Examples with MCODEClusterTaskFactory edu.ucsf.rbvi.clusterMaker2.internal.algorithms.networkClusterers.MCODE.MCODEClusterTaskFactory used on opensource projects

Example 1 with MCODEClusterTaskFactory

use of edu.ucsf.rbvi.clusterMaker2.internal.algorithms.networkClusterers.MCODE.MCODEClusterTaskFactory 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);
    }
}