From 87c9c6605ee2ae9d8024b0ac0a158f57f02f8ec0 Mon Sep 17 00:00:00 2001
From: Piotr Gawron <piotr.gawron@uni.lu>
Date: Fri, 4 Jan 2019 14:12:12 +0100
Subject: [PATCH] import/export of element full name added
---
.../model/sbml/extension/multi/BioEntityFeature.java | 3 +++
.../converter/model/sbml/species/SbmlSpeciesExporter.java | 6 ++++++
.../converter/model/sbml/species/SbmlSpeciesParser.java | 6 ++++++
3 files changed, 15 insertions(+)
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 02dfab98ff..e30f31ebf3 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
@@ -14,6 +14,9 @@ public enum BioEntityFeature {
SYNONYM("Synonym", null, new Class<?>[] { Element.class },
"minerva_synonym_"),
+ FULL_NAME("Full name", null, new Class<?>[] { Element.class },
+ "minerva_full_name_"),
+
SYMBOL("Symbol", null, new Class<?>[] { Element.class },
"minerva_symbol_");
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 9356fb591e..316c0b0b7e 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
@@ -100,6 +100,7 @@ public class SbmlSpeciesExporter extends SbmlElementExporter<Species, org.sbml.j
assignElementModificationResiduesToMulti(element, multiExtension, speciesType);
assignListOfSynonymsToMulti(element, multiExtension, speciesType);
assignSymbolToMulti(element, multiExtension, speciesType);
+ assignFullNameToMulti(element, multiExtension, speciesType);
}
private void assignElementModificationResiduesToMulti(Species element, MultiSpeciesPlugin multiExtension,
@@ -275,6 +276,11 @@ public class SbmlSpeciesExporter extends SbmlElementExporter<Species, org.sbml.j
assignValueToFeature(element, multiExtension, speciesType, element.getSymbol(), BioEntityFeature.SYMBOL);
}
+ private void assignFullNameToMulti(Species element, MultiSpeciesPlugin multiExtension,
+ MultiSpeciesType speciesType) {
+ assignValueToFeature(element, multiExtension, speciesType, element.getFullName(), BioEntityFeature.FULL_NAME);
+ }
+
private void assignValueToFeature(Species element, MultiSpeciesPlugin multiExtension, MultiSpeciesType speciesType,
String value, BioEntityFeature feature) {
SpeciesFeatureType structuralStateFeature = getFeature(element.getClass(), speciesType, feature);
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 e34dac0312..90754235bf 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
@@ -151,6 +151,12 @@ public class SbmlSpeciesParser extends SbmlElementParser<org.sbml.jsbml.Species>
} else {
minervaElement.setSymbol(featureValues.get(0));
}
+ } else if (MultiPackageNamingUtils.isFeatureId(featureTypeString, BioEntityFeature.FULL_NAME)) {
+ if (featureValues.size() != 1) {
+ logger.warn(warnPrefix + "Full name must have exactly one value");
+ } else {
+ minervaElement.setFullName(featureValues.get(0));
+ }
} else if (MultiPackageNamingUtils.isModificationFeatureId(featureTypeString)) {
createModificationResidues(minervaElement, speciesType, feature);
} else {
--
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