Author: pwang
Date: 2011-10-19 10:00:57 -0700 (Wed, 19 Oct 2011)
New Revision: 27231
Modified:
csplugins/trunk/ucsd/pwang/jActiveModules31/src/main/java/csplugins/jActiveModules/ParamStatistics.java
Log:
Refactored to work with Cy3
Modified:
csplugins/trunk/ucsd/pwang/jActiveModules31/src/main/java/csplugins/jActiveModules/ParamStatistics.java
===================================================================
---
csplugins/trunk/ucsd/pwang/jActiveModules31/src/main/java/csplugins/jActiveModules/ParamStatistics.java
2011-10-19 16:52:08 UTC (rev 27230)
+++
csplugins/trunk/ucsd/pwang/jActiveModules31/src/main/java/csplugins/jActiveModules/ParamStatistics.java
2011-10-19 17:00:57 UTC (rev 27231)
@@ -3,8 +3,10 @@
package csplugins.jActiveModules;
//imported packages
-import giny.model.Node;
+import org.cytoscape.view.model.CyNetworkView;
+import org.cytoscape.model.CyNode;
+
import java.io.Serializable;
import java.util.Arrays;
import java.util.Collections;
@@ -12,7 +14,9 @@
import java.util.Random;
import java.util.Vector;
-import cytoscape.logger.CyLogger;
+import org.cytoscape.application.swing.AbstractCyAction;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
/**
@@ -24,6 +28,9 @@
* networks so that larger networks do not dominate
*/
public class ParamStatistics implements Serializable{
+
+ private static final Logger logger =
LoggerFactory.getLogger(ParamStatistics.class);
+
/**
* means[i] is the mean of networks of size i+1
*/
@@ -76,7 +83,7 @@
* @param nodes Array of nodes to use for the determination
* @param trials Number of times to repeat the scoring process to determine
the stats
*/
- public void calculateMeanAndStd(Node [] nodes,int trials, int maxThreads,
MyProgressMonitor progress){
+ public void calculateMeanAndStd(CyNode [] nodes,int trials, int maxThreads,
MyProgressMonitor progress){
double [] overall_tallyx = new double[nodes.length];
double [] overall_tallyx_2 = new double[nodes.length];
means = new double[nodes.length];
@@ -111,7 +118,7 @@
try{
((Thread)it.next()).join();
}catch(Exception e){
- CyLogger.getLogger(ParamStatistics.class).error("Unable to join worker
thread",e);
+ logger.error("Unable to join worker thread",e);
return;
}
}
@@ -251,10 +258,10 @@
private double [] overall_tallyx_2;
private int total_trials;
private static int current_trials = 0;
- private Node[] nodes;
+ private CyNode[] nodes;
private MyProgressMonitor progress;
private Random rand;
- public MeanAndStdThread(double [] overall_tallyx,double []
overall_tallyx_2,int total_trials,Node [] nodes,MyProgressMonitor
progress,Random rand){
+ public MeanAndStdThread(double [] overall_tallyx,double []
overall_tallyx_2,int total_trials,CyNode [] nodes,MyProgressMonitor
progress,Random rand){
this.overall_tallyx = overall_tallyx;
this.overall_tallyx_2 = overall_tallyx_2;
this.total_trials = total_trials;
@@ -296,7 +303,7 @@
Iterator it = nodeList.iterator();
int i = 0;
while(it.hasNext()){
- comp.addNode((Node)it.next());
+ comp.addNode((CyNode)it.next());
double score = comp.calculateSimpleScore();
tallyx[i] += score;
tallyx_2[i] += score*score;
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