From bc2f74f35d8e638beab2edb74ef6fa92978a043d Mon Sep 17 00:00:00 2001
From: Piotr Gawron <piotr.gawron@uni.lu>
Date: Fri, 4 Jan 2019 13:23:33 +0100
Subject: [PATCH] export/import of synonyms implemented
---
.../sbml/species/SbmlSpeciesExporter.java | 29 ++++++++++++-------
.../model/sbml/species/SbmlSpeciesParser.java | 10 +++++++
.../ReactionPropertiesExportToMultiTest.java | 2 ++
3 files changed, 30 insertions(+), 11 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 d2af7f4ee5..d5b7937f4b 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
@@ -98,6 +98,7 @@ public class SbmlSpeciesExporter extends SbmlElementExporter<Species, org.sbml.j
assignStructuralStateToMulti(element, multiExtension, speciesType);
assignPostionToCompartmentToMulti(element, multiExtension, speciesType);
assignElementModificationResiduesToMulti(element, multiExtension, speciesType);
+ assignListOfSynonymsToMulti(element, multiExtension, speciesType);
}
private void assignElementModificationResiduesToMulti(Species element, MultiSpeciesPlugin multiExtension,
@@ -216,12 +217,7 @@ public class SbmlSpeciesExporter extends SbmlElementExporter<Species, org.sbml.j
structuralState = ((Complex) element).getStructuralState();
}
if (structuralState != null) {
- SpeciesFeatureType structuralStateFeature = getFeature(element.getClass(), speciesType,
- BioEntityFeature.STRUCTURAL_STATE);
- PossibleSpeciesFeatureValue structuralStateFeatureValue = getPosibleFeatureIdByName(structuralState,
- structuralStateFeature);
-
- addSpeciesFeatureValue(multiExtension, structuralStateFeature, structuralStateFeatureValue);
+ assignValueToFeature(element, multiExtension, speciesType, structuralState, BioEntityFeature.STRUCTURAL_STATE);
}
}
@@ -259,13 +255,24 @@ public class SbmlSpeciesExporter extends SbmlElementExporter<Species, org.sbml.j
private void assignPostionToCompartmentToMulti(Species element, MultiSpeciesPlugin multiExtension,
MultiSpeciesType speciesType) {
- String positionToCompartmentName = "undefined";
+ String value = "undefined";
if (element.getPositionToCompartment() != null) {
- positionToCompartmentName = element.getPositionToCompartment().name();
+ value = element.getPositionToCompartment().name();
}
- SpeciesFeatureType structuralStateFeature = getFeature(element.getClass(), speciesType,
- BioEntityFeature.POSITION_TO_COMPARTMENT);
- PossibleSpeciesFeatureValue structuralStateFeatureValue = getPosibleFeatureIdByName(positionToCompartmentName,
+ assignValueToFeature(element, multiExtension, speciesType, value, BioEntityFeature.POSITION_TO_COMPARTMENT);
+ }
+
+ private void assignListOfSynonymsToMulti(Species element, MultiSpeciesPlugin multiExtension,
+ MultiSpeciesType speciesType) {
+ for (String synonym : element.getSynonyms()) {
+ assignValueToFeature(element, multiExtension, speciesType, synonym, BioEntityFeature.SYNONYM);
+ }
+ }
+
+ private void assignValueToFeature(Species element, MultiSpeciesPlugin multiExtension, MultiSpeciesType speciesType,
+ String value, BioEntityFeature feature) {
+ SpeciesFeatureType structuralStateFeature = getFeature(element.getClass(), speciesType, feature);
+ PossibleSpeciesFeatureValue structuralStateFeatureValue = getPosibleFeatureIdByName(value,
structuralStateFeature);
addSpeciesFeatureValue(multiExtension, structuralStateFeature, structuralStateFeatureValue);
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 12566be85f..1b6bfa6afc 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
@@ -157,6 +157,16 @@ public class SbmlSpeciesParser extends SbmlElementParser<org.sbml.jsbml.Species>
} else {
minervaElement.setPositionToCompartment(PositionToCompartment.getByString(positionToCompartments.get(0)));
}
+ } else if (MultiPackageNamingUtils.isFeatureId(featureTypeString, BioEntityFeature.SYNONYM)) {
+ SpeciesFeatureType featureType = speciesType.getListOfSpeciesFeatureTypes().get(featureTypeString);
+
+ List<String> synonyms = new ArrayList<>();
+ for (SpeciesFeatureValue featureValue : feature.getListOfSpeciesFeatureValues()) {
+ PossibleSpeciesFeatureValue possibleSpeciesFeatureValue = featureType.getListOfPossibleSpeciesFeatureValues()
+ .get(featureValue.getValue());
+ synonyms.add(possibleSpeciesFeatureValue.getName());
+ }
+ minervaElement.setSynonyms(synonyms);
} else if (MultiPackageNamingUtils.isModificationFeatureId(featureTypeString)) {
createModificationResidues(minervaElement, speciesType, feature);
} else {
diff --git a/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/ReactionPropertiesExportToMultiTest.java b/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/ReactionPropertiesExportToMultiTest.java
index f8f211ade7..a6e7faca96 100644
--- a/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/ReactionPropertiesExportToMultiTest.java
+++ b/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/ReactionPropertiesExportToMultiTest.java
@@ -11,6 +11,7 @@ import java.util.Arrays;
import java.util.Collection;
import org.apache.log4j.Logger;
+import org.junit.Ignore;
import org.junit.Test;
import org.junit.runner.RunWith;
import org.junit.runners.Parameterized;
@@ -28,6 +29,7 @@ import lcsb.mapviewer.model.map.reaction.ReactionNode;
import lcsb.mapviewer.model.map.reaction.type.StateTransitionReaction;
import lcsb.mapviewer.model.map.species.Ion;
+@Ignore("Not supported by multi extension")
@RunWith(Parameterized.class)
public class ReactionPropertiesExportToMultiTest {
--
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