From 9713e553b1245d6b2078b50c27d916b4241b3971 Mon Sep 17 00:00:00 2001
From: Piotr Gawron <piotr.gawron@uni.lu>
Date: Fri, 4 Jan 2019 14:23:21 +0100
Subject: [PATCH] import export of element abbreviation implemented
---
.../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 d51503dc71..32df3fa608 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
@@ -20,6 +20,9 @@ public enum BioEntityFeature {
FORMULA("Formula", null, new Class<?>[] { Element.class },
"minerva_formula_"),
+ ABBREVIATION("Abbreviation", null, new Class<?>[] { Element.class },
+ "minerva_abbreviation_"),
+
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 0f2951dfc3..b9bacc64e8 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
@@ -102,6 +102,7 @@ public class SbmlSpeciesExporter extends SbmlElementExporter<Species, org.sbml.j
assignSymbolToMulti(element, multiExtension, speciesType);
assignFullNameToMulti(element, multiExtension, speciesType);
assignFormulaToMulti(element, multiExtension, speciesType);
+ assignAbbreviationToMulti(element, multiExtension, speciesType);
}
private void assignElementModificationResiduesToMulti(Species element, MultiSpeciesPlugin multiExtension,
@@ -287,6 +288,11 @@ public class SbmlSpeciesExporter extends SbmlElementExporter<Species, org.sbml.j
assignValueToFeature(element, multiExtension, speciesType, element.getFormula(), BioEntityFeature.FORMULA);
}
+ private void assignAbbreviationToMulti(Species element, MultiSpeciesPlugin multiExtension,
+ MultiSpeciesType speciesType) {
+ assignValueToFeature(element, multiExtension, speciesType, element.getAbbreviation(), BioEntityFeature.ABBREVIATION);
+ }
+
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 680044ff49..7b19918850 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
@@ -163,6 +163,12 @@ public class SbmlSpeciesParser extends SbmlElementParser<org.sbml.jsbml.Species>
} else {
minervaElement.setFormula(featureValues.get(0));
}
+ } else if (MultiPackageNamingUtils.isFeatureId(featureTypeString, BioEntityFeature.ABBREVIATION)) {
+ if (featureValues.size() != 1) {
+ logger.warn(warnPrefix + "Abbreviation must have exactly one value");
+ } else {
+ minervaElement.setAbbreviation(featureValues.get(0));
+ }
} else if (MultiPackageNamingUtils.isModificationFeatureId(featureTypeString)) {
createModificationResidues(minervaElement, speciesType, feature);
} else {
--
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