From 7aea8b7b28265f4bd167bf10ec3deb3e68850a70 Mon Sep 17 00:00:00 2001
From: Piotr Gawron <piotr.gawron@uni.lu>
Date: Fri, 16 Nov 2018 12:29:39 +0100
Subject: [PATCH] gpml parser doesn't put compartment into element inside
complexes
---
.../wikipathway/XML/ModelContructor.java | 26 ++++++++++---------
1 file changed, 14 insertions(+), 12 deletions(-)
diff --git a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/ModelContructor.java b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/ModelContructor.java
index a051eda38e..f340ba5f5b 100644
--- a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/ModelContructor.java
+++ b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/ModelContructor.java
@@ -983,15 +983,17 @@ public class ModelContructor {
* {@link Compartment} into a proper compartment.
*
* @param model
- * model where aliases will be modifed
+ * model where aliases will be modified
*/
private void putAliasesIntoCompartments(Model model) {
- for (Element alias : model.getElements()) {
- if (alias.getCompartment() == null) {
- if (alias instanceof Species) {
+ for (Element element : model.getElements()) {
+ if (element instanceof Species) {
+ if (((Species) element).getComplex() != null) {
+ element.setCompartment(null);
+ } else if (element.getCompartment() == null) {
Compartment selectedAlias = null;
for (Compartment cAlias : model.getCompartments()) {
- if (cAlias.cross(alias)) {
+ if (cAlias.cross(element)) {
if (selectedAlias == null) {
selectedAlias = cAlias;
} else if (selectedAlias.getSize() > cAlias.getSize()) {
@@ -1000,7 +1002,7 @@ public class ModelContructor {
}
}
if (selectedAlias != null) {
- selectedAlias.addElement(alias);
+ selectedAlias.addElement(element);
}
}
}
@@ -1128,16 +1130,16 @@ public class ModelContructor {
compartmentAlias.getElements().clear();
}
- for (Element alias : model.getElements()) {
+ for (Element element : model.getElements()) {
// elements inside complexes shouldn't be considered
- if (alias instanceof Species) {
- if (((Species) alias).getComplex() != null) {
+ if (element instanceof Species) {
+ if (((Species) element).getComplex() != null) {
continue;
}
}
Compartment parentAlias = null;
for (Compartment compartmentAlias : aliases) {
- if (compartmentAlias.contains(alias)) {
+ if (compartmentAlias.contains(element)) {
if (parentAlias == null) {
parentAlias = compartmentAlias;
} else if (parentAlias.getSize() > compartmentAlias.getSize()) {
@@ -1146,8 +1148,8 @@ public class ModelContructor {
}
}
if (parentAlias != null) {
- parentAlias.addElement(alias);
- alias.setCompartment(parentAlias);
+ parentAlias.addElement(element);
+ element.setCompartment(parentAlias);
}
}
}
--
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