From e4fb01674127a040209af8d2ca6ab31cf8c06810 Mon Sep 17 00:00:00 2001
From: Piotr Gawron <piotr.gawron@uni.lu>
Date: Fri, 4 Jan 2019 13:54:50 +0100
Subject: [PATCH] featureValues extracted to common function
---
.../model/sbml/species/SbmlSpeciesParser.java | 55 ++++++++++---------
1 file changed, 28 insertions(+), 27 deletions(-)
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 1b6bfa6afc..b504bb60d5 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
@@ -21,6 +21,7 @@ import org.sbml.jsbml.ext.multi.PossibleSpeciesFeatureValue;
import org.sbml.jsbml.ext.multi.SpeciesFeature;
import org.sbml.jsbml.ext.multi.SpeciesFeatureType;
import org.sbml.jsbml.ext.multi.SpeciesFeatureValue;
+import org.sbml.jsbml.ext.multi.SpeciesTypeInstance;
import org.sbml.jsbml.ext.multi.SubListOfSpeciesFeature;
import org.sbml.jsbml.ext.render.LocalStyle;
@@ -127,51 +128,51 @@ public class SbmlSpeciesParser extends SbmlElementParser<org.sbml.jsbml.Species>
SpeciesFeature feature) {
String warnPrefix = new ElementUtils().getElementTag(minervaElement);
String featureTypeString = feature.getSpeciesFeatureType();
+ List<String> featureValues = getFeatureValues(speciesType, feature);
if (MultiPackageNamingUtils.isFeatureId(featureTypeString, BioEntityFeature.STRUCTURAL_STATE)) {
- SpeciesFeatureType featureType = speciesType.getListOfSpeciesFeatureTypes().get(featureTypeString);
-
- List<String> structuralStates = new ArrayList<>();
- for (SpeciesFeatureValue featureValue : feature.getListOfSpeciesFeatureValues()) {
- PossibleSpeciesFeatureValue possibleSpeciesFeatureValue = featureType.getListOfPossibleSpeciesFeatureValues()
- .get(featureValue.getValue());
- structuralStates.add(possibleSpeciesFeatureValue.getName());
- }
if (minervaElement instanceof Protein) {
- ((Protein) minervaElement).setStructuralState(String.join("; ", structuralStates));
+ ((Protein) minervaElement).setStructuralState(String.join("; ", featureValues));
} else if (minervaElement instanceof Complex) {
- ((Complex) minervaElement).setStructuralState(String.join("; ", structuralStates));
+ ((Complex) minervaElement).setStructuralState(String.join("; ", featureValues));
} else {
logger.warn(warnPrefix + "Structural state not supported");
}
} else if (MultiPackageNamingUtils.isFeatureId(featureTypeString, BioEntityFeature.POSITION_TO_COMPARTMENT)) {
- 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) {
+ if (featureValues.size() != 1) {
logger.warn(warnPrefix + "Position to compartment must exactly one value");
} else {
- minervaElement.setPositionToCompartment(PositionToCompartment.getByString(positionToCompartments.get(0)));
+ minervaElement.setPositionToCompartment(PositionToCompartment.getByString(featureValues.get(0)));
}
} else if (MultiPackageNamingUtils.isFeatureId(featureTypeString, BioEntityFeature.SYNONYM)) {
- SpeciesFeatureType featureType = speciesType.getListOfSpeciesFeatureTypes().get(featureTypeString);
+ minervaElement.setSynonyms(featureValues);
+ } else if (MultiPackageNamingUtils.isModificationFeatureId(featureTypeString)) {
+ createModificationResidues(minervaElement, speciesType, feature);
+ } else {
+ logger.warn(warnPrefix + "Feature not supported: " + featureTypeString);
+ }
+ }
+
+ private List<String> getFeatureValues(MultiSpeciesType speciesType, SpeciesFeature feature) {
+ SpeciesFeatureType featureType = speciesType.getListOfSpeciesFeatureTypes().get(feature.getSpeciesFeatureType());
- List<String> synonyms = new ArrayList<>();
+ List<String> result = new ArrayList<>();
+ if (featureType != null) {
for (SpeciesFeatureValue featureValue : feature.getListOfSpeciesFeatureValues()) {
PossibleSpeciesFeatureValue possibleSpeciesFeatureValue = featureType.getListOfPossibleSpeciesFeatureValues()
.get(featureValue.getValue());
- synonyms.add(possibleSpeciesFeatureValue.getName());
+ result.add(possibleSpeciesFeatureValue.getName());
}
- minervaElement.setSynonyms(synonyms);
- } else if (MultiPackageNamingUtils.isModificationFeatureId(featureTypeString)) {
- createModificationResidues(minervaElement, speciesType, feature);
} else {
- logger.warn(warnPrefix + "Feature not supported: " + featureTypeString);
+ for (SpeciesTypeInstance speciesTypeInstance : speciesType.getListOfSpeciesTypeInstances()) {
+ speciesType = getMultiPlugin().getSpeciesType(speciesTypeInstance.getSpeciesType());
+ result = getFeatureValues(speciesType, feature);
+ if (result.size() > 0) {
+ return result;
+ }
+ }
+
}
+ return result;
}
private void createModificationResidues(Species minervaElement, MultiSpeciesType speciesType,
--
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