From f67b3a3895f7b682595eaef2c4ae12d7cb916f31 Mon Sep 17 00:00:00 2001
From: Piotr Gawron <piotr.gawron@uni.lu>
Date: Fri, 4 Jan 2019 14:25:43 +0100
Subject: [PATCH] import/export of element former symbols implemented
---
.../extension/multi/BioEntityFeature.java | 29 ++++++++++---------
.../sbml/species/SbmlSpeciesExporter.java | 8 +++++
.../model/sbml/species/SbmlSpeciesParser.java | 2 ++
3 files changed, 26 insertions(+), 13 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 32df3fa608..b1f3403977 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
@@ -7,25 +7,28 @@ import lcsb.mapviewer.model.map.species.Protein;
public enum BioEntityFeature {
STRUCTURAL_STATE("Structural state", "", new Class<?>[] { Protein.class, Complex.class },
"minerva_structural_state_"),
-
+
POSITION_TO_COMPARTMENT("Position to compartment", "undefined", new Class<?>[] { Element.class },
- "minerva_position_to_compartment_"),
-
+ "minerva_position_to_compartment_"),
+
SYNONYM("Synonym", null, new Class<?>[] { Element.class },
- "minerva_synonym_"),
-
+ "minerva_synonym_"),
+
+ FORMER_SYMBOL("Former symbol", null, new Class<?>[] { Element.class },
+ "minerva_former_symbol_"),
+
FULL_NAME("Full name", null, new Class<?>[] { Element.class },
- "minerva_full_name_"),
-
+ "minerva_full_name_"),
+
FORMULA("Formula", null, new Class<?>[] { Element.class },
- "minerva_formula_"),
-
+ "minerva_formula_"),
+
ABBREVIATION("Abbreviation", null, new Class<?>[] { Element.class },
- "minerva_abbreviation_"),
-
+ "minerva_abbreviation_"),
+
SYMBOL("Symbol", null, new Class<?>[] { Element.class },
- "minerva_symbol_");
-
+ "minerva_symbol_");
+
private String featureName;
private String defaultValue;
private Class<?>[] properClasses;
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 b9bacc64e8..a0ea4fa473 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);
+ assignListOfFormerSymbolsToMulti(element, multiExtension, speciesType);
assignSymbolToMulti(element, multiExtension, speciesType);
assignFullNameToMulti(element, multiExtension, speciesType);
assignFormulaToMulti(element, multiExtension, speciesType);
@@ -273,6 +274,13 @@ public class SbmlSpeciesExporter extends SbmlElementExporter<Species, org.sbml.j
}
}
+ private void assignListOfFormerSymbolsToMulti(Species element, MultiSpeciesPlugin multiExtension,
+ MultiSpeciesType speciesType) {
+ for (String formerSymbol : element.getFormerSymbols()) {
+ assignValueToFeature(element, multiExtension, speciesType, formerSymbol, BioEntityFeature.FORMER_SYMBOL);
+ }
+ }
+
private void assignSymbolToMulti(Species element, MultiSpeciesPlugin multiExtension,
MultiSpeciesType speciesType) {
assignValueToFeature(element, multiExtension, speciesType, element.getSymbol(), BioEntityFeature.SYMBOL);
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 7b19918850..1de4988a3f 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
@@ -145,6 +145,8 @@ public class SbmlSpeciesParser extends SbmlElementParser<org.sbml.jsbml.Species>
}
} else if (MultiPackageNamingUtils.isFeatureId(featureTypeString, BioEntityFeature.SYNONYM)) {
minervaElement.setSynonyms(featureValues);
+ } else if (MultiPackageNamingUtils.isFeatureId(featureTypeString, BioEntityFeature.FORMER_SYMBOL)) {
+ minervaElement.setFormerSymbols(featureValues);
} else if (MultiPackageNamingUtils.isFeatureId(featureTypeString, BioEntityFeature.SYMBOL)) {
if (featureValues.size() != 1) {
logger.warn(warnPrefix + "Symbol must have exactly one value");
--
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