residue;
@@ -431,26 +426,6 @@ public class SbmlExporterTest {
assertTrue("Species types are not exported", multiPlugin.getListOfSpeciesTypes().size() > 0);
}
- @Test
- public void testMultiExtensionTypeWithStructuralState() throws Exception {
- SbmlExporter exporter = new SbmlExporter();
- SBMLDocument doc = new SBMLDocument(3, 2);
- org.sbml.jsbml.Model result = doc.createModel("id");
- MultiModelPlugin multiPlugin = exporter.createSbmlMultiPlugin(result);
-
- Set<Class<?>> typesWithStructuralStates = new HashSet<>();
- typesWithStructuralStates.addAll(Arrays.asList(new Class<?>[] { GenericProtein.class, TruncatedProtein.class,
- Complex.class, IonChannelProtein.class, ReceptorProtein.class }));
-
- for (Class<?> clazz : typesWithStructuralStates) {
- MultiSpeciesType speciesType = multiPlugin.getSpeciesType(MultiPackageNamingUtils.getSpeciesTypeId(clazz));
- assertTrue(clazz.getSimpleName() + " doesn't have any features, but at least structuralState expected",
- speciesType.getListOfSpeciesFeatureTypes().size() > 0);
-
- }
-
- }
-
@Test
public void testMultiExtensionSBOTermsForTypes() throws Exception {
SbmlExporter exporter = new SbmlExporter();