Author: pwang
Date: 2011-10-19 09:21:44 -0700 (Wed, 19 Oct 2011)
New Revision: 27228
Modified:
csplugins/trunk/ucsd/pwang/jActiveModules31/src/main/java/csplugins/jActiveModules/SearchThread.java
Log:
Refactored to work with Cy3
Modified:
csplugins/trunk/ucsd/pwang/jActiveModules31/src/main/java/csplugins/jActiveModules/SearchThread.java
===================================================================
---
csplugins/trunk/ucsd/pwang/jActiveModules31/src/main/java/csplugins/jActiveModules/SearchThread.java
2011-10-19 16:06:52 UTC (rev 27227)
+++
csplugins/trunk/ucsd/pwang/jActiveModules31/src/main/java/csplugins/jActiveModules/SearchThread.java
2011-10-19 16:21:44 UTC (rev 27228)
@@ -1,8 +1,9 @@
package csplugins.jActiveModules;
//------------------------------------------------------------------------------
-import giny.model.GraphPerspective;
-import giny.model.Node;
+import org.cytoscape.model.CyEdge.Type;
+import org.cytoscape.model.CyNetwork;
+import org.cytoscape.model.CyNode;
import java.util.HashMap;
import java.util.HashSet;
@@ -14,16 +15,16 @@
import csplugins.jActiveModules.data.ActivePathFinderParameters;
public abstract class SearchThread extends Thread{
- protected GraphPerspective graph;
+ protected CyNetwork graph;
protected SortedVector oldPaths,newPaths;
protected Vector resultPaths;
protected Vector hiddenNodes;
protected HashSet nodeSet;
//protected HashMap node2edges;
- protected Node [] nodes;
+ protected CyNode [] nodes;
protected HashMap node2component;
protected ActivePathFinderParameters apfParams;
- public SearchThread(GraphPerspective graph, Vector resultPaths,Node []
nodes, ActivePathFinderParameters apfParams){
+ public SearchThread(CyNetwork graph, Vector resultPaths,CyNode [] nodes,
ActivePathFinderParameters apfParams){
this.graph = graph;
this.resultPaths = resultPaths;
//this.node2edges = node2edges;
@@ -40,7 +41,7 @@
* be present if we toggled the state of Node current
* @return A vector of new Components created by applying this change
*/
- protected Vector updatePaths(Node current){
+ protected Vector updatePaths(CyNode current){
//first make a (shallow) copy of oldPaths as our newPaths
//this copy will be update in upate_remove and update_add
newPaths = (SortedVector)((SortedVector)oldPaths).clone();
@@ -69,7 +70,7 @@
* @param current The node which was just added
* @return A vector of newly generated components
*/
- protected Vector update_add(Node current){
+ protected Vector update_add(CyNode current){
//get a list of components
//for the neighboring nodes
//first get the list of neighboring nodes
@@ -78,10 +79,10 @@
Set nComponents = new HashSet();
//Iterator it = graph.nodesIterator();
//CHANGE HERE
- Iterator it =
graph.neighborsList(current).iterator();
+ Iterator it = graph.getNeighborList(current,
Type.ANY).iterator(); //.neighborsList(current).iterator();
while(it.hasNext()){
//check for self loops
- Node myNode = (Node)it.next();
+ CyNode myNode = (CyNode)it.next();
if(current != myNode && nodeSet.contains(myNode)){
nComponents.add(node2component.get(myNode));
}
@@ -117,7 +118,7 @@
* @param removed The node which was removed
* @return A vector of newly created components
*/
- protected Vector update_remove(Node removed){
+ protected Vector update_remove(CyNode removed){
Vector temp = new Vector();
temp.add(removed);
return update_remove(temp);
@@ -187,7 +188,7 @@
*it will also reinsert any possible associated edges
* @param toggle The node to be toggled.
*/
- protected void toggleNode(Node toggle){
+ protected void toggleNode(CyNode toggle){
//If the graph contains the node, remove it
//this will also automatically remove any
//associated edges
@@ -220,7 +221,7 @@
*It sets a global vector of nodes that were hidden
* @param toggle The node to be toggled
*/
- protected void toggleNodeWithHiding(Node toggle){
+ protected void toggleNodeWithHiding(CyNode toggle){
//If the graph contains the node, we dont' have to do
//anything special
if(nodeSet.contains(toggle)){
@@ -228,7 +229,7 @@
}
else{
nodeSet.add(toggle);
- List neighborList = graph.neighborsList(toggle);
+ List neighborList = graph.getNeighborList(toggle, Type.ANY);
//.neighborsList(toggle);
//check if it is a hub according ot the user's
//parameters
if(neighborList.size() >= apfParams.getMinHubSize()){
@@ -249,7 +250,7 @@
//score is low, then that node gets that axe.
double min_score = ((Component)it.next()).getScore();
for(Iterator neighborIt =
neighborList.iterator();neighborIt.hasNext();){
- Node neighbor = (Node)neighborIt.next();
+ CyNode neighbor = (CyNode)neighborIt.next();
//make sure to include a check for self edges here
if(!neighbor.equals(toggle) && nodeSet.contains(neighbor)){
//get the component that this node belongs to
--
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