Java CyNetworkViewManager类代码示例

import org.cytoscape.view.model.CyNetworkViewManager; //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.view.model.CyNetworkViewManager; //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.view.model.CyNetworkViewManager; //导入依赖的package包/类
CyNetwork createOrGetNetwork()
{
	if (myNet == null)
	{
		myNet = adapter.getCyNetworkFactory().createNetwork();
		myNet.getRow(myNet).set(CyNetwork.NAME, cyNetworkNaming.getSuggestedNetworkTitle("General SPARQL"));
		adapter.getCyNetworkManager().addNetwork(myNet);
		createNodeAttributeIfNotExists("id");
		
		myView = null;
	}
	
	// create a network view if necessary (regardless of whether the network was just created
	if (myView == null) 
	{
		CyNetworkViewManager cyNetworkViewManager = adapter.getCyNetworkViewManager(); 
		myView = adapter.getCyNetworkViewFactory().createNetworkView(myNet);
		cyNetworkViewManager.addNetworkView(myView);
	}
	return myNet;
}
 

import org.cytoscape.view.model.CyNetworkViewManager; //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.view.model.CyNetworkViewManager; //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.view.model.CyNetworkViewManager; //导入依赖的package包/类
public JGFNetworkReader(InputStream inputStream, String inputName,
        GraphReader graphReader, GraphConverter belGraphConverter,
        BELEvidenceMapper belEvidenceMapper, 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);

    if (inputStream == null) throw new NullPointerException("inputStream cannot be null");
    if (inputName == null) throw new NullPointerException("inputName cannot be null");
    if (appMgr == null) throw new NullPointerException("appMgr cannot be null");
    if (networkMgr == null) throw new NullPointerException("networkMgr cannot be null");
    this.inputStream = inputStream;
    this.inputName = inputName;
    this.graphReader = graphReader;
    this.belGraphConverter = belGraphConverter;
    this.belEvidenceMapper = belEvidenceMapper;
    this.appMgr = appMgr;
    this.networkMgr = networkMgr;
    this.networkViewMgr = networkViewMgr;
    this.tableFactory = tableFactory;
    this.tableMgr = tableMgr;
    this.visMgr = visMgr;
    this.eventHelper = eventHelper;
}
 

import org.cytoscape.view.model.CyNetworkViewManager; //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.view.model.CyNetworkViewManager; //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.view.model.CyNetworkViewManager; //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.view.model.CyNetworkViewManager; //导入依赖的package包/类
public SafeAction(Map<String, String> properties,
                  CyApplicationManager applicationManager,
                  CyNetworkViewManager networkViewManager,
                  SafeController importController) {
    super(properties, applicationManager, networkViewManager);
    this.importController = importController;
}
 

import org.cytoscape.view.model.CyNetworkViewManager; //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.view.model.CyNetworkViewManager; //导入依赖的package包/类
public CyServices(CySwingApplication cySwingApplication,
		TaskManager taskManager, OpenBrowser openBrowser,
		CyNetworkManager networkManager,
		CyApplicationManager applicationManager,
		CyNetworkViewManager networkViewManager,
		CyNetworkReaderManager networkViewReaderManager,
		CyNetworkNaming naming, CyNetworkFactory networkFactory,
		CyLayoutAlgorithmManager layoutManager, UndoSupport undoSupport,
		VisualMappingManager mappingManager,
		CyProperty<Properties> cyProperty,
		CyNetworkViewFactory networkViewFactory,
		CyRootNetworkManager rootNetworkManager ) 
{
	this.cySwingApplication = cySwingApplication;
	this.taskManager = taskManager;
	this.openBrowser = openBrowser;
	this.networkManager = networkManager;
	this.applicationManager = applicationManager;
	this.networkViewManager = networkViewManager;
	this.networkViewReaderManager = networkViewReaderManager;
	this.naming = naming;
	this.networkFactory = networkFactory;
	this.layoutManager = layoutManager;
	this.undoSupport = undoSupport;
	this.mappingManager = mappingManager;
	this.cyProperty = cyProperty;
	this.networkViewFactory = networkViewFactory;
	this.rootNetworkManager = rootNetworkManager;
}
 

import org.cytoscape.view.model.CyNetworkViewManager; //导入依赖的package包/类
/**
 * @desc - Adds nodes to the protein network from the information returned by the Slim* run.
 * @param uniprotIDs - list of all Uniprot IDs input to the returned run.
 * @param nodeIds - map linking all selected Uniprot IDs to their CyNodes, for easy access to the network.
 * @param newNetwork - CyNetwork of the network being altered.
 * @param networkViewManager - NetworkViewManager for the network being altered. Initialised in CyActivator.
 * @param manager - CyApplicationManager for the network being altered. Initialised in CyActivator.
 */
public void addNodes (List<String> uniprotIDs, Map<String, CyNode> nodeIds, CyNetwork newNetwork,
                      CyNetworkViewManager networkViewManager, CyApplicationManager manager) {

    // Add network view
    final Collection<CyNetworkView> views = networkViewManager.getNetworkViews(newNetwork);
    CyNetworkView myView = null;
    if(views.size() != 0) {
        myView = views.iterator().next();
    }

    if (myView == null) {
        // create a new view for my network
        myView = networkViewFactory.createNetworkView(newNetwork);
        networkViewManager.addNetworkView(myView);
    } else {
        System.out.println("networkView already existed.");
    }

    CyNetworkView networkView =  manager.getCurrentNetworkView();
    for (Object o : nodeIds.entrySet()) {
        Map.Entry pairs = (Map.Entry) o;
        CyNode node = (CyNode) pairs.getValue();
        View<CyNode> nodeView = networkView.getNodeView(node);
        nodeView.setLockedValue(BasicVisualLexicon.NODE_SHAPE, NodeShapeVisualProperty.ELLIPSE);
        nodeView.setLockedValue(BasicVisualLexicon.NODE_BORDER_PAINT, Color.BLACK);
        nodeView.setLockedValue(BasicVisualLexicon.NODE_SIZE, 60.0);
    }
}
 

import org.cytoscape.view.model.CyNetworkViewManager; //导入依赖的package包/类
@Override
public void start(BundleContext context) throws Exception {
	networkFactory = getService(context, CyNetworkFactory.class);
	networkManager = getService(context, CyNetworkManager.class);
	networkNaming = getService(context, CyNetworkNaming.class);
	networkViewFactory = getService(context, CyNetworkViewFactory.class);
	networkViewManager = getService(context, CyNetworkViewManager.class);
	serviceRegistrar = getService(context, CyServiceRegistrar.class);
	
	//Set up tabbed panel in Control Panel
	CySwingApplication cytoscapeDesktopService = getService(context,CySwingApplication.class);
	
	
	CyApplicationManager appManager = getService(context, CyApplicationManager.class);
	
	OpenTaskFactory openTaskFactory = new OpenTaskFactory(cytoscapeDesktopService, serviceRegistrar, appManager);
	Properties openTaskFactoryProps = new Properties();
	openTaskFactoryProps.setProperty("preferredMenu", "Apps.SCODE");
	openTaskFactoryProps.setProperty("title", "Open SCODE");
	openTaskFactoryProps.setProperty("menuGravity","1.0");
	
	registerService(context, openTaskFactory, TaskFactory.class, openTaskFactoryProps);
	
	CloseTaskFactory closeTaskFactory = new CloseTaskFactory(cytoscapeDesktopService, serviceRegistrar);
	Properties closeTaskFactoryProps = new Properties();
	closeTaskFactoryProps.setProperty("preferredMenu", "Apps.SCODE");
	closeTaskFactoryProps.setProperty("title", "Close SCODE");
	closeTaskFactoryProps.setProperty("menuGravity","2.0");
	
	registerService(context, closeTaskFactory, TaskFactory.class, closeTaskFactoryProps);

}
 

import org.cytoscape.view.model.CyNetworkViewManager; //导入依赖的package包/类
public Plugin(CyNetworkFactory cyNetFct, 
		CyNetworkManager cyNetMgr, 
		DialogTaskManager dialogTaskManager, 
		CyNetworkViewFactory networkViewFactory,
		VisualMappingManager vmmServiceRef, 
		VisualStyleFactory visualStyleFactoryServiceRef, 
		VisualMappingFunctionFactory vmfFactoryC, 
		VisualMappingFunctionFactory vmfFactoryD, 
		VisualMappingFunctionFactory vmfFactoryP, 
		CyLayoutAlgorithmManager cyAlgorithmManager, 
		CyApplicationManager cyApplicationManager,
		CyNetworkViewManager cyNetworkViewManager,
		CySwingApplication cySwingApplication) {
	
	extensionManager = new HashMap<CyNetwork, ExtensionManager>();
	this.cyNetworkFactory = cyNetFct;
	this.cyNetworkManager = cyNetMgr;
	this.dialogTaskManager = dialogTaskManager;
	this.cyNetworkViewFactory = networkViewFactory;
	this.visualMappingManager = vmmServiceRef;
	this.visualStyleFactory = visualStyleFactoryServiceRef;
	this.visualMappingFunctionFactoryContinous = vmfFactoryC;
	this.visualMappingFunctionFactoryDiscrete = vmfFactoryD;
	this.visualMappingFunctionFactoryPassthrough = vmfFactoryP;
	this.cyLayoutAlgorithmManager = cyAlgorithmManager;
	this.cyApplicationManager = cyApplicationManager;
	this.cyNetworkViewManager = cyNetworkViewManager;
	this.cySwingApplication = cySwingApplication;
}