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Example 26 with CyServiceRegistrar

use of org.cytoscape.service.util.CyServiceRegistrar in project cytoscape-impl by cytoscape.

the class GMLFileFilterTest method setUp.

@Before
public void setUp() {
    Set<String> extensions = new HashSet<String>();
    Set<String> contentTypes = new HashSet<String>();
    String description = "GML";
    Properties properties = new Properties();
    CyProperty<Properties> cyProperties = new SimpleCyProperty<Properties>("test", properties, Properties.class, SavePolicy.DO_NOT_SAVE);
    CyServiceRegistrar serviceRegistrar = mock(CyServiceRegistrar.class);
    when(serviceRegistrar.getService(CyProperty.class, "(cyPropertyName=cytoscape3.props)")).thenReturn(cyProperties);
    filter = new GMLFileFilter(extensions, contentTypes, description, DataCategory.NETWORK, new StreamUtilImpl(serviceRegistrar));
}
Also used : Properties(java.util.Properties) SimpleCyProperty(org.cytoscape.property.SimpleCyProperty) CyServiceRegistrar(org.cytoscape.service.util.CyServiceRegistrar) StreamUtilImpl(org.cytoscape.io.internal.util.StreamUtilImpl) HashSet(java.util.HashSet) Before(org.junit.Before)

Example 27 with CyServiceRegistrar

use of org.cytoscape.service.util.CyServiceRegistrar in project cytoscape-impl by cytoscape.

the class SessionFileFilterTest method setUp.

@Before
public void setUp() {
    extensions = new HashSet<String>();
    contentTypes = new HashSet<String>();
    Properties properties = new Properties();
    CyProperty<Properties> cyProperties = new SimpleCyProperty<Properties>("test", properties, Properties.class, SavePolicy.DO_NOT_SAVE);
    CyServiceRegistrar serviceRegistrar = mock(CyServiceRegistrar.class);
    when(serviceRegistrar.getService(CyProperty.class, "(cyPropertyName=cytoscape3.props)")).thenReturn(cyProperties);
    streamUtil = new StreamUtilImpl(serviceRegistrar);
}
Also used : Properties(java.util.Properties) SimpleCyProperty(org.cytoscape.property.SimpleCyProperty) CyServiceRegistrar(org.cytoscape.service.util.CyServiceRegistrar) StreamUtilImpl(org.cytoscape.io.internal.util.StreamUtilImpl) Before(org.junit.Before)

Example 28 with CyServiceRegistrar

use of org.cytoscape.service.util.CyServiceRegistrar in project PhenomeScape by soulj.

the class NetworkNameChangedListener method handleEvent.

public void handleEvent(RowsSetEvent e) {
    // First check whether the Name field of any of the rows got changed.
    if (e.containsColumn(CyNetwork.NAME)) {
        CyServiceRegistrar cyServiceRegistrar = controlPanel.cyServiceRegistrar;
        DefaultComboBoxModel networkModel = (DefaultComboBoxModel) networkComboBox.getModel();
        networkModel.removeAllElements();
        for (CyNetwork cyNetwork : cyServiceRegistrar.getService(CyNetworkManager.class).getNetworkSet()) {
            String cyNetworkName = cyNetwork.getRow(cyNetwork).get(CyNetwork.NAME, String.class);
            networkModel.addElement(cyNetworkName);
        }
    }
}
Also used : CyNetworkManager(org.cytoscape.model.CyNetworkManager) CyNetwork(org.cytoscape.model.CyNetwork) DefaultComboBoxModel(javax.swing.DefaultComboBoxModel) CyServiceRegistrar(org.cytoscape.service.util.CyServiceRegistrar)

Example 29 with CyServiceRegistrar

use of org.cytoscape.service.util.CyServiceRegistrar 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);
    }
}
Also used : MCODEClusterTaskFactory(edu.ucsf.rbvi.clusterMaker2.internal.algorithms.networkClusterers.MCODE.MCODEClusterTaskFactory) MAMTaskFactory(edu.ucsf.rbvi.clusterMaker2.internal.algorithms.ranking.MAM.MAMTaskFactory) HITSTaskFactory(edu.ucsf.rbvi.clusterMaker2.internal.algorithms.ranking.HITS.HITSTaskFactory) CyServiceRegistrar(org.cytoscape.service.util.CyServiceRegistrar) BestNeighborFilterTaskFactory(edu.ucsf.rbvi.clusterMaker2.internal.algorithms.clusterFilters.BestNeighbor.BestNeighborFilterTaskFactory) FilterTaskFactory(edu.ucsf.rbvi.clusterMaker2.internal.algorithms.clusterFilters.FilterTaskFactory) DensityFilterTaskFactory(edu.ucsf.rbvi.clusterMaker2.internal.algorithms.clusterFilters.Density.DensityFilterTaskFactory) HairCutFilterTaskFactory(edu.ucsf.rbvi.clusterMaker2.internal.algorithms.clusterFilters.HairCut.HairCutFilterTaskFactory) CuttingEdgeFilterTaskFactory(edu.ucsf.rbvi.clusterMaker2.internal.algorithms.clusterFilters.CuttingEdge.CuttingEdgeFilterTaskFactory) FCMClusterTaskFactory(edu.ucsf.rbvi.clusterMaker2.internal.algorithms.networkClusterers.FCM.FCMClusterTaskFactory) CyGroupFactory(org.cytoscape.group.CyGroupFactory) KMedoidTaskFactory(edu.ucsf.rbvi.clusterMaker2.internal.algorithms.attributeClusterers.kmedoid.KMedoidTaskFactory) CySwingApplication(org.cytoscape.application.swing.CySwingApplication) HairCutFilterTaskFactory(edu.ucsf.rbvi.clusterMaker2.internal.algorithms.clusterFilters.HairCut.HairCutFilterTaskFactory) PCATaskFactory(edu.ucsf.rbvi.clusterMaker2.internal.algorithms.pca.PCATaskFactory) HopachPAMTaskFactory(edu.ucsf.rbvi.clusterMaker2.internal.algorithms.attributeClusterers.hopach.HopachPAMTaskFactory) FuzzifierTaskFactory(edu.ucsf.rbvi.clusterMaker2.internal.algorithms.networkClusterers.Fuzzifier.FuzzifierTaskFactory) MAATaskFactory(edu.ucsf.rbvi.clusterMaker2.internal.algorithms.ranking.MAA.MAATaskFactory) MCLClusterTaskFactory(edu.ucsf.rbvi.clusterMaker2.internal.algorithms.networkClusterers.MCL.MCLClusterTaskFactory) CuttingEdgeFilterTaskFactory(edu.ucsf.rbvi.clusterMaker2.internal.algorithms.clusterFilters.CuttingEdge.CuttingEdgeFilterTaskFactory) CyApplicationManager(org.cytoscape.application.CyApplicationManager) FFTTaskFactory(edu.ucsf.rbvi.clusterMaker2.internal.algorithms.attributeClusterers.fft.FFTTaskFactory) HierarchicalTaskFactory(edu.ucsf.rbvi.clusterMaker2.internal.algorithms.attributeClusterers.hierarchical.HierarchicalTaskFactory) KMeansTaskFactory(edu.ucsf.rbvi.clusterMaker2.internal.algorithms.attributeClusterers.kmeans.KMeansTaskFactory) ChengChurchTaskFactory(edu.ucsf.rbvi.clusterMaker2.internal.algorithms.attributeClusterers.ChengChurch.ChengChurchTaskFactory) GLayClusterTaskFactory(edu.ucsf.rbvi.clusterMaker2.internal.algorithms.networkClusterers.GLay.GLayClusterTaskFactory) PCoATaskFactory(edu.ucsf.rbvi.clusterMaker2.internal.algorithms.pcoa.PCoATaskFactory) PAMTaskFactory(edu.ucsf.rbvi.clusterMaker2.internal.algorithms.attributeClusterers.pam.PAMTaskFactory) HopachPAMTaskFactory(edu.ucsf.rbvi.clusterMaker2.internal.algorithms.attributeClusterers.hopach.HopachPAMTaskFactory) NetworkClusterTaskFactory(edu.ucsf.rbvi.clusterMaker2.internal.algorithms.networkClusterers.NetworkClusterTaskFactory) Properties(java.util.Properties) FeatureVectorTaskFactory(edu.ucsf.rbvi.clusterMaker2.internal.algorithms.attributeClusterers.featureVector.FeatureVectorTaskFactory) PRTaskFactory(edu.ucsf.rbvi.clusterMaker2.internal.algorithms.ranking.PR.PRTaskFactory) BestNeighborFilterTaskFactory(edu.ucsf.rbvi.clusterMaker2.internal.algorithms.clusterFilters.BestNeighbor.BestNeighborFilterTaskFactory) CyGroupManager(org.cytoscape.group.CyGroupManager) ConnectedComponentsTaskFactory(edu.ucsf.rbvi.clusterMaker2.internal.algorithms.networkClusterers.ConnectedComponents.ConnectedComponentsTaskFactory) TransClustClusterTaskFactory(edu.ucsf.rbvi.clusterMaker2.internal.algorithms.networkClusterers.TransClust.TransClustClusterTaskFactory) AutoSOMETaskFactory(edu.ucsf.rbvi.clusterMaker2.internal.algorithms.attributeClusterers.autosome.AutoSOMETaskFactory) DBSCANTaskFactory(edu.ucsf.rbvi.clusterMaker2.internal.algorithms.attributeClusterers.DBSCAN.DBSCANTaskFactory) AttributeClusterTaskFactory(edu.ucsf.rbvi.clusterMaker2.internal.algorithms.attributeClusterers.AttributeClusterTaskFactory) APClusterTaskFactory(edu.ucsf.rbvi.clusterMaker2.internal.algorithms.networkClusterers.AP.APClusterTaskFactory) PRWPTaskFactory(edu.ucsf.rbvi.clusterMaker2.internal.algorithms.ranking.PRWP.PRWPTaskFactory) SCPSClusterTaskFactory(edu.ucsf.rbvi.clusterMaker2.internal.algorithms.networkClusterers.SCPS.SCPSClusterTaskFactory) CommandTaskFactory(edu.ucsf.rbvi.clusterMaker2.internal.commands.CommandTaskFactory) CyTableFactory(org.cytoscape.model.CyTableFactory) edu.ucsf.rbvi.clusterMaker2.internal.algorithms.tSNEWrapper.tSNETaskFactory(edu.ucsf.rbvi.clusterMaker2.internal.algorithms.tSNEWrapper.tSNETaskFactory) CyTableManager(org.cytoscape.model.CyTableManager) DensityFilterTaskFactory(edu.ucsf.rbvi.clusterMaker2.internal.algorithms.clusterFilters.Density.DensityFilterTaskFactory) NetworkTaskFactory(org.cytoscape.task.NetworkTaskFactory) HITSTaskFactory(edu.ucsf.rbvi.clusterMaker2.internal.algorithms.ranking.HITS.HITSTaskFactory) AutoSOMETaskFactory(edu.ucsf.rbvi.clusterMaker2.internal.algorithms.attributeClusterers.autosome.AutoSOMETaskFactory) FCMClusterTaskFactory(edu.ucsf.rbvi.clusterMaker2.internal.algorithms.networkClusterers.FCM.FCMClusterTaskFactory) KMeansTaskFactory(edu.ucsf.rbvi.clusterMaker2.internal.algorithms.attributeClusterers.kmeans.KMeansTaskFactory) TransClustClusterTaskFactory(edu.ucsf.rbvi.clusterMaker2.internal.algorithms.networkClusterers.TransClust.TransClustClusterTaskFactory) PCAMenuTaskFactory(edu.ucsf.rbvi.clusterMaker2.internal.algorithms.pca.PCAMenuTaskFactory) FFTTaskFactory(edu.ucsf.rbvi.clusterMaker2.internal.algorithms.attributeClusterers.fft.FFTTaskFactory) KMedoidTaskFactory(edu.ucsf.rbvi.clusterMaker2.internal.algorithms.attributeClusterers.kmedoid.KMedoidTaskFactory) SCPSClusterTaskFactory(edu.ucsf.rbvi.clusterMaker2.internal.algorithms.networkClusterers.SCPS.SCPSClusterTaskFactory) MCLClusterTaskFactory(edu.ucsf.rbvi.clusterMaker2.internal.algorithms.networkClusterers.MCL.MCLClusterTaskFactory) NetworkClusterTaskFactory(edu.ucsf.rbvi.clusterMaker2.internal.algorithms.networkClusterers.NetworkClusterTaskFactory) PCATaskFactory(edu.ucsf.rbvi.clusterMaker2.internal.algorithms.pca.PCATaskFactory) ChengChurchTaskFactory(edu.ucsf.rbvi.clusterMaker2.internal.algorithms.attributeClusterers.ChengChurch.ChengChurchTaskFactory) APClusterTaskFactory(edu.ucsf.rbvi.clusterMaker2.internal.algorithms.networkClusterers.AP.APClusterTaskFactory) edu.ucsf.rbvi.clusterMaker2.internal.algorithms.tSNEWrapper.tSNETaskFactory(edu.ucsf.rbvi.clusterMaker2.internal.algorithms.tSNEWrapper.tSNETaskFactory) DBSCANTaskFactory(edu.ucsf.rbvi.clusterMaker2.internal.algorithms.attributeClusterers.DBSCAN.DBSCANTaskFactory) FeatureVectorTaskFactory(edu.ucsf.rbvi.clusterMaker2.internal.algorithms.attributeClusterers.featureVector.FeatureVectorTaskFactory) HierarchicalTaskFactory(edu.ucsf.rbvi.clusterMaker2.internal.algorithms.attributeClusterers.hierarchical.HierarchicalTaskFactory) PAMTaskFactory(edu.ucsf.rbvi.clusterMaker2.internal.algorithms.attributeClusterers.pam.PAMTaskFactory) BestNeighborFilterTaskFactory(edu.ucsf.rbvi.clusterMaker2.internal.algorithms.clusterFilters.BestNeighbor.BestNeighborFilterTaskFactory) AttributeClusterTaskFactory(edu.ucsf.rbvi.clusterMaker2.internal.algorithms.attributeClusterers.AttributeClusterTaskFactory) ConnectedComponentsTaskFactory(edu.ucsf.rbvi.clusterMaker2.internal.algorithms.networkClusterers.ConnectedComponents.ConnectedComponentsTaskFactory) PRWPTaskFactory(edu.ucsf.rbvi.clusterMaker2.internal.algorithms.ranking.PRWP.PRWPTaskFactory) FilterTaskFactory(edu.ucsf.rbvi.clusterMaker2.internal.algorithms.clusterFilters.FilterTaskFactory) ClusterTaskFactory(edu.ucsf.rbvi.clusterMaker2.internal.api.ClusterTaskFactory) TaskFactory(org.cytoscape.work.TaskFactory) DensityFilterTaskFactory(edu.ucsf.rbvi.clusterMaker2.internal.algorithms.clusterFilters.Density.DensityFilterTaskFactory) HairCutFilterTaskFactory(edu.ucsf.rbvi.clusterMaker2.internal.algorithms.clusterFilters.HairCut.HairCutFilterTaskFactory) NetworkTaskFactory(org.cytoscape.task.NetworkTaskFactory) MAATaskFactory(edu.ucsf.rbvi.clusterMaker2.internal.algorithms.ranking.MAA.MAATaskFactory) FuzzifierTaskFactory(edu.ucsf.rbvi.clusterMaker2.internal.algorithms.networkClusterers.Fuzzifier.FuzzifierTaskFactory) PCoATaskFactory(edu.ucsf.rbvi.clusterMaker2.internal.algorithms.pcoa.PCoATaskFactory) GLayClusterTaskFactory(edu.ucsf.rbvi.clusterMaker2.internal.algorithms.networkClusterers.GLay.GLayClusterTaskFactory) MAMTaskFactory(edu.ucsf.rbvi.clusterMaker2.internal.algorithms.ranking.MAM.MAMTaskFactory) PRTaskFactory(edu.ucsf.rbvi.clusterMaker2.internal.algorithms.ranking.PR.PRTaskFactory) CommandTaskFactory(edu.ucsf.rbvi.clusterMaker2.internal.commands.CommandTaskFactory) HopachPAMTaskFactory(edu.ucsf.rbvi.clusterMaker2.internal.algorithms.attributeClusterers.hopach.HopachPAMTaskFactory) MCODEClusterTaskFactory(edu.ucsf.rbvi.clusterMaker2.internal.algorithms.networkClusterers.MCODE.MCODEClusterTaskFactory) CuttingEdgeFilterTaskFactory(edu.ucsf.rbvi.clusterMaker2.internal.algorithms.clusterFilters.CuttingEdge.CuttingEdgeFilterTaskFactory)

Example 30 with CyServiceRegistrar

use of org.cytoscape.service.util.CyServiceRegistrar in project clusterMaker2 by RBVI.

the class RunPCA method runOnNodeToAttributeMatrix.

// this method assumes that eigen values
// are sorted in increasing order
public void runOnNodeToAttributeMatrix() {
    // System.out.println("runOnNodeToAttributeMatrix");
    CyMatrix matrix = CyMatrixFactory.makeLargeMatrix(network, weightAttributes, context.selectedOnly, context.ignoreMissing, false, false);
    // System.out.println("Computing principle components");
    components = computePCs(matrix);
    final Matrix loadingMatrix = calculateLoadingMatrix(matrix);
    if (context.pcaResultPanel) {
        CyServiceRegistrar registrar = manager.getService(CyServiceRegistrar.class);
        CySwingApplication swingApplication = manager.getService(CySwingApplication.class);
        ResultPanelPCA panel = new ResultPanelPCA(components, variance, network, networkView);
        CytoPanel cytoPanel = swingApplication.getCytoPanel(CytoPanelName.EAST);
        registrar.registerService(panel, CytoPanelComponent.class, new Properties());
        if (cytoPanel.getState() == CytoPanelState.HIDE)
            cytoPanel.setState(CytoPanelState.DOCK);
    }
    if (context.pcaPlot) {
        if (components.length < 2) {
            monitor.showMessage(TaskMonitor.Level.ERROR, "Only found " + components.length + " components. Need 2 for scatterplot. " + "Perhaps minimum variance is set too high?");
            return;
        }
        SwingUtilities.invokeLater(new Runnable() {

            public void run() {
                // System.out.println("Scatter plot dialog call");
                ScatterPlotDialog dialog = new ScatterPlotDialog(manager, "PCA", monitor, components, loadingMatrix, variance);
            }
        });
    }
}
Also used : CyMatrix(edu.ucsf.rbvi.clusterMaker2.internal.api.CyMatrix) Matrix(edu.ucsf.rbvi.clusterMaker2.internal.api.Matrix) ColtMatrix(edu.ucsf.rbvi.clusterMaker2.internal.algorithms.matrix.ColtMatrix) CyMatrix(edu.ucsf.rbvi.clusterMaker2.internal.api.CyMatrix) CySwingApplication(org.cytoscape.application.swing.CySwingApplication) ScatterPlotDialog(edu.ucsf.rbvi.clusterMaker2.internal.ui.ScatterPlotDialog) CytoPanel(org.cytoscape.application.swing.CytoPanel) Properties(java.util.Properties) CyServiceRegistrar(org.cytoscape.service.util.CyServiceRegistrar)

Aggregations

CyServiceRegistrar (org.cytoscape.service.util.CyServiceRegistrar)62 Properties (java.util.Properties)32 CyEventHelper (org.cytoscape.event.CyEventHelper)14 VisualMappingManager (org.cytoscape.view.vizmap.VisualMappingManager)13 CyApplicationManager (org.cytoscape.application.CyApplicationManager)12 UndoSupport (org.cytoscape.work.undo.UndoSupport)12 TaskIterator (org.cytoscape.work.TaskIterator)11 CyNetwork (org.cytoscape.model.CyNetwork)10 Task (org.cytoscape.work.Task)10 Before (org.junit.Before)10 Test (org.junit.Test)10 CyNetworkManager (org.cytoscape.model.CyNetworkManager)7 CyNetworkViewManager (org.cytoscape.view.model.CyNetworkViewManager)7 TaskFactory (org.cytoscape.work.TaskFactory)7 CyGroupManager (org.cytoscape.group.CyGroupManager)6 CyNetworkFactory (org.cytoscape.model.CyNetworkFactory)6 CyRootNetworkManager (org.cytoscape.model.subnetwork.CyRootNetworkManager)6 CyNetworkNaming (org.cytoscape.session.CyNetworkNaming)6 RenderingEngineManager (org.cytoscape.view.presentation.RenderingEngineManager)6 CyNetworkView (org.cytoscape.view.model.CyNetworkView)5