Java CyApplicationManager类代码示例

import org.cytoscape.application.CyApplicationManager; //导入依赖的package包/类
public MapColumnTask(CyServiceRegistrar registrar) {
	this.applicationManager = registrar.getService(CyApplicationManager.class);
	this.mappingManager = registrar.getService(DataSeriesMappingManager.class);
	
	DataSeriesManager dataSeriesManager = registrar.getService(DataSeriesManager.class);
	CyNetworkManager networkManager = registrar.getService(CyNetworkManager.class);
	
	targetClass = new ListSingleSelection<>(new TargetClassInfo("Nodes", CyNode.class), new TargetClassInfo("Edges", CyEdge.class));
	dataSeries = new ListSingleSelection<>(dataSeriesManager.getAllDataSeries());
	existingColumnForMapping = new ListSingleSelection<>();
	mapRowNamesWithColumn = new ListSingleSelection<>();
	
	targetNetwork = new ListSingleSelection<>(networkManager.getNetworkSet().stream().toArray(CyNetwork[]::new));
	if(applicationManager.getCurrentNetwork() != null)
	{
		targetNetwork.setSelectedValue(applicationManager.getCurrentNetwork());
	}
	
	updateExistingColumnForMapping(CyNode.class);
	updateMapRowNamesWithColumn(CyNode.class);
	
}
 

import org.cytoscape.application.CyApplicationManager; //导入依赖的package包/类
public SafeController(CyServiceRegistrar registrar,
                      CySwingApplication application,
                      CyApplicationManager applicationManager,
                      ImportPanelController importPanel,
                      AttributeBrowserController attributeBrowser,
                      CompositeMapController compositeMapPanel,
                      DomainBrowserController domainBrowser,
                      EventService eventService,
                      SafeSessionSerializer serializer,
                      SelectionTracker selectionTracker) {

    this.registrar = registrar;
    this.application = application;
    this.applicationManager = applicationManager;

    this.importPanel = importPanel;
    this.attributeBrowser = attributeBrowser;
    this.compositeMapPanel = compositeMapPanel;
    this.domainBrowser = domainBrowser;
    this.eventService = eventService;
    this.serializer = serializer;
    this.selectionTracker = selectionTracker;

    sessionsBySuid = new LongObjectHashMap<>();
}
 

import org.cytoscape.application.CyApplicationManager; //导入依赖的package包/类
public void makeMap (CyApplicationManager manager){

		netMap=new HashMap<String,List<Double>>();
		networkView = manager.getCurrentNetworkView();
		network = manager.getCurrentNetwork();
		nameNetwork = network.getRow(network).get("name", String.class);
		//System.out.println("curr net 2 one" + network);
		List<CyNode> nodes = network.getNodeList();
		//networkView.setVisualProperty(BasicVisualLexicon.NETWORK_CENTER_X_LOCATION, 0.0);
		//networkView.setVisualProperty(BasicVisualLexicon.NETWORK_CENTER_Y_LOCATION, 0.0);


		for (CyNode node: nodes ){
			String name = network.getRow(node).get("name", String.class);
			nodeView= networkView.getNodeView(node) ;
			List<Double> XY = new ArrayList<Double>();
			Double xref = nodeView.getVisualProperty(BasicVisualLexicon.NODE_X_LOCATION);
			Double yref = nodeView.getVisualProperty(BasicVisualLexicon.NODE_Y_LOCATION);

			XY.add(xref);
			XY.add(yref);
			netMap.put(name, XY);
		}
	}
 

import org.cytoscape.application.CyApplicationManager; //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.application.CyApplicationManager; //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.application.CyApplicationManager; //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.application.CyApplicationManager; //导入依赖的package包/类
@Override
public void start(BundleContext context) throws Exception {
    CyApplicationManager applicationManager = getService(context, CyApplicationManager.class);
    CySwingApplication swingApplication = getService(context, CySwingApplication.class);
    CyServiceRegistrar serviceRegistrar = getService(context, CyServiceRegistrar.class);
    VisualMappingManager visualMappingManager = getService(context, VisualMappingManager.class);
    VizmapReaderManager vizmapReaderManager = getService(context, VizmapReaderManager.class);
    TaskManager taskManager = getService(context, TaskManager.class);
    
    CySwing.init(swingApplication, serviceRegistrar); 
    NetworkController.init(applicationManager, visualMappingManager);
    
    // UI controls
    MenuAction menuAction = new MenuAction(taskManager);
    registerService(context, menuAction, CyAction.class, new Properties());


    taskManager.execute(new TaskIterator(new ImportGFDNetVisualStylesTask(visualMappingManager, vizmapReaderManager)));
    
    serviceRegistrar.registerService(new ClickOnViewListener(), RowsSetListener.class, new Properties());
    serviceRegistrar.registerService(new NetworkClosedListener(), NetworkAboutToBeDestroyedListener.class, new Properties());
}
 

import org.cytoscape.application.CyApplicationManager; //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.application.CyApplicationManager; //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.application.CyApplicationManager; //导入依赖的package包/类
/**
 * Create a new variation action.
 *
 * @param applicationManager application manager, must not be null
 * @param dialogTaskManager dialog task manager, must not be null
 * @param visualMappingManager visual mapping manager, must not be null
 * @param continuousMappingFactory continuous mapping factory, must not be null
 * @param discreteMappingFactory discrete mapping factory, must not be null
 * @param passthroughMappingFactory passthrough mapping factory, must not be null
 */
VariationAction(final CyApplicationManager applicationManager,
                final DialogTaskManager dialogTaskManager,
                final VisualMappingManager visualMappingManager,
                final VisualMappingFunctionFactory continuousMappingFactory,
                final VisualMappingFunctionFactory discreteMappingFactory,
                final VisualMappingFunctionFactory passthroughMappingFactory)
{
    super("Variation");
    setPreferredMenu("Apps");

    checkNotNull(applicationManager);
    checkNotNull(dialogTaskManager);
    checkNotNull(visualMappingManager);
    checkNotNull(continuousMappingFactory);
    checkNotNull(discreteMappingFactory);
    checkNotNull(passthroughMappingFactory);
    this.applicationManager = applicationManager;
    this.dialogTaskManager = dialogTaskManager;
    this.visualMappingManager = visualMappingManager;
    this.continuousMappingFactory = continuousMappingFactory;
    this.discreteMappingFactory = discreteMappingFactory;
    this.passthroughMappingFactory = passthroughMappingFactory;
}
 

import org.cytoscape.application.CyApplicationManager; //导入依赖的package包/类
@Override
public void start(final BundleContext bundleContext)
{
    if (bundleContext == null)
    {
        throw new NullPointerException("bundleContext must not be null");
    }
    CyApplicationManager applicationManager = getService(bundleContext, CyApplicationManager.class);
    DialogTaskManager dialogTaskManager = getService(bundleContext, DialogTaskManager.class);
    VisualMappingManager visualMappingManager = getService(bundleContext, VisualMappingManager.class);
    VisualMappingFunctionFactory continuousMappingFactory = getService(bundleContext, VisualMappingFunctionFactory.class, "(mapping.type=continuous)");
    VisualMappingFunctionFactory discreteMappingFactory = getService(bundleContext, VisualMappingFunctionFactory.class, "(mapping.type=discrete)");
    VisualMappingFunctionFactory passthroughMappingFactory = getService(bundleContext, VisualMappingFunctionFactory.class, "(mapping.type=passthrough)");

    VariationAction variationAction = new VariationAction(applicationManager,
                                                          dialogTaskManager,
                                                          visualMappingManager,
                                                          continuousMappingFactory,
                                                          discreteMappingFactory,
                                                          passthroughMappingFactory);

    Properties properties = new Properties();
    registerService(bundleContext, variationAction, CyAction.class, properties);
}
 

import org.cytoscape.application.CyApplicationManager; //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.application.CyApplicationManager; //导入依赖的package包/类
public static boolean checkNetwork(CyApplicationManager applicationManager) {
    boolean result = false;
    
    CyNetworkView view = applicationManager.getCurrentNetworkView();
    CyNetwork network = applicationManager.getCurrentNetwork();
        
    // Cannot continue if either of these is null.
    if (network == null || view == null) {
        JOptionPane.showMessageDialog(
                null,
                "No network and/or view to link to.",
                "Missing network",
                JDialog.ERROR);
    } else {
        result = true;
    }
    
    return result;
}
 

import org.cytoscape.application.CyApplicationManager; //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.application.CyApplicationManager; //导入依赖的package包/类
@Inject
public CreateAnnotationSetDialog(JFrame jFrame, CyApplicationManager appManager) {
	super(jFrame, true);
	setTitle("AutoAnnotate: Create Annotation Set");
	this.networkView = appManager.getCurrentNetworkView();
	setMinimumSize(new Dimension(500, 400));
}