From 29c25fc9bc62d70271199feee34d671951076dce Mon Sep 17 00:00:00 2001
From: Piotr Gawron <piotr.gawron@uni.lu>
Date: Wed, 2 Jan 2019 09:55:41 +0100
Subject: [PATCH] export/import of position to compartment implemented
---
.../converter/model/sbml/SbmlExporter.java | 62 ++++++++++++++-----
.../sbml/species/SbmlSpeciesExporter.java | 33 ++++++++++
.../model/sbml/species/SbmlSpeciesParser.java | 19 ++++++
.../model/sbml/SbmlExporterTest.java | 17 +++++
4 files changed, 115 insertions(+), 16 deletions(-)
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 d9ec1fc0ca..99a4a95a00 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
@@ -37,6 +37,7 @@ 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.model.map.species.field.PositionToCompartment;
import lcsb.mapviewer.modelutils.map.ElementUtils;
public class SbmlExporter {
@@ -97,7 +98,7 @@ public class SbmlExporter {
MultiModelPlugin multiPlugin = null;
if (usedExtensions.contains(SbmlExtension.MULTI)) {
multiPlugin = createSbmlMultiPlugin(result);
- assignStructuralStatesToTypes(multiPlugin, model);
+ assignModelDataToTypes(multiPlugin, model);
}
SbmlCompartmentExporter compartmentExporter = new SbmlCompartmentExporter(result, model, usedExtensions);
@@ -119,18 +120,21 @@ public class SbmlExporter {
return doc;
}
- private void assignStructuralStatesToTypes(MultiModelPlugin multiPlugin, lcsb.mapviewer.model.map.model.Model model) {
+ private void assignModelDataToTypes(MultiModelPlugin multiPlugin, lcsb.mapviewer.model.map.model.Model model) {
for (Element element : model.getElements()) {
String structuralState = null;
+ MultiSpeciesType speciesType = speciesTypeByClass.get(element.getClass());
if (element instanceof Protein) {
structuralState = ((Protein) element).getStructuralState();
} else if (element instanceof Complex) {
structuralState = ((Complex) element).getStructuralState();
}
if (structuralState != null) {
- MultiSpeciesType speciesType = speciesTypeByClass.get(element.getClass());
addStructuralStateToPossibleValues(speciesType, structuralState);
}
+ if (element instanceof Species) {
+ addPositionToCompartmentToPossibleValues(speciesType, ((Species) element).getPositionToCompartment());
+ }
}
}
@@ -141,6 +145,14 @@ public class SbmlExporter {
addPosibleValueToFeature(feature, structuralState);
}
+ private void addPositionToCompartmentToPossibleValues(MultiSpeciesType speciesType, PositionToCompartment position) {
+ SpeciesFeatureType feature = speciesType.getListOfSpeciesFeatureTypes()
+ .get("minerva_position_to_compartment_" + speciesType.getName());
+ if (position != null) {
+ addPosibleValueToFeature(feature, position.name());
+ }
+ }
+
/**
* Create SBML layout for the given model.
*
@@ -183,24 +195,42 @@ public class SbmlExporter {
result.addExtension("multi", multiPlugin);
for (Class<? extends Element> clazz : new ElementUtils().getAvailableElementSubclasses()) {
if (Species.class.isAssignableFrom(clazz)) {
- MultiSpeciesType speciesType = new MultiSpeciesType();
- speciesType.setName(clazz.getSimpleName());
- speciesType.setId("minerva_species_type_" + clazz.getSimpleName());
- if (Protein.class.isAssignableFrom(clazz) || Complex.class.isAssignableFrom(clazz)) {
- SpeciesFeatureType feature = new SpeciesFeatureType();
- feature.setName("Structural state");
- feature.setId("minerva_structural_state_" + clazz.getSimpleName());
- addPosibleValueToFeature(feature, "");
- speciesType.getListOfSpeciesFeatureTypes().add(feature);
- }
- multiPlugin.getListOfSpeciesTypes().add(speciesType);
- speciesTypeByClass.put(clazz, speciesType);
- speciesType.setSBOTerm(SBOTermSpeciesType.getTermByType((Class<? extends Species>) 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("minerva_species_type_" + clazz.getSimpleName());
+ 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("minerva_structural_state_" + clazz.getSimpleName());
+ 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("minerva_position_to_compartment_" + clazz.getSimpleName());
+ addPosibleValueToFeature(feature, "undefined");
+ speciesType.getListOfSpeciesFeatureTypes().add(feature);
+ }
+
private void addPosibleValueToFeature(SpeciesFeatureType feature, String value) {
boolean alreadyExists = false;
for (PossibleSpeciesFeatureValue existingValue : feature.getListOfPossibleSpeciesFeatureValues()) {
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 b636d3937c..313f3cdf73 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
@@ -70,6 +70,12 @@ public class SbmlSpeciesExporter extends SbmlElementExporter<Species, org.sbml.j
MultiSpeciesType speciesType = getMultiSpeciesType(element);
multiExtension.setSpeciesType(speciesType.getId());
result.addExtension("multi", multiExtension);
+ assignStructuralStateToMulti(element, multiExtension, speciesType);
+ assignPostionToCompartmentToMulti(element, multiExtension, speciesType);
+ }
+
+ private void assignStructuralStateToMulti(Species element, MultiSpeciesPlugin multiExtension,
+ MultiSpeciesType speciesType) {
String structuralState = null;
if (element instanceof Protein) {
structuralState = ((Protein) element).getStructuralState();
@@ -98,6 +104,33 @@ 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("minerva_position_to_compartment_" + element.getClass().getSimpleName());
+ PossibleSpeciesFeatureValue structuralStateFeatureValue = null;
+ for (PossibleSpeciesFeatureValue value : structuralStateFeature.getListOfPossibleSpeciesFeatureValues()) {
+ if (value.getName().equals(positionToCompartmentName)) {
+ structuralStateFeatureValue = value;
+ }
+ }
+ if (structuralStateFeatureValue == null) {
+ throw new InvalidStateException(
+ new ElementUtils().getElementTag(element) + "Cannot find position to compartment value for: "
+ + positionToCompartmentName);
+ }
+
+ SpeciesFeature feature = multiExtension.createSpeciesFeature();
+ feature.setSpeciesFeatureType(structuralStateFeature.getId());
+ SpeciesFeatureValue value = new SpeciesFeatureValue();
+ value.setValue(structuralStateFeatureValue.getId());
+ feature.addSpeciesFeatureValue(value);
+ }
+
private MultiSpeciesType getMultiSpeciesType(Species element) {
MultiSpeciesType speciesType = getMultiPlugin()
.getSpeciesType("minerva_species_type_" + element.getClass().getSimpleName());
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 9308131a7f..aeff43bca2 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
@@ -32,6 +32,7 @@ import lcsb.mapviewer.model.map.species.Element;
import lcsb.mapviewer.model.map.species.Protein;
import lcsb.mapviewer.model.map.species.Species;
import lcsb.mapviewer.model.map.species.Unknown;
+import lcsb.mapviewer.model.map.species.field.PositionToCompartment;
import lcsb.mapviewer.modelutils.map.ElementUtils;
public class SbmlSpeciesParser extends SbmlElementParser<org.sbml.jsbml.Species> {
@@ -124,6 +125,24 @@ public class SbmlSpeciesParser extends SbmlElementParser<org.sbml.jsbml.Species>
} else {
logger.warn(warnPrefix + "Invalid structural state for class " + featureTypeString);
}
+ } else if (featureTypeString.startsWith("minerva_position_to_compartment_")) {
+ if (featureTypeString.equals("minerva_position_to_compartment_" + minervaElement.getClass().getSimpleName())) {
+ SpeciesFeatureType featureType = speciesType.getListOfSpeciesFeatureTypes().get(featureTypeString);
+
+ List<String> positionToCompartments = new ArrayList<>();
+ for (SpeciesFeatureValue featureValue : feature.getListOfSpeciesFeatureValues()) {
+ PossibleSpeciesFeatureValue possibleSpeciesFeatureValue = featureType.getListOfPossibleSpeciesFeatureValues()
+ .get(featureValue.getValue());
+ positionToCompartments.add(possibleSpeciesFeatureValue.getName());
+ }
+ if (positionToCompartments.size() != 1) {
+ logger.warn(warnPrefix + "Position to compartment must exactly one value");
+ } else {
+ minervaElement.setPositionToCompartment(PositionToCompartment.getByString(positionToCompartments.get(0)));
+ }
+ } else {
+ logger.warn(warnPrefix + "Invalid structural state for class " + featureTypeString);
+ }
} else {
logger.warn(warnPrefix + "Feature not supported: " + featureTypeString);
}
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 aff6bc9be3..23bcd786c0 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
@@ -50,6 +50,7 @@ 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.PositionToCompartment;
public class SbmlExporterTest {
Logger logger = Logger.getLogger(SbmlExporterTest.class);
@@ -479,6 +480,22 @@ public class SbmlExporterTest {
assertEquals("Structural state not exported/imported properly", 0, comparator.compare(model, deserializedModel));
}
+ @Test
+ public void testExportPositionToCompartment() throws Exception {
+ Model model = createEmptyModel();
+ GenericProtein element = new GenericProtein("id");
+ element.setName("test name");
+ element.setX(10);
+ element.setWidth(10);
+ element.setY(10);
+ element.setHeight(10);
+ element.setPositionToCompartment(PositionToCompartment.INSIDE);
+ model.addElement(element);
+ Model deserializedModel = getModelAfterSerializing(model);
+
+ assertEquals("Postion to compartment not exported/imported properly", 0, comparator.compare(model, deserializedModel));
+ }
+
@Test
public void testMultiExtensionProteinStateInTypes() throws Exception {
String structuralState = "xxx";
--
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