Java Interaction类代码示例

import org.biopax.paxtools.model.level3.Interaction; //导入依赖的package包/类
private void createInteractionEdges(CyNetwork network) {
	//  Extract the List of all Interactions
	Collection<Interaction> interactionList = model.getObjects(Interaction.class);

	for (Interaction itr : interactionList) {	
		if(log.isTraceEnabled()) {
			log.trace("Mapping " + itr.getModelInterface().getSimpleName() 
				+ " edges : " + itr.getUri());
		}
		
		if (itr instanceof Conversion) {
			addConversionInteraction(network, (Conversion)itr);
		} else if (itr instanceof Control) {
			addControlInteraction(network, (Control) itr);
		} else {
			addPhysicalInteraction(network, itr);
		}
	}
}
 

import org.biopax.paxtools.model.level3.Interaction; //导入依赖的package包/类
/**
 * Creates a name for to the BioPAX model
 * using its top-level process name(s). 
 * 
 * @param model
 * @return
 */
public static String getName(Model model) {		
	StringBuffer modelName = new StringBuffer();
	
	Collection<Pathway> pws = ModelUtils.getRootElements(model, Pathway.class);
	for(Pathway pw: pws) {
			modelName.append(" ").append(getName(pw)); 
	}
	
	if(modelName.length()==0) {
		Collection<Interaction> itrs = ModelUtils.getRootElements(model, Interaction.class);
		for(Interaction it: itrs) {
			modelName.append(" ").append(getName(it));
		}	
	}
	
	if(modelName.length()==0) {
		modelName.append(model.getXmlBase());
	}
	
	String name = modelName.toString().trim();

	return name;
}
 

import org.biopax.paxtools.model.level3.Interaction; //导入依赖的package包/类
private void addPhysicalInteraction(CyNetwork network, Interaction interactionElement) {
	//  Add all Participants
	Collection<Entity> participantElements = interactionElement.getParticipant();
	for (Entity participantElement : participantElements) {
		linkNodes(network, interactionElement, participantElement, "participant");
	}
}
 

import org.biopax.paxtools.model.level3.Interaction; //导入依赖的package包/类
private JTextPane createSummaryHtmlTextPane() {
    final JTextPane textPane = new JTextPane();
    textPane.setEditable(false);
    textPane.setBorder(new EmptyBorder(7,7,7,7));
    textPane.setContentType("text/html");
    textPane.putClientProperty(JEditorPane.HONOR_DISPLAY_PROPERTIES, Boolean.TRUE);
    textPane.addHyperlinkListener(new HyperlinkListener() {
        public void hyperlinkUpdate(HyperlinkEvent hyperlinkEvent) {
            if (hyperlinkEvent.getEventType() == HyperlinkEvent.EventType.ACTIVATED) {
            	//import/create a network if the link is clicked
           		SearchHit currentItem = current;
           		String uri = hyperlinkEvent.getURL().toString();

	boolean isProccess = "Pathway".equalsIgnoreCase(currentItem.getBiopaxClass());
	if(!isProccess) {
		for(Class<? extends BioPAXElement> t : SimpleEditorMap.L3.getKnownSubClassesOf(Interaction.class)) {
			if(t.getSimpleName().equalsIgnoreCase(currentItem.getBiopaxClass())) {
				isProccess = true;
				break;
			}
		}
	}
           		if(!isProccess) {
    	        	// create new 'neighborhood' query for a physical entity or entity reference type hit;
		// use global organism and datasource filters
           			final CPathGraphQuery graphQuery = App.client.createGraphQuery()
           				.datasourceFilter(App.options.selectedDatasources())
           				.organismFilter(App.options.selectedOrganisms())
           				.sources(Collections.singleton(uri))
           				.kind(GraphType.NEIGHBORHOOD);
           			App.cyServices.taskManager.execute(new TaskIterator(
               			new NetworkAndViewTask(graphQuery, currentItem.toString())));
           		} else { // for a biological process (pathway or interaction), use '/get' command
           			final CPathGetQuery getQuery = App.client.createGetQuery()
           				.sources(Collections.singleton(uri));
           			App.cyServices.taskManager.execute(new TaskIterator(
               			new NetworkAndViewTask(getQuery, currentItem.toString())));
           		}
            }
        }
    });
    
    style(textPane);
    
    return textPane;
}