Author: pwang
Date: 2011-10-31 16:41:19 -0700 (Mon, 31 Oct 2011)
New Revision: 27351
Modified:
csplugins/trunk/ucsd/pwang/jActiveModules31/src/main/java/csplugins/jActiveModules/ActivePaths.java
Log:
Bug 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
2011-10-31 21:37:25 UTC (rev 27350)
+++
csplugins/trunk/ucsd/pwang/jActiveModules31/src/main/java/csplugins/jActiveModules/ActivePaths.java
2011-10-31 23:41:19 UTC (rev 27351)
@@ -161,17 +161,17 @@
// this.cyEventHelperService.fireEvent();
//}
- Set<VisualStyle> visualStyles =
this.visualMappingManager.getAllVisualStyles();
- Iterator<VisualStyle> it = visualStyles.iterator();
- while (it.hasNext()){
- VisualStyle vs = it.next();
- if (vs.getTitle().equalsIgnoreCase(VS_OVERVIEW_NAME)){
- overviewVS = vs;
- }
- if (vs.getTitle().equalsIgnoreCase(VS_MODULE_NAME)){
- moduleVS = vs;
- }
- }
+// Set<VisualStyle> visualStyles =
this.visualMappingManager.getAllVisualStyles();
+// Iterator<VisualStyle> it = visualStyles.iterator();
+// while (it.hasNext()){
+// VisualStyle vs = it.next();
+// if (vs.getTitle().equalsIgnoreCase(VS_OVERVIEW_NAME)){
+// overviewVS = vs;
+// }
+// if (vs.getTitle().equalsIgnoreCase(VS_MODULE_NAME)){
+// moduleVS = vs;
+// }
+// }
if (cyNetwork == null || cyNetwork.getNodeCount() == 0) {
@@ -226,6 +226,10 @@
newNode.setNetwork(subnetworks[i]);
// create an attribute for this new node
//Cytoscape.getNodeAttributes().setAttribute(newNode.getIdentifier(),
NODE_SCORE, new Double(activePaths[i].getScore()));
+
+ if
(overview.getDefaultNodeTable().getColumn(NODE_SCORE)== null){
+
overview.getDefaultNodeTable().createColumn(NODE_SCORE, Double.class, false);
+ }
newNode.getCyRow().set(NODE_SCORE, new
Double(activePaths[i].getScore()));
}
@@ -235,6 +239,12 @@
//3. Create an edge attribute "overlapScore", which is defined
as NumberOfSharedNodes/min(two network sizes)
+
+
overview.getDefaultEdgeTable().createColumn("jActiveModules_nodeCount_min_two",
Integer.class, false);
+
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()){
@@ -263,7 +273,13 @@
newView.updateView();
// Create view for top n modules
- int n = new
Integer(this.cytoscapeProperties.getProperties().getProperty(ActiveModulesUI.JACTIVEMODULES_TOP_N_MODULE)).intValue();
+ int n = -1;
+ try {
+ n= new
Integer(this.cytoscapeProperties.getProperties().getProperty(ActiveModulesUI.JACTIVEMODULES_TOP_N_MODULE)).intValue();
+ }
+ catch(Exception e){
+ n= 5;
+ }
if (n> subnetworks.length){
n = subnetworks.length;
@@ -391,8 +407,8 @@
//final CyNetworkView moduleView =
Cytoscape.createNetworkView(subnetworks[i], subnetworks[i].getTitle(),
tuning());
final CyNetworkView moduleView =
this.cyNetworkViewManager.getNetworkView(subnetworks2[i].getSUID());
//moduleView.setVisualStyle(moduleVS.getTitle()); //.getName());
-
this.visualMappingManager.setVisualStyle(moduleVS, moduleView);
//Cytoscape.getVisualMappingManager().setVisualStyle(moduleVS);
- moduleView.updateView(); //.redrawGraph(false,
true);
+
+// moduleView.updateView(); //.redrawGraph(false,
true);
}
}
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