Author: pwang
Date: 2009-06-11 14:57:19 -0700 (Thu, 11 Jun 2009)
New Revision: 16931
Modified:
csplugins/trunk/ucsd/pwang/jActiveModules3/src/csplugins/jActiveModules/ActivePaths.java
Log:
Create group only, the result will not be displayed on JPanel
Modified:
csplugins/trunk/ucsd/pwang/jActiveModules3/src/csplugins/jActiveModules/ActivePaths.java
===================================================================
---
csplugins/trunk/ucsd/pwang/jActiveModules3/src/csplugins/jActiveModules/ActivePaths.java
2009-06-11 21:50:42 UTC (rev 16930)
+++
csplugins/trunk/ucsd/pwang/jActiveModules3/src/csplugins/jActiveModules/ActivePaths.java
2009-06-11 21:57:19 UTC (rev 16931)
@@ -76,6 +76,9 @@
public MyGroupViewer myGroupViewer = null;
private static int groupViewerCount = 0;
private static int groupCount = 0;
+
+ public static String groupViewerName = "moduleFinderViewer";
+
// ----------------------------------------------------------------
public ActivePaths(CyNetwork cyNetwork, ActivePathFinderParameters
apfParams, ActiveModulesUI parentUI) {
this.apfParams = apfParams;
@@ -95,9 +98,8 @@
this.cyNetwork = cyNetwork;
this.parentUI = parentUI;
- // Generate a unique id for each groupViewer
- myGroupViewer = new MyGroupViewer("MyGroupViewer" +
groupViewerCount++);
-
+ // Create a groupViewer and register it
+ myGroupViewer = new MyGroupViewer(groupViewerName);
CyGroupManager.registerGroupViewer(myGroupViewer);
} // ctor
@@ -125,11 +127,13 @@
}
activePaths = apf.findActivePaths();
- Vector tableData = createTableData(attrNames);
+ Vector groupData = createGroupData();
//
+ printGroupData(groupData);
+ /*
tableDialog = null;
if (showTable) {
@@ -143,40 +147,38 @@
}
if(apfParams.getExit() && !apfParams.getRandomizeExpression()){
System.exit(0);
- }
+ }
+ */
}
+
//
- private Vector<Object> createTableData(String [] attrNames) {
+ private Vector<Object> createGroupData() {
Vector<CyGroup> groupVect = new Vector<CyGroup>();
Double[] scores = new Double[activePaths.length];
Boolean[][] data = new
Boolean[activePaths.length][activePaths[0].getConditions().length];
-
+
for (int i=0; i<activePaths.length; i++){
Component thePath = activePaths[i];
// Create group for this pathway
// 1. Define the group name
String groupName = "Group_" + groupCount++;
- System.out.println("ActivePaths: groupName = "+
groupName);
// 2. create an empty group
-
- CyGroup theGroup =
CyGroupManager.createGroup(groupName,
ActivePaths.this.myGroupViewer.getViewerName());
-
- System.out.println("ActivePaths: theGroup = " +
theGroup);
-
- Vector nodeVect = thePath.getNodes();
+ //CyGroup theGroup =
CyGroupManager.createGroup(groupName, ActivePaths.this.groupViewerName);
+ CyGroup theGroup =
CyGroupManager.createGroup(groupName, ActivePaths.this.groupViewerName);
// 3. add nodes to the group
+ Vector nodeVect = (Vector) thePath.getDisplayNodes();
for (int j=0; j< nodeVect.size(); j++){
CyNode oneNode = (CyNode) nodeVect.elementAt(j);
if (oneNode != null){
theGroup.addNode(oneNode);
}
else {
- System.out.println("ActivePaths:
createTableData(): oneNode = null");
+ //System.out.println("ActivePaths:
createTableData(): oneNode = null");
}
}
@@ -215,8 +217,22 @@
}
+ private void printGroupData(Vector groupData){
+ Vector<CyGroup> groupVect = (Vector<CyGroup>)
groupData.elementAt(0);
+ Double[] scores = (Double[]) groupData.elementAt(1);
+ Boolean[][] data = (Boolean[][]) groupData.elementAt(2);
+
+ System.out.println("\n================\nNumber of Groups = " +
groupVect.size());
+ for (int i=0; i<groupVect.size(); i++ ){
+ CyGroup theGroup = groupVect.elementAt(i);
+ System.out.println( theGroup.getGroupName()+ ": size =
"+ theGroup.getNodes().size()+ ": score =" + scores[i]);
+ }
+ System.out.println("");
+ }
+
+
public class MyGroupViewer implements CyGroupViewer {
- private String viewerName = "MyGroupViewer";
+ private String viewerName = ActivePaths.groupViewerName;
public MyGroupViewer(String viewerName){
this.viewerName = viewerName;
@@ -227,10 +243,11 @@
}
public void groupCreated(CyGroup group) {
-
+ System.out.println("MyGroupViewer: groupCreated(): "+
group.getGroupName());
}
+
public void groupCreated(CyGroup group, CyNetworkView myView){
-
+ System.out.println("MyGroupViewer: groupCreated(): "+
group.getGroupName() + " for " + myView.getTitle());
}
public void groupWillBeRemoved(CyGroup group){
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