Author: pwang
Date: 2011-10-19 09:48:10 -0700 (Wed, 19 Oct 2011)
New Revision: 27229
Modified:
csplugins/trunk/ucsd/pwang/jActiveModules31/src/main/java/csplugins/jActiveModules/GreedySearchThread.java
Log:
Refactored to work with Cy3
Modified:
csplugins/trunk/ucsd/pwang/jActiveModules31/src/main/java/csplugins/jActiveModules/GreedySearchThread.java
===================================================================
---
csplugins/trunk/ucsd/pwang/jActiveModules31/src/main/java/csplugins/jActiveModules/GreedySearchThread.java
2011-10-19 16:21:44 UTC (rev 27228)
+++
csplugins/trunk/ucsd/pwang/jActiveModules31/src/main/java/csplugins/jActiveModules/GreedySearchThread.java
2011-10-19 16:48:10 UTC (rev 27229)
@@ -1,21 +1,25 @@
package csplugins.jActiveModules;
//------------------------------------------------------------------------------
-import giny.model.GraphPerspective;
-import giny.model.Node;
+import org.cytoscape.model.CyNetwork;
+import org.cytoscape.model.CyNode;
+import org.cytoscape.model.CyEdge.Type;
+
import java.util.Collection;
import java.util.HashMap;
import java.util.HashSet;
import java.util.Iterator;
import java.util.LinkedList;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
import csplugins.jActiveModules.data.ActivePathFinderParameters;
-import cytoscape.logger.CyLogger;
+
public class GreedySearchThread extends Thread {
- private static CyLogger logger =
CyLogger.getLogger(GreedySearchThread.class);
+ private static final Logger logger =
LoggerFactory.getLogger(GreedySearchThread.class);
int max_depth, search_depth;
ActivePathFinderParameters apfParams;
@@ -49,11 +53,11 @@
* Determines which nodes are within max depth of the starting point
*/
HashSet withinMaxDepth;
- Node[] nodes;
- GraphPerspective graph;
- public GreedySearchThread(GraphPerspective graph,
ActivePathFinderParameters apfParams,
+ CyNode[] nodes;
+ CyNetwork graph;
+ public GreedySearchThread(CyNetwork graph, ActivePathFinderParameters
apfParams,
Collection nodeList, MyProgressMonitor tpm, HashMap
temp_hash,
- Node[] node_array) {
+ CyNode[] node_array) {
this.apfParams = apfParams;
max_depth = apfParams.getMaxDepth();
search_depth = apfParams.getSearchDepth();
@@ -68,12 +72,12 @@
/**
* Recursively find the nodes within a max depth
*/
- private void initializeMaxDepth(Node current, int depth) {
+ private void initializeMaxDepth(CyNode current, int depth) {
withinMaxDepth.add(current);
if (depth > 0) {
- Iterator listIt =
graph.neighborsList(current).iterator();
+ Iterator listIt =
graph.getNeighborList(current,Type.ANY).iterator();
//.neighborsList(current).iterator();
while (listIt.hasNext()) {
- Node myNode = (Node) listIt.next();
+ CyNode myNode = (CyNode) listIt.next();
if (!withinMaxDepth.contains(myNode)) {
initializeMaxDepth(myNode, depth - 1);
}
@@ -87,10 +91,10 @@
*/
public void run() {
boolean done = false;
- Node seed = null;
+ CyNode seed = null;
synchronized (nodeIterator) {
if (nodeIterator.hasNext()) {
- seed = (Node) nodeIterator.next();
+ seed = (CyNode) nodeIterator.next();
} else {
done = true;
}
@@ -135,7 +139,7 @@
// node2BestComponent.put(seed,component);
// }
while (it.hasNext()) {
- Node current = (Node) it.next();
+ CyNode current = (CyNode) it.next();
Component oldBest = (Component)
node2BestComponent
.get(current);
if (oldBest == null
@@ -152,7 +156,7 @@
synchronized (nodeIterator) {
if (nodeIterator.hasNext()) {
- seed = (Node) nodeIterator.next();
+ seed = (CyNode) nodeIterator.next();
} else {
done = true;
}
@@ -180,7 +184,7 @@
* Nodes that can be removed.
*/
private boolean runGreedySearchRecursive(int depth, Component component,
- Node lastAdded, HashSet removableNodes) {
+ CyNode lastAdded, HashSet removableNodes) {
boolean improved = false;
// score this component, check and see if the global top scores
should
// be updated, if we have found a better score, then return true
@@ -194,12 +198,12 @@
// if depth > 0, otherwise we are out of depth and the
recursive
// calls will end
// Get an iterator of nodes which are next to the
- Iterator nodeIt =
graph.neighborsList(lastAdded).iterator();
+ Iterator nodeIt = graph.getNeighborList(lastAdded,
Type.ANY).iterator(); //.neighborsList(lastAdded).iterator();
boolean anyCallImproved = false;
removableNodes.remove(lastAdded);
int dependentCount = 0;
while (nodeIt.hasNext()) {
- Node newNeighbor = (Node) nodeIt.next();
+ CyNode newNeighbor = (CyNode) nodeIt.next();
// this node is only a new neighbor if it is
not currently
// in the component.
if (withinMaxDepth.contains(newNeighbor)
@@ -233,12 +237,12 @@
HashSet removableNodes) {
LinkedList list = new LinkedList(removableNodes);
while (!list.isEmpty()) {
- Node current = (Node) list.removeFirst();
+ CyNode current = (CyNode) list.removeFirst();
component.removeNode(current);
double score = component.getScore();
if (score > bestScore) {
bestScore = score;
- Node predecessor = (Node)
node2Predecessor.get(current);
+ CyNode predecessor = (CyNode)
node2Predecessor.get(current);
int dependentCount = ((Integer)
node2DependentCount
.get(predecessor)).intValue();
dependentCount -= 1;
--
You received this message because you are subscribed to the Google Groups
"cytoscape-cvs" group.
To post to this group, send email to [email protected].
To unsubscribe from this group, send email to
[email protected].
For more options, visit this group at
http://groups.google.com/group/cytoscape-cvs?hl=en.
