From 3724bc1a867c182c949dd045a33c98d2ed5ed400 Mon Sep 17 00:00:00 2001
From: Piotr Gawron <piotr.gawron@uni.lu>
Date: Fri, 4 Jan 2019 14:05:07 +0100
Subject: [PATCH] export import of element symbol property added
---
.../extension/multi/BioEntityFeature.java | 7 +++++--
.../multi/MultiPackageNamingUtils.java | 2 ++
.../sbml/species/SbmlSpeciesExporter.java | 20 ++++++++++++++-----
.../model/sbml/species/SbmlSpeciesParser.java | 14 +++++++++++--
4 files changed, 34 insertions(+), 9 deletions(-)
diff --git a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/extension/multi/BioEntityFeature.java b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/extension/multi/BioEntityFeature.java
index b34767108a..02dfab98ff 100644
--- a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/extension/multi/BioEntityFeature.java
+++ b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/extension/multi/BioEntityFeature.java
@@ -12,8 +12,11 @@ public enum BioEntityFeature {
"minerva_position_to_compartment_"),
SYNONYM("Synonym", null, new Class<?>[] { Element.class },
- "minerva_synonym_");
-
+ "minerva_synonym_"),
+
+ SYMBOL("Symbol", null, new Class<?>[] { Element.class },
+ "minerva_symbol_");
+
private String featureName;
private String defaultValue;
private Class<?>[] properClasses;
diff --git a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/extension/multi/MultiPackageNamingUtils.java b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/extension/multi/MultiPackageNamingUtils.java
index eefbd1bd25..1ef585cd49 100644
--- a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/extension/multi/MultiPackageNamingUtils.java
+++ b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/extension/multi/MultiPackageNamingUtils.java
@@ -27,6 +27,8 @@ public final class MultiPackageNamingUtils {
private static final String MINERVA_MODIFICATION_TYPE_PREFIX = "minerva_modification_type_";
+ public static final String NULL_REPRESENTATION = "NULL";
+
/**
* Returns id of the {@link MultiSpeciesType} for a given minerva class.
*
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 d5b7937f4b..9356fb591e 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
@@ -99,6 +99,7 @@ public class SbmlSpeciesExporter extends SbmlElementExporter<Species, org.sbml.j
assignPostionToCompartmentToMulti(element, multiExtension, speciesType);
assignElementModificationResiduesToMulti(element, multiExtension, speciesType);
assignListOfSynonymsToMulti(element, multiExtension, speciesType);
+ assignSymbolToMulti(element, multiExtension, speciesType);
}
private void assignElementModificationResiduesToMulti(Species element, MultiSpeciesPlugin multiExtension,
@@ -241,16 +242,16 @@ public class SbmlSpeciesExporter extends SbmlElementExporter<Species, org.sbml.j
private PossibleSpeciesFeatureValue getPosibleFeatureIdByName(String featureValueName,
SpeciesFeatureType speciesFeature) {
- PossibleSpeciesFeatureValue structuralStateFeatureValue = null;
+ PossibleSpeciesFeatureValue result = null;
for (PossibleSpeciesFeatureValue value : speciesFeature.getListOfPossibleSpeciesFeatureValues()) {
if (value.getName().equals(featureValueName)) {
- structuralStateFeatureValue = value;
+ result = value;
}
}
- if (structuralStateFeatureValue == null) {
- structuralStateFeatureValue = addPosibleValueToFeature(speciesFeature, featureValueName);
+ if (result == null) {
+ result = addPosibleValueToFeature(speciesFeature, featureValueName);
}
- return structuralStateFeatureValue;
+ return result;
}
private void assignPostionToCompartmentToMulti(Species element, MultiSpeciesPlugin multiExtension,
@@ -269,6 +270,11 @@ public class SbmlSpeciesExporter extends SbmlElementExporter<Species, org.sbml.j
}
}
+ private void assignSymbolToMulti(Species element, MultiSpeciesPlugin multiExtension,
+ MultiSpeciesType speciesType) {
+ assignValueToFeature(element, multiExtension, speciesType, element.getSymbol(), BioEntityFeature.SYMBOL);
+ }
+
private void assignValueToFeature(Species element, MultiSpeciesPlugin multiExtension, MultiSpeciesType speciesType,
String value, BioEntityFeature feature) {
SpeciesFeatureType structuralStateFeature = getFeature(element.getClass(), speciesType, feature);
@@ -370,6 +376,10 @@ public class SbmlSpeciesExporter extends SbmlElementExporter<Species, org.sbml.j
}
private PossibleSpeciesFeatureValue addPosibleValueToFeature(SpeciesFeatureType feature, String value) {
+ if (value == null) {
+ value = MultiPackageNamingUtils.NULL_REPRESENTATION;
+ }
+
PossibleSpeciesFeatureValue result = null;
for (PossibleSpeciesFeatureValue existingValue : feature.getListOfPossibleSpeciesFeatureValues()) {
if (existingValue.getName().equals(value)) {
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 b504bb60d5..e34dac0312 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
@@ -139,12 +139,18 @@ public class SbmlSpeciesParser extends SbmlElementParser<org.sbml.jsbml.Species>
}
} else if (MultiPackageNamingUtils.isFeatureId(featureTypeString, BioEntityFeature.POSITION_TO_COMPARTMENT)) {
if (featureValues.size() != 1) {
- logger.warn(warnPrefix + "Position to compartment must exactly one value");
+ logger.warn(warnPrefix + "Position to compartment must have exactly one value");
} else {
minervaElement.setPositionToCompartment(PositionToCompartment.getByString(featureValues.get(0)));
}
} else if (MultiPackageNamingUtils.isFeatureId(featureTypeString, BioEntityFeature.SYNONYM)) {
minervaElement.setSynonyms(featureValues);
+ } else if (MultiPackageNamingUtils.isFeatureId(featureTypeString, BioEntityFeature.SYMBOL)) {
+ if (featureValues.size() != 1) {
+ logger.warn(warnPrefix + "Symbol must have exactly one value");
+ } else {
+ minervaElement.setSymbol(featureValues.get(0));
+ }
} else if (MultiPackageNamingUtils.isModificationFeatureId(featureTypeString)) {
createModificationResidues(minervaElement, speciesType, feature);
} else {
@@ -160,7 +166,11 @@ public class SbmlSpeciesParser extends SbmlElementParser<org.sbml.jsbml.Species>
for (SpeciesFeatureValue featureValue : feature.getListOfSpeciesFeatureValues()) {
PossibleSpeciesFeatureValue possibleSpeciesFeatureValue = featureType.getListOfPossibleSpeciesFeatureValues()
.get(featureValue.getValue());
- result.add(possibleSpeciesFeatureValue.getName());
+ if (possibleSpeciesFeatureValue.getName().equals(MultiPackageNamingUtils.NULL_REPRESENTATION)) {
+ result.add(null);
+ } else {
+ result.add(possibleSpeciesFeatureValue.getName());
+ }
}
} else {
for (SpeciesTypeInstance speciesTypeInstance : speciesType.getListOfSpeciesTypeInstances()) {
--
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