Author: pwang
Date: 2009-06-10 17:05:12 -0700 (Wed, 10 Jun 2009)
New Revision: 16911
Modified:
csplugins/trunk/ucsd/pwang/jActiveModules3/src/csplugins/jActiveModules/ActivePaths.java
Log:
use CyGroup
Modified:
csplugins/trunk/ucsd/pwang/jActiveModules3/src/csplugins/jActiveModules/ActivePaths.java
===================================================================
---
csplugins/trunk/ucsd/pwang/jActiveModules3/src/csplugins/jActiveModules/ActivePaths.java
2009-06-11 00:03:57 UTC (rev 16910)
+++
csplugins/trunk/ucsd/pwang/jActiveModules3/src/csplugins/jActiveModules/ActivePaths.java
2009-06-11 00:05:12 UTC (rev 16911)
@@ -29,15 +29,22 @@
import javax.swing.SwingConstants;
import csplugins.jActiveModules.data.ActivePathFinderParameters;
-import csplugins.jActiveModules.dialogs.ConditionsVsPathwaysTable;
+import csplugins.jActiveModules.dialogs.ConditionsVsPathwaysTable2;
import cytoscape.CyNetwork;
+import cytoscape.CyNode;
+import cytoscape.groups.CyGroup;
+import cytoscape.groups.CyGroupManager;
+import cytoscape.groups.CyGroupViewer;
+import cytoscape.groups.CyGroupViewer.ChangeType;
import cytoscape.Cytoscape;
import cytoscape.data.CyAttributes;
import cytoscape.data.ExpressionData;
import cytoscape.data.SelectFilter;
import cytoscape.data.mRNAMeasurement;
+import cytoscape.view.CyNetworkView;
import cytoscape.view.cytopanels.CytoPanel;
import cytoscape.view.cytopanels.CytoPanelState;
+import csplugins.jActiveModules.Component;
//import cytoscape.data.CyNetworkFactory;
//-----------------------------------------------------------------------------------
@@ -50,7 +57,7 @@
//protected ExpressionData expressionData = null;
protected JMenuBar menubar;
protected JMenu expressionConditionsMenu;
- protected ConditionsVsPathwaysTable tableDialog;
+ protected ConditionsVsPathwaysTable2 tableDialog;
protected String currentCondition = "none";
protected csplugins.jActiveModules.Component[] activePaths;
protected String[] attrNames;
@@ -65,7 +72,10 @@
protected static int resultsCount = 1;
protected ActiveModulesUI parentUI;
-
+
+ public MyGroupViewer myGroupViewer = null;
+ private static int groupViewerCount = 0;
+ private static int groupCount = 0;
// ----------------------------------------------------------------
public ActivePaths(CyNetwork cyNetwork, ActivePathFinderParameters
apfParams, ActiveModulesUI parentUI) {
this.apfParams = apfParams;
@@ -84,6 +94,12 @@
mainFrame = Cytoscape.getDesktop();
this.cyNetwork = cyNetwork;
this.parentUI = parentUI;
+
+ // Generate a unique id for each groupViewer
+ myGroupViewer = new MyGroupViewer("MyGroupViewer" +
groupViewerCount++);
+
+ CyGroupManager.registerGroupViewer(myGroupViewer);
+
} // ctor
// --------------------------------------------------------------
@@ -108,10 +124,19 @@
cyNetwork, apfParams,
mainFrame, parentUI);
}
activePaths = apf.findActivePaths();
+
+ Vector tableData = createTableData(attrNames);
+ //
+
+
tableDialog = null;
+
if (showTable) {
- showConditionsVsPathwaysTable();
+ tableDialog = new ConditionsVsPathwaysTable2(cyNetwork,
+ attrNames, tableData, ActivePaths.this,
parentUI);
+
+ showConditionsVsPathwaysTable();
}
if(apfParams.getSave() && !apfParams.getRandomizeExpression()){
tableDialog.saveState(apfParams.getOutputFile());
@@ -121,7 +146,101 @@
}
}
-
+
+ //
+ private Vector<Object> createTableData(String [] attrNames) {
+ 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();
+
+ // 3. add nodes to the group
+ 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");
+ }
+ }
+
+ //
+ groupVect.add(theGroup);
+
+ // get score for this pathway
+ scores[i] = new Double(thePath.getScore());
+
+ //populate data items
+ String[] conditions = thePath.getConditions();
+ for (int j=0; j<thePath.getConditions().length; j++ ){
+ boolean matchedCondition = false;
+
+ for (int cond = 0; cond < conditions.length;
cond++) {
+ //String condition =
conditionsForThisPath[cond];
+ if
(attrNames[cond].equalsIgnoreCase(conditions[cond])) {
+ matchedCondition = true;
+ break;
+ }
+ }
+
+ if (matchedCondition)
+ data[i][j] = new Boolean(true);
+ else
+ data[i][j] = new Boolean(false);
+ }
+ }
+
+ Vector<Object> retVect = new Vector<Object>();
+ retVect.add(groupVect);
+ retVect.add(scores);
+ retVect.add(data);
+
+ return retVect;
+ }
+
+
+ public class MyGroupViewer implements CyGroupViewer {
+ private String viewerName = "MyGroupViewer";
+
+ public MyGroupViewer(String viewerName){
+ this.viewerName = viewerName;
+ }
+
+ public String getViewerName(){
+ return viewerName;
+ }
+
+ public void groupCreated(CyGroup group) {
+
+ }
+ public void groupCreated(CyGroup group, CyNetworkView myView){
+
+ }
+ public void groupWillBeRemoved(CyGroup group){
+
+ }
+ public void groupChanged(CyGroup group, CyNode changedNode,
ChangeType change){
+
+ }
+
+ }
+
/**
* Returns the best scoring path from the last run. This is mostly used
by
* the score distribution when calculating the distribution
@@ -202,10 +321,11 @@
return tempHash;
}
+
protected void showConditionsVsPathwaysTable() {
CytoPanel cytoPanel =
Cytoscape.getDesktop().getCytoPanel(SwingConstants.EAST);
- tableDialog = new ConditionsVsPathwaysTable(mainFrame,
cyNetwork,
- attrNames, activePaths, this, parentUI);
+ //tableDialog = new ConditionsVsPathwaysTable2(mainFrame,
cyNetwork,
+ // attrNames, activePaths, this, parentUI);
cytoPanel.add("jActiveModules Results " + (resultsCount++),
tableDialog);
cytoPanel.setSelectedIndex(cytoPanel.indexOfComponent(tableDialog));
@@ -214,7 +334,7 @@
addActivePathToolbarButton();
}
- protected ConditionsVsPathwaysTable getConditionsVsPathwaysTable() {
+ protected ConditionsVsPathwaysTable2 getConditionsVsPathwaysTable() {
return tableDialog;
}
@@ -242,14 +362,16 @@
JOptionPane.showMessageDialog(mainFrame, "Score: " + score);
} // scoreActivePath
+ /*
protected class ActivePathControllerLauncherAction extends
AbstractAction {
ActivePathControllerLauncherAction() {
super("Active Modules");
} // ctor
public void actionPerformed(ActionEvent e) {
- showConditionsVsPathwaysTable();
+ //showConditionsVsPathwaysTable();
}
}
+ */
/**
* find all of the unique node names in the full set of active paths.
there
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