Code cleanup and built-in template update

Author: smm8ec

src/main/java/edu/virginia/uvacluster/internal/ClusterUtil.java

@@ -19,6 +19,7 @@ public static CyNetwork getDefaultModel(String weightFeatureName, SavePolicy pol
 		                         "Variance : Degree (4)",
 		                         "Median : Degree (4)",
 		                         "Max : Degree (4)",
+		                         "Count : Node (5)",
 		                         String.format("Mean : weight{%s} (4)",weightFeatureName),
 		                         String.format("Variance : weight{%s} (4)",weightFeatureName),
 		                         String.format("Density at cutoff %s (6)",weightCutoffs[0]),

src/main/java/edu/virginia/uvacluster/internal/CyActivator.java

@@ -35,35 +35,9 @@ public void start(BundleContext context) throws Exception {
 		networkViewManager = getService(context, CyNetworkViewManager.class);
 		serviceRegistrar = getService(context, CyServiceRegistrar.class);
 
-		
-		/* ******SupervisedComplexTaskFactory clusterFactory= new SupervisedComplexTaskFactory();
-		
-		//TODO re-enable
-		//GenModelTaskFactory modelFactory = new GenModelTaskFactory();
-		
-		//Set service properties
-		Properties clusterFactoryProperties = new Properties();
-		clusterFactoryProperties.setProperty("preferredMenu", "Apps.SCODE");
-		clusterFactoryProperties.setProperty("title","Analyze Network");      ************/
-		
-		/* TODO This option is disabled because a network only appears once the session file is reloaded.  
-		Properties genNetworkProperties = new Properties();
-		genNetworkProperties.setProperty("preferredMenu", "Apps.Supervised Complex");
-		genNetworkProperties.setProperty("title", "Generate Default Model");
-		*/
-		
 		//Set up tabbed panel in Control Panel
 		CySwingApplication cytoscapeDesktopService = getService(context,CySwingApplication.class);
 
-		/*
-		MyControlPanel myControlPanel = new MyControlPanel();
-		ControlPanelAction controlPanelAction = new ControlPanelAction(cytoscapeDesktopService,myControlPanel);
-		
-		registerService(context,myControlPanel,CytoPanelComponent.class, new Properties());
-		registerService(context,controlPanelAction,CyAction.class, new Properties());
-		*/
-		//register services
-		//registerService(context, clusterFactory, NetworkTaskFactory.class, clusterFactoryProperties);
 
 		CyApplicationManager appManager = getService(context, CyApplicationManager.class);
 
@@ -82,8 +56,6 @@ public void start(BundleContext context) throws Exception {
 		closeTaskFactoryProps.setProperty("menuGravity","2.0");
 
 		registerService(context, closeTaskFactory, TaskFactory.class, closeTaskFactoryProps);
-		
-		//TODO re-enable when cytoscape bug is fixed
-		//registerService(context, modelFactory, NetworkTaskFactory.class,genNetworkProperties);
+
 	}
 }