Author: pwang
Date: 2011-10-19 09:06:52 -0700 (Wed, 19 Oct 2011)
New Revision: 27227
Modified:
csplugins/trunk/ucsd/pwang/jActiveModules31/src/main/java/csplugins/jActiveModules/ScoreDistributionThread.java
Log:
Refactored to work with Cy3
Modified:
csplugins/trunk/ucsd/pwang/jActiveModules31/src/main/java/csplugins/jActiveModules/ScoreDistributionThread.java
===================================================================
---
csplugins/trunk/ucsd/pwang/jActiveModules31/src/main/java/csplugins/jActiveModules/ScoreDistributionThread.java
2011-10-19 01:05:08 UTC (rev 27226)
+++
csplugins/trunk/ucsd/pwang/jActiveModules31/src/main/java/csplugins/jActiveModules/ScoreDistributionThread.java
2011-10-19 16:06:52 UTC (rev 27227)
@@ -10,21 +10,28 @@
import javax.swing.JOptionPane;
import csplugins.jActiveModules.data.ActivePathFinderParameters;
-import cytoscape.CyNetwork;
-import cytoscape.Cytoscape;
-import cytoscape.data.ExpressionData;
-import cytoscape.logger.CyLogger;
+import org.cytoscape.application.swing.AbstractCyAction;
+import org.cytoscape.model.CyNetwork;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+//import cytoscape.data.ExpressionData;
+
+
public class ScoreDistributionThread extends Thread{
- private static CyLogger logger = CyLogger.getLogger(
ScoreDistributionThread.class );
+ private static final Logger logger =
LoggerFactory.getLogger(ScoreDistributionThread.class);
CyNetwork cyNetwork;
ActivePaths activePaths;
ActivePathFinderParameters apfParams;
- public ScoreDistributionThread(CyNetwork cyNetwork,
+ private final JFrame desktopFrame;
+
+ public ScoreDistributionThread(JFrame desktopFrame, CyNetwork cyNetwork,
ActivePaths activePaths,
ActivePathFinderParameters apfParams){
- this.cyNetwork = cyNetwork;
+ this.desktopFrame = desktopFrame;
+ this.cyNetwork = cyNetwork;
this.activePaths = activePaths;
this.apfParams = apfParams;
}
@@ -38,14 +45,13 @@
*/
public void run() {
int i;
- JFrame mainFrame = Cytoscape.getDesktop();
int numberOfRuns = 100;
if(apfParams.getRun()){
numberOfRuns = apfParams.getRandomIterations();
}
else{
- String inputValue = JOptionPane.showInputDialog(mainFrame, "Number of
runs");
+ String inputValue = JOptionPane.showInputDialog(desktopFrame, "Number
of runs");
numberOfRuns = Integer.parseInt(inputValue);
}
PrintStream p = null;
@@ -56,7 +62,7 @@
}
else{
JFileChooser chooser = new JFileChooser();
- int result = chooser.showSaveDialog(mainFrame);
+ int result = chooser.showSaveDialog(desktopFrame);
if(result == JFileChooser.APPROVE_OPTION){
FileOutputStream out = new
FileOutputStream(chooser.getSelectedFile());
p = new PrintStream(out);
@@ -86,7 +92,7 @@
apfParams.setToUseMCFile(true);
apfParams.setMcFileName("last.mc");
}
- MyProgressMonitor monitor = new
MyProgressMonitor(mainFrame,"Running random trials","",0,numberOfRuns);
+ MyProgressMonitor monitor = new
MyProgressMonitor(desktopFrame,"Running random trials","",0,numberOfRuns);
for (i=1; i<numberOfRuns; i++) {
t = new Thread(activePaths);
t.start();
--
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