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

Example 66 with CyApplicationManager

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

the class GenerateNetworkViewsTask method setCurrentNetworkAndViewTask.

public void setCurrentNetworkAndViewTask(final CyNetwork network) {
    final CyNetworkViewManager netViewManager = serviceRegistrar.getService(CyNetworkViewManager.class);
    final List<CyNetworkView> views = new ArrayList<>(netViewManager.getNetworkViews(network));
    final CyApplicationManager applicationManager = serviceRegistrar.getService(CyApplicationManager.class);
    boolean currentViewSet = false;
    for (CyNetworkView v : views) {
        if (v.getModel().equals(network)) {
            applicationManager.setCurrentNetworkView(v);
            currentViewSet = true;
            break;
        }
    }
    if (!currentViewSet)
        applicationManager.setCurrentNetwork(network);
}

Example 67 with CyApplicationManager

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

the class LoadMultipleNetworksTask method init.

private void init() {
    // otherwise let the reader's tunables handle it.
    if (readers != null && readers.size() > 1) {
        // Initialize column list
        if (rootNetwork != null)
            setTargetColumnList(getTargetColumns(rootNetwork));
        else
            setTargetColumnList(new ListSingleSelection<>());
        // Initialize renderer list
        final List<NetworkViewRenderer> renderers = new ArrayList<>();
        NetworkViewRenderer defViewRenderer = null;
        final CyApplicationManager applicationManager = serviceRegistrar.getService(CyApplicationManager.class);
        final Set<NetworkViewRenderer> rendererSet = applicationManager.getNetworkViewRendererSet();
        // so the combo-box does not appear to the user, since there is nothing to select anyway.
        if (rendererSet.size() > 1) {
            renderers.addAll(rendererSet);
            Collections.sort(renderers, new Comparator<NetworkViewRenderer>() {

                @Override
                public int compare(NetworkViewRenderer r1, NetworkViewRenderer r2) {
                    return r1.toString().compareToIgnoreCase(r2.toString());
                }
            });
        }
        defViewRenderer = applicationManager.getDefaultNetworkViewRenderer();
        rendererList = new ListSingleSelection<>(renderers);
        if (defViewRenderer != null && renderers.contains(defViewRenderer))
            rendererList.setSelectedValue(defViewRenderer);
    }
}

Example 68 with CyApplicationManager

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

the class ExportSelectedNetworkTaskFactoryImpl method createTaskIterator.

@Override
public TaskIterator createTaskIterator(File file) {
    final CyApplicationManager applicationManager = serviceRegistrar.getService(CyApplicationManager.class);
    CyNetworkView view = applicationManager.getCurrentNetworkView();
    if (view != null)
        return getExportNetworkViewTaskFactory().createTaskIterator(view, file);
    CyNetwork network = applicationManager.getCurrentNetwork();
    if (network != null)
        return getExportNetworkTaskFactory().createTaskIterator(network, file);
    return null;
}

Example 69 with CyApplicationManager

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

the class OpenSessionCommandTask method changeCurrentSession.

private void changeCurrentSession(CySessionManager sessionManager, TaskMonitor tm) throws Exception {
    final CySession newSession = reader.getSession();
    if (newSession == null)
        throw new NullPointerException("Session could not be read for file: " + file);
    String fileName = file != null ? file.getAbsolutePath() : new URI(url).getPath().replace("/", "");
    sessionManager.setCurrentSession(newSession, fileName);
    // Set Current network: this is necessary to update GUI
    final CyApplicationManager appManager = serviceRegistrar.getService(CyApplicationManager.class);
    final RenderingEngine<CyNetwork> currentEngine = appManager.getCurrentRenderingEngine();
    if (currentEngine != null)
        appManager.setCurrentRenderingEngine(currentEngine);
    tm.setProgress(1.0);
    tm.setStatusMessage("Session file " + fileName + " successfully loaded.");
    // Add this session file URL as the most recent file
    if (file != null)
        serviceRegistrar.getService(RecentlyOpenedTracker.class).add(file.toURI().toURL());
}

Example 70 with CyApplicationManager

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

the class NewNetworkSelectedNodesOnlyTaskFactoryTest method testObserver.

@Test
public void testObserver() throws Exception {
    NetworkViewTestSupport viewSupport = new NetworkViewTestSupport();
    NetworkTestSupport networkSupport = new NetworkTestSupport();
    CyNetworkFactory networkFactory = networkSupport.getNetworkFactory();
    UndoSupport undoSupport = mock(UndoSupport.class);
    CyRootNetworkManager crnf = new CyRootNetworkManagerImpl();
    CyNetworkViewFactory cnvf = viewSupport.getNetworkViewFactory();
    CyNetworkManager netmgr = mock(CyNetworkManager.class);
    CyNetworkViewManager networkViewManager = mock(CyNetworkViewManager.class);
    CyNetworkNaming naming = mock(CyNetworkNaming.class);
    VisualMappingManager vmm = mock(VisualMappingManager.class);
    CyApplicationManager appManager = mock(CyApplicationManager.class);
    CyEventHelper eventHelper = mock(CyEventHelper.class);
    CyGroupManager groupMgr = mock(CyGroupManager.class);
    RenderingEngineManager renderingEngineMgr = mock(RenderingEngineManager.class);
    CyLayoutAlgorithm defLayout = mock(CyLayoutAlgorithm.class);
    CyLayoutAlgorithmManager layoutMgr = mock(CyLayoutAlgorithmManager.class);
    when(layoutMgr.getDefaultLayout()).thenReturn(defLayout);
    CyServiceRegistrar serviceRegistrar = mock(CyServiceRegistrar.class);
    when(serviceRegistrar.getService(CyLayoutAlgorithmManager.class)).thenReturn(layoutMgr);
    NewNetworkSelectedNodesOnlyTaskFactoryImpl factory = new NewNetworkSelectedNodesOnlyTaskFactoryImpl(undoSupport, crnf, cnvf, netmgr, networkViewManager, naming, vmm, appManager, eventHelper, groupMgr, renderingEngineMgr, serviceRegistrar);
    CyNetwork network = networkFactory.createNetwork();
    CyNode node = network.addNode();
    network.getRow(node).set(CyNetwork.SELECTED, true);
    TaskObserver observer = mock(TaskObserver.class);
    TaskMonitor taskMonitor = mock(TaskMonitor.class);
    TaskIterator iterator = factory.createTaskIterator(network);
    while (iterator.hasNext()) {
        Task t = iterator.next();
        t.run(taskMonitor);
        if (t instanceof ObservableTask)
            observer.taskFinished((ObservableTask) t);
    }
    verify(observer, times(1)).taskFinished(any(ObservableTask.class));
}