import org.cytoscape.model.CyTableUtil; //导入依赖的package包/类
private void createCluster(AnnotationSet annotationSet) {
	LabelMaker labelMaker = labelManager.get().getLabelMaker(annotationSet);
	if(!labelMaker.isReady()) {
		return;
	}
	
	List<CyNode> nodes = CyTableUtil.getNodesInState(networkView.getModel(), CyNetwork.SELECTED, true);
	CyNetwork network = networkView.getModel();
	
	// Remove selected nodes from existing clusters. Bug #37
	annotationSet.removeNodes(nodes);
			
	String label = labelMaker.makeLabel(network, nodes, annotationSet.getLabelColumn());
	Cluster cluster = annotationSet.createCluster(nodes, label, false);
	
	// It was the intention to only allow ModelEvents to be fired from inside the model package.
	// But the cluster is already selected and firing the event here is much simpler than 
	// re-selecting the nodes to get the event to fire.
	EventBus eventBus = eventBusProvider.get();
	eventBus.post(new ModelEvents.ClustersSelected(annotationSet, Collections.singleton(cluster)));
}
 

import org.cytoscape.model.CyTableUtil; //导入依赖的package包/类
private void createAnnotationSetAndCluster() {
	// Automatically create an annotation set
	ModelManager modelManager = modelManagerProvider.get();
	NetworkViewSet nvs = modelManager.getNetworkViewSet(networkView);
	List<CyNode> nodes = CyTableUtil.getNodesInState(networkView.getModel(), CyNetwork.SELECTED, true);
	String labelColumn = getLabelColumn();
	
	@SuppressWarnings("rawtypes")
	LabelMakerFactory labelMakerFactory = labelManagerProvider.get().getDefaultFactory();
	@SuppressWarnings("unchecked")
	LabelMaker labelMaker = labelMakerFactory.createLabelMaker(labelMakerFactory.getDefaultContext());
	String label = labelMaker.makeLabel(networkView.getModel(), nodes, labelColumn);
	
	String suggestedName = nvs.suggestName();
	AnnotationSetBuilder builder = nvs.getAnnotationSetBuilder(suggestedName, labelColumn);
	builder.addCluster(nodes, label, false);
	AnnotationSet as = builder.build();
	
	nvs.select(as);
}
 

import org.cytoscape.model.CyTableUtil; //导入依赖的package包/类
@Override
public void handleEvent(RowsSetEvent e) {
	if(safeRunner.shouldIgnore(EventType.SELECTION)) {
		return;
	}
	if(!e.containsColumn(CyNetwork.SELECTED))
		return;
	
	Optional<AnnotationSet> active = getActiveNetworkViewSet().flatMap(NetworkViewSet::getActiveAnnotationSet);
	if(active.isPresent()) {
		AnnotationSet annotationSet = active.get();
		CyNetwork network = annotationSet.getParent().getNetwork();
		
		if(network.getDefaultNodeTable().equals(e.getSource())) {
			List<Cluster> selectedClusters = new ArrayList<>();
			List<CyNode> selectedNodes = CyTableUtil.getNodesInState(network, CyNetwork.SELECTED, true);
			
			for(Cluster cluster : annotationSet.getClusters()) {
				if(selectedNodes.containsAll(cluster.getNodes())) {
					selectedClusters.add(cluster);
				}
			}
			
			// Fire event even when selectedClusters is empty
			postEventOffEDT(new ModelEvents.ClustersSelected(annotationSet, selectedClusters));
		}
	}
}
 

import org.cytoscape.model.CyTableUtil; //导入依赖的package包/类
public List<String> getSelectedElements() {
    List<CyNode> nodes = CyTableUtil.getNodesInState(network, CyNetwork.SELECTED, true);
    List<CyEdge> edges = CyTableUtil.getEdgesInState(network, CyNetwork.SELECTED, true);
    if(nodes.size() == 1 && edges.isEmpty()) {
        CyNode node = nodes.get(0);
        String nodeGOTerm = network.getRow(node).get(GOTermColumn, String.class);
        
        if (Unknown.equals(nodeGOTerm) || Unnanotated.equals(nodeGOTerm)) {
           return null;
        }
        
        return Arrays.asList(network.getRow(node).get(CyNetwork.NAME, String.class));
    } 
    else if (nodes.isEmpty() && edges.size() == 1) {
        CyEdge edge = edges.get(0);
        CyRow sourceRow = network.getRow(edge.getSource());
        CyRow targetRow = network.getRow(edge.getTarget());
        String sourceGOTerm = sourceRow.get(GOTermColumn, String.class);
        String targetGOTerm = targetRow.get(GOTermColumn, String.class);
        
        if (Unknown.equals(sourceGOTerm) || Unnanotated.equals(sourceGOTerm)
                || Unknown.equals(targetGOTerm) || Unnanotated.equals(targetGOTerm)) {
           return null;
        }
        
        return Arrays.asList(sourceRow.get(CyNetwork.NAME, String.class), targetRow.get(CyNetwork.NAME, String.class));
    }
    return null;
}
 

import org.cytoscape.model.CyTableUtil; //导入依赖的package包/类
@Override
public boolean collectParameters() {
	CyNetwork currNet = getPlugin().getCyApplicationManager().getCurrentNetwork();
	List<CyNode> selectedNodes = CyTableUtil.getNodesInState(currNet, "selected", true);
	
	if(selectedNodes.size() == 2){
		setFrom(selectedNodes.get(0));
		setTo(selectedNodes.get(1));
		setNet(currNet);
	} else {
		JOptionPane.showMessageDialog(plugin.getCySwingApplication().getJFrame(), "Please select only two nodes!");
	}
	
	return from != null && to != null && depth != null && net != null;
}
 

import org.cytoscape.model.CyTableUtil; //导入依赖的package包/类
@Override
public boolean isReady(CyNetworkView networkView) {
	List<CyNode> nodes = CyTableUtil.getNodesInState(networkView.getModel(), CyNetwork.SELECTED, true);
	return !nodes.isEmpty();
}
 

import org.cytoscape.model.CyTableUtil; //导入依赖的package包/类
@Override
public void actionPerformed(ActionEvent e) 
{
	MarrsProject project = projectMgr.getProject();
	CyNetwork myNet = mapper.createOrGetNetwork();
	
	String filter = project.getQueryParameterFilter(mq, "ID");			
	if ("uri-list".equals (filter))
	{
		// active nodes is the union of selected nodes and the right-clicked node.
		List<CyNode> activeNodes = new ArrayList<CyNode>();
		activeNodes.addAll (CyTableUtil.getNodesInState(myNet,"selected",true));
		if (!activeNodes.contains (clickedNode))
		{
			activeNodes.add (clickedNode);
		}
		
		CyTable nodeTable = myNet.getDefaultNodeTable();
		
		StringBuilder builder = new StringBuilder();
		String sep = "<";
	
		for (CyNode n : activeNodes)
		{
			String nid = nodeTable.getRow(n.getSUID()).get("id", String.class);
			builder.append (sep);
			builder.append (nid);
			sep = ">, <";
		}
		builder.append (">");
		
		project.setQueryParameter("ID", builder.toString());
	}
	else if ("uri".equals(filter))
	{
		project.setQueryParameter("ID", "<" + id + ">");
	}
	else if ("uri-bracketed".equals(filter))
	{
		project.setQueryParameter("ID", "<" + id + ">");
	}
	else
	{
		project.setQueryParameter("ID", id);
	}
	
	String qtext;
	try {
		QueryStatus result = ProjectDlg.run(mapper, project, frame, mq);
		if (!result.userCancelled && (result.resultNum == 0))
			JOptionPane.showMessageDialog(frame, "Zero results");
	} catch (MarrsException e2) {
		JOptionPane.showMessageDialog(frame, "<html>Error fetching results<br>" + StringUtils.escapeHtml(e2.getMessage()), "Error preparing query", JOptionPane.ERROR_MESSAGE);
	}
	catch (StreamException e1) {
		JOptionPane.showMessageDialog(frame, "<html>Error fetching results<br>" + StringUtils.escapeHtml(e1.getMessage()), "Error executing query", JOptionPane.ERROR_MESSAGE);
	}
	System.out.println ("Query done");
}