From 4cd685fae8e5c40048c57b2daf700be6617b4aa8 Mon Sep 17 00:00:00 2001
From: Piotr Gawron <piotr.gawron@uni.lu>
Date: Thu, 15 Nov 2018 15:47:10 +0100
Subject: [PATCH] when exporting celldesigner aliases inside complex include
either compartmentAlias or complexAlias - including both result in weird
things inside CellDesigner
---
.../model/celldesigner/alias/SpeciesAliasXmlParser.java | 7 +++----
1 file changed, 3 insertions(+), 4 deletions(-)
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/alias/SpeciesAliasXmlParser.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/alias/SpeciesAliasXmlParser.java
index 30ab817536..631685017f 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/alias/SpeciesAliasXmlParser.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/alias/SpeciesAliasXmlParser.java
@@ -143,7 +143,6 @@ public class SpeciesAliasXmlParser extends AbstractAliasXmlParser<Species> {
complex.addSpecies(result);
}
}
-
species.updateModelElementAfterLayoutAdded(result);
return result;
@@ -205,12 +204,12 @@ public class SpeciesAliasXmlParser extends AbstractAliasXmlParser<Species> {
sb.append("<celldesigner:speciesAlias ");
sb.append("id=\"" + species.getElementId() + "\" ");
sb.append("species=\"" + elements.getElementId(species) + "\" ");
- if (compartmentAliasId != null) {
- sb.append("compartmentAlias=\"" + compartmentAliasId + "\" ");
- }
if (complex != null) {
sb.append("complexSpeciesAlias=\"" + complex.getElementId() + "\" ");
+ } else if (compartmentAliasId != null) {
+ // you cannot have both if there are both then CellDesigner behaves improperly
+ sb.append("compartmentAlias=\"" + compartmentAliasId + "\" ");
}
sb.append(">\n");
--
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