Author: pwang
Date: 2011-11-01 09:26:24 -0700 (Tue, 01 Nov 2011)
New Revision: 27357
Modified:
csplugins/trunk/ucsd/pwang/jActiveModules31/src/main/java/csplugins/jActiveModules/ActivePaths.java
Log:
More bugs fixed
Modified:
csplugins/trunk/ucsd/pwang/jActiveModules31/src/main/java/csplugins/jActiveModules/ActivePaths.java
===================================================================
---
csplugins/trunk/ucsd/pwang/jActiveModules31/src/main/java/csplugins/jActiveModules/ActivePaths.java
2011-11-01 15:23:53 UTC (rev 27356)
+++
csplugins/trunk/ucsd/pwang/jActiveModules31/src/main/java/csplugins/jActiveModules/ActivePaths.java
2011-11-01 16:26:24 UTC (rev 27357)
@@ -199,7 +199,7 @@
}
public void run() {
-
+
System.gc();
//long start = System.currentTimeMillis();
HashMap expressionMap = generateExpressionMap();
@@ -214,6 +214,10 @@
//1 . create subnetwork for each path
CyNetwork[] subnetworks = createSubnetworks();
+ for (int i=0; i<subnetworks.length; i++){
+ this.cyNetworkManager.addNetwork(subnetworks[i]);
+ }
+
//2. create an overview network for all nested network
final CyNetwork overview = this.cyNetworkFactory.getInstance();
overview.getCyRow().set("name", "jActiveModules Search Result
"+ runCount++);
@@ -232,6 +236,8 @@
}
newNode.getCyRow().set(NODE_SCORE, new
Double(activePaths[i].getScore()));
}
+
+ this.cyNetworkManager.addNetwork(overview);
//Edges indicate that nodes in nested networks exist in both
nested networks
Set<CyEdge> path_edges = getPathEdges(overview, path_nodes);
//new HashSet<CyEdge>();
@@ -244,7 +250,6 @@
overview.getDefaultEdgeTable().createColumn("jActiveModules_nodeOverlapCount",
Integer.class, false);
overview.getDefaultEdgeTable().createColumn(EDGE_SCORE,
Double.class, false);
-
CyTable cyEdgeAttrs = this.cyNetwork.getDefaultEdgeTable();
//Cytoscape.getEdgeAttributes();
Iterator it = path_edges.iterator();
while(it.hasNext()){
@@ -264,13 +269,21 @@
//cyEdgeAttrs.setAttribute(aEdge.getIdentifier(),
EDGE_SCORE, overlapScore);
aEdge.getCyRow().set(EDGE_SCORE, overlapScore);
}
-
+
//4. Create an view for overview network and apply visual style
//Cytoscape.createNetworkView(overview,
overview.getIdentifier(), tuning(), null);
final CyNetworkView newView =
this.cyNetworkViewFactory.getNetworkView(overview);
+ this.cyNetworkViewManager.addNetworkView(newView);
- this.visualMappingManager.setVisualStyle(overviewVS, newView);
- newView.updateView();
+// this.visualMappingManager.setVisualStyle(overviewVS, newView);
+
+ //newView.updateView();
+
+ // Apply layout for overview
+ CyLayoutAlgorithm alg =
this.cyLayoutsService.getLayout("force-directed");
+ alg.setNetworkView(newView);
+ this.taskManagerService.execute(alg);
+
// Create view for top n modules
int n = -1;
@@ -287,14 +300,15 @@
for (int i=0; i<n; i++){
CyNetworkView theView =
this.cyNetworkViewFactory.getNetworkView(subnetworks[i]);
+
this.cyNetworkViewManager.addNetworkView(theView);
-
this.visualMappingManager.setVisualStyle(moduleVS, theView);
- theView.updateView();
+//
this.visualMappingManager.setVisualStyle(moduleVS, theView);
+// theView.updateView();
- CyLayoutAlgorithm alg =
this.cyLayoutsService.getLayout("force-directed");
+ CyLayoutAlgorithm alg_f =
this.cyLayoutsService.getLayout("force-directed");
alg.setNetworkView(theView);
- this.taskManagerService.execute(alg);
+ this.taskManagerService.execute(alg_f);
}
}
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