Author: scooter
Date: 2010-08-11 15:33:23 -0700 (Wed, 11 Aug 2010)
New Revision: 21339
Modified:
csplugins/trunk/ucsf/scooter/clusterMaker/src/clusterMaker/ClusterMaker.java
csplugins/trunk/ucsf/scooter/clusterMaker/src/clusterMaker/commands/VizCommandHandler.java
csplugins/trunk/ucsf/scooter/clusterMaker/src/clusterMaker/ui/NestedNetworkView.java
Log:
Added some clean-up for the nested network case
Modified:
csplugins/trunk/ucsf/scooter/clusterMaker/src/clusterMaker/ClusterMaker.java
===================================================================
---
csplugins/trunk/ucsf/scooter/clusterMaker/src/clusterMaker/ClusterMaker.java
2010-08-11 22:31:47 UTC (rev 21338)
+++
csplugins/trunk/ucsf/scooter/clusterMaker/src/clusterMaker/ClusterMaker.java
2010-08-11 22:33:23 UTC (rev 21339)
@@ -136,7 +136,13 @@
item = new JMenuItem(viz3.getName());
item.addActionListener(new
ClusterMakerCommandListener((ClusterAlgorithm)viz3));
menu.add(item);
+
+ // Because this overlaps with the new network visualization, it
doesn't show
+ // up in our vizMap automatically -- add it here so it will
show up in our
+ // command list.
+ vizMap.put(viz3.getShortName(), viz3);
+
// Catch new network loaded and change events so we can update
our visualization menus
Cytoscape.getPropertyChangeSupport()
.addPropertyChangeListener( Cytoscape.NETWORK_LOADED, this );
Modified:
csplugins/trunk/ucsf/scooter/clusterMaker/src/clusterMaker/commands/VizCommandHandler.java
===================================================================
---
csplugins/trunk/ucsf/scooter/clusterMaker/src/clusterMaker/commands/VizCommandHandler.java
2010-08-11 22:31:47 UTC (rev 21338)
+++
csplugins/trunk/ucsf/scooter/clusterMaker/src/clusterMaker/commands/VizCommandHandler.java
2010-08-11 22:33:23 UTC (rev 21339)
@@ -64,8 +64,8 @@
for (String vizName: vizMap.keySet()) {
ClusterViz viz = vizMap.get(vizName);
ClusterProperties props = viz.getSettings();
- addDescription(vizName, vizName+" cluster visualizer");
- addArguments(vizName, props);
+ addDescription(vizName.toLowerCase(), vizName+" cluster
visualizer");
+ addArguments(vizName.toLowerCase(), props);
}
}
Modified:
csplugins/trunk/ucsf/scooter/clusterMaker/src/clusterMaker/ui/NestedNetworkView.java
===================================================================
---
csplugins/trunk/ucsf/scooter/clusterMaker/src/clusterMaker/ui/NestedNetworkView.java
2010-08-11 22:31:47 UTC (rev 21338)
+++
csplugins/trunk/ucsf/scooter/clusterMaker/src/clusterMaker/ui/NestedNetworkView.java
2010-08-11 22:33:23 UTC (rev 21339)
@@ -146,7 +146,7 @@
String cluster_type =
networkAttributes.getStringAttribute(netId,
ClusterMaker.CLUSTER_TYPE_ATTRIBUTE);
if (cluster_type != "MCL" && cluster_type != "GLay" &&
cluster_type != "AP" && cluster_type != "FORCE" &&
- cluster_type != "MCODE")
+ cluster_type != "MCODE" && cluster_type != "TransClust")
return false;
if (networkAttributes.hasAttribute(netId,
ClusterMaker.CLUSTER_ATTRIBUTE)) {
@@ -334,10 +334,10 @@
// Get the list of edges
List<CyEdge> edgeList =
currentNetwork.getConnectingEdges(nodeList);
String title = currentNetwork.getTitle()+"--cluster
"+cluster;
- CyNetwork net = Cytoscape.createNetwork(nodeList,
edgeList, title, parentNet);
+ CyNetwork net = Cytoscape.createNetwork(nodeList,
edgeList, title, parentNet, false);
// Create our view and lay it out
- // CyNetworkView v = Cytoscape.createNetworkView(net,
title, alg);
+ CyNetworkView v = Cytoscape.createNetworkView(net,
title, alg);
// Get the clustered node
CyNode node = Cytoscape.getCyNode(title, true);
--
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