From b5a4d8a71c2d74f9c8b1249145eec62a998ce744 Mon Sep 17 00:00:00 2001
From: Piotr Gawron <piotr.gawron@uni.lu>
Date: Fri, 9 Feb 2018 16:01:41 +0100
Subject: [PATCH] fix on kinetics in reactions with complex modifiers
---
.../reaction/KineticsXmlParser.java | 9 ++++++---
.../reaction/ReactionFromXml.java | 20 ++++++++++++++-----
2 files changed, 21 insertions(+), 8 deletions(-)
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/reaction/KineticsXmlParser.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/reaction/KineticsXmlParser.java
index e77e87b9d8..103ad6f643 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/reaction/KineticsXmlParser.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/reaction/KineticsXmlParser.java
@@ -55,15 +55,18 @@ public class KineticsXmlParser extends XmlParser {
if (element == null) {
element = model.getFunctionById(id);
}
+ if (element == null) {
+ element = model.getElementByElementId(id);
+ }
if (element != null) {
ciNode.setTextContent(element.getElementId());
- } else {
+ elementsUsedInKinetics.add(element);
+ } else if (!id.equals("default")) {
throw new InvalidXmlSchemaException("Unknown symbol in kinetics: " + id);
}
- elementsUsedInKinetics.add(element);
}
result.addArguments(elementsUsedInKinetics);
-
+
String definition = super.nodeToString(mathNode, true);
definition = definition.replace(" xmlns=\"http://www.sbml.org/sbml/level2/version4\"", "");
definition = definition.replace("<math>", "<math xmlns=\"http://www.w3.org/1998/Math/MathML\">");
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/reaction/ReactionFromXml.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/reaction/ReactionFromXml.java
index a5efde95d9..8eb79c0076 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/reaction/ReactionFromXml.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/reaction/ReactionFromXml.java
@@ -233,20 +233,30 @@ public class ReactionFromXml extends XmlParser {
String aliasId = super.getNodeAttr("alias", node);
addElementMapping(model, result, speciesId, aliasId);
}
-
+
for (Node node : super.getAllNotNecessirellyDirectChild("celldesigner:productLink", annotationNode)) {
String speciesId = super.getNodeAttr("product", node);
String aliasId = super.getNodeAttr("alias", node);
addElementMapping(model, result, speciesId, aliasId);
}
-
+ for (Node node : super.getAllNotNecessirellyDirectChild("celldesigner:modification", annotationNode)) {
+ String speciesId = super.getNodeAttr("modifiers", node);
+ String aliasId = super.getNodeAttr("aliases", node);
+ addElementMapping(model, result, speciesId, aliasId);
+ }
+
return result;
}
private void addElementMapping(Model model, Map<String, Element> result, String speciesId, String aliasId) {
- Element element = model.getElementByElementId(aliasId);
- result.put(speciesId, element);
- addCompartmentMapping(result, element);
+ String[] aliasIds = aliasId.split(",");
+ String[] speciesIds = speciesId.split(",");
+ for (int i = 0; i < aliasIds.length; i++) {
+
+ Element element = model.getElementByElementId(aliasIds[i]);
+ result.put(speciesIds[i], element);
+ addCompartmentMapping(result, element);
+ }
}
private void addCompartmentMapping(Map<String, Element> result, Element element) {
--
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