Java CyNetworkView类代码示例

import org.cytoscape.view.model.CyNetworkView; //导入依赖的package包/类
void setAttributeBrowserStyle(CyNetworkView view) {
    if (!SwingUtilities.isEventDispatchThread()) {
        SwingUtilities.invokeLater(() -> setAttributeBrowserStyle(view));
        return;
    }

    VisualStyle style = visualMappingManager.getAllVisualStyles()
                                            .stream()
                                            .filter(s -> s.getTitle()
                                                          .equals(StyleFactory.ATTRIBUTE_BROWSER_STYLE))
                                            .findFirst()
                                            .orElse(null);

    if (style == null) {
        style = styleFactory.createAttributeBrowserStyle();
        visualMappingManager.addVisualStyle(style);
    }

    VisualStyle viewStyle = visualMappingManager.getVisualStyle(view);
    if (viewStyle != style) {
        visualMappingManager.setVisualStyle(style, view);
    }
}
 

import org.cytoscape.view.model.CyNetworkView; //导入依赖的package包/类
private void updateEdgeWeightColumnList() {
    weightColumnModel.removeAllElements();

    if (session == null) {
        return;
    }

    CyNetworkView view = session.getNetworkView();
    CyNetwork model = view.getModel();
    CyTable table = model.getDefaultEdgeTable();
    table.getColumns()
         .stream()
         .filter(c -> !CyIdentifiable.SUID.equals(c.getName()) && Number.class.isAssignableFrom(c.getType()))
         .map(c -> c.getName())
         .sorted(String.CASE_INSENSITIVE_ORDER)
         .forEach(name -> weightColumnModel.addElement(name));

    weightColumn.setSelectedItem(session.getWeightColumn());

    if (weightColumn.getSelectedIndex() == -1 && weightColumnModel.getSize() > 0) {
        weightColumn.setSelectedIndex(0);
    }
}
 

import org.cytoscape.view.model.CyNetworkView; //导入依赖的package包/类
void setDomainBrowserStyle(CyNetworkView view) {
    if (!SwingUtilities.isEventDispatchThread()) {
        SwingUtilities.invokeLater(() -> setDomainBrowserStyle(view));
        return;
    }

    VisualStyle style = visualMappingManager.getAllVisualStyles()
                                            .stream()
                                            .filter(s -> s.getTitle()
                                                          .equals(StyleFactory.DOMAIN_BROWSER_STYLE))
                                            .findFirst()
                                            .orElse(null);

    if (style == null) {
        style = styleFactory.createDomainBrowserStyle();
        visualMappingManager.addVisualStyle(style);
    }

    VisualStyle viewStyle = visualMappingManager.getVisualStyle(view);
    if (viewStyle != style) {
        visualMappingManager.setVisualStyle(style, view);
    }
}
 

import org.cytoscape.view.model.CyNetworkView; //导入依赖的package包/类
void updateColumnList(SafeSession session) {
    lastAnnotationPath = null;
    this.session = session;

    nodeIdsModel.removeAllElements();

    if (session == null) {
        return;
    }

    CyNetworkView view = session.getNetworkView();
    CyNetwork model = view.getModel();
    CyTable table = model.getDefaultNodeTable();
    SafeUtil.getStringColumnNames(table)
            .forEach(name -> {
                nodeIdsModel.addElement(name);
            });

    nodeIds.setSelectedItem(session.getIdColumn());
}
 

import org.cytoscape.view.model.CyNetworkView; //导入依赖的package包/类
void setNetworkView(CyNetworkView view) {
    if (view == null) {
        setSession(null);
        return;
    }

    long suid = view.getSUID();
    synchronized (sessionMutex) {
        SafeSession session = sessionsBySuid.get(suid);
        if (session == null) {
            session = createNewSession(view);
            sessionsBySuid.put(suid, session);

            CyNetwork network = view.getModel();
            CyTable nodeTable = network.getDefaultNodeTable();
            sessionsBySuid.put(nodeTable.getSUID(), session);
        }
        setSession(session);
    }
}
 

import org.cytoscape.view.model.CyNetworkView; //导入依赖的package包/类
void serializeSession(CyTable dataTable,
                      SafeSession session) {
    CyNetworkView networkView = session.getNetworkView();
    CyNetwork network = networkView.getModel();
    CyTable networkTable = network.getDefaultNetworkTable();
    CyRow row = networkTable.getRow(network.getSUID());

    checkColumn(networkTable, DATA_TABLE_COLUMN, Long.class);
    Long suid = dataTable.getSUID();
    row.set(DATA_TABLE_COLUMN, suid);

    CyRow viewRow = dataTable.getRow(networkView.getSUID());
    try (StringWriter writer = new StringWriter()) {
        toJson(session, writer);
        String json = writer.toString();
        viewRow.set(SAFE_DATA_COLUMN, json);
    } catch (IOException e) {
        e.printStackTrace();
    }
}
 

import org.cytoscape.view.model.CyNetworkView; //导入依赖的package包/类
public LongObjectMap<SafeSession> loadFromSession(CySession cySession) throws IOException {

        CyTable dataTable = cySession.getTables()
                                     .stream()
                                     .map(metadata -> metadata.getTable())
                                     .filter(table -> DATA_TABLE_TITLE.equals(table.getTitle()))
                                     .findFirst()
                                     .orElse(null);

        LongObjectMap<SafeSession> sessions = new LongObjectHashMap<>();
        if (dataTable == null) {
            return sessions;
        }

        for (CyRow row : dataTable.getAllRows()) {
            String json = row.get(SAFE_DATA_COLUMN, String.class);
            SafeSession session = parseSession(json);

            Long oldSuid = row.get(CyIdentifiable.SUID, Long.class);
            CyNetworkView view = cySession.getObject(oldSuid, CyNetworkView.class);
            session.setNetworkView(view);
            sessions.put(view.getSUID(), session);
        }
        return sessions;
    }
 

import org.cytoscape.view.model.CyNetworkView; //导入依赖的package包/类
public static CoordinateData forNodes(CyNetworkView networkView, Collection<CyNode> nodes) {
	double xmin = 100000000;
	double xmax = -100000000;
	double ymin = 100000000;
	double ymax = -100000000;
	
	Map<CyNode,double[]> coordinates = new HashMap<>();
	Map<CyNode,Double> radii = new HashMap<>();
	
	for(CyNode node : nodes) {
		View<CyNode> nodeView = networkView.getNodeView(node);
		if(nodeView != null) {
			double x = nodeView.getVisualProperty(BasicVisualLexicon.NODE_X_LOCATION);
			double y = nodeView.getVisualProperty(BasicVisualLexicon.NODE_Y_LOCATION);
			double radius = nodeView.getVisualProperty(BasicVisualLexicon.NODE_WIDTH);
			
			coordinates.put(node, new double[]{x,y});
			radii.put(node, radius);
			
			xmin = Double.min(xmin, x);
			xmax = Double.max(xmax, x);
			ymin = Double.min(ymin, y);
			ymax = Double.max(ymax, y);
		}
	}
	
	return new CoordinateData(xmin, xmax, ymin, ymax, coordinates, radii);
}
 

import org.cytoscape.view.model.CyNetworkView; //导入依赖的package包/类
/**
 * This is a huge hack to get around a bug in cytoscape.
 * All groups must be expanded before the session is saved.
 */
private void expandAllClusters() {
	Collection<CyNetworkView> networkViews = 
		modelManagerProvider.get()
		.getNetworkViewSets()
		.stream()
		.map(NetworkViewSet::getNetworkView)
		.collect(Collectors.toSet());
	
	if(networkViews.isEmpty())
		return;
	
	TaskIterator tasks = getExpandTasks(networkViews);
	
	Semaphore semaphore = new Semaphore(0);
	dialogTaskManager.execute(tasks, TaskTools.allFinishedObserver(() -> semaphore.release()));
	
	// We need to block while the groups are expanding because this must happen before the session is saved.
	semaphore.acquireUninterruptibly();
}
 

import org.cytoscape.view.model.CyNetworkView; //导入依赖的package包/类
public void exportModel() {
	for(CyNetwork network: networkManager.getNetworkSet()) {
		CyTable asTable = createAnnotationSetTable(network);
		CyTable clusterTable = createClusterTable(network);
		
		Ids ids = new Ids();
		
		Collection<CyNetworkView> networkViews = networkViewManager.getNetworkViews(network);
		for(CyNetworkView networkView : networkViews) {
			Optional<NetworkViewSet> nvs = modelManagerProvider.get().getExistingNetworkViewSet(networkView);
			if(nvs.isPresent()) {
				try {
					exportModel(nvs.get(), asTable, clusterTable, ids);
				}catch(Exception ex) {
					ex.printStackTrace();
				}
				continue;
			}
		}
	}
}
 

import org.cytoscape.view.model.CyNetworkView; //导入依赖的package包/类
@Override
public void run(TaskMonitor taskMonitor) {
	taskMonitor.setTitle(BuildProperties.APP_NAME);
	taskMonitor.setStatusMessage("Removing Annotations");
	
	CyNetworkView networkView = networkViewSet.getNetworkView();
	List<Annotation> annotations = annotationManager.getAnnotations(networkView);
	if(annotations != null) { // seriously?
		for(Annotation annotation : annotations) {
			try {
				SwingUtilities.invokeAndWait(annotation::removeAnnotation);
			} catch (Exception e) {}
		}
	}
	
	for(Cluster cluster : networkViewSet.getAllClusters()) {
		annotationRenderer.removeShapeAnnoation(cluster);
		annotationRenderer.removeTextAnnotation(cluster);
	}
}
 

import org.cytoscape.view.model.CyNetworkView; //导入依赖的package包/类
private Map<String,Collection<CyNode>> runClusterMaker(Optional<Double> cutoff) {
	CyNetworkView networkView = params.getNetworkView();
	CyNetwork network = networkView.getModel();
	boolean hasHidden = hasHiddenNodes(networkView);
	if(hasHidden) {
		Collection<CyNode> visibleNodes = getVisibleNodes(networkView);
		CreateSubnetworkTask subnetworkTask = subnetworkTaskFactory.create(network, visibleNodes);
		ResultObserver<CyNetwork> observer = new ResultObserver<>(subnetworkTask, CyNetwork.class);
		syncTaskManager.execute(new TaskIterator(subnetworkTask), observer);
		network = observer.getResults().get();
		networkManager.addNetwork(network, false);
	}
	
	RunClusterMakerTaskFactory clusterMakerTaskFactory = 
			clusterMakerFactoryFactory.create(network, params.getClusterAlgorithm(), params.getClusterMakerEdgeAttribute(), cutoff.orElse(null));
	RunClusterMakerResultObserver clusterResultObserver = new RunClusterMakerResultObserver();
	TaskIterator tasks = clusterMakerTaskFactory.createTaskIterator(clusterResultObserver);
	syncTaskManager.execute(tasks);
	Map<String,Collection<CyNode>> result =  clusterResultObserver.getResult();
	
	if(hasHidden) {
		networkManager.destroyNetwork(network);
	}
	
	return result;
}
 

import org.cytoscape.view.model.CyNetworkView; //导入依赖的package包/类
/**
 * This is fast because no events are fired while the summary network is being built. 
 * The summary network and view are registered at the end.
 */
@Override
public void run(TaskMonitor taskMonitor) {
	taskMonitor.setTitle(BuildProperties.APP_NAME);
	taskMonitor.setStatusMessage(SummaryNetworkAction.TITLE);
	
	
	CyNetwork originNetwork = annotationSet.getParent().getNetwork();
	List<SummaryCluster> summaryClusters = getSummaryClusters();
	
	// create summary network
	SummaryNetwork summaryNetwork = createSummaryNetwork(originNetwork, summaryClusters);
	
	// create summary network view
	CyNetworkView summaryNetworkView = createNetworkView(summaryNetwork);
	
	// apply visual style
	applyVisualStyle(annotationSet.getParent().getNetworkView(), summaryNetworkView, summaryNetwork);
	
	// register
	networkManager.addNetwork(summaryNetwork.network);
	networkViewManager.addNetworkView(summaryNetworkView);
	summaryNetworkView.fitContent();
	
	resultNetwork = summaryNetwork.network;
}
 

import org.cytoscape.view.model.CyNetworkView; //导入依赖的package包/类
private void applyVisualStyle(CyNetworkView originNetworkView, CyNetworkView summaryNetworkView, SummaryNetwork summaryNetwork) {
	VisualStyle vs = visualMappingManager.getVisualStyle(originNetworkView);
	
	for(View<CyNode> nodeView : summaryNetworkView.getNodeViews()) {
		// Label
		String name = summaryNetworkView.getModel().getRow(nodeView.getModel()).get("name", String.class);
		nodeView.setLockedValue(BasicVisualLexicon.NODE_LABEL, name);
		
		// Node size
		CyNode node = nodeView.getModel();
		SummaryCluster cluster = summaryNetwork.getClusterFor(node);
		int numNodes = cluster.getNodes().size();
		nodeView.setLockedValue(BasicVisualLexicon.NODE_SIZE, (double)numNodes);
	}
	
	visualMappingManager.setVisualStyle(vs, summaryNetworkView);
}
 

import org.cytoscape.view.model.CyNetworkView; //导入依赖的package包/类
private CyNetworkView getNetworkView() throws IllegalArgumentException {
	if(network == null) {
		network = applicationManager.getCurrentNetwork();
		if(network == null)
			throw new IllegalArgumentException("Please create a network first.");
	}
	else {
		// Unfortunatly clusterMaker2 is buggy regarding the network parameter,
		// the only way to get clusterMaker2 to run without problems is to make the desired network the current one.
		applicationManager.setCurrentNetwork(network);
	}
	
	Collection<CyNetworkView> netViews = networkViewManager.getNetworkViews(network);
	if(netViews == null || netViews.isEmpty())
		throw new IllegalArgumentException("Selected network does not have a view.");
	
	return netViews.iterator().next();
}