本文整理汇总了Java中org.cytoscape.view.model.CyNetworkViewFactory类的典型用法代码示例。如果您正苦于以下问题:Java CyNetworkViewFactory类的具体用法?Java CyNetworkViewFactory怎么用?Java CyNetworkViewFactory使用的例子?那么恭喜您, 这里精选的类代码示例或许可以为您提供帮助。
CyNetworkViewFactory类属于org.cytoscape.view.model包,在下文中一共展示了CyNetworkViewFactory类的20个代码示例,这些例子默认根据受欢迎程度排序。您可以为喜欢或者感觉有用的代码点赞,您的评价将有助于我们的系统推荐出更棒的Java代码示例。
示例1: configureTest
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());
}
开发者ID:BaderLab,项目名称:AutoAnnotateApp,代码行数:20,代码来源:NetworkTestUtil.java
示例2: AdjNetworkReaderFactory
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;
}
开发者ID:srikanthBezawada,项目名称:AdjacencyMatrixExporter,代码行数:19,代码来源:AdjNetworkReaderFactory.java
示例3: AdjNetworkReader
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;
}
开发者ID:srikanthBezawada,项目名称:AdjacencyMatrixExporter,代码行数:20,代码来源:AdjNetworkReader.java
示例4: start
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);
}
开发者ID:passeridae,项目名称:SLiMscape,代码行数:23,代码来源:CyActivator.java
示例5: JGFNetworkReaderFactory
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;
}
开发者ID:jsongraph,项目名称:jgf-app,代码行数:24,代码来源:JGFNetworkReaderFactory.java
示例6: JGFNetworkReader
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;
}
开发者ID:jsongraph,项目名称:jgf-app,代码行数:27,代码来源:JGFNetworkReader.java
示例7: start
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());
}
开发者ID:gsummer,项目名称:cyNeo4j,代码行数:26,代码来源:CyActivator.java
示例8: SyncDownTaskFactory
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;
}
开发者ID:gsummer,项目名称:cyNeo4j,代码行数:21,代码来源:SyncDownTaskFactory.java
示例9: SyncDownTask
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;
}
开发者ID:gsummer,项目名称:cyNeo4j,代码行数:22,代码来源:SyncDownTask.java
示例10: configure
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());
}
开发者ID:BaderLab,项目名称:AutoAnnotateApp,代码行数:39,代码来源:CytoscapeServiceModule.java
示例11: CyServices
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;
}
开发者ID:cytoscape,项目名称:biopax,代码行数:30,代码来源:CyServices.java
示例12: start
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);
}
开发者ID:DataFusion4NetBio,项目名称:Paper16-SCODE,代码行数:33,代码来源:CyActivator.java
示例13: Plugin
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;
}
开发者ID:CyTargetLinker,项目名称:cytargetlinker,代码行数:30,代码来源:Plugin.java
示例14: start
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());
}
开发者ID:CyTargetLinker,项目名称:cytargetlinker,代码行数:38,代码来源:CyActivator.java
示例15: CyServices
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;
}
开发者ID:PathwayCommons,项目名称:CyPath2,代码行数:40,代码来源:CyServices.java
示例16: start
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...
}
开发者ID:cytoscape,项目名称:biopax,代码行数:50,代码来源:CyActivator.java
示例17: getNetworkViewFactory
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;
}
开发者ID:cytoscape,项目名称:biopax,代码行数:7,代码来源:BioPaxReaderTask.java
示例18: SlimPanel
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);
}
开发者ID:passeridae,项目名称:SLiMscape,代码行数:45,代码来源:SlimPanel.java
示例19: start
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);
}
开发者ID:jsongraph,项目名称:jgf-app,代码行数:77,代码来源:CyActivator.java
示例20: KddnExperiment
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;
}
开发者ID:tianye03,项目名称:kddn-cytoscape,代码行数:79,代码来源:KddnExperiment.java
注:本文中的org.cytoscape.view.model.CyNetworkViewFactory类示例整理自Github/MSDocs等源码及文档管理平台,相关代码片段筛选自各路编程大神贡献的开源项目,源码版权归原作者所有,传播和使用请参考对应项目的License;未经允许,请勿转载。 |
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