use of edu.ucsf.rbvi.clusterMaker2.internal.algorithms.attributeClusterers.DBSCAN.DBSCANTaskFactory in project clusterMaker2 by RBVI.
the class CyActivator method start.
public void start(BundleContext bc) {
// See if we have a graphics console or not
boolean haveGUI = true;
CySwingApplication swingAppRef = getService(bc, CySwingApplication.class);
if (swingAppRef == null) {
// if haveGUI is false, we don't want to provide any hooks to the treeview
haveGUI = false;
}
CyApplicationManager appRef = getService(bc, CyApplicationManager.class);
CyServiceRegistrar serviceRegistrar = getService(bc, CyServiceRegistrar.class);
CyGroupManager groupManager = getService(bc, CyGroupManager.class);
CyGroupFactory groupFactory = getService(bc, CyGroupFactory.class);
CyTableFactory tableFactory = getService(bc, CyTableFactory.class);
CyTableManager tableManager = getService(bc, CyTableManager.class);
// Create our context object. This will probably keep track of all of the
// registered clustering algorithms, settings, etc.
ClusterManagerImpl clusterManager = new ClusterManagerImpl(appRef, serviceRegistrar, groupFactory, groupManager, tableFactory, tableManager);
registerServiceListener(bc, clusterManager, "addClusterAlgorithm", "removeClusterAlgorithm", ClusterTaskFactory.class);
registerServiceListener(bc, clusterManager, "addClusterVisualizer", "removeClusterVisualizer", ClusterVizFactory.class);
registerServiceListener(bc, clusterManager, "addRankingAlgorithm", "removeRankingAlgorithm", RankFactory.class);
// Register each of our algorithms
// Attribute clusterers
registerService(bc, new AttributeClusterTaskFactory(clusterManager), ClusterTaskFactory.class, new Properties());
registerService(bc, new AutoSOMETaskFactory(clusterManager, true), ClusterTaskFactory.class, new Properties());
registerService(bc, new FeatureVectorTaskFactory(clusterManager), ClusterTaskFactory.class, new Properties());
registerService(bc, new HierarchicalTaskFactory(clusterManager), ClusterTaskFactory.class, new Properties());
registerService(bc, new KMeansTaskFactory(clusterManager), ClusterTaskFactory.class, new Properties());
registerService(bc, new KMedoidTaskFactory(clusterManager), ClusterTaskFactory.class, new Properties());
registerService(bc, new HopachPAMTaskFactory(clusterManager), ClusterTaskFactory.class, new Properties());
registerService(bc, new PAMTaskFactory(clusterManager), ClusterTaskFactory.class, new Properties());
// FIXME: FFT is seriously broken!
registerService(bc, new FFTTaskFactory(clusterManager), ClusterTaskFactory.class, new Properties());
registerService(bc, new DBSCANTaskFactory(clusterManager), ClusterTaskFactory.class, new Properties());
/*
* Hold off on these until we get improve the performance sufficiently
* to allow them to be useful
*/
// registerService(bc, new BicFinderTaskFactory(clusterManager),
// ClusterTaskFactory.class, new Properties());
// registerService(bc, new BiMineTaskFactory(clusterManager),
// ClusterTaskFactory.class, new Properties());
registerService(bc, new ChengChurchTaskFactory(clusterManager), ClusterTaskFactory.class, new Properties());
// Network clusterers
registerService(bc, new NetworkClusterTaskFactory(clusterManager), ClusterTaskFactory.class, new Properties());
registerService(bc, new APClusterTaskFactory(clusterManager), ClusterTaskFactory.class, new Properties());
registerService(bc, new AutoSOMETaskFactory(clusterManager, false), ClusterTaskFactory.class, new Properties());
registerService(bc, new FuzzifierTaskFactory(clusterManager), ClusterTaskFactory.class, new Properties());
registerService(bc, new GLayClusterTaskFactory(clusterManager), ClusterTaskFactory.class, new Properties());
registerService(bc, new ConnectedComponentsTaskFactory(clusterManager), ClusterTaskFactory.class, new Properties());
registerService(bc, new FCMClusterTaskFactory(clusterManager), ClusterTaskFactory.class, new Properties());
registerService(bc, new MCLClusterTaskFactory(clusterManager), ClusterTaskFactory.class, new Properties());
registerService(bc, new MCODEClusterTaskFactory(clusterManager), ClusterTaskFactory.class, new Properties());
registerService(bc, new SCPSClusterTaskFactory(clusterManager), ClusterTaskFactory.class, new Properties());
registerService(bc, new TransClustClusterTaskFactory(clusterManager), ClusterTaskFactory.class, new Properties());
// Cluster ranking
registerService(bc, new MAATaskFactory(clusterManager), RankFactory.class, new Properties());
registerService(bc, new MAMTaskFactory(clusterManager), RankFactory.class, new Properties());
registerService(bc, new PRWPTaskFactory(clusterManager), RankFactory.class, new Properties());
registerService(bc, new PRTaskFactory(clusterManager), RankFactory.class, new Properties());
registerService(bc, new HITSTaskFactory(clusterManager), RankFactory.class, new Properties());
// Filters
registerService(bc, new FilterTaskFactory(clusterManager), ClusterTaskFactory.class, new Properties());
registerService(bc, new BestNeighborFilterTaskFactory(clusterManager), ClusterTaskFactory.class, new Properties());
registerService(bc, new CuttingEdgeFilterTaskFactory(clusterManager), ClusterTaskFactory.class, new Properties());
registerService(bc, new DensityFilterTaskFactory(clusterManager), ClusterTaskFactory.class, new Properties());
registerService(bc, new HairCutFilterTaskFactory(clusterManager), ClusterTaskFactory.class, new Properties());
// registerService(bc, new UITaskFactory(clusterManager), ClusterTaskFactory.class, new Properties());
// Visualizations
registerService(bc, new NewNetworkViewFactory(clusterManager, false), ClusterVizFactory.class, new Properties());
registerService(bc, new NewNetworkViewFactory(clusterManager, true), ClusterVizFactory.class, new Properties());
registerService(bc, new HeatMapViewTaskFactory(clusterManager), ClusterVizFactory.class, new Properties());
registerService(bc, new KnnViewTaskFactory(clusterManager), ClusterVizFactory.class, new Properties());
registerService(bc, new BiclusterViewTaskFactory(clusterManager), ClusterVizFactory.class, new Properties());
registerService(bc, new TreeViewTaskFactory(clusterManager), ClusterVizFactory.class, new Properties());
registerService(bc, new CreateResultsPanelTaskFactory(clusterManager, true), ClusterVizFactory.class, new Properties());
registerService(bc, new CreateRankingPanelTaskFactory(clusterManager, true), ClusterVizFactory.class, new Properties());
registerService(bc, new DestroyResultsPanelTaskFactory(clusterManager, true), ClusterVizFactory.class, new Properties());
registerService(bc, new DestroyRankingPanelTaskFactory(clusterManager, true), ClusterVizFactory.class, new Properties());
// Dimensionality Reduction
// registerService(bc, new PCAMenuTaskFactory(clusterManager), ClusterTaskFactory.class, new Properties());
registerService(bc, new PCATaskFactory(clusterManager), ClusterTaskFactory.class, new Properties());
registerService(bc, new PCoATaskFactory(clusterManager), ClusterTaskFactory.class, new Properties());
registerService(bc, new tSNETaskFactory(clusterManager), ClusterTaskFactory.class, new Properties());
{
// Link Network Selections
LinkSelectionTaskFactory linkTaskFactory = new LinkSelectionTaskFactory(clusterManager);
Properties linkSelectionProps = new Properties();
linkSelectionProps.setProperty(INSERT_SEPARATOR_BEFORE, "true");
linkSelectionProps.setProperty(PREFERRED_MENU, "Apps.clusterMaker Visualizations");
linkSelectionProps.setProperty(TITLE, "Link selection across networks");
linkSelectionProps.setProperty(COMMAND, "linkSelection");
linkSelectionProps.setProperty(COMMAND_NAMESPACE, "clusterviz");
linkSelectionProps.setProperty(ENABLE_FOR, "networkAndView");
linkSelectionProps.setProperty(IN_MENU_BAR, "true");
linkSelectionProps.setProperty(MENU_GRAVITY, "100.0");
registerService(bc, linkTaskFactory, NetworkTaskFactory.class, linkSelectionProps);
}
{
// UnLink Network Selections
UnlinkSelectionTaskFactory unlinkTaskFactory = new UnlinkSelectionTaskFactory(clusterManager);
Properties unlinkSelectionProps = new Properties();
unlinkSelectionProps.setProperty(PREFERRED_MENU, "Apps.clusterMaker Visualizations");
unlinkSelectionProps.setProperty(TITLE, "Unlink selection across networks");
unlinkSelectionProps.setProperty(COMMAND, "unlinkSelection");
unlinkSelectionProps.setProperty(COMMAND_NAMESPACE, "clusterviz");
unlinkSelectionProps.setProperty(ENABLE_FOR, "networkAndView");
unlinkSelectionProps.setProperty(IN_MENU_BAR, "true");
unlinkSelectionProps.setProperty(MENU_GRAVITY, "100.0");
registerService(bc, unlinkTaskFactory, NetworkTaskFactory.class, unlinkSelectionProps);
}
// Commands
// These task factories provide useful commands that only make sense in the context of REST or
// the command interface
{
TaskFactory commandTaskFactory = new CommandTaskFactory(clusterManager, "hascluster");
Properties props = new Properties();
props.setProperty(COMMAND_NAMESPACE, "cluster");
props.setProperty(COMMAND, CommandTaskFactory.HASCLUSTER);
props.setProperty(COMMAND_DESCRIPTION, "Test to see if this network has a cluster of the requested type");
registerService(bc, commandTaskFactory, TaskFactory.class, props);
}
{
TaskFactory commandTaskFactory = new CommandTaskFactory(clusterManager, "getnetworkcluster");
Properties props = new Properties();
props.setProperty(COMMAND_NAMESPACE, "cluster");
props.setProperty(COMMAND, CommandTaskFactory.GETNETWORKCLUSTER);
props.setProperty(COMMAND_DESCRIPTION, "Get a cluster network cluster result");
registerService(bc, commandTaskFactory, TaskFactory.class, props);
}
{
TaskFactory commandTaskFactory = new CommandTaskFactory(clusterManager, "getcluster");
Properties props = new Properties();
props.setProperty(COMMAND_NAMESPACE, "cluster");
props.setProperty(COMMAND, CommandTaskFactory.GETCLUSTER);
props.setProperty(COMMAND_DESCRIPTION, "Get an attribute cluster result");
registerService(bc, commandTaskFactory, TaskFactory.class, props);
}
}
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