本文整理汇总了Java中org.cytoscape.model.CyNetworkFactory类的典型用法代码示例。如果您正苦于以下问题:Java CyNetworkFactory类的具体用法?Java CyNetworkFactory怎么用?Java CyNetworkFactory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。
CyNetworkFactory类属于org.cytoscape.model包,在下文中一共展示了CyNetworkFactory类的15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,您的评价将有助于系统推荐出更棒的Java代码示例。
示例1: setUp
import org.cytoscape.model.CyNetworkFactory; //导入依赖的package包/类
@Before
public void setUp(CyNetworkFactory networkFactory, CyNetworkManager networkManager) {
networkView = NetworkTestUtil.createNetwork(networkFactory, networkManager);
CyNetwork network = networkView.getModel();
nodes = new HashMap<>();
nodes.put("n1", createNode(network, "n1", "cluster_1"));
nodes.put("n2", createNode(network, "n2", "cluster_1"));
nodes.put("n3", createNode(network, "n3", "cluster_1"));
nodes.put("n4", createNode(network, "n4", "cluster_2"));
nodes.put("n5", createNode(network, "n5", "cluster_2"));
nodes.put("n6", createNode(network, "n6", "cluster_3"));
nodes.put("n7", createNode(network, "n7", null));
nodes.put("n8", createNode(network, "n8", null));
nodes.put("n9", createNode(network, "n9", null));
}
示例2: setUp
import org.cytoscape.model.CyNetworkFactory; //导入依赖的package包/类
@Before
public void setUp(CyNetworkFactory networkFactory, CyNetworkManager networkManager) {
networkView = NetworkTestUtil.createNetwork(networkFactory, networkManager);
CyNetwork network = networkView.getModel();
nodes = new HashMap<>();
nodes.put("n1", createNode(network, "n1", "cluster_1"));
nodes.put("n2", createNode(network, "n2", "cluster_1"));
nodes.put("n3", createNode(network, "n3", "cluster_1"));
nodes.put("n4", createNode(network, "n4", "cluster_2"));
nodes.put("n5", createNode(network, "n5", "cluster_2"));
nodes.put("n6", createNode(network, "n6", "cluster_3"));
nodes.put("n7", createNode(network, "n7", "cluster_4"));
nodes.put("n8", createNode(network, "n8", "cluster_5"));
nodes.put("n9", createNode(network, "n9", "cluster_6"));
}
示例3: setUp
import org.cytoscape.model.CyNetworkFactory; //导入依赖的package包/类
@Before
public void setUp(CyNetworkFactory networkFactory, CyNetworkManager networkManager) {
networkView = NetworkTestUtil.createNetwork(networkFactory, networkManager);
CyNetwork network = networkView.getModel();
createNode(network, "n1", "cluster_1");
createNode(network, "n2", "cluster_1");
createNode(network, "n3", "cluster_1");
createNode(network, "n4", "cluster_2");
createNode(network, "n5", "cluster_2");
createNode(network, "n6", "cluster_3");
createNode(network, "n7", "cluster_4");
createNode(network, "n8", "cluster_5");
createNode(network, "n9", "cluster_6");
}
示例4: configureTest
import org.cytoscape.model.CyNetworkFactory; //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());
}
示例5: AdjNetworkReaderFactory
import org.cytoscape.model.CyNetworkFactory; //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;
}
示例6: AdjNetworkReader
import org.cytoscape.model.CyNetworkFactory; //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;
}
示例7: start
import org.cytoscape.model.CyNetworkFactory; //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);
}
示例8: JGFNetworkReaderFactory
import org.cytoscape.model.CyNetworkFactory; //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;
}
示例9: start
import org.cytoscape.model.CyNetworkFactory; //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());
}
示例10: SyncDownTaskFactory
import org.cytoscape.model.CyNetworkFactory; //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;
}
示例11: SyncDownTask
import org.cytoscape.model.CyNetworkFactory; //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;
}
示例12: configure
import org.cytoscape.model.CyNetworkFactory; //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());
}
示例13: configureTest
import org.cytoscape.model.CyNetworkFactory; //导入依赖的package包/类
@Override
protected void configureTest() {
NetworkTestSupport networkTestSupport = new NetworkTestSupport();
TableTestSupport tableTestSupport = new TableTestSupport();
bind(CyNetworkFactory.class).toInstance(networkTestSupport.getNetworkFactory());
bind(CyNetworkTableManager.class).toInstance(networkTestSupport.getNetworkTableManager());
bind(CyNetworkManager.class).toInstance(networkTestSupport.getNetworkManager());
bind(CyTableFactory.class).toInstance(tableTestSupport.getTableFactory());
bind(EventBus.class).toInstance(new EventBus());
TypeLiteral<LabelMakerFactory<?>> labelMakerFactoryType = new TypeLiteral<LabelMakerFactory<?>>() {};
Multibinder<LabelMakerFactory<?>> labelFactoryBinder = Multibinder.newSetBinder(binder(), labelMakerFactoryType);
labelFactoryBinder.addBinding().toInstance(mock(LabelMakerFactory.class));
}
示例14: createNetwork
import org.cytoscape.model.CyNetworkFactory; //导入依赖的package包/类
public static CyNetworkView createNetwork(CyNetworkFactory networkFactory, CyNetworkManager networkManager) {
CyNetworkView networkView = mock(CyNetworkView.class);
CyNetwork network = networkFactory.createNetwork();
networkManager.addNetwork(network);
when(networkView.getModel()).thenReturn(network);
network.getDefaultNodeTable().createColumn(CLUSTER_COL, String.class, false);
return networkView;
}
示例15: setup
import org.cytoscape.model.CyNetworkFactory; //导入依赖的package包/类
@Before
public void setup(CyApplicationManager appManager, ModelManager modelManager, AnnotationRenderer renderer,
RemoveAllAnnotationsTask.Factory removeTaskFactory, DrawClusterTask.Factory drawTaskFactory,
EraseClusterTask.Factory eraseTaskFactory, SelectClusterTask.Factory selectTaskFactory) {
// set up stubbing
CyNetworkView networkView = mock(CyNetworkView.class);
when(appManager.getCurrentNetworkView()).thenReturn(networkView);
when(drawTaskFactory.create(any())).thenReturn(mock(DrawClusterTask.class));
when(removeTaskFactory.create(any())).thenReturn(mock(RemoveAllAnnotationsTask.class));
when(eraseTaskFactory.create(any())).thenReturn(mock(EraseClusterTask.class));
when(selectTaskFactory.create(any(), anyBoolean())).thenReturn(mock(SelectClusterTask.class));
NetworkTestSupport networkTestSupport = new NetworkTestSupport();
CyNetworkFactory networkFactory = networkTestSupport.getNetworkFactory();
CyNetworkManager networkManager = networkTestSupport.getNetworkManager();
CyNetwork network = networkFactory.createNetwork();
networkManager.addNetwork(network);
when(networkView.getModel()).thenReturn(network);
// create model fixture
NetworkViewSet nvs = modelManager.getNetworkViewSet(networkView);
AnnotationSet as = nvs.createAnnotationSet("as1", "lc1");
as.createCluster(createNodes(network,10), "cluster1", false);
as.createCluster(createNodes(network,10), "cluster2", false);
as.createCluster(createNodes(network,10), "cluster3", false);
nvs.select(as);
// Reset invocation counts from fixture initialization.
// Unfortunately reset() also resets the stubbing so we need to redo it.
reset(removeTaskFactory, drawTaskFactory, eraseTaskFactory, selectTaskFactory);
when(drawTaskFactory.create(any())).thenReturn(mock(DrawClusterTask.class));
when(removeTaskFactory.create(any())).thenReturn(mock(RemoveAllAnnotationsTask.class));
when(eraseTaskFactory.create(any())).thenReturn(mock(EraseClusterTask.class));
when(selectTaskFactory.create(any(), anyBoolean())).thenReturn(mock(SelectClusterTask.class));
}