From 47679cc55a6341c79c83691aecd421ef5240a6b4 Mon Sep 17 00:00:00 2001
From: Piotr Gawron <piotr.gawron@uni.lu>
Date: Wed, 23 Oct 2019 13:28:26 +0200
Subject: [PATCH] import/export of new structural state implemented
---
.../sbml/species/SbmlSpeciesExporter.java | 79 ++++++++++++++++++-
.../model/sbml/species/SbmlSpeciesParser.java | 79 +++++++++++++++++--
.../model/sbml/SbmlExporterTest.java | 25 +++---
.../sbml/species/SbmlSpeciesExporterTest.java | 5 +-
4 files changed, 169 insertions(+), 19 deletions(-)
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 a7cf1fdfd1..3688c5e1e8 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
@@ -32,6 +32,7 @@ public class SbmlSpeciesExporter extends SbmlElementExporter<Species, org.sbml.j
private SbmlCompartmentExporter compartmentExporter;
private int modificationResidueCounter = 0;
+ private int structuralStateCounter = 0;
private Map<String, String> modificationResidueIds = new HashMap<>();
public SbmlSpeciesExporter(Model sbmlModel,
@@ -172,14 +173,15 @@ public class SbmlSpeciesExporter extends SbmlElementExporter<Species, org.sbml.j
private void assignStructuralStateToMulti(Species element, MultiSpeciesPlugin multiExtension,
MultiSpeciesType speciesType) {
- String structuralState = null;
+ StructuralState structuralState = null;
if (element instanceof Protein) {
structuralState = ((Protein) element).getStructuralState();
} else if (element instanceof Complex) {
structuralState = ((Complex) element).getStructuralState();
}
if (structuralState != null) {
- assignValueToFeature(element, multiExtension, speciesType, structuralState, BioEntityFeature.STRUCTURAL_STATE);
+ assignValueToFeature(element, multiExtension, speciesType, structuralState.getValue(),
+ BioEntityFeature.STRUCTURAL_STATE);
}
}
@@ -374,13 +376,16 @@ public class SbmlSpeciesExporter extends SbmlElementExporter<Species, org.sbml.j
String multiDistinguisher = null;
if (isExtensionEnabled(SbmlExtension.MULTI)) {
- String structuralState = null;
+ StructuralState structuralState = null;
if (element instanceof Protein) {
+
structuralState = ((Protein) element).getStructuralState();
} else if (element instanceof Complex) {
structuralState = ((Complex) element).getStructuralState();
}
- multiDistinguisher = structuralState;
+ if (structuralState != null) {
+ multiDistinguisher = structuralState.getValue();
+ }
if (element instanceof SpeciesWithModificationResidue) {
List<String> modifications = new ArrayList<>();
@@ -465,6 +470,9 @@ public class SbmlSpeciesExporter extends SbmlElementExporter<Species, org.sbml.j
createModificationGlyph(mr, speciesGlyph);
}
}
+ if (element.getStructuralState() != null) {
+ createStructuralStateGlyph(element, speciesGlyph);
+ }
}
TextGlyph textGlyph = getLayout().createTextGlyph("text_" + element.getElementId(), element.getName());
textGlyph
@@ -484,6 +492,44 @@ public class SbmlSpeciesExporter extends SbmlElementExporter<Species, org.sbml.j
}
+ private void createStructuralStateGlyph(Species element, AbstractReferenceGlyph speciesGlyph) {
+ org.sbml.jsbml.Species sbmlSpecies = getSbmlModel().getSpecies(speciesGlyph.getReference());
+
+ MultiSpeciesPlugin speciesExtension = (MultiSpeciesPlugin) sbmlSpecies.getExtension("multi");
+
+ SpeciesFeatureType structuralStateFeature = getFeature(element.getClass(), getMultiSpeciesType(element),
+ BioEntityFeature.STRUCTURAL_STATE);
+
+ PossibleSpeciesFeatureValue possibleSpeciesFeatureValue = getPosibleFeatureIdByName(
+ element.getStructuralState().getValue(), structuralStateFeature);
+
+ SpeciesFeature feature = null;
+ for (SpeciesFeature existingFeature : speciesExtension.getListOfSpeciesFeatures()) {
+ if (existingFeature.getSpeciesFeatureType().equals(structuralStateFeature.getId())) {
+ feature = existingFeature;
+ }
+ }
+
+ SpeciesFeatureValue modificationFeatureValue = null;
+ for (SpeciesFeatureValue featureValue : feature.getListOfSpeciesFeatureValues()) {
+ if (possibleSpeciesFeatureValue.getId().equals(featureValue.getValue())) {
+ modificationFeatureValue = featureValue;
+ }
+ }
+
+ modificationFeatureValue.setId(getStructuralStateUniqueId(element.getStructuralState()));
+
+ GeneralGlyph modificationGlyph = getLayout().createGeneralGlyph("structural_state_" + (idCounter++),
+ modificationFeatureValue.getId());
+ ReferenceGlyph referenceGlyph = new ReferenceGlyph("structural_state_reference_" + (idCounter++));
+ referenceGlyph.setGlyph(speciesGlyph.getId());
+ referenceGlyph.setBoundingBox(createBoundingBoxForStructuralState(element.getStructuralState()));
+
+ modificationGlyph.addReferenceGlyph(referenceGlyph);
+ modificationGlyph.setBoundingBox(createBoundingBoxForStructuralState(element.getStructuralState()));
+
+ }
+
@SuppressWarnings("unchecked")
private MultiSpeciesType createSpeciesTypeForClass(MultiModelPlugin multiPlugin, Class<? extends Element> clazz) {
MultiSpeciesType speciesType = new MultiSpeciesType();
@@ -560,6 +606,20 @@ public class SbmlSpeciesExporter extends SbmlElementExporter<Species, org.sbml.j
modificationGlyph.setBoundingBox(createBoundingBoxForModification(mr));
}
+ private BoundingBox createBoundingBoxForStructuralState(StructuralState structuralState) {
+ double width = structuralState.getWidth();
+ double height = structuralState.getHeight();
+ double x = structuralState.getPosition().getX();
+ double y = structuralState.getPosition().getY();
+ BoundingBox boundingBox = new BoundingBox();
+ boundingBox.setPosition(new Point(x, y, structuralState.getSpecies().getZ() + 1));
+ Dimensions dimensions = new Dimensions();
+ dimensions.setWidth(width);
+ dimensions.setHeight(height);
+ boundingBox.setDimensions(dimensions);
+ return boundingBox;
+ }
+
private BoundingBox createBoundingBoxForModification(ModificationResidue mr) {
double width, height;
if (mr instanceof AbstractRegionModification) {
@@ -592,4 +652,15 @@ public class SbmlSpeciesExporter extends SbmlElementExporter<Species, org.sbml.j
return result;
}
+ private String getStructuralStateUniqueId(StructuralState mr) {
+ String modificationId = "structural_state_" + getSbmlIdKey(mr.getSpecies());
+ String result = modificationResidueIds.get(modificationId);
+ if (result == null) {
+ result = "structural_state_" + (structuralStateCounter++);
+ modificationResidueIds.put(modificationId, result);
+ }
+ return result;
+
+ }
+
}
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 d6c62603e5..7a98e43eea 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
@@ -2,8 +2,7 @@ package lcsb.mapviewer.converter.model.sbml.species;
import java.awt.geom.Point2D;
import java.lang.reflect.InvocationTargetException;
-import java.util.ArrayList;
-import java.util.List;
+import java.util.*;
import org.apache.logging.log4j.LogManager;
import org.apache.logging.log4j.Logger;
@@ -31,6 +30,8 @@ public class SbmlSpeciesParser extends SbmlElementParser<org.sbml.jsbml.Species>
private static String ARTIFITIAL_SOURCE_ID = "sbml_artifitial_source";
Logger logger = LogManager.getLogger(SbmlSpeciesParser.class);
+ Map<String, String> structuralStateIdMap = new HashMap<>();
+
public SbmlSpeciesParser(Model model, lcsb.mapviewer.model.map.model.Model minervaModel) {
super(model, minervaModel);
}
@@ -65,13 +66,20 @@ public class SbmlSpeciesParser extends SbmlElementParser<org.sbml.jsbml.Species>
String featureTypeString = feature.getSpeciesFeatureType();
List<String> featureValues = getFeatureValues(speciesType, feature);
if (MultiPackageNamingUtils.isFeatureId(featureTypeString, BioEntityFeature.STRUCTURAL_STATE)) {
+ String structuralStateId = null;
+ for (SpeciesFeatureValue featureValue : feature.getListOfSpeciesFeatureValues()) {
+ if (featureValue.getId() != null) {
+ structuralStateId = featureValue.getId();
+ }
+ }
if (minervaElement instanceof Protein) {
- ((Protein) minervaElement).setStructuralState(String.join("; ", featureValues));
+ minervaElement.setStructuralState(createStructuralState(featureValues));
} else if (minervaElement instanceof Complex) {
- ((Complex) minervaElement).setStructuralState(String.join("; ", featureValues));
+ minervaElement.setStructuralState(createStructuralState(featureValues));
} else {
logger.warn(warnPrefix + "Structural state not supported");
}
+ structuralStateIdMap.put(minervaElement.getElementId(), structuralStateId);
} else if (MultiPackageNamingUtils.isFeatureId(featureTypeString, BioEntityFeature.POSITION_TO_COMPARTMENT)) {
if (featureValues.size() != 1) {
logger.warn(warnPrefix + "Position to compartment must have exactly one value");
@@ -161,6 +169,12 @@ public class SbmlSpeciesParser extends SbmlElementParser<org.sbml.jsbml.Species>
}
}
+ private StructuralState createStructuralState(List<String> featureValues) {
+ StructuralState structuralState = new StructuralState();
+ structuralState.setValue(String.join("; ", featureValues));
+ return structuralState;
+ }
+
private List<String> getFeatureValues(MultiSpeciesType speciesType, SpeciesFeature feature) {
SpeciesFeatureType featureType = speciesType.getListOfSpeciesFeatureTypes().get(feature.getSpeciesFeatureType());
@@ -320,7 +334,29 @@ public class SbmlSpeciesParser extends SbmlElementParser<org.sbml.jsbml.Species>
// find a reference to the alias in layout, so we know it's the proper value
ReferenceGlyph referenceGlyph = ((GeneralGlyph) graphicalObject).getListOfReferenceGlyphs().get(0);
if (Objects.equal(referenceGlyph.getGlyph(), mr.getSpecies().getElementId())) {
-// if (referenceGlyph.getGlyph().equals(mr.getSpecies().getElementId())) {
+ // if (referenceGlyph.getGlyph().equals(mr.getSpecies().getElementId())) {
+ residueGlyph = (GeneralGlyph) graphicalObject;
+ }
+ } else {
+ residueGlyph = (GeneralGlyph) graphicalObject;
+ }
+ }
+ }
+ }
+ return residueGlyph;
+ }
+
+ private GeneralGlyph getResidueGlyphForStructuralState(StructuralState mr) {
+ GeneralGlyph residueGlyph = null;
+ String structurlaStateId = structuralStateIdMap.get(mr.getSpecies().getElementId());
+ for (GraphicalObject graphicalObject : getLayout().getListOfAdditionalGraphicalObjects()) {
+ if (graphicalObject instanceof GeneralGlyph) {
+ if (Objects.equal(((GeneralGlyph) graphicalObject).getReference(), structurlaStateId)) {
+ if (((GeneralGlyph) graphicalObject).getListOfReferenceGlyphs().size() > 0) {
+ // find a reference to the alias in layout, so we know it's the proper value
+ ReferenceGlyph referenceGlyph = ((GeneralGlyph) graphicalObject).getListOfReferenceGlyphs().get(0);
+ if (Objects.equal(referenceGlyph.getGlyph(), mr.getSpecies().getElementId())) {
+ // if (referenceGlyph.getGlyph().equals(mr.getSpecies().getElementId())) {
residueGlyph = (GeneralGlyph) graphicalObject;
}
} else {
@@ -366,21 +402,54 @@ public class SbmlSpeciesParser extends SbmlElementParser<org.sbml.jsbml.Species>
for (Element element : result) {
String compartmentId = null;
+ String speciesId = element.getElementId();
if (getLayout().getSpeciesGlyph(element.getElementId()) != null) {
compartmentId = ((org.sbml.jsbml.Species) getLayout().getSpeciesGlyph(element.getElementId())
.getSpeciesInstance()).getCompartment();
+ speciesId = ((org.sbml.jsbml.Species) getLayout().getSpeciesGlyph(element.getElementId()).getSpeciesInstance())
+ .getId();
} else {
if (!element.getElementId().equals(ARTIFITIAL_SINK_ID)
&& !element.getElementId().equals(ARTIFITIAL_SOURCE_ID)) {
compartmentId = getSbmlModel().getSpecies(element.getElementId()).getCompartment();
}
}
+ structuralStateIdMap.put(element.getElementId(), structuralStateIdMap.get(speciesId));
assignCompartment(element, compartmentId);
assignModificationResiduesLayout(element);
+ assignStructuralStateLayout(element);
}
return result;
}
+ private void assignStructuralStateLayout(Element element) {
+ if (element instanceof Protein || element instanceof Complex) {
+ StructuralState state = ((Species) element).getStructuralState();
+ if (state != null) {
+ state.setFontSize(10);
+ state.setHeight(20);
+ state.setWidth(element.getWidth());
+ state.setPosition(new Point2D.Double(element.getX(), element.getY() - 10));
+ GeneralGlyph residueGlyph = getResidueGlyphForStructuralState(state);
+ if (residueGlyph != null) {
+ if (residueGlyph.getBoundingBox() == null || residueGlyph.getBoundingBox().getDimensions() == null) {
+ logger.warn(
+ new ElementUtils().getElementTag(element) + " Layout doesn't contain coordinates for structural state");
+ } else {
+ double width = residueGlyph.getBoundingBox().getDimensions().getWidth();
+ double height = residueGlyph.getBoundingBox().getDimensions().getHeight();
+ double x = residueGlyph.getBoundingBox().getPosition().getX();
+ double y = residueGlyph.getBoundingBox().getPosition().getY();
+ state.setPosition(new Point2D.Double(x, y));
+ state.setWidth(width);
+ state.setHeight(height);
+ }
+ }
+
+ }
+ }
+ }
+
@Override
protected void applyStyleToElement(Element elementWithLayout, LocalStyle style) {
super.applyStyleToElement(elementWithLayout, style);
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 145e36e21b..6a2c07c771 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
@@ -3,7 +3,6 @@ package lcsb.mapviewer.converter.model.sbml;
import static org.junit.Assert.*;
import java.awt.Color;
-import java.awt.geom.Line2D;
import java.awt.geom.Point2D;
import java.io.File;
import java.lang.reflect.Modifier;
@@ -17,7 +16,6 @@ import org.sbml.jsbml.SBMLDocument;
import org.sbml.jsbml.ext.multi.*;
import lcsb.mapviewer.common.Configuration;
-import lcsb.mapviewer.common.comparator.LineComparator;
import lcsb.mapviewer.common.comparator.ListComparator;
import lcsb.mapviewer.converter.ConverterParams;
import lcsb.mapviewer.converter.model.celldesigner.CellDesignerXmlParser;
@@ -397,7 +395,7 @@ public class SbmlExporterTest extends SbmlTestFunctions {
public void testExportProteinState() throws Exception {
Model model = createEmptyModel();
GenericProtein element = createProtein();
- element.setStructuralState("xxx");
+ element.setStructuralState(createStructuralState(element));
model.addElement(element);
Model deserializedModel = getModelAfterSerializing(model);
@@ -430,9 +428,9 @@ public class SbmlExporterTest extends SbmlTestFunctions {
@Test
public void testMultiExtensionProteinStateInTypes() throws Exception {
- String structuralState = "xxx";
Model model = createEmptyModel();
GenericProtein element = createProtein();
+ StructuralState structuralState = createStructuralState(element);
element.setStructuralState(structuralState);
model.addElement(element);
org.sbml.jsbml.Model sbmlModel = exporter.toSbmlDocument(model).getModel();
@@ -442,7 +440,7 @@ public class SbmlExporterTest extends SbmlTestFunctions {
for (MultiSpeciesType speciesType : multiPlugin.getListOfSpeciesTypes()) {
for (SpeciesFeatureType featureType : speciesType.getListOfSpeciesFeatureTypes()) {
for (PossibleSpeciesFeatureValue featureValue : featureType.getListOfPossibleSpeciesFeatureValues()) {
- if (featureValue.getName().equals(structuralState)) {
+ if (featureValue.getName().equals(structuralState.getValue())) {
structuralStateValueFound = true;
}
}
@@ -454,13 +452,12 @@ public class SbmlExporterTest extends SbmlTestFunctions {
@Test
public void testMultiExtensionProteinStateSuplicateInTypes() throws Exception {
- String structuralState = "xxx";
Model model = createEmptyModel();
GenericProtein element = createProtein();
- element.setStructuralState(structuralState);
+ element.setStructuralState(createStructuralState(element));
model.addElement(element);
element = createProtein();
- element.setStructuralState(structuralState);
+ element.setStructuralState(createStructuralState(element));
model.addElement(element);
org.sbml.jsbml.Model sbmlModel = exporter.toSbmlDocument(model).getModel();
MultiModelPlugin multiPlugin = (MultiModelPlugin) sbmlModel.getExtension("multi");
@@ -498,9 +495,9 @@ public class SbmlExporterTest extends SbmlTestFunctions {
@Test
public void testMultiExtensionStructuralStateTypeDefinition() throws Exception {
- String structuralState = "xxx";
Model model = createEmptyModel();
GenericProtein element = createProtein();
+ StructuralState structuralState = createStructuralState(element);
element.setStructuralState(structuralState);
model.addElement(element);
org.sbml.jsbml.Model sbmlModel = exporter.toSbmlDocument(model).getModel();
@@ -512,6 +509,16 @@ public class SbmlExporterTest extends SbmlTestFunctions {
speciesExtension.getListOfSpeciesFeatures().size() > 0);
}
+ private StructuralState createStructuralState(Element element) {
+ StructuralState structuralState = new StructuralState();
+ structuralState.setValue("xxx");
+ structuralState.setPosition(new Point2D.Double(element.getX(), element.getY() - 10));
+ structuralState.setWidth(element.getWidth());
+ structuralState.setHeight(20.0);
+ structuralState.setFontSize(10.0);
+ return structuralState;
+ }
+
@Test
public void testExportResidue() throws Exception {
Model model = createEmptyModel();
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 190972f434..caa0240f2b 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
@@ -18,6 +18,7 @@ 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.species.*;
+import lcsb.mapviewer.model.map.species.field.StructuralState;
public class SbmlSpeciesExporterTest extends SbmlTestFunctions {
@@ -84,7 +85,9 @@ public class SbmlSpeciesExporterTest extends SbmlTestFunctions {
public void testIdsOfSpeciesWithStructuralStates() throws InconsistentModelException {
Species protein1 = createProtein();
Protein protein2 = createProtein();
- protein2.setStructuralState("X");
+ StructuralState state = new StructuralState();
+ state.setValue("X");
+ protein2.setStructuralState(state);
Model model = new ModelFullIndexed(null);
model.addElement(protein1);
model.addElement(protein2);
--
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