Examples with CyRootNetworkManager org.cytoscape.model.subnetwork.CyRootNetworkManager used on opensource projects

Example 1 with CyRootNetworkManager

use of org.cytoscape.model.subnetwork.CyRootNetworkManager 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 CyRootNetworkManager

use of org.cytoscape.model.subnetwork.CyRootNetworkManager in project cytoscape-impl by cytoscape.

the class AbstractSessionReader method cleanUp.

/**
 * Use this methods to dispose temporary resources.
 * This method must always be invoked, even if this task is cancelled.
 */
protected void cleanUp(TaskMonitor tm) {
    try {
        ((ReusableInputStream) sourceInputStream).reallyClose();
    } catch (Exception e) {
        logger.error("Error closing source input stream.", e);
    }
    if (cancelled) {
        // Destroy groups
        final Set<CyGroup> groups = groupUtil.getGroups(cache.getNetworks());
        groupUtil.destroyGroups(groups);
        // Dispose CyNetworkViews and CyNetworks
        for (final CyNetworkView view : networkViews) view.dispose();
        final CyRootNetworkManager rootNetworkManager = serviceRegistrar.getService(CyRootNetworkManager.class);
        final Set<CyRootNetwork> rootNetworks = new HashSet<>();
        // such as group networks.
        for (final CyNetwork net : cache.getNetworks()) {
            net.dispose();
            rootNetworks.add(rootNetworkManager.getRootNetwork(net));
        }
        for (final CyRootNetwork rootNet : rootNetworks) rootNet.dispose();
        networkViews.clear();
        networks.clear();
    }
    cache.dispose();
    SessionUtil.setReadingSessionFile(false);
}

Example 3 with CyRootNetworkManager

use of org.cytoscape.model.subnetwork.CyRootNetworkManager in project cytoscape-impl by cytoscape.

the class Cy2SessionReaderImpl method extractNetworks.

private void extractNetworks(TaskMonitor tm) throws JAXBException, IOException {
    // Extract the XGMML files
    Map<String, Network> netMap = new HashMap<>();
    for (Network curNet : cysession.getNetworkTree().getNetwork()) {
        netMap.put(curNet.getId(), curNet);
    }
    final CyRootNetworkManager rootNetworkManager = serviceRegistrar.getService(CyRootNetworkManager.class);
    walkNetworkTree(netMap.get(NETWORK_ROOT), null, netMap, tm, rootNetworkManager);
}

Example 4 with CyRootNetworkManager

use of org.cytoscape.model.subnetwork.CyRootNetworkManager in project cytoscape-impl by cytoscape.

the class CloneNetworkTaskFactoryTest method testObserver.

@Test
public void testObserver() throws Exception {
    NetworkViewTestSupport viewSupport = new NetworkViewTestSupport();
    NetworkTestSupport networkSupport = new NetworkTestSupport();
    CyNetworkManager networkMgr = Mockito.mock(CyNetworkManager.class);
    CyNetworkViewManager networkViewMgr = Mockito.mock(CyNetworkViewManager.class);
    VisualMappingManager vmm = Mockito.mock(VisualMappingManager.class);
    CyNetworkFactory netFactory = networkSupport.getNetworkFactory();
    CyNetworkViewFactory netViewFactory = viewSupport.getNetworkViewFactory();
    CyNetworkNaming naming = Mockito.mock(CyNetworkNaming.class);
    CyApplicationManager appMgr = Mockito.mock(CyApplicationManager.class);
    CyNetworkTableManager netTableMgr = Mockito.mock(CyNetworkTableManager.class);
    CyRootNetworkManager rootNetMgr = new CyRootNetworkManagerImpl();
    CyGroupManager groupMgr = Mockito.mock(CyGroupManager.class);
    CyGroupFactory groupFactory = Mockito.mock(CyGroupFactory.class);
    RenderingEngineManager renderingEngineMgr = Mockito.mock(RenderingEngineManager.class);
    CyNetworkViewFactory nullNetworkViewFactory = new NullCyNetworkViewFactory();
    CyServiceRegistrar serviceRegistrar = Mockito.mock(CyServiceRegistrar.class);
    CloneNetworkTaskFactoryImpl factory = new CloneNetworkTaskFactoryImpl(networkMgr, networkViewMgr, vmm, netFactory, netViewFactory, naming, appMgr, netTableMgr, rootNetMgr, groupMgr, groupFactory, renderingEngineMgr, nullNetworkViewFactory, serviceRegistrar);
    CyNetwork network = netFactory.createNetwork();
    TaskObserver observer = Mockito.mock(TaskObserver.class);
    TaskIterator iterator = factory.createTaskIterator(network);
    TaskMonitor taskMonitor = Mockito.mock(TaskMonitor.class);
    while (iterator.hasNext()) {
        Task t = iterator.next();
        t.run(taskMonitor);
        if (t instanceof ObservableTask)
            observer.taskFinished((ObservableTask) t);
    }
    Mockito.verify(observer, Mockito.times(1)).taskFinished(Mockito.any(ObservableTask.class));
}

Example 5 with CyRootNetworkManager

use of org.cytoscape.model.subnetwork.CyRootNetworkManager in project cytoscape-impl by cytoscape.

the class NewNetworkSelectedNodesEdgesTaskFactoryTest 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);
    NewNetworkSelectedNodesEdgesTaskFactoryImpl factory = new NewNetworkSelectedNodesEdgesTaskFactoryImpl(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));
}