Examples with CyTableFactory org.cytoscape.model.CyTableFactory used on opensource projects

Example 1 with CyTableFactory

use of org.cytoscape.model.CyTableFactory in project cytoscape-impl by cytoscape.

the class CyActivator method start.

@Override
public void start(BundleContext bc) {
    CyServiceRegistrar serviceRegistrar = getService(bc, CyServiceRegistrar.class);
    CyEventHelper cyEventHelperRef = getService(bc, CyEventHelper.class);
    CyNetworkNaming cyNetworkNamingServiceRef = getService(bc, CyNetworkNaming.class);
    UndoSupport undoSupportServiceRef = getService(bc, UndoSupport.class);
    CyNetworkViewFactory cyNetworkViewFactoryServiceRef = getService(bc, CyNetworkViewFactory.class);
    CyNetworkFactory cyNetworkFactoryServiceRef = getService(bc, CyNetworkFactory.class);
    CyRootNetworkManager cyRootNetworkFactoryServiceRef = getService(bc, CyRootNetworkManager.class);
    VisualMappingManager visualMappingManagerServiceRef = getService(bc, VisualMappingManager.class);
    CyNetworkViewWriterManager networkViewWriterManagerServiceRef = getService(bc, CyNetworkViewWriterManager.class);
    CyNetworkManager cyNetworkManagerServiceRef = getService(bc, CyNetworkManager.class);
    CyNetworkViewManager cyNetworkViewManagerServiceRef = getService(bc, CyNetworkViewManager.class);
    CyApplicationManager cyApplicationManagerServiceRef = getService(bc, CyApplicationManager.class);
    CySessionManager cySessionManagerServiceRef = getService(bc, CySessionManager.class);
    CyTableFactory cyTableFactoryServiceRef = getService(bc, CyTableFactory.class);
    CyTableManager cyTableManagerServiceRef = getService(bc, CyTableManager.class);
    CyLayoutAlgorithmManager cyLayoutsServiceRef = getService(bc, CyLayoutAlgorithmManager.class);
    CyTableWriterManager cyTableWriterManagerRef = getService(bc, CyTableWriterManager.class);
    SynchronousTaskManager<?> synchronousTaskManagerServiceRef = getService(bc, SynchronousTaskManager.class);
    TunableSetter tunableSetterServiceRef = getService(bc, TunableSetter.class);
    CyRootNetworkManager rootNetworkManagerServiceRef = getService(bc, CyRootNetworkManager.class);
    CyNetworkTableManager cyNetworkTableManagerServiceRef = getService(bc, CyNetworkTableManager.class);
    RenderingEngineManager renderingEngineManagerServiceRef = getService(bc, RenderingEngineManager.class);
    CyNetworkViewFactory nullNetworkViewFactory = getService(bc, CyNetworkViewFactory.class, "(id=NullCyNetworkViewFactory)");
    CyGroupManager cyGroupManager = getService(bc, CyGroupManager.class);
    CyGroupFactory cyGroupFactory = getService(bc, CyGroupFactory.class);
    {
        DynamicTaskFactoryProvisionerImpl factory = new DynamicTaskFactoryProvisionerImpl(serviceRegistrar);
        registerAllServices(bc, factory);
    }
    createPreferencesTaskFactories(bc, serviceRegistrar);
    createFilterTaskFactories(bc, serviceRegistrar);
    createTableTaskFactories(bc, serviceRegistrar, undoSupportServiceRef, cyNetworkManagerServiceRef, cyApplicationManagerServiceRef, cyTableFactoryServiceRef, cyTableManagerServiceRef, cyTableWriterManagerRef, tunableSetterServiceRef, rootNetworkManagerServiceRef, cyNetworkTableManagerServiceRef);
    createNetworkTaskFactories(bc, serviceRegistrar, cyEventHelperRef, cyNetworkNamingServiceRef, undoSupportServiceRef, cyNetworkViewFactoryServiceRef, cyNetworkFactoryServiceRef, cyRootNetworkFactoryServiceRef, visualMappingManagerServiceRef, cyNetworkManagerServiceRef, cyNetworkViewManagerServiceRef, cyApplicationManagerServiceRef, synchronousTaskManagerServiceRef, rootNetworkManagerServiceRef, cyNetworkTableManagerServiceRef, renderingEngineManagerServiceRef, nullNetworkViewFactory, cyGroupManager, cyGroupFactory, networkViewWriterManagerServiceRef, tunableSetterServiceRef);
    createViewTaskFactories(bc, cyEventHelperRef, undoSupportServiceRef, visualMappingManagerServiceRef, networkViewWriterManagerServiceRef, cyNetworkViewManagerServiceRef, cyApplicationManagerServiceRef, cyLayoutsServiceRef, tunableSetterServiceRef, renderingEngineManagerServiceRef, cyNetworkManagerServiceRef, cySessionManagerServiceRef, serviceRegistrar);
    createVizmapTaskFactories(bc, serviceRegistrar);
    createSessionTaskFactories(bc, serviceRegistrar);
    createGroupTaskFactories(bc, undoSupportServiceRef, cyApplicationManagerServiceRef, cyGroupManager, cyGroupFactory, serviceRegistrar);
    createNodeEdgeTaskFactories(bc, serviceRegistrar, cyEventHelperRef, undoSupportServiceRef, cyNetworkViewManagerServiceRef, tunableSetterServiceRef, cyApplicationManagerServiceRef, cyTableManagerServiceRef, renderingEngineManagerServiceRef, visualMappingManagerServiceRef);
    createLayoutTaskFactories(bc, serviceRegistrar);
    createHelpTaskFactories(bc, serviceRegistrar);
}

Example 2 with CyTableFactory

use of org.cytoscape.model.CyTableFactory in project cytoscape-impl by cytoscape.

the class LoadTableReaderTask method loadAnnotation.

private void loadAnnotation(TaskMonitor tm) {
    tm.setProgress(0.0);
    TextTableReader reader = this.reader;
    AttributeMappingParameters readerAMP = (AttributeMappingParameters) reader.getMappingParameter();
    String primaryKey = readerAMP.getAttributeNames()[readerAMP.getKeyIndex()];
    tm.setProgress(0.1);
    final CyTableFactory tableFactory = serviceRegistrar.getService(CyTableFactory.class);
    final CyTable table = tableFactory.createTable("AttrTable " + inputName.substring(inputName.lastIndexOf('/') + 1) + " " + Integer.toString(numImports++), primaryKey, String.class, true, true);
    cyTables = new CyTable[] { table };
    tm.setProgress(0.3);
    try {
        this.reader.readTable(table);
    } catch (IOException e) {
        e.printStackTrace();
    }
    tm.setProgress(1.0);
}

Example 3 with CyTableFactory

use of org.cytoscape.model.CyTableFactory in project cytoscape-impl by cytoscape.

the class Cy3SessionReaderImplTest method testRestoreVirtualColumnsWithCircularDependencies.

@Test(expected = Exception.class)
public void testRestoreVirtualColumnsWithCircularDependencies() throws Exception {
    // This should never happen, but let's make sure it doesn't get into an infinite loop
    {
        VirtualColumn vc = new VirtualColumn();
        vc.setName("a");
        vc.setSourceColumn("a");
        vc.setSourceJoinKey("id");
        vc.setTargetJoinKey("id");
        vc.setSourceTable("t2");
        vc.setTargetTable("t3");
        reader.virtualColumns.add(vc);
    }
    {
        VirtualColumn vc = new VirtualColumn();
        vc.setName("a");
        vc.setSourceColumn("a");
        vc.setSourceJoinKey("id");
        vc.setTargetJoinKey("id");
        vc.setSourceTable("t1");
        vc.setTargetTable("t2");
        reader.virtualColumns.add(vc);
    }
    {
        VirtualColumn vc = new VirtualColumn();
        vc.setName("a");
        vc.setSourceColumn("a");
        vc.setSourceJoinKey("id");
        vc.setTargetJoinKey("id");
        vc.setSourceTable("t2");
        vc.setTargetTable("t3");
        reader.virtualColumns.add(vc);
    }
    CyTableFactory tblFactory = tblTestSupport.getTableFactory();
    CyTable tbl1 = tblFactory.createTable("t1", "id", Integer.class, true, true);
    CyTable tbl2 = tblFactory.createTable("t2", "id", Integer.class, true, true);
    CyTable tbl3 = tblFactory.createTable("t3", "id", Integer.class, true, true);
    reader.filenameTableMap.put(tbl1.getTitle(), tbl1);
    reader.filenameTableMap.put(tbl2.getTitle(), tbl2);
    reader.filenameTableMap.put(tbl3.getTitle(), tbl3);
    reader.restoreVirtualColumns();
}

Example 4 with CyTableFactory

use of org.cytoscape.model.CyTableFactory 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);
    }
}

Example 5 with CyTableFactory

use of org.cytoscape.model.CyTableFactory in project cytoscape-impl by cytoscape.

the class ExpressionReader method copyToAttribs.

/**
 * Copies ExpressionData data structure into CyAttributes data structure.
 *
 * @param nodeAttribs Node Attributes CyTable.
 * @param taskMonitor Task Monitor. Can be null.
 */
private void copyToAttribs(TaskMonitor taskMonitor) {
    String[] condNames = getConditionNames();
    final CyTableFactory tableFactory = serviceRegistrar.getService(CyTableFactory.class);
    table = tableFactory.createTable("Expression Matrix", "geneName", String.class, /* public = */
    true, /* mutable = */
    true);
    // first set up the columns
    for (int condNum = 0; condNum < condNames.length; condNum++) {
        String condName = condNames[condNum];
        String eStr = condName + "exp";
        String sStr = condName + "sig";
        table.createColumn(eStr, Double.class, false);
        table.createColumn(sStr, Double.class, false);
    }
    // now create the rows and populate
    for (int i = 0; i < geneNames.size(); i++) {
        String canName = geneNames.get(i);
        CyRow row = table.getRow(canName);
        for (int condNum = 0; condNum < condNames.length; condNum++) {
            String condName = condNames[condNum];
            String eStr = condName + "exp";
            String sStr = condName + "sig";
            mRNAMeasurement mm = getMeasurement(canName, condName);
            if (mm != null) {
                row.set(eStr, new Double(mm.getRatio()));
                row.set(sStr, new Double(mm.getSignificance()));
            }
            // Report on Progress to the Task Monitor.
            if (taskMonitor != null) {
                int currentCoordinate = (condNum * geneNames.size()) + i;
                int matrixSize = condNames.length * geneNames.size();
                double percent = ((double) currentCoordinate / matrixSize) * 100.0;
                taskMonitor.setProgress(percent);
            }
        }
    }
}