From 3f760694ad77d89f577a7830e9d73835aeca95f5 Mon Sep 17 00:00:00 2001
From: Piotr Gawron <piotr.gawron@uni.lu>
Date: Fri, 4 Jan 2019 15:16:38 +0100
Subject: [PATCH] export/import of charge implemented
---
.../sbml/extension/multi/BioEntityFeature.java | 3 +++
.../model/sbml/species/SbmlSpeciesExporter.java | 8 ++++++++
.../model/sbml/species/SbmlSpeciesParser.java | 13 +++++++++++++
.../sbml/ElementPropertiesExportToMultiTest.java | 4 ++++
4 files changed, 28 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 93db74e678..a1b95b4d59 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
@@ -29,6 +29,9 @@ public enum BioEntityFeature {
DIMER("Dimer", null, new Class<?>[] { Element.class },
"minerva_dimer_"),
+ CHARGE("Charge", null, new Class<?>[] { Element.class },
+ "minerva_charge_"),
+
ABBREVIATION("Abbreviation", null, new Class<?>[] { Element.class },
"minerva_abbreviation_"),
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 532aa20056..a3c6131fb7 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
@@ -106,6 +106,7 @@ public class SbmlSpeciesExporter extends SbmlElementExporter<Species, org.sbml.j
assignDimerToMulti(element, multiExtension, speciesType);
assignHypotheticalToMulti(element, multiExtension, speciesType);
assignAbbreviationToMulti(element, multiExtension, speciesType);
+ assignChargeToMulti(element, multiExtension, speciesType);
}
private void assignElementModificationResiduesToMulti(Species element, MultiSpeciesPlugin multiExtension,
@@ -305,6 +306,13 @@ public class SbmlSpeciesExporter extends SbmlElementExporter<Species, org.sbml.j
}
}
+ private void assignChargeToMulti(Species element, MultiSpeciesPlugin multiExtension,
+ MultiSpeciesType speciesType) {
+ if (element.getCharge() != null) {
+ assignValueToFeature(element, multiExtension, speciesType, element.getCharge().toString(), BioEntityFeature.CHARGE);
+ }
+ }
+
private void assignHypotheticalToMulti(Species element, MultiSpeciesPlugin multiExtension,
MultiSpeciesType speciesType) {
if (element.getHypothetical() != null) {
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 3022498a91..de9ba5546d 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
@@ -86,6 +86,9 @@ public class SbmlSpeciesParser extends SbmlElementParser<org.sbml.jsbml.Species>
if (species.isSetConstant()) {
result.setConstant(species.getConstant());
}
+ if (species.isSetCharge()) {
+ result.setCharge(species.getCharge());
+ }
assignBioEntityData(species, result);
if (getLayout() == null) {
assignCompartment(result, species.getCompartment());
@@ -157,6 +160,16 @@ public class SbmlSpeciesParser extends SbmlElementParser<org.sbml.jsbml.Species>
logger.warn(warnPrefix + "Dimer must have integer value, instead found: " + featureValues.get(0));
}
}
+ } else if (MultiPackageNamingUtils.isFeatureId(featureTypeString, BioEntityFeature.CHARGE)) {
+ if (featureValues.size() != 1) {
+ logger.warn(warnPrefix + "Charge must have exactly one value");
+ } else {
+ try {
+ minervaElement.setCharge(Integer.parseInt(featureValues.get(0)));
+ } catch (NumberFormatException e) {
+ logger.warn(warnPrefix + "Charge must have integer value, instead found: " + featureValues.get(0));
+ }
+ }
} else if (MultiPackageNamingUtils.isFeatureId(featureTypeString, BioEntityFeature.SYMBOL)) {
if (featureValues.size() != 1) {
logger.warn(warnPrefix + "Symbol must have exactly one value");
diff --git a/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/ElementPropertiesExportToMultiTest.java b/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/ElementPropertiesExportToMultiTest.java
index ad4ba2ac9d..ea0af3d658 100644
--- a/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/ElementPropertiesExportToMultiTest.java
+++ b/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/ElementPropertiesExportToMultiTest.java
@@ -60,6 +60,10 @@ public class ElementPropertiesExportToMultiTest {
element.setHomodimer(4);
data.add(createTestEntry("Homodimer", element));
+ element = createElement();
+ element.setCharge(5);
+ data.add(createTestEntry("Charge", element));
+
element = createElement();
element.setHypothetical(true);
data.add(createTestEntry("Hypothetical", element));
--
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