Author: pwang
Date: 2012-02-15 16:51:16 -0800 (Wed, 15 Feb 2012)
New Revision: 28296
Modified:
csplugins/trunk/ucsd/pwang/subnetworkByCategory/src/main/java/org/cytoscape/subnetwork/SubnetworkByCategory.java
csplugins/trunk/ucsd/pwang/subnetworkByCategory/src/main/java/org/cytoscape/subnetwork/SubnetworkByCategoryAction.java
csplugins/trunk/ucsd/pwang/subnetworkByCategory/src/main/java/org/cytoscape/subnetwork/SubnetworkByCategoryPlugin.java
Log:
updated
Modified:
csplugins/trunk/ucsd/pwang/subnetworkByCategory/src/main/java/org/cytoscape/subnetwork/SubnetworkByCategory.java
===================================================================
---
csplugins/trunk/ucsd/pwang/subnetworkByCategory/src/main/java/org/cytoscape/subnetwork/SubnetworkByCategory.java
2012-02-16 00:50:50 UTC (rev 28295)
+++
csplugins/trunk/ucsd/pwang/subnetworkByCategory/src/main/java/org/cytoscape/subnetwork/SubnetworkByCategory.java
2012-02-16 00:51:16 UTC (rev 28296)
@@ -16,14 +16,15 @@
public class SubnetworkByCategory {
- public CyNetwork execute(CyNetwork net, String attributeName){
+ public CyNetwork execute(CyNetwork parentNetwork, String attributeName){
// 1. get the node list for each category
- HashMap categoryMap = getNodeCategoryMap(net, attributeName);
+ HashMap categoryMap = getNodeCategoryMap(parentNetwork,
attributeName);
// 2. create subnetwork for each category
- CyNetwork[] subnetworks = createSubnetworks(net, categoryMap);
+ CyNetwork[] subnetworks = createSubnetworks(parentNetwork,
categoryMap);
//3. create an overview network for all nested network
+ CyAttributes nodeAttr = Cytoscape.getNodeAttributes();
Set overview_nodes = new HashSet();
for (int i=0; i< subnetworks.length; i++){
CyNode newNode
=Cytoscape.getCyNode(subnetworks[i].getTitle(), true);
@@ -31,9 +32,13 @@
overview_nodes.add(newNode);
}
- Set overview_edges = getOverviewEdges(net, overview_nodes);
- final CyNetwork overview =
Cytoscape.createNetwork(overview_nodes, overview_edges, "Overview of category
", net, false);
+ Set overview_edges = getOverviewEdges(parentNetwork,
overview_nodes);
+ final CyNetwork overview =
Cytoscape.createNetwork(overview_nodes, overview_edges,
SubnetworkByCategoryPlugin.overviewTitle, parentNetwork, false);
+ // add a network attribute for overview network
+ CyAttributes networkAttr = Cytoscape.getNetworkAttributes();
+ networkAttr.setAttribute(overview.getIdentifier(),
"parentNetworkId", parentNetwork.getIdentifier());
+
// 4. Create a view for overview network
Cytoscape.createNetworkView(overview, overview.getTitle());
Modified:
csplugins/trunk/ucsd/pwang/subnetworkByCategory/src/main/java/org/cytoscape/subnetwork/SubnetworkByCategoryAction.java
===================================================================
---
csplugins/trunk/ucsd/pwang/subnetworkByCategory/src/main/java/org/cytoscape/subnetwork/SubnetworkByCategoryAction.java
2012-02-16 00:50:50 UTC (rev 28295)
+++
csplugins/trunk/ucsd/pwang/subnetworkByCategory/src/main/java/org/cytoscape/subnetwork/SubnetworkByCategoryAction.java
2012-02-16 00:51:16 UTC (rev 28296)
@@ -7,6 +7,7 @@
import cytoscape.CyNetwork;
import cytoscape.view.CyNetworkView;
+import cytoscape.data.CyAttributes;
import cytoscape.layout.CyLayoutAlgorithm;
import cytoscape.visual.VisualStyle;
@@ -52,11 +53,12 @@
return;
}
- CyNetwork net = Cytoscape.getCurrentNetwork();
+ CyNetwork parentNetwork = Cytoscape.getCurrentNetwork();
SubnetworkByCategory w = new SubnetworkByCategory();
- CyNetwork overviewNetwork = w.execute(net,
dlg.getSelectedAttribute());
+ CyNetwork overviewNetwork = w.execute(parentNetwork,
dlg.getSelectedAttribute());
+
CyNetworkView view =
Cytoscape.getNetworkView(overviewNetwork.getIdentifier());
if (view != null){
@@ -68,7 +70,7 @@
// apply layout -- force-directed
CyLayoutAlgorithm alg =
cytoscape.layout.CyLayouts.getLayout("force-directed");
- view.applyLayout(alg);
+ view.applyLayout(alg);
}
}
}
Modified:
csplugins/trunk/ucsd/pwang/subnetworkByCategory/src/main/java/org/cytoscape/subnetwork/SubnetworkByCategoryPlugin.java
===================================================================
---
csplugins/trunk/ucsd/pwang/subnetworkByCategory/src/main/java/org/cytoscape/subnetwork/SubnetworkByCategoryPlugin.java
2012-02-16 00:50:50 UTC (rev 28295)
+++
csplugins/trunk/ucsd/pwang/subnetworkByCategory/src/main/java/org/cytoscape/subnetwork/SubnetworkByCategoryPlugin.java
2012-02-16 00:51:16 UTC (rev 28296)
@@ -13,6 +13,8 @@
*/
public class SubnetworkByCategoryPlugin extends CytoscapePlugin {
+ public static String overviewTitle = "Overview of category";
+
public SubnetworkByCategoryPlugin() {
// Properly initializes things.
super();
@@ -20,5 +22,7 @@
// This action represents the actual behavior of the plugin.
SubnetworkByCategoryAction action = new
SubnetworkByCategoryAction();
Cytoscape.getDesktop().getCyMenus().addAction(action);
+
+ Cytoscape.getPropertyChangeSupport().addPropertyChangeListener(
new NNTKNetworkListener() );
}
}
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