Author: pwang
Date: 2011-10-19 11:57:46 -0700 (Wed, 19 Oct 2011)
New Revision: 27235
Modified:
csplugins/trunk/ucsd/pwang/jActiveModules31/src/main/java/csplugins/jActiveModules/ActivePathsFinder.java
Log:
Refactored to work with Cy3
Modified:
csplugins/trunk/ucsd/pwang/jActiveModules31/src/main/java/csplugins/jActiveModules/ActivePathsFinder.java
===================================================================
---
csplugins/trunk/ucsd/pwang/jActiveModules31/src/main/java/csplugins/jActiveModules/ActivePathsFinder.java
2011-10-19 18:52:32 UTC (rev 27234)
+++
csplugins/trunk/ucsd/pwang/jActiveModules31/src/main/java/csplugins/jActiveModules/ActivePathsFinder.java
2011-10-19 18:57:46 UTC (rev 27235)
@@ -1,9 +1,10 @@
package csplugins.jActiveModules;
//------------------------------------------------------------------------------
-import giny.model.GraphPerspective;
-import giny.model.Node;
+import org.cytoscape.model.CyNetwork;
+import org.cytoscape.model.CyNode;
+
import java.io.FileInputStream;
import java.io.FileOutputStream;
import java.io.ObjectInputStream;
@@ -19,10 +20,13 @@
import javax.swing.JFrame;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
import csplugins.jActiveModules.data.ActivePathFinderParameters;
-import cytoscape.CyNetwork;
-import cytoscape.logger.CyLogger;
+import csplugins.jActiveModules.util.SelectUtil;
+
/**
* This class contains the main logic for finding Active Paths The important
* function is findActivePaths() which calls the simulated annealing subroutine
@@ -30,8 +34,9 @@
*/
public class ActivePathsFinder {
- private static CyLogger logger = CyLogger.getLogger(
ActivePathsFinder.class );
+ private static final Logger logger =
LoggerFactory.getLogger(ActivePathsFinder.class);
+
/**
* See constructor
*/
@@ -47,7 +52,7 @@
/**
* an array containing all of the nodes initially in the graph
*/
- private Node[] nodes;
+ private CyNode[] nodes;
/**
* This is a hashmap which maps from nodes to an array of edges (Edge
[]).
* This is used to determine which edges belonged to which nodes before
any
@@ -129,7 +134,7 @@
* actually done
*/
private void setupScoring() {
- GraphPerspective perspective = cyNetwork;
+ CyNetwork perspective = cyNetwork;
// Here we initialize the z table. We use this data structure
when we
// want to get an adjusted z score
// based on how many conditions we are looking at.
@@ -137,8 +142,8 @@
Component.zStats = new ZStatistics(attrNames.length);
logger.info("Done initializing Z Table");
- nodes = new Node[1];
- nodes = (Node[]) (perspective.nodesList().toArray(nodes));
+ nodes = new CyNode[1];
+ nodes = (CyNode[]) (perspective.getNodeList().toArray(nodes));
// Edge [] e_array;
// This has is used to store all the edges that were connected
@@ -347,9 +352,9 @@
*/
private void runGreedySearch() {
if (apfParams.getSearchFromNodes()) {
- runGreedySearch(cyNetwork.getSelectedNodes());
+
runGreedySearch(SelectUtil.getSelectedNodes(cyNetwork));
//cyNetwork.getSelectedNodes());
} else {
- runGreedySearch(cyNetwork.nodesList());
+ runGreedySearch(cyNetwork.getNodeList());
}
}
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