Java ObjectType.DATANODE属性代码示例

/**
 * generates html for a given PathwayElement. Combines the base
 * header with fragments from all BackpageHooks into one html String.
 */
public String getBackpageHTML(PathwayElement e)
{
	if (e == null) {
		return "<p>No pathway element is selected.</p>";
	} else if (e.getObjectType() != ObjectType.DATANODE && e.getObjectType() != ObjectType.LINE) {
		return "<p>Backpage is not available for this type of element.<BR>Only DataNodes or Interactions can have a backpage.</p>";
	} else if (e.getDataSource() == null || e.getXref().getId().equals("")) {
		return "<p>There is no annotation for this pathway element defined.</p>";
	}
	StringBuilder builder = new StringBuilder(backpagePanelHeader);
	for (BackpageHook h : hooks)
	{
		builder.append(h.getHtml(e));
	}
	builder.append ("</body></html>");
	return builder.toString();
}
 

private boolean usesOldEnsembl(Pathway pwy)
{
	Organism org = Organism.fromLatinName(pwy.getMappInfo().getOrganism());
	if (!ensSpecies.containsKey(org))
		return false; // this pwy is not one of the species to be converted

	for (PathwayElement elt : pwy.getDataObjects())
	{
		if (elt.getObjectType() == ObjectType.DATANODE &&
				elt.getDataSource() == BioDataSource.ENSEMBL)
		{
			return true;
		}
	}
	return false;
}
 

/**
 * Ensembl considers each species database as separate,
 * and thus they should have separate system codes as well.
 * This method will convert generic Ensembl datanodes
 * to species specific datanodes if possible.
 */
private void convertEnsembl(Pathway pwy)
{
	Organism org = Organism.fromLatinName(pwy.getMappInfo().getOrganism());
	if (!ensSpecies.containsKey(org))
		return; // this pwy is not one of the species to be converted

	for (PathwayElement elt : pwy.getDataObjects())
	{
		if (elt.getObjectType() == ObjectType.DATANODE &&
				elt.getDataSource() == BioDataSource.ENSEMBL)
		{
			elt.setDataSource (ensSpecies.get (org));
		}
	}

}
 

/**
 * generates html for a given PathwayElement. Combines the base header with
 * fragments from all BackpageHooks into one html String.
 */
public String getAnnotationHTML(PathwayElement e) {
	if (e == null) {
		return "<p>No pathway element is selected.</p>";
	} else if (e.getObjectType() != ObjectType.DATANODE
			&& e.getObjectType() != ObjectType.LINE) {
		return "<p>It is currently not possible to annotate this type of pathway element." +
				"<BR>Only DataNodes and Interactions can be annotated.</p>";
	} else if (e.getDataSource() == null || e.getXref().getId().equals("")) {
		return "<p>This pathway element has not yet been annotated.</p>";
	}
	StringBuilder builder = new StringBuilder(backpagePanelHeader);
	for (DataHook h : hooks) {
		builder.append(h.getHtml(e));
	}
	builder.append("</body></html>");
	return builder.toString();
}
 

/**
 * Highlight all object but DataNodes and Groups. Only the first color
 * from the hashmap will be used.
 */
private void doHighlight() {
	for(VPathwayElement vpe : vPathway.getDrawingObjects()) {
		if(vpe instanceof Graphics) {
			PathwayElement pwe = ((Graphics)vpe).getPathwayElement();
			List<Color> elmColors = colors.get(pwe);
			if(elmColors != null && elmColors.size() > 0) {
				ObjectType ot = pwe.getObjectType();
				if(ot != ObjectType.DATANODE && ot != ObjectType.GROUP) {
					vpe.highlight(elmColors.get(0));
				}
			}
		}
	}
}
 

public static void main(String[] args) throws Exception {
	//Create a client to the WikiPathways web service
	URL wsURL = new URL("http://webservice.wikipathways.org");
	WikiPathwaysClient client = new WikiPathwaysClient(wsURL);
		
	//////////////////////////
	// EXAMPLE (FIND BY XREF)
	// Find a pathway by affymetrix probeset
	Xref affy = new Xref("201746_at", DataSource.getBySystemCode("X"));
		
	System.out.println("Searching for pathways with Affymetrix probeset " + affy);

	WSSearchResult[] result = client.findPathwaysByXref(affy);
	for(WSSearchResult r : result) {
		System.out.println("Found pathway: " + r.getName() + " (" + r.getSpecies() + ")");
	}
		
	////////////////////////////////////
	// EXAMPLE (GET PATHWAY - SAVE GPML)
	//Download a pathway from WikiPathways
	WSPathway wsPathway = client.getPathway("WP274");
		
	System.out.println("Downloaded pathway " + wsPathway.getName() + ", revision " + wsPathway.getRevision());
		
	//Create a pathway object
	Pathway pathway = WikiPathwaysClient.toPathway(wsPathway);
		
	//Get all genes, proteins and metabolites for a pathway
	for(PathwayElement pwElm : pathway.getDataObjects()) {
		//Only take elements with type DATANODE (genes, proteins, metabolites)
		if(pwElm.getObjectType() == ObjectType.DATANODE) {
			//Print information to the screen
			System.out.println(pwElm.getTextLabel());
			System.out.println("\t" + pwElm.getXref());
			System.out.println("\t" + pwElm.getDataNodeType());
		}
	}
		
	//Save the pathway locally
	pathway.writeToXml(new File(wsPathway.getName() + ".gpml"), true);
		
	///////////////////////////////
	// EXAMPLE (LIST ALL PATHWAYS)
	//Print info for all WikiPathways pathways
	WSPathwayInfo[] pathwayList = client.listPathways();
		
	for(WSPathwayInfo pathwayInfo : pathwayList) {
		System.out.println("Pathway:");
		System.out.println("\tIdentifier:\t" + pathwayInfo.getId());
		System.out.println("\tName:\t" + pathwayInfo.getName());
		System.out.println("\tOrganism:\t" + pathwayInfo.getSpecies());
	}
}