From c1b0296b139769acd33bf65a06ecd232c93d671a Mon Sep 17 00:00:00 2001
From: Piotr Gawron <piotr.gawron@uni.lu>
Date: Tue, 19 Dec 2017 10:32:19 +0100
Subject: [PATCH] handling of the situation when layout ids are not unique for
reactions
---
.../model/sbml/SbmlReactionParser.java | 22 +++++++++----------
1 file changed, 11 insertions(+), 11 deletions(-)
diff --git a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlReactionParser.java b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlReactionParser.java
index 3a633ce4f7..88c9883007 100644
--- a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlReactionParser.java
+++ b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlReactionParser.java
@@ -72,26 +72,27 @@ public class SbmlReactionParser {
return sbmlModel.getListOfReactions();
}
- protected void mergeLayout(Collection<Reaction> elements, Layout sbmlLayout, Model sbmlModel)
+ protected void mergeLayout(Collection<Reaction> reactions, Layout sbmlLayout, Model sbmlModel)
throws InvalidInputDataExecption {
Set<Reaction> used = new HashSet<>();
- Map<String, Reaction> elementById = new HashMap<>();
- for (Reaction species : elements) {
- if (elementById.get(species.getIdReaction()) != null) {
- throw new InvalidInputDataExecption("Duplicated reaction id: " + species.getIdReaction());
+ Map<String, Reaction> reactionById = new HashMap<>();
+ for (Reaction reaction : reactions) {
+ if (reactionById.get(reaction.getIdReaction()) != null) {
+ throw new InvalidInputDataExecption("Duplicated reaction id: " + reaction.getIdReaction());
}
- elementById.put(species.getIdReaction(), species);
+ reactionById.put(reaction.getIdReaction(), reaction);
}
for (ReactionGlyph glyph : sbmlLayout.getListOfReactionGlyphs()) {
- Reaction source = elementById.get(glyph.getReaction());
+ Reaction source = reactionById.get(glyph.getReaction());
if (source == null) {
throw new InvalidInputDataExecption("Layout contains invalid Species id: " + glyph.getReaction());
}
used.add(source);
try {
Reaction reactionWithLayout = source.copy();
- reactionWithLayout.setIdReaction(glyph.getId());
+ // getId doesn't have to be unique, therefore we concatenate with reaction
+ reactionWithLayout.setIdReaction(glyph.getId() + "_" + glyph.getReaction());
for (SpeciesReferenceGlyph speciesRefernceGlyph : glyph.getListOfSpeciesReferenceGlyphs()) {
SpeciesGlyph speciesGlyph = layout.getSpeciesGlyph(speciesRefernceGlyph.getSpeciesGlyph());
ReactionNode minervaNode = null;
@@ -206,16 +207,15 @@ public class SbmlReactionParser {
operator.setLine(line);
reactionWithLayout.addNode(operator);
}
-
minervaModel.addReaction(new StateTransitionReaction(reactionWithLayout));
} catch (InvalidArgumentException e) {
throw new InvalidInputDataExecption(e);
}
}
Set<Reaction> elementsToRemove = new HashSet<>();
- for (Reaction reaction : elements) {
+ for (Reaction reaction : reactions) {
if (!used.contains(reaction)) {
- logger.warn("Layout doesn't contain information about Element: " + reaction.getIdReaction());
+ logger.warn("Layout doesn't contain information about Reaction: " + reaction.getIdReaction());
} else {
elementsToRemove.add(reaction);
}
--
GitLab