Author: pwang
Date: 2011-10-19 09:52:08 -0700 (Wed, 19 Oct 2011)
New Revision: 27230
Modified:
csplugins/trunk/ucsd/pwang/jActiveModules31/src/main/java/csplugins/jActiveModules/ComponentFinder.java
Log:
Refactored to work with Cy3
Modified:
csplugins/trunk/ucsd/pwang/jActiveModules31/src/main/java/csplugins/jActiveModules/ComponentFinder.java
===================================================================
---
csplugins/trunk/ucsd/pwang/jActiveModules31/src/main/java/csplugins/jActiveModules/ComponentFinder.java
2011-10-19 16:48:10 UTC (rev 27229)
+++
csplugins/trunk/ucsd/pwang/jActiveModules31/src/main/java/csplugins/jActiveModules/ComponentFinder.java
2011-10-19 16:52:08 UTC (rev 27230)
@@ -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.HashSet;
import java.util.Iterator;
@@ -21,7 +22,7 @@
/**
*The graph which contains the nodes we are searching on
*/
- GraphPerspective graph;
+ CyNetwork graph;
/**
*A list of nodes that have been found in the current component search.
*/
@@ -40,7 +41,7 @@
* Make a new component finder with the specified graph
* @param g the graph on which to search
*/
- public ComponentFinder(GraphPerspective g,HashSet valid){
+ public ComponentFinder(CyNetwork g,HashSet valid){
graph = g;
this.valid = valid;
}
@@ -71,10 +72,10 @@
//call back to postVisit after it is done searching any node. This is
//where we will update the status of that node
if(!valid.contains(nodes.get(start))){
- throw new RuntimeException("Starting node for a component search was
not present in the graph, this is an ActiveModules
bug."+((Node)nodes.get(start)).getIdentifier());
+ throw new RuntimeException("Starting node for a component search was
not present in the graph, this is an ActiveModules
bug."+((CyNode)nodes.get(start)).getCyRow().get("name", String.class));
//.getIdentifier());
}
- search((Node)nodes.get(start));
+ search((CyNode)nodes.get(start));
result.add(new Component(current));
finalSize += current.size();
while(start<nodes.size() && reached.contains(nodes.get(start))){
@@ -88,12 +89,12 @@
return result;
}
- private void search(Node root){
+ private void search(CyNode root){
current.add(root);
reached.add(root);
- Iterator nodeIt = graph.neighborsList(root).iterator();
+ Iterator nodeIt = graph.getNeighborList(root, Type.ANY).iterator();
//.neighborsList(root).iterator();
while(nodeIt.hasNext()){
- Node myNode = (Node)nodeIt.next();
+ CyNode myNode = (CyNode)nodeIt.next();
if(valid.contains(myNode) && !reached.contains(myNode)){
search(myNode);
}
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