Author: pwang
Date: 2011-11-29 14:55:50 -0800 (Tue, 29 Nov 2011)
New Revision: 27638
Modified:
csplugins/trunk/ucsd/pwang/jActiveModules-impl/src/main/java/csplugins/jActiveModules/ActivePaths.java
Log:
Fixed syntax error caused by API change
Modified:
csplugins/trunk/ucsd/pwang/jActiveModules-impl/src/main/java/csplugins/jActiveModules/ActivePaths.java
===================================================================
---
csplugins/trunk/ucsd/pwang/jActiveModules-impl/src/main/java/csplugins/jActiveModules/ActivePaths.java
2011-11-29 19:50:56 UTC (rev 27637)
+++
csplugins/trunk/ucsd/pwang/jActiveModules-impl/src/main/java/csplugins/jActiveModules/ActivePaths.java
2011-11-29 22:55:50 UTC (rev 27638)
@@ -228,7 +228,7 @@
CyNode newNode = overview.addNode();
//Cytoscape.getCyNode(subnetworks[i].getTitle(), true);
newNode.getCyRow().set("name",
subnetworks[i].getCyRow().get("name", String.class));
path_nodes.add(newNode);
- newNode.setNetwork(subnetworks[i]);
+ newNode.setNetworkPointer(subnetworks[i]);
// create an attribute for this new node
//Cytoscape.getNodeAttributes().setAttribute(newNode.getIdentifier(),
NODE_SCORE, new Double(activePaths[i].getScore()));
@@ -258,11 +258,11 @@
Iterator it = path_edges.iterator();
while(it.hasNext()){
CyEdge aEdge = (CyEdge) it.next();
- int NumberOfSharedNodes =
getNumberOfSharedNodes((CyNetwork)aEdge.getSource().getNetwork(),
-
(CyNetwork)aEdge.getTarget().getNetwork());
+ int NumberOfSharedNodes =
getNumberOfSharedNodes((CyNetwork)aEdge.getSource().getNetworkPointer(),
+
(CyNetwork)aEdge.getTarget().getNetworkPointer());
- int minNodeCount =
Math.min(aEdge.getSource().getNetwork().getNodeCount(),
-
aEdge.getTarget().getNetwork().getNodeCount());
+ int minNodeCount =
Math.min(aEdge.getSource().getNetworkPointer().getNodeCount(),
+
aEdge.getTarget().getNetworkPointer().getNodeCount());
//cyEdgeAttrs.setAttribute(aEdge.getIdentifier(),
"jActiveModules_nodeCount_min_two", minNodeCount);
aEdge.getCyRow().set("jActiveModules_nodeCount_min_two", minNodeCount);
@@ -361,7 +361,7 @@
HashSet[] hashSet = new HashSet[nodes.length];
for (int i=0; i< nodes.length; i++){
- hashSet[i] = new
HashSet<CyNode>(((CyNode)nodes[i]).getNetwork().getNodeList());
+ hashSet[i] = new
HashSet<CyNode>(((CyNode)nodes[i]).getNetworkPointer().getNodeList());
}
for (int i=0; i< nodes.length-1; i++){
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