From 2e3ca9ce97deb80ee4ad4134cb93e385b9de210f Mon Sep 17 00:00:00 2001
From: Piotr Gawron <piotr.gawron@uni.lu>
Date: Fri, 4 Jan 2019 14:59:36 +0100
Subject: [PATCH] import/export of hypothetical implemented
---
.../sbml/extension/multi/BioEntityFeature.java | 3 +++
.../model/sbml/species/SbmlSpeciesExporter.java | 9 +++++++++
.../model/sbml/species/SbmlSpeciesParser.java | 14 ++++++++++++++
.../sbml/ElementPropertiesExportToMultiTest.java | 4 ++++
4 files changed, 30 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 bb89d16008..93db74e678 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
@@ -23,6 +23,9 @@ public enum BioEntityFeature {
FORMULA("Formula", null, new Class<?>[] { Element.class },
"minerva_formula_"),
+ HYPOTHETICAL("Hypothetical", null, new Class<?>[] { Element.class },
+ "minerva_hypothetical_"),
+
DIMER("Dimer", null, new Class<?>[] { Element.class },
"minerva_dimer_"),
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 7dad53fae4..532aa20056 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
@@ -104,6 +104,7 @@ public class SbmlSpeciesExporter extends SbmlElementExporter<Species, org.sbml.j
assignFullNameToMulti(element, multiExtension, speciesType);
assignFormulaToMulti(element, multiExtension, speciesType);
assignDimerToMulti(element, multiExtension, speciesType);
+ assignHypotheticalToMulti(element, multiExtension, speciesType);
assignAbbreviationToMulti(element, multiExtension, speciesType);
}
@@ -304,6 +305,14 @@ public class SbmlSpeciesExporter extends SbmlElementExporter<Species, org.sbml.j
}
}
+ private void assignHypotheticalToMulti(Species element, MultiSpeciesPlugin multiExtension,
+ MultiSpeciesType speciesType) {
+ if (element.getHypothetical() != null) {
+ assignValueToFeature(element, multiExtension, speciesType, element.getHypothetical().toString(),
+ BioEntityFeature.HYPOTHETICAL);
+ }
+ }
+
private void assignAbbreviationToMulti(Species element, MultiSpeciesPlugin multiExtension,
MultiSpeciesType speciesType) {
assignValueToFeature(element, multiExtension, speciesType, element.getAbbreviation(),
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 b2a3de6028..3022498a91 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
@@ -181,6 +181,20 @@ public class SbmlSpeciesParser extends SbmlElementParser<org.sbml.jsbml.Species>
} else {
minervaElement.setAbbreviation(featureValues.get(0));
}
+ } else if (MultiPackageNamingUtils.isFeatureId(featureTypeString, BioEntityFeature.HYPOTHETICAL)) {
+ if (featureValues.size() != 1) {
+ logger.warn(warnPrefix + "Hypothetical must have exactly one value");
+ } else {
+ Boolean value = null;
+ if (featureValues.get(0).equalsIgnoreCase("true")) {
+ value = true;
+ } else if (featureValues.get(0).equalsIgnoreCase("false")) {
+ value = false;
+ } else {
+ logger.warn(warnPrefix + "Hypothetical must be true/false value. Found: " + featureValues.get(0));
+ }
+ minervaElement.setHypothetical(value);
+ }
} else if (MultiPackageNamingUtils.isModificationFeatureId(featureTypeString)) {
createModificationResidues(minervaElement, speciesType, feature);
} else {
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 50f4af36da..ad4ba2ac9d 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.setHypothetical(true);
+ data.add(createTestEntry("Hypothetical", element));
+
element = createElement();
element.setSymbol("H2O");
data.add(createTestEntry("Symbol", element));
--
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