Java CyNetworkFactory类代码示例

import org.cytoscape.model.CyNetworkFactory; //导入依赖的package包/类
@Before
public void setUp(CyNetworkFactory networkFactory, CyNetworkManager networkManager) {
	networkView = NetworkTestUtil.createNetwork(networkFactory, networkManager);
	CyNetwork network = networkView.getModel();
	
	nodes = new HashMap<>();
	nodes.put("n1", createNode(network, "n1", "cluster_1"));
	nodes.put("n2", createNode(network, "n2", "cluster_1"));
	nodes.put("n3", createNode(network, "n3", "cluster_1"));
	
	nodes.put("n4", createNode(network, "n4", "cluster_2"));
	nodes.put("n5", createNode(network, "n5", "cluster_2"));
	
	nodes.put("n6", createNode(network, "n6", "cluster_3"));
	
	nodes.put("n7", createNode(network, "n7", null));
	nodes.put("n8", createNode(network, "n8", null));
	nodes.put("n9", createNode(network, "n9", null));
}
 

import org.cytoscape.model.CyNetworkFactory; //导入依赖的package包/类
@Before
public void setUp(CyNetworkFactory networkFactory, CyNetworkManager networkManager) {
	networkView = NetworkTestUtil.createNetwork(networkFactory, networkManager);
	CyNetwork network = networkView.getModel();
	
	nodes = new HashMap<>();
	nodes.put("n1", createNode(network, "n1", "cluster_1"));
	nodes.put("n2", createNode(network, "n2", "cluster_1"));
	nodes.put("n3", createNode(network, "n3", "cluster_1"));
	
	nodes.put("n4", createNode(network, "n4", "cluster_2"));
	nodes.put("n5", createNode(network, "n5", "cluster_2"));
	
	nodes.put("n6", createNode(network, "n6", "cluster_3"));
	
	nodes.put("n7", createNode(network, "n7", "cluster_4"));
	nodes.put("n8", createNode(network, "n8", "cluster_5"));
	nodes.put("n9", createNode(network, "n9", "cluster_6"));
}
 

import org.cytoscape.model.CyNetworkFactory; //导入依赖的package包/类
@Before
public void setUp(CyNetworkFactory networkFactory, CyNetworkManager networkManager) {
	networkView = NetworkTestUtil.createNetwork(networkFactory, networkManager);
	CyNetwork network = networkView.getModel();
	
	createNode(network, "n1", "cluster_1");
	createNode(network, "n2", "cluster_1");
	createNode(network, "n3", "cluster_1");
	
	createNode(network, "n4", "cluster_2");
	createNode(network, "n5", "cluster_2");
	
	createNode(network, "n6", "cluster_3");
	
	createNode(network, "n7", "cluster_4");
	createNode(network, "n8", "cluster_5");
	createNode(network, "n9", "cluster_6");
}
 

import org.cytoscape.model.CyNetworkFactory; //导入依赖的package包/类
@Override
protected void configureTest() {
	TableTestSupport tableTestSupport = new TableTestSupport();
	NetworkViewTestSupport networkViewTestSupport = new NetworkViewTestSupport();
	
	bind(CyNetworkFactory.class).toInstance(networkViewTestSupport.getNetworkFactory());
	bind(CyNetworkTableManager.class).toInstance(networkViewTestSupport.getNetworkTableManager());
	bind(CyNetworkManager.class).toInstance(networkViewTestSupport.getNetworkManager());
	bind(CyTableFactory.class).toInstance(tableTestSupport.getTableFactory());
	bind(CyNetworkViewFactory.class).toInstance(networkViewTestSupport.getNetworkViewFactory());
	
	TypeLiteral<TaskManager<?,?>> taskManager = new TypeLiteral<TaskManager<?,?>>(){};
	bind(taskManager).annotatedWith(Names.named("sync")).to(SerialTestTaskManager.class);
	bind(taskManager).annotatedWith(Names.named("dialog")).to(SerialTestTaskManager.class);
	bind(LabelMakerManager.class).toInstance(mock(LabelMakerManager.class));
	bind(IconManager.class).toInstance(mock(IconManager.class));
	// Bind all AssistedInjection factories
	install(ApplicationModule.createFactoryModule());
}
 

import org.cytoscape.model.CyNetworkFactory; //导入依赖的package包/类
public AdjNetworkReaderFactory(final CyFileFilter adjFileFilter, final CyApplicationManager appMgr,
        final CyNetworkViewFactory cyNetworkViewFactory, final CyNetworkFactory cyNetworkFactory,
        final CyNetworkManager cyNetworkManager, final CyNetworkViewManager cyNetworkViewManager,
        final CyRootNetworkManager cyRootNetworkManager, final CyTableFactory cyTableFactory,
        final CyTableManager cyTableManager, final VisualMappingManager visMgr,
        final CyEventHelper eventHelper) {
    this.adjFileFilter = adjFileFilter;
    this.appMgr = appMgr;
    this.cyNetworkFactory = cyNetworkFactory;
    this.cyNetworkViewFactory = cyNetworkViewFactory;
    this.cyNetworkManager = cyNetworkManager;
    this.cyNetworkViewManager = cyNetworkViewManager;
    this.cyRootNetworkManager = cyRootNetworkManager;
    this.cyTableFactory = cyTableFactory;
    this.cyTableManager = cyTableManager;
    this.visMgr = visMgr;
    this.eventHelper = eventHelper;
}
 

import org.cytoscape.model.CyNetworkFactory; //导入依赖的package包/类
public AdjNetworkReader(InputStream inputStream, String inputName,
        CyApplicationManager appMgr, CyNetworkViewFactory networkViewFactory,
        CyNetworkFactory networkFactory, CyNetworkManager networkMgr,
        CyNetworkViewManager networkViewMgr, CyRootNetworkManager rootNetworkMgr, 
        CyTableFactory tableFactory, CyTableManager tableMgr, 
        VisualMappingManager visMgr, CyEventHelper eventHelper) {
    super(inputStream, networkViewFactory, networkFactory, networkMgr, rootNetworkMgr);
    this.inputStream = inputStream;
    this.inputName = inputName;
    this.appMgr = appMgr;
    this.networkMgr = networkMgr;
    this.networkViewMgr = networkViewMgr;
    this.tableFactory = tableFactory;
    this.tableMgr = tableMgr;
    this.visMgr = visMgr;
    this.eventHelper = eventHelper;
    this.networkFactory = networkFactory;
    this.networkViewFactory = networkViewFactory;
}
 

import org.cytoscape.model.CyNetworkFactory; //导入依赖的package包/类
@Override
public void start(BundleContext context) throws Exception {
	CyApplicationManager manager = getService(context, CyApplicationManager.class);
	CySwingAppAdapter adapter = getService(context, CySwingAppAdapter.class);
	CySwingApplication desktopApp = adapter.getCySwingApplication();
       OpenBrowser openBrowser = getService(context,OpenBrowser.class);
       CyEventHelper eventHelper = getService(context, CyEventHelper.class);
       CyNetworkFactory networkFactory = getService(context, CyNetworkFactory.class);
       CyNetworkManager networkManager = getService(context, CyNetworkManager.class);
       CyNetworkViewFactory networkViewFactory = getService(context, CyNetworkViewFactory.class);
       CyNetworkViewManager networkViewManager = getService(context, CyNetworkViewManager.class);
       VisualMappingManager visualMappingManager = getService(context,VisualMappingManager.class);

	Properties properties = new Properties();

	SlimPanel slimPanel = new SlimPanel(manager, adapter, openBrowser, eventHelper, networkFactory, networkManager,
               networkViewFactory, networkViewManager, visualMappingManager);
	registerService(context, slimPanel, CytoPanelComponent.class, properties);

	SlimscapePluginAction slimscapePluginAction = new SlimscapePluginAction(manager, adapter, desktopApp, slimPanel);
	registerService(context, slimscapePluginAction, CyAction.class, properties);
}
 

import org.cytoscape.model.CyNetworkFactory; //导入依赖的package包/类
public JGFNetworkReaderFactory(final CyFileFilter cyFileFilter, final CyApplicationManager appMgr,
        final CyNetworkViewFactory cyNetworkViewFactory, final CyNetworkFactory cyNetworkFactory,
        final CyNetworkManager cyNetworkManager, final CyNetworkViewManager cyNetworkViewManager,
        final CyRootNetworkManager cyRootNetworkManager, final CyTableFactory cyTableFactory,
        final CyTableManager cyTableManager, final VisualMappingManager visMgr,
        final CyEventHelper eventHelper, final GraphReader graphReader,
        final GraphConverter belGraphConverter, final BELEvidenceMapper belEvidenceMapper) {

    this.cyFileFilter = cyFileFilter;
    this.appMgr = appMgr;
    this.cyNetworkFactory = cyNetworkFactory;
    this.cyNetworkViewFactory = cyNetworkViewFactory;
    this.cyNetworkManager = cyNetworkManager;
    this.cyNetworkViewManager = cyNetworkViewManager;
    this.cyRootNetworkManager = cyRootNetworkManager;
    this.cyTableFactory = cyTableFactory;
    this.cyTableManager = cyTableManager;
    this.visMgr = visMgr;
    this.eventHelper = eventHelper;
    this.graphReader = graphReader;
    this.belGraphConverter = belGraphConverter;
    this.belEvidenceMapper = belEvidenceMapper;
}
 

import org.cytoscape.model.CyNetworkFactory; //导入依赖的package包/类
@Override
public void start(BundleContext context) throws Exception {
	
	CyApplicationManager cyApplicationManager = getService(context, CyApplicationManager.class);
	CySwingApplication cySwingApplication = getService(context, CySwingApplication.class);
	CyNetworkFactory cyNetworkFactory = getService(context, CyNetworkFactory.class);
	CyNetworkManager cyNetMgr = getService(context,CyNetworkManager.class);
	CyTableFactory tableFactory = getService(context, CyTableFactory.class);
	CyNetworkViewManager cyNetViewMgr = getService(context, CyNetworkViewManager.class);
	DialogTaskManager diagTaskManager = getService(context, DialogTaskManager.class);
	CyNetworkViewFactory cyNetworkViewFactory = getService(context, CyNetworkViewFactory.class);
	CyLayoutAlgorithmManager cyLayoutAlgorithmMgr = getService(context,CyLayoutAlgorithmManager.class);
	VisualMappingManager visualMappingMgr = getService(context,VisualMappingManager.class);
	
	plugin = new Plugin(cyApplicationManager,cySwingApplication,cyNetworkFactory,tableFactory,cyNetMgr,cyNetViewMgr,diagTaskManager,cyNetworkViewFactory,cyLayoutAlgorithmMgr,visualMappingMgr);
			
	ConnectInstanceMenuAction connectAction = new ConnectInstanceMenuAction(cyApplicationManager,plugin);	
	SyncUpMenuAction syncUpAction = new SyncUpMenuAction(cyApplicationManager, plugin);
	SyncDownMenuAction syncDownAction = new SyncDownMenuAction(cyApplicationManager, plugin);
	
	registerAllServices(context, connectAction, new Properties());
	registerAllServices(context, syncUpAction, new Properties());
	registerAllServices(context, syncDownAction, new Properties());
	
}
 

import org.cytoscape.model.CyNetworkFactory; //导入依赖的package包/类
public SyncDownTaskFactory(CyNetworkManager cyNetworkMgr,
		boolean mergeInCurrent, CyNetworkFactory cyNetworkFactory,
		String instanceLocation, String cypherURL,
		String auth,
		CyNetworkViewManager cyNetworkViewMgr,
		CyNetworkViewFactory cyNetworkViewFactory,
		CyLayoutAlgorithmManager cyLayoutAlgorithmMgr,
		VisualMappingManager visualMappingMgr) {
	super();
	this.cyNetworkMgr = cyNetworkMgr;
	this.mergeInCurrent = mergeInCurrent;
	this.cyNetworkFactory = cyNetworkFactory;
	this.instanceLocation = instanceLocation;
	this.cypherURL = cypherURL;
	this.auth = auth;
	this.cyNetworkViewMgr = cyNetworkViewMgr;
	this.cyNetworkViewFactory = cyNetworkViewFactory;
	this.cyLayoutAlgorithmMgr = cyLayoutAlgorithmMgr;
	this.visualMappingMgr = visualMappingMgr;
}
 

import org.cytoscape.model.CyNetworkFactory; //导入依赖的package包/类
public SyncDownTask(boolean mergeInCurrent, String cypherURL,
		String instanceLocation, 
		String auth,
		CyNetworkFactory cyNetworkFactory,
		CyNetworkManager cyNetworkMgr,
		CyNetworkViewManager cyNetworkViewMgr,
		CyNetworkViewFactory cyNetworkViewFactory,
		CyLayoutAlgorithmManager cyLayoutAlgorithmMgr,
		VisualMappingManager visualMappingMgr) {
	super();
	this.mergeInCurrent = mergeInCurrent;
	this.cypherURL = cypherURL;
	this.instanceLocation = instanceLocation;
	this.auth = auth;
	this.cyNetworkFactory = cyNetworkFactory;
	this.cyNetworkMgr = cyNetworkMgr;
	this.cyNetworkViewMgr = cyNetworkViewMgr;
	this.cyNetworkViewFactory = cyNetworkViewFactory;
	this.cyLayoutAlgorithmMgr = cyLayoutAlgorithmMgr;
	this.visualMappingMgr = visualMappingMgr;
}
 

import org.cytoscape.model.CyNetworkFactory; //导入依赖的package包/类
@Override
protected void configure() {
	// Bind cytoscape OSGi services
	bindService(CyServiceRegistrar.class);
	bindService(CyApplicationManager.class);
	bindService(CySwingApplication.class);
	bindService(CyNetworkManager.class);
	bindService(CyNetworkViewFactory.class);
	bindService(CyNetworkViewManager.class);
	bindService(CyNetworkFactory.class);
	bindService(IconManager.class);
	bindService(CyLayoutAlgorithmManager.class);
	bindService(CyGroupManager.class);
	bindService(CyGroupFactory.class);
	bindService(CyGroupAggregationManager.class);
	bindService(CyGroupSettingsManager.class);
	bindService(AvailableCommands.class);
	bindService(CommandExecutorTaskFactory.class);
	bindService(CySessionManager.class);
	bindService(CyEventHelper.class);
	bindService(OpenBrowser.class);
	bindService(VisualMappingManager.class);
	bindService(CyNetworkTableManager.class);
	bindService(CyTableManager.class);
	bindService(CyTableFactory.class);
	bindService(FileUtil.class);
	bindService(CyRootNetworkManager.class);
	
	bindService(DialogTaskManager.class);
	TypeLiteral<SynchronousTaskManager<?>> synchronousManager = new TypeLiteral<SynchronousTaskManager<?>>(){};
	bind(synchronousManager).toProvider(service(synchronousManager).single());
	
	bindService(AnnotationManager.class);
	TypeLiteral<AnnotationFactory<ShapeAnnotation>> shapeFactory = new TypeLiteral<AnnotationFactory<ShapeAnnotation>>(){};
	bind(shapeFactory).toProvider(service(shapeFactory).filter(ldap("(type=ShapeAnnotation.class)")).single());
	TypeLiteral<AnnotationFactory<TextAnnotation>> textFactory = new TypeLiteral<AnnotationFactory<TextAnnotation>>(){};
	bind(textFactory).toProvider(service(textFactory).filter(ldap("(type=TextAnnotation.class)")).single());
}
 

import org.cytoscape.model.CyNetworkFactory; //导入依赖的package包/类
@Override
protected void configureTest() {
	NetworkTestSupport networkTestSupport = new NetworkTestSupport();
	TableTestSupport tableTestSupport = new TableTestSupport();
	bind(CyNetworkFactory.class).toInstance(networkTestSupport.getNetworkFactory());
	bind(CyNetworkTableManager.class).toInstance(networkTestSupport.getNetworkTableManager());
	bind(CyNetworkManager.class).toInstance(networkTestSupport.getNetworkManager());
	bind(CyTableFactory.class).toInstance(tableTestSupport.getTableFactory());
	
	bind(EventBus.class).toInstance(new EventBus());
	
	TypeLiteral<LabelMakerFactory<?>> labelMakerFactoryType = new TypeLiteral<LabelMakerFactory<?>>() {};
	Multibinder<LabelMakerFactory<?>> labelFactoryBinder = Multibinder.newSetBinder(binder(), labelMakerFactoryType);
	labelFactoryBinder.addBinding().toInstance(mock(LabelMakerFactory.class));
}
 

import org.cytoscape.model.CyNetworkFactory; //导入依赖的package包/类
public static CyNetworkView createNetwork(CyNetworkFactory networkFactory, CyNetworkManager networkManager) {
	CyNetworkView networkView = mock(CyNetworkView.class);
	CyNetwork network = networkFactory.createNetwork();
	networkManager.addNetwork(network);
	when(networkView.getModel()).thenReturn(network);
	network.getDefaultNodeTable().createColumn(CLUSTER_COL, String.class, false);
	return networkView;
}
 

import org.cytoscape.model.CyNetworkFactory; //导入依赖的package包/类
@Before
public void setup(CyApplicationManager appManager, ModelManager modelManager, AnnotationRenderer renderer,
		RemoveAllAnnotationsTask.Factory removeTaskFactory, DrawClusterTask.Factory drawTaskFactory,
		EraseClusterTask.Factory eraseTaskFactory, SelectClusterTask.Factory selectTaskFactory) {
	
	// set up stubbing
	CyNetworkView networkView = mock(CyNetworkView.class);
	when(appManager.getCurrentNetworkView()).thenReturn(networkView);
	
	when(drawTaskFactory.create(any())).thenReturn(mock(DrawClusterTask.class));
	when(removeTaskFactory.create(any())).thenReturn(mock(RemoveAllAnnotationsTask.class));
	when(eraseTaskFactory.create(any())).thenReturn(mock(EraseClusterTask.class));
	when(selectTaskFactory.create(any(), anyBoolean())).thenReturn(mock(SelectClusterTask.class));
	
	NetworkTestSupport networkTestSupport = new NetworkTestSupport();
	CyNetworkFactory networkFactory = networkTestSupport.getNetworkFactory();
	CyNetworkManager networkManager = networkTestSupport.getNetworkManager();
	
	CyNetwork network = networkFactory.createNetwork();
	networkManager.addNetwork(network);
	when(networkView.getModel()).thenReturn(network);

	// create model fixture
	NetworkViewSet nvs = modelManager.getNetworkViewSet(networkView);
	AnnotationSet as = nvs.createAnnotationSet("as1", "lc1");
	as.createCluster(createNodes(network,10), "cluster1", false);
	as.createCluster(createNodes(network,10), "cluster2", false);
	as.createCluster(createNodes(network,10), "cluster3", false);
	nvs.select(as);
	
	// Reset invocation counts from fixture initialization.
	// Unfortunately reset() also resets the stubbing so we need to redo it.
	reset(removeTaskFactory, drawTaskFactory, eraseTaskFactory, selectTaskFactory);
	when(drawTaskFactory.create(any())).thenReturn(mock(DrawClusterTask.class));
	when(removeTaskFactory.create(any())).thenReturn(mock(RemoveAllAnnotationsTask.class));
	when(eraseTaskFactory.create(any())).thenReturn(mock(EraseClusterTask.class));
	when(selectTaskFactory.create(any(), anyBoolean())).thenReturn(mock(SelectClusterTask.class));
}