Author: rodche
Date: 2012-05-14 12:33:46 -0700 (Mon, 14 May 2012)
New Revision: 29262
Modified:
csplugins/trunk/toronto/rodche/cpathsquared-impl/pom.xml
csplugins/trunk/toronto/rodche/cpathsquared-impl/src/main/java/org/cytoscape/cpathsquared/internal/task/ExecuteGetRecordByCPathIdTask.java
csplugins/trunk/toronto/rodche/cpathsquared-impl/src/main/java/org/cytoscape/cpathsquared/internal/util/BioPaxUtil.java
Log:
updated to paxtools 4.1.5-SNAPSHOTs
Modified: csplugins/trunk/toronto/rodche/cpathsquared-impl/pom.xml
===================================================================
--- csplugins/trunk/toronto/rodche/cpathsquared-impl/pom.xml 2012-05-14
19:15:18 UTC (rev 29261)
+++ csplugins/trunk/toronto/rodche/cpathsquared-impl/pom.xml 2012-05-14
19:33:46 UTC (rev 29262)
@@ -199,12 +199,12 @@
<dependency>
<groupId>org.biopax.paxtools</groupId>
<artifactId>paxtools-core</artifactId>
- <version>4.1.4-SNAPSHOT</version>
+ <version>4.1.5-SNAPSHOT</version>
</dependency>
<dependency>
<groupId>org.biopax.paxtools</groupId>
<artifactId>biopax-converter</artifactId>
- <version>4.1.4-SNAPSHOT</version>
+ <version>4.1.5-SNAPSHOT</version>
</dependency>
<!-- Spring Dependencies to embed (temporary; must use/start
Spring EBR
bundles instead) -->
Modified:
csplugins/trunk/toronto/rodche/cpathsquared-impl/src/main/java/org/cytoscape/cpathsquared/internal/task/ExecuteGetRecordByCPathIdTask.java
===================================================================
---
csplugins/trunk/toronto/rodche/cpathsquared-impl/src/main/java/org/cytoscape/cpathsquared/internal/task/ExecuteGetRecordByCPathIdTask.java
2012-05-14 19:15:18 UTC (rev 29261)
+++
csplugins/trunk/toronto/rodche/cpathsquared-impl/src/main/java/org/cytoscape/cpathsquared/internal/task/ExecuteGetRecordByCPathIdTask.java
2012-05-14 19:33:46 UTC (rev 29262)
@@ -5,11 +5,9 @@
import java.io.FileWriter;
import java.io.IOException;
import java.util.ArrayList;
-import java.util.Collections;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
-import java.util.Set;
import javax.swing.SwingUtilities;
@@ -297,9 +295,8 @@
}
//normalize/infer properties: displayName,
organism, dataSource
fixDisplayName(model);
- ModelUtils mu = new ModelUtils(model);
- mu.inferPropertyFromParent("dataSource");
- mu.inferPropertyFromParent("organism");
+ ModelUtils.inferPropertyFromParent(model,
"dataSource");
+ ModelUtils.inferPropertyFromParent(model,
"organism");
//map biopax properties to Cy attributes for
SIF nodes
for (BioPAXElement e : model.getObjects()) {
if(e instanceof EntityReference
Modified:
csplugins/trunk/toronto/rodche/cpathsquared-impl/src/main/java/org/cytoscape/cpathsquared/internal/util/BioPaxUtil.java
===================================================================
---
csplugins/trunk/toronto/rodche/cpathsquared-impl/src/main/java/org/cytoscape/cpathsquared/internal/util/BioPaxUtil.java
2012-05-14 19:15:18 UTC (rev 29261)
+++
csplugins/trunk/toronto/rodche/cpathsquared-impl/src/main/java/org/cytoscape/cpathsquared/internal/util/BioPaxUtil.java
2012-05-14 19:33:46 UTC (rev 29262)
@@ -456,15 +456,13 @@
public static String getName(Model model) {
StringBuffer modelName = new StringBuffer();
- ModelUtils mu = new ModelUtils(model);
-
- Collection<Pathway> pws = mu.getRootElements(Pathway.class);
+ Collection<Pathway> pws = ModelUtils.getRootElements(model,
Pathway.class);
for(Pathway pw: pws) {
modelName.append(" ").append(getNodeName(pw));
}
if(modelName.length()==0) {
- Collection<Interaction> itrs =
mu.getRootElements(Interaction.class);
+ Collection<Interaction> itrs =
ModelUtils.getRootElements(model, Interaction.class);
for(Interaction it: itrs) {
modelName.append(" ").append(getNodeName(it));
}
--
You received this message because you are subscribed to the Google Groups
"cytoscape-cvs" group.
To post to this group, send email to [email protected].
To unsubscribe from this group, send email to
[email protected].
For more options, visit this group at
http://groups.google.com/group/cytoscape-cvs?hl=en.
