Author: pwang
Date: 2011-10-19 10:48:44 -0700 (Wed, 19 Oct 2011)
New Revision: 27233
Modified:
csplugins/trunk/ucsd/pwang/jActiveModules31/src/main/java/csplugins/jActiveModules/SimulatedAnnealingSearchThread.java
Log:
Refactored to work with Cy3
Modified:
csplugins/trunk/ucsd/pwang/jActiveModules31/src/main/java/csplugins/jActiveModules/SimulatedAnnealingSearchThread.java
===================================================================
---
csplugins/trunk/ucsd/pwang/jActiveModules31/src/main/java/csplugins/jActiveModules/SimulatedAnnealingSearchThread.java
2011-10-19 17:39:55 UTC (rev 27232)
+++
csplugins/trunk/ucsd/pwang/jActiveModules31/src/main/java/csplugins/jActiveModules/SimulatedAnnealingSearchThread.java
2011-10-19 17:48:44 UTC (rev 27233)
@@ -1,24 +1,28 @@
package csplugins.jActiveModules;
//------------------------------------------------------------------------------
-import giny.model.GraphPerspective;
-import giny.model.Node;
-
+import org.cytoscape.model.CyNetwork;
+import org.cytoscape.model.CyNode;
import java.util.HashMap;
import java.util.HashSet;
import java.util.Iterator;
import java.util.Random;
import java.util.Vector;
+import org.cytoscape.application.swing.AbstractCyAction;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
import csplugins.jActiveModules.data.ActivePathFinderParameters;
-import cytoscape.logger.CyLogger;
public class SimulatedAnnealingSearchThread extends SearchThread{
- MyProgressMonitor progress;
- public SimulatedAnnealingSearchThread(GraphPerspective graph, Vector
resultPaths, Node [] nodes, ActivePathFinderParameters apfParams,
MyProgressMonitor progress){
+
+ private static final Logger logger =
LoggerFactory.getLogger(SimulatedAnnealingSearchThread.class);
+ MyProgressMonitor progress;
+ public SimulatedAnnealingSearchThread(CyNetwork graph, Vector resultPaths,
CyNode [] nodes, ActivePathFinderParameters apfParams, MyProgressMonitor
progress){
super(graph,resultPaths,nodes,apfParams);
this.progress = progress;
- super.nodeSet = new HashSet(graph.nodesList());
+ super.nodeSet = new HashSet(graph.getNodeList());
}
/**
@@ -39,18 +43,18 @@
boolean hubFinding = apfParams.getMinHubSize() > 0;
if(hubFinding){
- CyLogger.getLogger(
SimulatedAnnealingSearchThread.class).info("Using hub finding:
"+apfParams.getMinHubSize());
+ logger.info("Using hub finding: "+apfParams.getMinHubSize());
}
//NodeList [] components = GraphConnectivity.connectedComponents(graph);
ComponentFinder cf = new ComponentFinder(graph,nodeSet);
- //Vector components = cf.getComponents(new Vector(graph.nodesList()));
+ //Vector components = cf.getComponents(new Vector(graph.getNodeList()));
//why is a new vector being creater here?
//Iterator compIt = cf.getComponents(new
Vector(graph.nodesList())).iterator();
- Iterator compIt = cf.getComponents(graph.nodesList()).iterator();
+ Iterator compIt = cf.getComponents(graph.getNodeList()).iterator();
while(compIt.hasNext()){
//Component tempComponent = new Component((Vector)compIt.next());
oldPaths.sortedAdd((Component)compIt.next());
@@ -89,7 +93,7 @@
hiddenNodes.clear();
//select a node
- Node current_node = nodes[rand.nextInt(nodes.length)];
+ CyNode current_node = nodes[rand.nextInt(nodes.length)];
//toggle the state of that node, it we are doing hubfinding, this
may
//also involve toggling the state of the surrrounding nodes
if(hubFinding){
@@ -159,7 +163,7 @@
if(hubFinding){
it = hiddenNodes.iterator();
while(it.hasNext()){
- toggleNode((Node)it.next());
+ toggleNode((CyNode)it.next());
}
}
}
@@ -169,7 +173,7 @@
if(hubFinding){
it = hiddenNodes.iterator();
while(it.hasNext()){
- toggleNode((Node)it.next());
+ toggleNode((CyNode)it.next());
}
}
}
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