From a123fb5807c9479699f71bbc2c0b73bb165c1eeb Mon Sep 17 00:00:00 2001
From: Piotr Gawron <piotr.gawron@uni.lu>
Date: Thu, 3 Jan 2019 15:30:14 +0100
Subject: [PATCH] basic export of modificationrediues implemented
---
.../model/sbml/MultiPackageNamingUtils.java | 38 +++
.../converter/model/sbml/SbmlParser.java | 8 +
.../sbml/species/SbmlSpeciesExporter.java | 244 ++++++++++++++++--
.../model/sbml/species/SbmlSpeciesParser.java | 132 +++++++++-
.../model/sbml/SbmlExporterTest.java | 3 +
.../modelutils/map/ElementUtils.java | 6 +
6 files changed, 414 insertions(+), 17 deletions(-)
diff --git a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/MultiPackageNamingUtils.java b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/MultiPackageNamingUtils.java
index c2905e08ce..a4f69ebc8e 100644
--- a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/MultiPackageNamingUtils.java
+++ b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/MultiPackageNamingUtils.java
@@ -1,9 +1,12 @@
package lcsb.mapviewer.converter.model.sbml;
+import org.apache.log4j.Logger;
import org.sbml.jsbml.ext.multi.MultiSpeciesType;
import lcsb.mapviewer.model.map.species.Element;
import lcsb.mapviewer.model.map.species.Species;
+import lcsb.mapviewer.model.map.species.field.ModificationResidue;
+import lcsb.mapviewer.model.map.species.field.ModificationState;
/**
* Class responsible for providing identifiers of structures inside multi
@@ -13,7 +16,9 @@ import lcsb.mapviewer.model.map.species.Species;
*
*/
public final class MultiPackageNamingUtils {
+ private static Logger logger = Logger.getLogger(MultiPackageNamingUtils.class);
+ private static final String MINERVA_MODIFICATION_TYPE_PREFIX = "minerva_modification_type_";
private static final String MINERVA_POSITION_TO_COMPARTMENT_PREFIX = "minerva_position_to_compartment_";
private static final String MINERVA_STRUCTURAL_STATE_PREFIX = "minerva_structural_state_";
@@ -65,4 +70,37 @@ public final class MultiPackageNamingUtils {
return featureTypeId.startsWith(MINERVA_POSITION_TO_COMPARTMENT_PREFIX);
}
+ public static String getModificationFeatureId(Species species, Class<? extends ModificationResidue> class1) {
+ return MINERVA_MODIFICATION_TYPE_PREFIX + species.getClass().getSimpleName() + "_" + class1.getSimpleName();
+ }
+
+ public static String getModificationFeatureId(Species species, Class<? extends ModificationResidue> class1,
+ ModificationState state) {
+ String stateName = "null";
+ if (state != null) {
+ stateName = state.name();
+ }
+
+ return MINERVA_MODIFICATION_TYPE_PREFIX + species.getClass().getSimpleName() + "_" + class1.getSimpleName() + "_"
+ + stateName;
+ }
+
+ public static boolean isModificationFeatureId(String featureTypeString) {
+ return featureTypeString.startsWith(MINERVA_MODIFICATION_TYPE_PREFIX);
+ }
+
+ public static boolean isModificationFeatureId(String speciesFeatureType,
+ Class<? extends ModificationResidue> class1) {
+ return isModificationFeatureId(speciesFeatureType) && speciesFeatureType.contains("_" + class1.getSimpleName());
+ }
+
+ public static ModificationState getModificationStateFromFeatureTypeName(String featureTypeString) {
+ for (ModificationState state : ModificationState.values()) {
+ if (featureTypeString.endsWith(state.name())) {
+ return state;
+ }
+ }
+ return null;
+ }
+
}
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 bacbc97877..48f4e8d3ac 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
@@ -46,6 +46,8 @@ import lcsb.mapviewer.model.map.reaction.type.BooleanLogicGateReaction;
import lcsb.mapviewer.model.map.species.Complex;
import lcsb.mapviewer.model.map.species.Element;
import lcsb.mapviewer.model.map.species.Species;
+import lcsb.mapviewer.model.map.species.field.ModificationResidue;
+import lcsb.mapviewer.model.map.species.field.SpeciesWithModificationResidue;
public class SbmlParser implements IConverter {
@@ -184,6 +186,12 @@ public class SbmlParser implements IConverter {
for (Element element : model.getElements()) {
if (element.getWidth() == 0 || element.getHeight() == 0) {
bioEntitesRequiringLayout.add(element);
+ } else if (element instanceof SpeciesWithModificationResidue) {
+ for (ModificationResidue mr : ((SpeciesWithModificationResidue) element).getModificationResidues()) {
+ if (mr.getPosition() == null) {
+ bioEntitesRequiringLayout.add(element);
+ }
+ }
}
}
for (Reaction reaction : model.getReactions()) {
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 eb1b3053c6..670c655dbc 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
@@ -1,11 +1,19 @@
package lcsb.mapviewer.converter.model.sbml.species;
+import java.util.ArrayList;
import java.util.Collection;
+import java.util.Collections;
+import java.util.HashMap;
import java.util.List;
+import java.util.Map;
+import org.apache.commons.lang3.StringUtils;
import org.apache.log4j.Logger;
import org.sbml.jsbml.Model;
import org.sbml.jsbml.ext.layout.AbstractReferenceGlyph;
+import org.sbml.jsbml.ext.layout.BoundingBox;
+import org.sbml.jsbml.ext.layout.Dimensions;
+import org.sbml.jsbml.ext.layout.Point;
import org.sbml.jsbml.ext.multi.MultiModelPlugin;
import org.sbml.jsbml.ext.multi.MultiSpeciesPlugin;
import org.sbml.jsbml.ext.multi.MultiSpeciesType;
@@ -20,10 +28,24 @@ 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.AntisenseRna;
import lcsb.mapviewer.model.map.species.Complex;
import lcsb.mapviewer.model.map.species.Element;
+import lcsb.mapviewer.model.map.species.Gene;
import lcsb.mapviewer.model.map.species.Protein;
+import lcsb.mapviewer.model.map.species.Rna;
import lcsb.mapviewer.model.map.species.Species;
+import lcsb.mapviewer.model.map.species.field.AbstractRegionModification;
+import lcsb.mapviewer.model.map.species.field.AbstractSiteModification;
+import lcsb.mapviewer.model.map.species.field.BindingRegion;
+import lcsb.mapviewer.model.map.species.field.CodingRegion;
+import lcsb.mapviewer.model.map.species.field.ModificationResidue;
+import lcsb.mapviewer.model.map.species.field.ModificationSite;
+import lcsb.mapviewer.model.map.species.field.ProteinBindingDomain;
+import lcsb.mapviewer.model.map.species.field.RegulatoryRegion;
+import lcsb.mapviewer.model.map.species.field.Residue;
+import lcsb.mapviewer.model.map.species.field.SpeciesWithModificationResidue;
+import lcsb.mapviewer.model.map.species.field.TranscriptionSite;
public class SbmlSpeciesExporter extends SbmlElementExporter<Species, org.sbml.jsbml.Species> {
@@ -32,7 +54,6 @@ public class SbmlSpeciesExporter extends SbmlElementExporter<Species, org.sbml.j
/**
* Default class logger.
*/
- @SuppressWarnings("unused")
private static Logger logger = Logger.getLogger(SbmlSpeciesExporter.class);
private SbmlCompartmentExporter compartmentExporter;
@@ -75,6 +96,113 @@ public class SbmlSpeciesExporter extends SbmlElementExporter<Species, org.sbml.j
result.addExtension("multi", multiExtension);
assignStructuralStateToMulti(element, multiExtension, speciesType);
assignPostionToCompartmentToMulti(element, multiExtension, speciesType);
+ assignElementModificationResiduesToMulti(element, multiExtension, speciesType);
+ }
+
+ private void assignElementModificationResiduesToMulti(Species element, MultiSpeciesPlugin multiExtension,
+ MultiSpeciesType speciesType) {
+ if (element instanceof Protein) {
+ assignModificationResiduesToMulti(((Protein) element).getModificationResidues(), multiExtension, speciesType);
+ } else if (element instanceof Gene) {
+ assignModificationResiduesToMulti(((Gene) element).getModificationResidues(), multiExtension, speciesType);
+ } else if (element instanceof Rna) {
+ assignModificationResiduesToMulti(((Rna) element).getRegions(), multiExtension, speciesType);
+ } else if (element instanceof AntisenseRna) {
+ assignModificationResiduesToMulti(((AntisenseRna) element).getRegions(), multiExtension, speciesType);
+ }
+
+ }
+
+ private void assignModificationResiduesToMulti(Collection<ModificationResidue> modificationResidues,
+ MultiSpeciesPlugin multiExtension, MultiSpeciesType speciesType) {
+ for (ModificationResidue mr : modificationResidues) {
+ SpeciesFeatureType feature = null;
+ PossibleSpeciesFeatureValue value;
+
+ if (mr instanceof BindingRegion) {
+ feature = getBindingRegionFeature(mr.getSpecies(), speciesType);
+ } else if (mr instanceof CodingRegion) {
+ feature = getCodingRegionFeature(mr.getSpecies(), speciesType);
+ } else if (mr instanceof ProteinBindingDomain) {
+ feature = getProteinBindingDomainFeature(mr.getSpecies(), speciesType);
+ } else if (mr instanceof RegulatoryRegion) {
+ feature = getRegulatoryRegionFeature(mr.getSpecies(), speciesType);
+ } else if (mr instanceof TranscriptionSite) {
+ feature = getTranscriptionSiteFeature(mr.getSpecies(), speciesType);
+ } else if (mr instanceof ModificationSite) {
+ feature = getModificationSiteFeature((ModificationSite) mr, speciesType);
+ } else if (mr instanceof Residue) {
+ feature = getResidueFeature((Residue) mr, speciesType);
+ } else {
+ logger.warn("Don't know how to export modification: " + mr.getClass());
+ }
+ value = getPosibleFeatureIdByName(mr.getName(), feature);
+ SpeciesFeatureValue featureValue = addSpeciesFeatureValue(multiExtension, feature, value);
+ featureValue.setId(getModificationResidueUniqueId(mr));
+ }
+ }
+
+ private SpeciesFeatureType getCodingRegionFeature(Species species, MultiSpeciesType speciesType) {
+ String featureId = MultiPackageNamingUtils.getModificationFeatureId(species, CodingRegion.class);
+ String featureName = "Coding region";
+ return getOrCreateFeatureById(featureId, featureName, speciesType);
+ }
+
+ private SpeciesFeatureType getBindingRegionFeature(Species species, MultiSpeciesType speciesType) {
+ String featureId = MultiPackageNamingUtils.getModificationFeatureId(species, BindingRegion.class);
+ String featureName = "Binding region";
+ return getOrCreateFeatureById(featureId, featureName, speciesType);
+ }
+
+ private SpeciesFeatureType getProteinBindingDomainFeature(Species species, MultiSpeciesType speciesType) {
+ String featureId = MultiPackageNamingUtils.getModificationFeatureId(species, ProteinBindingDomain.class);
+ String featureName = "Protein binding domain";
+ return getOrCreateFeatureById(featureId, featureName, speciesType);
+ }
+
+ private SpeciesFeatureType getRegulatoryRegionFeature(Species species, MultiSpeciesType speciesType) {
+ String featureId = MultiPackageNamingUtils.getModificationFeatureId(species, RegulatoryRegion.class);
+ String featureName = "Regulatory region";
+ return getOrCreateFeatureById(featureId, featureName, speciesType);
+ }
+
+ private SpeciesFeatureType getTranscriptionSiteFeature(Species species, MultiSpeciesType speciesType) {
+ String featureId = MultiPackageNamingUtils.getModificationFeatureId(species, TranscriptionSite.class);
+ String featureName = "Transcription site";
+ return getOrCreateFeatureById(featureId, featureName, speciesType);
+ }
+
+ private SpeciesFeatureType getModificationSiteFeature(ModificationSite modificationSite,
+ MultiSpeciesType speciesType) {
+ String featureId = MultiPackageNamingUtils.getModificationFeatureId(modificationSite.getSpecies(),
+ ModificationSite.class, modificationSite.getState());
+ String featureName = "";
+ if (modificationSite.getState() != null) {
+ featureName = modificationSite.getState().getFullName();
+ }
+ return getOrCreateFeatureById(featureId, featureName, speciesType);
+ }
+
+ private SpeciesFeatureType getResidueFeature(Residue residue, MultiSpeciesType speciesType) {
+ String featureId = MultiPackageNamingUtils.getModificationFeatureId(residue.getSpecies(), Residue.class,
+ residue.getState());
+ String featureName = "";
+ if (residue.getState() != null) {
+ featureName = residue.getState().getFullName();
+ }
+ return getOrCreateFeatureById(featureId, featureName, speciesType);
+ }
+
+ private SpeciesFeatureType getOrCreateFeatureById(String featureId, String featureName,
+ MultiSpeciesType speciesType) {
+ SpeciesFeatureType feature = speciesType.getSpeciesFeatureType(featureId);
+ if (feature == null) {
+ feature = new SpeciesFeatureType();
+ feature.setName(featureName);
+ feature.setId(featureId);
+ speciesType.getListOfSpeciesFeatureTypes().add(feature);
+ }
+ return feature;
}
private void assignStructuralStateToMulti(Species element, MultiSpeciesPlugin multiExtension,
@@ -90,14 +218,28 @@ public class SbmlSpeciesExporter extends SbmlElementExporter<Species, org.sbml.j
PossibleSpeciesFeatureValue structuralStateFeatureValue = getPosibleFeatureIdByName(structuralState,
structuralStateFeature);
- SpeciesFeature feature = multiExtension.createSpeciesFeature();
- feature.setSpeciesFeatureType(structuralStateFeature.getId());
- SpeciesFeatureValue value = new SpeciesFeatureValue();
- value.setValue(structuralStateFeatureValue.getId());
- feature.addSpeciesFeatureValue(value);
+ addSpeciesFeatureValue(multiExtension, structuralStateFeature, structuralStateFeatureValue);
}
}
+ private SpeciesFeatureValue addSpeciesFeatureValue(MultiSpeciesPlugin multiExtension, SpeciesFeatureType fetureType,
+ PossibleSpeciesFeatureValue possibleValue) {
+ SpeciesFeature feature = null;
+ for (SpeciesFeature existingFeature : multiExtension.getListOfSpeciesFeatures()) {
+ if (existingFeature.getSpeciesFeatureType().equals(fetureType.getId())) {
+ feature = existingFeature;
+ }
+ }
+ if (feature == null) {
+ feature = multiExtension.createSpeciesFeature();
+ feature.setSpeciesFeatureType(fetureType.getId());
+ }
+ SpeciesFeatureValue value = new SpeciesFeatureValue();
+ value.setValue(possibleValue.getId());
+ feature.addSpeciesFeatureValue(value);
+ return value;
+ }
+
private PossibleSpeciesFeatureValue getPosibleFeatureIdByName(String featureValueName,
SpeciesFeatureType speciesFeature) {
PossibleSpeciesFeatureValue structuralStateFeatureValue = null;
@@ -122,11 +264,7 @@ public class SbmlSpeciesExporter extends SbmlElementExporter<Species, org.sbml.j
PossibleSpeciesFeatureValue structuralStateFeatureValue = getPosibleFeatureIdByName(positionToCompartmentName,
structuralStateFeature);
- SpeciesFeature feature = multiExtension.createSpeciesFeature();
- feature.setSpeciesFeatureType(structuralStateFeature.getId());
- SpeciesFeatureValue value = new SpeciesFeatureValue();
- value.setValue(structuralStateFeatureValue.getId());
- feature.addSpeciesFeatureValue(value);
+ addSpeciesFeatureValue(multiExtension, structuralStateFeature, structuralStateFeatureValue);
}
private MultiSpeciesType getMultiSpeciesType(Species element) {
@@ -168,6 +306,19 @@ public class SbmlSpeciesExporter extends SbmlElementExporter<Species, org.sbml.j
structuralState = ((Complex) element).getStructuralState();
}
multiDistinguisher = structuralState;
+
+ if (element instanceof SpeciesWithModificationResidue) {
+ List<String> modifications = new ArrayList<>();
+ for (ModificationResidue mr : ((SpeciesWithModificationResidue) element).getModificationResidues()) {
+ String modificationId = mr.getName() + mr.getClass().getSimpleName();
+ if (mr instanceof AbstractSiteModification) {
+ modificationId += ((AbstractSiteModification) mr).getState();
+ }
+ modifications.add(modificationId);
+ }
+ Collections.sort(modifications);
+ multiDistinguisher += "\n" + StringUtils.join(modifications, ",");
+ }
}
String result = element.getClass().getSimpleName() + "\n" + element.getName() + "\n" + compartmentName + "\n"
+ complexName
@@ -234,12 +385,73 @@ public class SbmlSpeciesExporter extends SbmlElementExporter<Species, org.sbml.j
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());
+ @Override
+ protected void assignLayoutToGlyph(Species element, AbstractReferenceGlyph speciesGlyph) {
+ super.assignLayoutToGlyph(element, speciesGlyph);
+ if (isExtensionEnabled(SbmlExtension.MULTI)) {
+ if (element instanceof SpeciesWithModificationResidue) {
+ for (ModificationResidue mr : ((SpeciesWithModificationResidue) element).getModificationResidues()) {
+ org.sbml.jsbml.Species sbmlSpecies = getSbmlModel().getSpecies(speciesGlyph.getReference());
+ createModificationGlyph(mr, sbmlSpecies);
+ }
+ }
}
}
+ private void createModificationGlyph(ModificationResidue mr, org.sbml.jsbml.Species sbmlSpecies) {
+ MultiSpeciesPlugin speciesExtension = (MultiSpeciesPlugin) sbmlSpecies.getExtension("multi");
+ SpeciesFeature feature = null;
+ String featureTypeId = MultiPackageNamingUtils.getModificationFeatureId(mr.getSpecies(), mr.getClass());
+ if (mr instanceof AbstractSiteModification) {
+ featureTypeId = MultiPackageNamingUtils.getModificationFeatureId(mr.getSpecies(), mr.getClass(),
+ ((AbstractSiteModification) mr).getState());
+ }
+ for (SpeciesFeature existingFeature : speciesExtension.getListOfSpeciesFeatures()) {
+ if (existingFeature.getSpeciesFeatureType().equals(featureTypeId)) {
+ feature = existingFeature;
+ }
+ }
+
+ SpeciesFeatureValue modificationFeatureValue = null;
+ for (SpeciesFeatureValue featureValue : feature.getListOfSpeciesFeatureValues()) {
+ if (featureValue.getId().equals(getModificationResidueUniqueId(mr))) {
+ modificationFeatureValue = featureValue;
+ }
+ }
+
+ AbstractReferenceGlyph modificationGlyph = getLayout().createGeneralGlyph("modification_" + (idCounter++),
+ modificationFeatureValue.getId());
+ double width, height;
+ if (mr instanceof AbstractRegionModification) {
+ width = ((AbstractRegionModification) mr).getWidth();
+ height = ((AbstractRegionModification) mr).getHeight();
+ } else {
+ width = 12;
+ height = 12;
+ }
+ double x = mr.getPosition().getX() - width / 2;
+ double y = mr.getPosition().getY() - height / 2;
+ logger.debug(mr.getPosition().getX() + ";" + mr.getPosition().getY() + ";" + modificationFeatureValue.getId());
+ logger.debug(x + ";" + y + ";" + modificationFeatureValue.getId());
+ BoundingBox boundingBox = new BoundingBox();
+ boundingBox.setPosition(new Point(x, y));
+ Dimensions dimensions = new Dimensions();
+ dimensions.setWidth(width);
+ dimensions.setHeight(height);
+ boundingBox.setDimensions(dimensions);
+ modificationGlyph.setBoundingBox(boundingBox);
+ }
+
+ private int modificationResidueCounter = 0;
+ private Map<String, String> modificationResidueIds = new HashMap<>();
+
+ private String getModificationResidueUniqueId(ModificationResidue mr) {
+ String result = modificationResidueIds.get(mr.getIdModificationResidue() + "_" + getSbmlIdKey(mr.getSpecies()));
+ if (result == null) {
+ result = "modification_residue_" + (modificationResidueCounter++);
+ modificationResidueIds.put(mr.getIdModificationResidue() + "_" + getSbmlIdKey(mr.getSpecies()), 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 1c184c1671..4fb0cf872e 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
@@ -1,5 +1,6 @@
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;
@@ -9,6 +10,8 @@ import org.sbml.jsbml.ListOf;
import org.sbml.jsbml.Model;
import org.sbml.jsbml.ext.layout.AbstractReferenceGlyph;
import org.sbml.jsbml.ext.layout.CompartmentGlyph;
+import org.sbml.jsbml.ext.layout.GeneralGlyph;
+import org.sbml.jsbml.ext.layout.GraphicalObject;
import org.sbml.jsbml.ext.layout.SpeciesGlyph;
import org.sbml.jsbml.ext.multi.MultiModelPlugin;
import org.sbml.jsbml.ext.multi.MultiSpeciesPlugin;
@@ -33,7 +36,24 @@ 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.AbstractRegionModification;
+import lcsb.mapviewer.model.map.species.field.BindingRegion;
+import lcsb.mapviewer.model.map.species.field.CodingRegion;
+import lcsb.mapviewer.model.map.species.field.ModificationResidue;
+import lcsb.mapviewer.model.map.species.field.ModificationSite;
import lcsb.mapviewer.model.map.species.field.PositionToCompartment;
+import lcsb.mapviewer.model.map.species.field.ProteinBindingDomain;
+import lcsb.mapviewer.model.map.species.field.RegulatoryRegion;
+import lcsb.mapviewer.model.map.species.field.Residue;
+import lcsb.mapviewer.model.map.species.field.SpeciesWithBindingRegion;
+import lcsb.mapviewer.model.map.species.field.SpeciesWithCodingRegion;
+import lcsb.mapviewer.model.map.species.field.SpeciesWithModificationResidue;
+import lcsb.mapviewer.model.map.species.field.SpeciesWithModificationSite;
+import lcsb.mapviewer.model.map.species.field.SpeciesWithProteinBindingDomain;
+import lcsb.mapviewer.model.map.species.field.SpeciesWithRegulatoryRegion;
+import lcsb.mapviewer.model.map.species.field.SpeciesWithResidue;
+import lcsb.mapviewer.model.map.species.field.SpeciesWithTranscriptionSite;
+import lcsb.mapviewer.model.map.species.field.TranscriptionSite;
import lcsb.mapviewer.modelutils.map.ElementUtils;
public class SbmlSpeciesParser extends SbmlElementParser<org.sbml.jsbml.Species> {
@@ -142,13 +162,91 @@ public class SbmlSpeciesParser extends SbmlElementParser<org.sbml.jsbml.Species>
minervaElement.setPositionToCompartment(PositionToCompartment.getByString(positionToCompartments.get(0)));
}
} else {
- logger.warn(warnPrefix + "Invalid structural state for class " + featureTypeString);
+ logger.warn(warnPrefix + "Position to compartment for class " + featureTypeString);
}
+ } else if (MultiPackageNamingUtils.isModificationFeatureId(featureTypeString)) {
+ createModificationResidues(minervaElement, speciesType, feature);
} else {
logger.warn(warnPrefix + "Feature not supported: " + featureTypeString);
}
}
+ private void createModificationResidues(Species minervaElement, MultiSpeciesType speciesType,
+ SpeciesFeature feature) {
+ String warnPrefix = new ElementUtils().getElementTag(minervaElement);
+ ModificationResidue mr = null;
+
+ String featureTypeString = feature.getSpeciesFeatureType();
+ SpeciesFeatureType featureType = speciesType.getListOfSpeciesFeatureTypes().get(featureTypeString);
+ for (SpeciesFeatureValue featureValue : feature.getListOfSpeciesFeatureValues()) {
+ if (MultiPackageNamingUtils.isModificationFeatureId(featureTypeString, BindingRegion.class)) {
+ mr = new BindingRegion();
+ if (minervaElement instanceof SpeciesWithBindingRegion) {
+ ((SpeciesWithBindingRegion) minervaElement).addBindingRegion((BindingRegion) mr);
+ } else {
+ logger.warn(warnPrefix + "Object class doesn't support " + mr.getClass());
+ }
+ } else if (MultiPackageNamingUtils.isModificationFeatureId(featureTypeString, CodingRegion.class)) {
+ mr = new CodingRegion();
+ if (minervaElement instanceof SpeciesWithCodingRegion) {
+ ((SpeciesWithCodingRegion) minervaElement).addCodingRegion((CodingRegion) mr);
+ } else {
+ logger.warn(warnPrefix + "Object class doesn't support " + mr.getClass());
+ }
+ } else if (MultiPackageNamingUtils.isModificationFeatureId(featureTypeString, ProteinBindingDomain.class)) {
+ mr = new ProteinBindingDomain();
+ if (minervaElement instanceof SpeciesWithProteinBindingDomain) {
+ ((SpeciesWithProteinBindingDomain) minervaElement).addProteinBindingDomain((ProteinBindingDomain) mr);
+ } else {
+ logger.warn(warnPrefix + "Object class doesn't support " + mr.getClass());
+ }
+ } else if (MultiPackageNamingUtils.isModificationFeatureId(featureTypeString, RegulatoryRegion.class)) {
+ mr = new RegulatoryRegion();
+ if (minervaElement instanceof SpeciesWithRegulatoryRegion) {
+ ((SpeciesWithRegulatoryRegion) minervaElement).addRegulatoryRegion((RegulatoryRegion) mr);
+ } else {
+ logger.warn(warnPrefix + "Object class doesn't support " + mr.getClass());
+ }
+ } else if (MultiPackageNamingUtils.isModificationFeatureId(featureTypeString, TranscriptionSite.class)) {
+ mr = new TranscriptionSite();
+ if (minervaElement instanceof SpeciesWithTranscriptionSite) {
+ ((SpeciesWithTranscriptionSite) minervaElement).addTranscriptionSite((TranscriptionSite) mr);
+ } else {
+ logger.warn(warnPrefix + "Object class doesn't support " + mr.getClass());
+ }
+ } else if (MultiPackageNamingUtils.isModificationFeatureId(featureTypeString, ModificationSite.class)) {
+ mr = new ModificationSite();
+ ((ModificationSite) mr)
+ .setState(MultiPackageNamingUtils.getModificationStateFromFeatureTypeName(featureTypeString));
+ if (minervaElement instanceof SpeciesWithModificationSite) {
+ ((SpeciesWithModificationSite) minervaElement).addModificationSite((ModificationSite) mr);
+ } else {
+ logger.warn(warnPrefix + "Object class doesn't support " + mr.getClass());
+ }
+ } else if (MultiPackageNamingUtils.isModificationFeatureId(featureTypeString, Residue.class)) {
+ mr = new Residue();
+ ((Residue) mr)
+ .setState(MultiPackageNamingUtils.getModificationStateFromFeatureTypeName(featureTypeString));
+ if (minervaElement instanceof SpeciesWithResidue) {
+ ((SpeciesWithResidue) minervaElement).addResidue((Residue) mr);
+ } else {
+ logger.warn(warnPrefix + "Object class doesn't support " + mr.getClass());
+ }
+ } else {
+ logger.warn(warnPrefix + "Unsupported modification type: " + featureTypeString);
+ }
+ PossibleSpeciesFeatureValue possibleSpeciesFeatureValue = featureType.getListOfPossibleSpeciesFeatureValues()
+ .get(featureValue.getValue());
+ if (possibleSpeciesFeatureValue != null) {
+ mr.setName(possibleSpeciesFeatureValue.getName());
+ mr.setIdModificationResidue(featureValue.getId());
+ } else {
+ logger.warn(warnPrefix + "Invalid feature value: " + featureValue.getValue());
+ }
+ }
+
+ }
+
private String extractSBOTermFromSpecies(org.sbml.jsbml.Species species) {
String sboTerm = species.getSBOTermID();
MultiSpeciesPlugin multiExtension = (MultiSpeciesPlugin) species.getExtension("multi");
@@ -184,10 +282,42 @@ public class SbmlSpeciesParser extends SbmlElementParser<org.sbml.jsbml.Species>
}
}
assignCompartment(element, compartmentId);
+ assignModificationResiduesLayout(element);
}
return result;
}
+ private void assignModificationResiduesLayout(Element element) {
+ if (element instanceof SpeciesWithModificationResidue) {
+ for (ModificationResidue mr : ((SpeciesWithModificationResidue) element).getModificationResidues()) {
+ GeneralGlyph residueGlyph = null;
+ for (GraphicalObject graphicalObject : getLayout().getListOfAdditionalGraphicalObjects()) {
+ if (graphicalObject instanceof GeneralGlyph) {
+ if (((GeneralGlyph) graphicalObject).getReference().equals(mr.getIdModificationResidue())) {
+ residueGlyph = (GeneralGlyph) graphicalObject;
+ }
+ }
+ }
+ if (residueGlyph != null) {
+ if (residueGlyph.getBoundingBox() == null || residueGlyph.getBoundingBox().getDimensions() == null) {
+ logger.warn(new ElementUtils().getElementTag(mr) + "Layout doesn't contain coordinates");
+ } 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();
+ mr.setPosition(new Point2D.Double(x + width / 2, y + height / 2));
+ if (mr instanceof AbstractRegionModification) {
+ ((AbstractRegionModification) mr).setWidth(width);
+ ((AbstractRegionModification) mr).setHeight(height);
+ }
+ }
+ }
+ }
+ }
+
+ }
+
private void assignCompartment(Element element, String compartmentId) {
Compartment compartment = getMinervaModel().getElementByElementId(compartmentId);
if (compartment == null && getLayout() != null) {
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 5181a0ff31..1a6733fff5 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
@@ -595,14 +595,17 @@ public class SbmlExporterTest {
Residue mr = new Residue("x1");
mr.setName("217U");
mr.setState(ModificationState.PHOSPHORYLATED);
+ mr.setPosition(new Point2D.Double(10,11));
element.addResidue(mr);
mr = new Residue("Y");
mr.setName("218");
mr.setState(ModificationState.PHOSPHORYLATED);
+ mr.setPosition(new Point2D.Double(10,12));
element.addResidue(mr);
mr = new Residue("Z");
mr.setName("219");
mr.setState(ModificationState.UBIQUITINATED);
+ mr.setPosition(new Point2D.Double(10,13));
element.addResidue(mr);
model.addElement(element);
Model deserializedModel = getModelAfterSerializing(model);
diff --git a/model/src/main/java/lcsb/mapviewer/modelutils/map/ElementUtils.java b/model/src/main/java/lcsb/mapviewer/modelutils/map/ElementUtils.java
index 94777c846e..5313c5b44f 100644
--- a/model/src/main/java/lcsb/mapviewer/modelutils/map/ElementUtils.java
+++ b/model/src/main/java/lcsb/mapviewer/modelutils/map/ElementUtils.java
@@ -16,6 +16,7 @@ import lcsb.mapviewer.model.map.BioEntity;
import lcsb.mapviewer.model.map.reaction.Reaction;
import lcsb.mapviewer.model.map.reaction.ReactionNode;
import lcsb.mapviewer.model.map.species.Element;
+import lcsb.mapviewer.model.map.species.field.ModificationResidue;
/**
* Class with some util method for {@link BioEntity} objects.
@@ -262,4 +263,9 @@ public final class ElementUtils {
return "[" + node.getClass().getSimpleName() + "]" + getElementTag(node.getElement());
}
+ public String getElementTag(ModificationResidue mr) {
+ return "[" + mr.getClass().getSimpleName() + "," + mr.getIdModificationResidue() + "]"
+ + getElementTag(mr.getSpecies());
+ }
+
}
--
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