import org.cytoscape.model.subnetwork.CyRootNetworkManager; //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.subnetwork.CyRootNetworkManager; //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.subnetwork.CyRootNetworkManager; //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.subnetwork.CyRootNetworkManager; //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.model.subnetwork.CyRootNetworkManager; //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.subnetwork.CyRootNetworkManager; //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.model.subnetwork.CyRootNetworkManager; //导入依赖的package包/类
public ControlPanel(CyNetworkManager networkManager,
		CyRootNetworkManager rootNetworkManager,
		CyApplicationManager applicationManager,
		CyGroupManager groupManager,
		CyGroupFactory groupFactory,
		TaskManager taskManager) {

	this.networkManager = networkManager;
	this.rootNetworkManager = rootNetworkManager;
	this.applicationManager = applicationManager;
	this.groupManager = groupManager;
	this.groupFactory = groupFactory;
	this.taskManager = taskManager;
	this.networkSettings = new HashMap<Long, NetworkSettings>();
	this.itemChangeListener = new ItemChangeListener();
	this.nSelectedNodes = 0;
	this.currentNetworkSUID = null;

	initUserInterface();
	
	CyNetwork network = applicationManager.getCurrentNetwork();
	if (network != null) {
		this.currentNetworkSUID = network.getSUID();
		this.networkSettings.put(currentNetworkSUID, new NetworkSettings(network));

		updateUserInterface();
		updateFeedbackTableModel();
		updateButtons();
	} else {
		disableUserInterface();
	}

	this.setVisible(true);
}
 

import org.cytoscape.model.subnetwork.CyRootNetworkManager; //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.model.subnetwork.CyRootNetworkManager; //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.model.subnetwork.CyRootNetworkManager; //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.model.subnetwork.CyRootNetworkManager; //导入依赖的package包/类
/**
 * Upon bundle activation (install or startup).
 */
public void start(BundleContext bc) {
    // Manager services.
    //CySwingApplication desktopManager = getService(bc, CySwingApplication.class);
    
    // Basic access to current and/or currently selected networks, 
    // views and rendering engines in an instance of Cytoscape.
    CyApplicationManager applicationManager = getService(bc, CyApplicationManager.class);
    
    // Access to all root networks
    CyRootNetworkManager rootNetworkManager = getService(bc, CyRootNetworkManager.class);
    
    // Access to all networks
    CyNetworkManager networkManager = getService(bc, CyNetworkManager.class);
    
    // This object manages mapping from view model to VisualStyle. 
    // User objects can access all VisualStyles and VisualMappingFunctions through this class.
    VisualMappingManager visualMappingManager = getService(bc, VisualMappingManager.class);
    
    // The CyGroupManager maintains information about all of the groups an instance of Cytoscape.
    CyGroupManager groupManager = getService(bc, CyGroupManager.class);
    
    // An interface describing a factory used for creating CyGroup objects.
    CyGroupFactory groupFactory = getService(bc, CyGroupFactory.class);
    
    TaskManager taskManager = getService(bc, TaskManager.class);
    
    // Action, the group viewer
    ViewerAction viewerAction =
            new ViewerAction(applicationManager,
                             visualMappingManager,
                             groupManager,
                             groupFactory);
    
    // Action, the group selector
    /*GroupsFromColumnsAction groupsAction =
            new GroupsFromColumnsAction(applicationManager,
                                        groupManager,
                                        groupFactory);*/
    
    // The eXamine control panel
    ControlPanel controlPanel = new ControlPanel(networkManager, rootNetworkManager, 
    		applicationManager, groupManager, groupFactory, taskManager);

    // Register it as a service.
    registerService(bc, viewerAction, CyAction.class, new Properties());
    //registerService(bc, groupsAction, CyAction.class, new Properties());
    registerService(bc, controlPanel, CytoPanelComponent.class, new Properties());
    registerService(bc, controlPanel, SetCurrentNetworkListener.class, new Properties());
    registerService(bc, controlPanel, RowsSetListener.class, new Properties());
    registerService(bc, controlPanel, ColumnNameChangedListener.class, new Properties());
    registerService(bc, controlPanel, ColumnDeletedListener.class, new Properties());
    registerService(bc, controlPanel, ColumnCreatedListener.class, new Properties());
    registerService(bc, controlPanel, NetworkDestroyedListener.class, new Properties());
    registerService(bc, controlPanel, SessionLoadedListener.class, new Properties());
}