Examples with CyApplicationManager org.cytoscape.application.CyApplicationManager used on opensource projects

Example 36 with CyApplicationManager

use of org.cytoscape.application.CyApplicationManager in project cytoscape-impl by cytoscape.

the class ImportTableDataTask method init.

private final void init() {
    this.name2NetworkMap = new HashMap<>();
    this.name2RootMap = new HashMap<>();
    this.source2targetColumnMap = new HashMap<>();
    this.mappedTables = new ArrayList<>();
    final CyNetworkManager netMgr = serviceRegistrar.getService(CyNetworkManager.class);
    if (netMgr.getNetworkSet().size() > 0) {
        whereImportTable = new ListSingleSelection<>(NETWORK_COLLECTION, NETWORK_SELECTION, UNASSIGNED_TABLE);
        whereImportTable.setSelectedValue(NETWORK_COLLECTION);
        networksPresent = true;
    } else {
        whereImportTable = new ListSingleSelection<>(UNASSIGNED_TABLE);
        whereImportTable.setSelectedValue(UNASSIGNED_TABLE);
    }
    if (byReader) {
        if (reader != null && reader.getTables() != null)
            newTableName = reader.getTables()[0].getTitle();
    } else
        newTableName = globalTable.getTitle();
    if (networksPresent) {
        final List<TableType> options = new ArrayList<>();
        for (TableType type : TableType.values()) options.add(type);
        dataTypeTargetForNetworkCollection = new ListSingleSelection<>(options);
        dataTypeTargetForNetworkCollection.setSelectedValue(TableType.NODE_ATTR);
        dataTypeTargetForNetworkList = new ListSingleSelection<>(options);
        dataTypeTargetForNetworkList.setSelectedValue(TableType.NODE_ATTR);
        for (CyNetwork net : netMgr.getNetworkSet()) {
            final String netName = net.getRow(net).get(CyNetwork.NAME, String.class);
            name2NetworkMap.put(netName, net);
        }
        final CyApplicationManager appMgr = serviceRegistrar.getService(CyApplicationManager.class);
        final List<String> names = new ArrayList<>();
        names.addAll(name2NetworkMap.keySet());
        sort(names);
        if (names.isEmpty()) {
            targetNetworkList = new ListMultipleSelection<>(NO_NETWORKS);
        } else {
            targetNetworkList = new ListMultipleSelection<>(names);
            final CyNetwork currNet = appMgr.getCurrentNetwork();
            if (currNet != null) {
                final String currName = currNet.getRow(currNet).get(CyNetwork.NAME, String.class);
                if (currName != null && targetNetworkList.getPossibleValues().contains(currName))
                    targetNetworkList.setSelectedValues(Collections.singletonList(currName));
            }
            final List<CyNetwork> selectedNetworks = new ArrayList<>();
            for (String netName : targetNetworkList.getSelectedValues()) {
                if (name2NetworkMap.containsKey(netName))
                    selectedNetworks.add(name2NetworkMap.get(netName));
            }
            keyColumnForMappingNetworkList = getColumns(selectedNetworks, dataTypeTargetForNetworkList.getSelectedValue(), CyRootNetwork.DEFAULT_ATTRS);
        }
        final CyRootNetworkManager rootNetMgr = serviceRegistrar.getService(CyRootNetworkManager.class);
        for (CyNetwork net : netMgr.getNetworkSet()) {
            final CyRootNetwork rootNet = rootNetMgr.getRootNetwork(net);
            if (!name2RootMap.containsValue(rootNet))
                name2RootMap.put(rootNet.getRow(rootNet).get(CyRootNetwork.NAME, String.class), rootNet);
        }
        final List<String> rootNames = new ArrayList<>();
        rootNames.addAll(name2RootMap.keySet());
        sort(rootNames);
        targetNetworkCollection = new ListSingleSelection<>(rootNames);
        if (!rootNames.isEmpty()) {
            targetNetworkCollection.setSelectedValue(rootNames.get(0));
            final CyNetwork currNet = appMgr.getCurrentNetwork();
            final CyRootNetwork currRootNet = currNet instanceof CySubNetwork ? rootNetMgr.getRootNetwork(currNet) : null;
            if (currRootNet != null) {
                final String currName = currRootNet.getRow(currRootNet).get(CyNetwork.NAME, String.class);
                if (currName != null && targetNetworkCollection.getPossibleValues().contains(currName))
                    targetNetworkCollection.setSelectedValue(currName);
            }
            keyColumnForMapping = getColumns(Collections.singletonList(name2RootMap.get(targetNetworkCollection.getSelectedValue())), dataTypeTargetForNetworkCollection.getSelectedValue(), CyRootNetwork.SHARED_ATTRS);
        }
    }
}

Example 37 with CyApplicationManager

use of org.cytoscape.application.CyApplicationManager 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 38 with CyApplicationManager

use of org.cytoscape.application.CyApplicationManager in project cytoscape-api by cytoscape.

the class SetCurrentNetworkViewEventTest method testGoodGetNetworkView.

@Test
public void testGoodGetNetworkView() {
    CyApplicationManager source = mock(CyApplicationManager.class);
    CyNetworkView n = mock(CyNetworkView.class);
    SetCurrentNetworkViewEvent e = new SetCurrentNetworkViewEvent(source, n);
    assertNotNull(e.getNetworkView());
    assertEquals(n, e.getNetworkView());
}

Example 39 with CyApplicationManager

use of org.cytoscape.application.CyApplicationManager in project cytoscape-impl by cytoscape.

the class CySessionManagerImpl method restoreNetworkViews.

private void restoreNetworkViews(final CySession sess, List<CyNetwork> selectedNetworks) {
    logger.debug("Restoring network views...");
    Set<CyNetworkView> netViews = sess.getNetworkViews();
    List<CyNetworkView> selectedViews = new ArrayList<>();
    for (CyNetworkView nv : netViews) {
        CyNetwork network = nv.getModel();
        if (selectedNetworks.contains(network)) {
            selectedViews.add(nv);
        }
    }
    Map<CyNetworkView, Map<VisualProperty<?>, Object>> viewVPMap = new HashMap<>();
    if (netViews != null) {
        final CyNetworkViewManager nvMgr = serviceRegistrar.getService(CyNetworkViewManager.class);
        for (CyNetworkView nv : netViews) {
            if (nv != null) {
                // Save the original values of these visual properties,
                // because we will have to set them again after the views are rendered
                Map<VisualProperty<?>, Object> vpMap = new HashMap<>();
                viewVPMap.put(nv, vpMap);
                vpMap.put(BasicVisualLexicon.NETWORK_HEIGHT, nv.getVisualProperty(BasicVisualLexicon.NETWORK_HEIGHT));
                vpMap.put(BasicVisualLexicon.NETWORK_WIDTH, nv.getVisualProperty(BasicVisualLexicon.NETWORK_WIDTH));
                nvMgr.addNetworkView(nv, false);
            }
        }
    }
    // Let's guarantee the network views are rendered
    final CyEventHelper eventHelper = serviceRegistrar.getService(CyEventHelper.class);
    eventHelper.flushPayloadEvents();
    // Set the saved visual properties again, because the renderer may have overwritten the original values
    for (Entry<CyNetworkView, Map<VisualProperty<?>, Object>> entry1 : viewVPMap.entrySet()) {
        CyNetworkView nv = entry1.getKey();
        for (Entry<VisualProperty<?>, Object> entry2 : entry1.getValue().entrySet()) nv.setVisualProperty(entry2.getKey(), entry2.getValue());
    }
    final CyApplicationManager appMgr = serviceRegistrar.getService(CyApplicationManager.class);
    if (!selectedViews.isEmpty())
        appMgr.setCurrentNetworkView(selectedViews.get(0));
    appMgr.setSelectedNetworkViews(selectedViews);
}

Example 40 with CyApplicationManager

use of org.cytoscape.application.CyApplicationManager in project cytoscape-impl by cytoscape.

the class CyNetworkManagerImpl method addNetwork.

@Override
public void addNetwork(final CyNetwork network, final boolean setCurrent) {
    if (network == null)
        throw new NullPointerException("Network is null");
    synchronized (lock) {
        logger.debug("Adding new Network Model: Model ID = " + network.getSUID());
        // Make sure the network has a name
        final CyRow row = network.getRow(network);
        final String name = row.get(CyNetwork.NAME, String.class);
        final String sharedName = row.get(CyRootNetwork.SHARED_NAME, String.class);
        if (name != null && !name.trim().isEmpty() && (sharedName == null || sharedName.trim().isEmpty())) {
            row.set(CyRootNetwork.SHARED_NAME, name);
        } else if (sharedName != null && !sharedName.trim().isEmpty() && (name == null || name.trim().isEmpty())) {
            row.set(CyNetwork.NAME, sharedName);
        } else if ((sharedName == null || sharedName.trim().isEmpty()) && (name == null || name.trim().isEmpty())) {
            final CyNetworkNaming namingUtil = serviceRegistrar.getService(CyNetworkNaming.class);
            final String newName = namingUtil.getSuggestedNetworkTitle("Network");
            row.set(CyNetwork.NAME, newName);
            row.set(CyRootNetwork.SHARED_NAME, newName);
        }
        // Add the new network to the internal map
        networkMap.put(network.getSUID(), network);
    }
    final CyEventHelper cyEventHelper = serviceRegistrar.getService(CyEventHelper.class);
    cyEventHelper.fireEvent(new NetworkAddedEvent(CyNetworkManagerImpl.this, network));
    if (setCurrent) {
        final CyApplicationManager applicationManager = serviceRegistrar.getService(CyApplicationManager.class);
        if (// It may be null when running unit tests
        applicationManager != null)
            applicationManager.setCurrentNetwork(network);
    }
}