import org.cytoscape.view.model.CyNetworkViewFactory; //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.view.model.CyNetworkViewFactory; //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.CyNetworkViewFactory; //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.CyNetworkViewFactory; //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.CyNetworkViewFactory; //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.CyNetworkViewFactory; //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.CyNetworkViewFactory; //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.CyNetworkViewFactory; //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.CyNetworkViewFactory; //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.CyNetworkViewFactory; //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.CyNetworkViewFactory; //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.CyNetworkViewFactory; //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.CyNetworkViewFactory; //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;
}
 

import org.cytoscape.view.model.CyNetworkViewFactory; //导入依赖的package包/类
@Override
public void start(BundleContext context) throws Exception {
	CyApplicationManager cyApplicationManager = getService(context, CyApplicationManager.class);
	CyNetworkViewFactory networkViewFactory = getService(context, CyNetworkViewFactory.class);
	CyNetworkFactory networkFactory = getService(context, CyNetworkFactory.class);
	CyNetworkManager networkManager = getService(context, CyNetworkManager.class);
	DialogTaskManager dialogTaskManager = getService(context, DialogTaskManager.class);
	VisualMappingManager vmmServiceRef = getService(context,VisualMappingManager.class);
	VisualStyleFactory visualStyleFactoryServiceRef = getService(context,VisualStyleFactory.class);
	VisualMappingFunctionFactory vmfFactoryC = getService(context,VisualMappingFunctionFactory.class, "(mapping.type=continuous)");
	VisualMappingFunctionFactory vmfFactoryD = getService(context,VisualMappingFunctionFactory.class, "(mapping.type=discrete)");
	VisualMappingFunctionFactory vmfFactoryP = getService(context,VisualMappingFunctionFactory.class, "(mapping.type=passthrough)");
	CyLayoutAlgorithmManager cyAlgorithmManager = getService(context, CyLayoutAlgorithmManager.class);
	CyNetworkViewManager cyNetworkViewManager = getService(context, CyNetworkViewManager.class);
	CySwingApplication cySwingApplication = getService(context, CySwingApplication.class);
	OpenBrowser openBrowser = getService(context, OpenBrowser.class);
					
	Plugin plugin = new Plugin(networkFactory, networkManager, dialogTaskManager, networkViewFactory, vmmServiceRef, visualStyleFactoryServiceRef,
			vmfFactoryC, vmfFactoryD, vmfFactoryP, cyAlgorithmManager, cyApplicationManager, cyNetworkViewManager, cySwingApplication);
	registerService(context, plugin, NetworkDestroyedListener.class, new Properties());
	
	// CyTargetLinker implements two actions: extend network and help
	ExtensionAction extAction = new ExtensionAction("Extend network", plugin);
	registerAllServices(context, extAction, new Properties());
	
	HelpAction helpAction = new HelpAction("Help", openBrowser);
	registerAllServices(context, helpAction, new Properties());
	
	// property stores last used RegIN directory
	CyTargetLinkerProperty property = new CyTargetLinkerProperty();
	CyProperty<Properties> prop = property.checkCyProperties(getService(context, CySessionManager.class));
	registerService(context, prop, CyProperty.class, new Properties());
	
	// registers the panel for CyTargetLinker
	CyTargetLinkerPanel panel = new CyTargetLinkerPanel(plugin);
	registerService(context, panel, CytoPanelComponent.class, new Properties());
}
 

import org.cytoscape.view.model.CyNetworkViewFactory; //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,
			CyRootNetworkManager rootNetworkManager, 
			UnHideAllEdgesTaskFactory unHideAllEdgesTaskFactory,
			CyNetworkViewFactory networkViewFactory,
			VisualStyleFactory visualStyleFactory,
			VisualMappingFunctionFactory discreteMappingFunctionFactory,
			VisualMappingFunctionFactory passthroughMappingFunctionFactory,
			StreamUtil streamUtil
	) {
		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;
		this.unHideAllEdgesTaskFactory = unHideAllEdgesTaskFactory;
		this.visualStyleFactory = visualStyleFactory;
		this.discreteMappingFunctionFactory = discreteMappingFunctionFactory;
		this.passthroughMappingFunctionFactory = passthroughMappingFunctionFactory;
		this.streamUtil = streamUtil;
	}
 

import org.cytoscape.view.model.CyNetworkViewFactory; //导入依赖的package包/类
public void start(BundleContext bc) {

		CySwingApplication cySwingApplication = getService(bc,CySwingApplication.class);
		OpenBrowser openBrowser = getService(bc,OpenBrowser.class);
		CyApplicationManager cyApplicationManager = getService(bc,CyApplicationManager.class);
		CyNetworkViewManager cyNetworkViewManager = getService(bc,CyNetworkViewManager.class);
		CyNetworkManager cyNetworkManager = getService(bc,CyNetworkManager.class);
		CyNetworkNaming cyNetworkNaming = getService(bc,CyNetworkNaming.class);
		CyNetworkFactory cyNetworkFactory = getService(bc,CyNetworkFactory.class);
		StreamUtil streamUtil = getService(bc,StreamUtil.class);
		VisualMappingManager visualMappingManager = getService(bc,VisualMappingManager.class);
		VisualStyleFactory visualStyleFactory = getService(bc,VisualStyleFactory.class);
		VisualMappingFunctionFactory discreteMappingFunctionFactory =
				getService(bc,VisualMappingFunctionFactory.class,"(mapping.type=discrete)");
		VisualMappingFunctionFactory passthroughMappingFunctionFactory =
				getService(bc,VisualMappingFunctionFactory.class,"(mapping.type=passthrough)");
		CyLayoutAlgorithmManager cyLayoutAlgorithmManager = getService(bc,CyLayoutAlgorithmManager.class);	
		TaskManager taskManager = getService(bc, DialogTaskManager.class);
		CyProperty<Properties> cyProperties = getService(bc, CyProperty.class, "(cyPropertyName=cytoscape3.props)");
		CyRootNetworkManager cyRootNetworkManager = getService(bc,CyRootNetworkManager.class);
		CyNetworkReaderManager cyNetworkReaderManager = getService(bc,CyNetworkReaderManager.class);
		UndoSupport undoSupport = getService(bc,UndoSupport.class);
		CyNetworkViewFactory networkViewFactory = getService(bc, CyNetworkViewFactory.class);
		
		
		// keep all the service references in one place -
		final CyServices cyServices = new CyServices(cySwingApplication, taskManager, openBrowser, 
				cyNetworkManager, cyApplicationManager, cyNetworkViewManager, cyNetworkReaderManager, 
				cyNetworkNaming, cyNetworkFactory, cyLayoutAlgorithmManager, undoSupport, visualMappingManager, 
				cyProperties, networkViewFactory, cyRootNetworkManager);
				
		BioPaxFilter bioPaxFilter = new BioPaxFilter(streamUtil);
				
		VisualStyleUtil visualStyleUtil = new VisualStyleUtil(visualStyleFactory,
				visualMappingManager, discreteMappingFunctionFactory, passthroughMappingFunctionFactory);
		visualStyleUtil.init(); //important

		// create the biopax reader object
		BioPaxReader biopaxReader = new BioPaxReader(bioPaxFilter, cyServices, visualStyleUtil);		
		// register/export osgi services
		Properties props = new Properties();
		props.setProperty("readerDescription","BioPAX reader");
		props.setProperty("readerId","biopaxNetworkReader");
		registerAllServices(bc, biopaxReader, props);

		System.setProperty("paxtools.CollectionsProvider","org.biopax.paxtools.trove.TProvider");

		//TODO move the CytoPanelComponent (results panel) and related code from CyPath2 app to here...
	}
 

import org.cytoscape.view.model.CyNetworkViewFactory; //导入依赖的package包/类
private CyNetworkViewFactory getNetworkViewFactory() {
	if (rendererList != null && rendererList.getSelectedValue() != null)
		return rendererList.getSelectedValue().getNetworkViewFactory();
	
	return cyServices.networkViewFactory;
}
 

import org.cytoscape.view.model.CyNetworkViewFactory; //导入依赖的package包/类
public SlimPanel(CyApplicationManager manager, CyAppAdapter adapter, OpenBrowser openBrowser,
                 CyEventHelper eventHelper, CyNetworkFactory networkFactory, CyNetworkManager networkManager,
                 CyNetworkViewFactory networkViewFactory, CyNetworkViewManager networkViewManager, VisualMappingManager visualMappingManager) {
    super();
    this.networkFactory = networkFactory;
    this.networkViewFactory = networkViewFactory;
    this.networkViewManager = networkViewManager;
    this.setBounds(100, 100, 725, 471);

    this.setLayout(new BoxLayout(this, BoxLayout.Y_AXIS));

    JTabbedPane tabbedPane = new JTabbedPane(JTabbedPane.TOP);
    GridBagConstraints gbc_tabbedPane = new GridBagConstraints();
    gbc_tabbedPane.fill = GridBagConstraints.BOTH;
    gbc_tabbedPane.gridx = 0;
    gbc_tabbedPane.gridy = 0;
    add(tabbedPane, gbc_tabbedPane);

    JTabbedPane slimfinder = new JTabbedPane();
    SlimfinderOptionsPanel slimfinderOptionsPanel = new SlimfinderOptionsPanel();
    slimfinder.addTab("Run", new SlimfinderRunPanel(manager, openBrowser, slimfinderOptionsPanel,
            eventHelper, networkFactory, networkManager, networkViewFactory, networkViewManager, visualMappingManager, adapter, slimfinder));
    slimfinder.addTab("Options", slimfinderOptionsPanel);

    JTabbedPane slimprob = new JTabbedPane();
    SlimprobOptionsPanel slimprobOptionsPanel = new SlimprobOptionsPanel();
    slimprob.addTab("Run", new SlimprobRunPanel(manager, openBrowser, slimprobOptionsPanel,
            eventHelper, networkFactory, networkManager, networkViewFactory, networkViewManager, visualMappingManager, adapter, slimprob));
    slimprob.addTab("Options", slimprobOptionsPanel);

    JTabbedPane qslimfinder = new JTabbedPane();
    QSlimfinderOptionsPanel qslimfinderOptionsPanel = new QSlimfinderOptionsPanel();
    qslimfinder.addTab("Run", new QSlimfinderRunPanel(manager, openBrowser, qslimfinderOptionsPanel,
            eventHelper, networkFactory, networkManager, networkViewFactory, networkViewManager, visualMappingManager, adapter, qslimfinder));
    qslimfinder.addTab("Options", qslimfinderOptionsPanel);

    // Add the slimprob and slimfinder tabs to tabbedPane
    tabbedPane.addTab("SLiMFinder", slimfinder);
    tabbedPane.addTab("SLiMProb", slimprob);
    tabbedPane.addTab("QSLiMFinder", qslimfinder);
    //tabbedPane.addTab("Domain", new JPanel());

    this.add(tabbedPane);
}
 

import org.cytoscape.view.model.CyNetworkViewFactory; //导入依赖的package包/类
/**
 * {@inheritDoc}
 */
@Override
public void start(BundleContext bc) throws Exception {

    // reference services
    final StreamUtil streamUtil = getService(bc, StreamUtil.class);
    final CyApplicationManager appMgr = getService(bc, CyApplicationManager.class);
    final CyNetworkViewFactory cyNetworkViewFactory = getService(bc, CyNetworkViewFactory.class);
    final CyNetworkFactory cyNetworkFactory = getService(bc, CyNetworkFactory.class);
    final CyNetworkManager cyNetworkManager = getService(bc, CyNetworkManager.class);
    final CyNetworkViewManager cyNetworkViewManager = getService(bc, CyNetworkViewManager.class);
    final CyRootNetworkManager cyRootNetworkManager = getService(bc, CyRootNetworkManager.class);
    final CyTableManager cyTableManager = getService(bc, CyTableManager.class);
    final CyTableFactory cyTableFactory = getService(bc, CyTableFactory.class);
    final VisualMappingManager visMgr = getService(bc, VisualMappingManager.class);
    final VizmapReaderManager vizmapReaderMgr = getService(bc, VizmapReaderManager.class);
    final CyEventHelper eventHelper = getService(bc, CyEventHelper.class);
    final CySwingApplication cySwingApplication = getService(bc, CySwingApplication.class);
    final CyApplicationConfiguration cyAppConfig = getService(bc, CyApplicationConfiguration.class);

    // contribute visual styles
    CyActivator.contributeStyles(visMgr, vizmapReaderMgr);

    // API implementations
    final GraphReader graphReader = new GraphReaderImpl();
    final GraphConverter belGraphConverter = new BELGraphConverterImpl(cyNetworkFactory);
    final BELEvidenceMapper belEvidenceMapper = new BELEvidenceMapperImpl();

    // register readers
    final CyFileFilter jgfReaderFilter = new JGFFileFilter(streamUtil);
    final JGFNetworkReaderFactory jgfReaderFactory = new JGFNetworkReaderFactory(
            jgfReaderFilter, appMgr, cyNetworkViewFactory, cyNetworkFactory,
            cyNetworkManager, cyNetworkViewManager, cyRootNetworkManager, cyTableFactory,
            cyTableManager, visMgr, eventHelper, graphReader, belGraphConverter,
            belEvidenceMapper);
    final Properties jgfNetworkReaderFactoryProps = new Properties();
    jgfNetworkReaderFactoryProps.put(ID, "JGFNetworkReaderFactory");
    registerService(bc, jgfReaderFactory, InputStreamTaskFactory.class, jgfNetworkReaderFactoryProps);

    // register listeners
    final Properties evidenceProps = new Properties();
    evidenceProps.put("name", "evidence");
    EvidencePanelComponent evidencePanelComponent = new EvidencePanelComponent(belEvidenceMapper, cyTableManager, cyNetworkManager);
    registerAllServices(bc, evidencePanelComponent, evidenceProps);
    registerAllServices(bc, new SessionListener(visMgr, vizmapReaderMgr), new Properties());

    final Properties evidenceFactoryProps = new Properties();
    evidenceFactoryProps.put(ID, "ShowEvidenceFactory");
    evidenceFactoryProps.put(PREFERRED_MENU, "Apps.JGF App");
    evidenceFactoryProps.put(MENU_GRAVITY, "14.0");
    evidenceFactoryProps.put(TITLE, "View Evidence");
    registerService(bc, new ShowEvidenceFactory(cyTableManager, cySwingApplication, evidencePanelComponent), EdgeViewTaskFactory.class, evidenceFactoryProps);

    // register about action
    AbstractCyAction aboutAction = new AbstractCyAction("About") {
        @Override
        public void actionPerformed(ActionEvent e) {
            About.showDialog(JGFApp.NAME, JGFApp.DESC, JGFApp.VERSION, JGFApp.ICON, JGFApp.LINKS);
        }
    };
    aboutAction.setMenuGravity(0.0f);
    aboutAction.setPreferredMenu("Apps.JGF App");
    final Properties aboutActionProps = new Properties();
    aboutActionProps.put("id", "jgfApp.about.action");
    registerService(bc, aboutAction, CyAction.class, aboutActionProps);

    // register help action
    AbstractCyAction helpAction = createBrowseHelpAction("/docs.zip", "docs/index.html", cyAppConfig, this);
    helpAction.setMenuGravity(1.0f);
    helpAction.setPreferredMenu("Apps.JGF App");
    final Properties helpActionProps = new Properties();
    helpActionProps.put("id", "jgfApp.help.action");
    registerService(bc, helpAction, CyAction.class, helpActionProps);
}
 

import org.cytoscape.view.model.CyNetworkViewFactory; //导入依赖的package包/类
/**
    * Constructor
    * @param cyNetworkManagerServiceRef
    * @param cyNetworkNamingServiceRef
    * @param cyNetworkFactoryServiceRef
    * @param networkViewFactory
    * @param networkViewManager
    * @param vmmServiceRef
    * @param vsfServiceRef
    * @param vmfFactoryC
    * @param vmfFactoryD
    * @param vmfFactoryP
    * @param clamRef
    * @param varList
    * @param data1
    * @param data2
    * @param priorKnowledge
    * @param useKnowledge
    * @param lambda1
    * @param lambda2
    * @param alpha
    * @param theta
    * @param delta
    * @param needPvalue
    * @param numPermutation
    * @param twoCondition
    * @param dataPanel
    * @param parameterPanel
    */
public KddnExperiment(CyNetworkManager cyNetworkManagerServiceRef,
		CyNetworkNaming cyNetworkNamingServiceRef, 
		CyNetworkFactory cyNetworkFactoryServiceRef, 
		CyNetworkViewFactory networkViewFactory, 
		CyNetworkViewManager networkViewManager,
		VisualMappingManager vmmServiceRef, 
		VisualStyleFactory vsfServiceRef, 
		VisualMappingFunctionFactory vmfFactoryC, 
		VisualMappingFunctionFactory vmfFactoryD, 
		VisualMappingFunctionFactory vmfFactoryP,
		CyLayoutAlgorithmManager clamRef, 
		String[] varList, double[][] data1, double[][] data2, 
		String[][] priorKnowledge, boolean useKnowledge, 
		double lambda1, double lambda2, 
		double alpha, double theta, double delta, boolean needPvalue,
		int numPermutation, boolean twoCondition, 
		KddnDataPanel dataPanel, KddnParameterPanel parameterPanel) {
	
	this.cyNetworkFactoryServiceRef = cyNetworkFactoryServiceRef;
	this.cyNetworkManagerServiceRef = cyNetworkManagerServiceRef;
	this.cyNetworkNamingServiceRef = cyNetworkNamingServiceRef;
	this.networkViewFactory = networkViewFactory;
	this.networkViewManager = networkViewManager;
	this.vmmServiceRef = vmmServiceRef;
	this.vsfServiceRef = vsfServiceRef;
	this.vmfFactoryC = vmfFactoryC;
	this.vmfFactoryD = vmfFactoryD;
	this.vmfFactoryP = vmfFactoryP;
	this.clamRef = clamRef;
	this.varList = varList;
	this.data1 = data1;	
	this.priorKnowledge = priorKnowledge;
	this.useKnowledge = useKnowledge;
	this.numPermutation = numPermutation;
	this.lambda1 = lambda1;
	this.lambda2 = lambda2;
	this.theta = theta;
	this.alpha = alpha;
	this.delta = delta;
	this.needPvalue = needPvalue;
	this.twoCondition = twoCondition;
	if(!twoCondition)
		this.data2 = data1;
	else
		this.data2 = data2;
	
	this.dataPanel = dataPanel;
	this.parameterPanel = parameterPanel;
}