use of org.cytoscape.application.CyApplicationManager 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);
}
use of org.cytoscape.application.CyApplicationManager in project cytoscape-impl by cytoscape.
the class NetworkViewMediator method handleEvent.
@Override
public void handleEvent(final SessionLoadedEvent e) {
loadingSession = false;
final CyNetworkView view = serviceRegistrar.getService(CyApplicationManager.class).getCurrentNetworkView();
if (view != null) {
final CyNetworkViewManager netViewMgr = serviceRegistrar.getService(CyNetworkViewManager.class);
if (netViewMgr.getNetworkViewSet().contains(view)) {
final CyApplicationManager appMgr = serviceRegistrar.getService(CyApplicationManager.class);
final RenderingEngine<CyNetwork> currentEngine = appMgr.getCurrentRenderingEngine();
if (currentEngine == null || currentEngine.getViewModel() != view)
appMgr.setCurrentRenderingEngine(presentationMap.get(view));
}
}
invokeOnEDT(() -> {
getNetworkViewMainPanel().setCurrentNetworkView(view);
// Always show the current view in the View Mode when opening older session files (up to version 3.3)
if (!getNetworkViewMainPanel().isGridMode()) {
if (view != null) {
getNetworkViewMainPanel().showViewContainer(view);
} else {
final CyNetwork net = serviceRegistrar.getService(CyApplicationManager.class).getCurrentNetwork();
if (net != null)
getNetworkViewMainPanel().showNullViewContainer(net);
}
} else {
getNetworkViewGrid().update(getNetworkViewGrid().getThumbnailSlider().getValue());
}
});
}
use of org.cytoscape.application.CyApplicationManager in project cytoscape-impl by cytoscape.
the class SetCurrentNetworkTaskTest method testRun.
@Test
public void testRun() throws Exception {
CyApplicationManager applicationManager = mock(CyApplicationManager.class);
CyNetworkManager netmgr = mock(CyNetworkManager.class);
;
TaskMonitor tm = mock(TaskMonitor.class);
CyNetwork net = mock(CyNetwork.class);
HashSet<CyNetwork> netSet = new HashSet<CyNetwork>();
netSet.add(net);
when(netmgr.getNetworkSet()).thenReturn(netSet);
SetCurrentNetworkTask t = new SetCurrentNetworkTask(applicationManager, netmgr);
t.run(tm);
verify(applicationManager, times(1)).setCurrentNetwork(net);
}
use of org.cytoscape.application.CyApplicationManager 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));
}
use of org.cytoscape.application.CyApplicationManager 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));
}
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