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Commit 47679cc5 authored by Piotr Gawron's avatar Piotr Gawron
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import/export of new structural state implemented

parent ff2ec80f
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1 merge request!978Resolve "species states size and position"
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with 169 additions and 19 deletions
converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/species/SbmlSpeciesExporter.java
+ 75
− 4
View file @ 47679cc5
......@@ -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;
}
}
converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/species/SbmlSpeciesParser.java
+ 74
− 5
View file @ 47679cc5
......@@ -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);
......
converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/SbmlExporterTest.java
+ 16
− 9
View file @ 47679cc5
......@@ -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();
......
converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/species/SbmlSpeciesExporterTest.java
+ 4
− 1
View file @ 47679cc5
......@@ -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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