Java Pathway.getDataObjects方法代码示例

import org.pathvisio.core.model.Pathway; //导入方法依赖的package包/类
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;
}
 

import org.pathvisio.core.model.Pathway; //导入方法依赖的package包/类
/**
 * 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));
		}
	}

}
 

import org.pathvisio.core.model.Pathway; //导入方法依赖的package包/类
public static void convertGpml(Pathway p, String wpId, String revision, Model pathwayModel) {
	Resource pathwayRes = PathwayConverter.parsePathwayInfoGpml(p, wpId, revision, pathwayModel);
	DataHandlerGpml data = new DataHandlerGpml(p, pathwayRes);
	
	for(PathwayElement e : p.getDataObjects()) {
		if(e.getObjectType().equals(ObjectType.DATANODE)) {
			DataNodeConverter.parseDataNodesGpml(e, pathwayModel, data);
		} else if(e.getObjectType().equals(ObjectType.STATE)) {
			StateConverter.parseStateGpml(e, pathwayModel, data);
		} else if(e.getObjectType().equals(ObjectType.LINE)) {
			InteractionConverter.parseInteractionGpml((MLine) e, pathwayModel, data);
		} else if(e.getObjectType().equals(ObjectType.GRAPHLINE)) {
			GraphicalLineConverter.parseInteractionGpml((MLine) e, pathwayModel, data);
		} else if(e.getObjectType().equals(ObjectType.LABEL)) {
			LabelConverter.parseLabelGpml(e, pathwayModel, data);
		} else if(e.getObjectType().equals(ObjectType.SHAPE)) {
			ShapeConverter.parseShapeGpml(e, pathwayModel, data);
		} else if(e.getObjectType().equals(ObjectType.GROUP)) {
			GroupConverter.parseGroupGpml((MGroup) e, pathwayModel, data);
		} else if(e.getObjectType().equals(ObjectType.INFOBOX)) {
			InfoBoxConverter.parseInfoBoxGpml(e, pathwayModel, data);
		}
	}
}
 

import org.pathvisio.core.model.Pathway; //导入方法依赖的package包/类
protected Result scanPathway(File pathwayFile) throws BotException {
	try {
		ConnectorBotResult report = new ConnectorBotResult(
				getCache().getPathwayInfo(pathwayFile));
		Pathway pathway = new Pathway();
		pathway.readFromXml(pathwayFile, true);

		String orgName = pathway.getMappInfo().getOrganism();
		Organism org = Organism.fromLatinName(orgName);
		if(org == null) org = Organism.fromShortName(orgName);

		for(PathwayElement pwe : pathway.getDataObjects()) {
			if(pwe.getObjectType() == ObjectType.LINE) {
				boolean valid =
					pwe.getMStart().isLinked() &&
					pwe.getMEnd().isLinked();

				report.addLine(pwe, valid);
			}
		}

		return report;
	} catch(Exception e) {
		throw new BotException(e);
	}
}
 

import org.pathvisio.core.model.Pathway; //导入方法依赖的package包/类
/**
 * Creates a pathway from the data in the provided {@link Transferable}.
 * @param t
 * @return
 * @throws ConverterException
 * @throws MalformedURLException
 * @throws UnsupportedFlavorException
 * @throws IOException
 */
public static Pathway pathwayFromTransferable(Transferable t) throws ConverterException, MalformedURLException, UnsupportedFlavorException, IOException {
	Pathway pnew = new Pathway();

	String xml = getText(t);
	if(xml != null) {
		GpmlFormat.readFromXml(pnew, new StringReader(xml), true);

		List<PathwayElement> elements = new ArrayList<PathwayElement>();
		for(PathwayElement elm : pnew.getDataObjects()) {
			if(elm.getObjectType() != ObjectType.MAPPINFO) {
				elements.add(elm);
			} else {
				//Only add mappinfo if it's not generated by the transferable
				String source = elm.getMapInfoDataSource();
				if(!PathwayTransferable.INFO_DATASOURCE.equals(source)) {
					elements.add(elm);
				}
			}
		}
		return pnew;
	}

	URL url = getFileURL(t);
	if(url != null) {
		File file = new File(url.getFile());
		pnew.readFromXml(file, true);
		return pnew;
	}
	return null;
}
 

import org.pathvisio.core.model.Pathway; //导入方法依赖的package包/类
public void testCopyPaste()
	{
    	Pathway pTarget = new Pathway();
    	VPathway vpTarget = new VPathway(null);
    	vpTarget.fromModel(pTarget);

		vPwy.selectObject(vDn);
		vPwy.copyToClipboard();

		vpTarget.pasteFromClipboard();

		PathwayElement pasted = null;
		for(PathwayElement e : pTarget.getDataObjects()) {
			if("1234".equals(e.getElementID())) {
				pasted = e;
			}
		}
		//TODO: does not work if VPathwayWrapper is not VPathwaySwing.
//		assertNotNull(pasted);

		//Now copy mappinfo
//		PathwayElement info = pSource.getMappInfo();
//		info.setMapInfoName("test pathway");
//		vpSource.selectObject(vpSource.getPathwayElementView(info));
//		vpSource.copyToClipboard();

//		vpTarget.pasteFromClipboard();

		//test if mappinfo has been pasted to the target pathway
//		assertTrue("test pathway".equals(pTarget.getMappInfo().getMapInfoName()));
    }
 

import org.pathvisio.core.model.Pathway; //导入方法依赖的package包/类
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());
	}
}
 

import org.pathvisio.core.model.Pathway; //导入方法依赖的package包/类
/**
 * Test if tag is removed when needed.
 */
private void removeConnectorTag(String pwId) {
	try {
		WSPathway wsp = client.getPathway(pwId);
		//Connect the line and update the pathway
		Pathway pathway = WikiPathwaysClient.toPathway(wsp);
		PathwayElement line = null;
		for(PathwayElement pwe : pathway.getDataObjects()) {
			if(pwe.getObjectType() == ObjectType.LINE) {
				line = pwe;
				break;
			}
		}
		assertNotNull(line);

		PathwayElement e1 = PathwayElement.createPathwayElement(ObjectType.DATANODE);
		PathwayElement e2 = PathwayElement.createPathwayElement(ObjectType.DATANODE);
		pathway.add(e1);
		pathway.add(e2);
		e1.setGeneratedGraphId(); e2.setGeneratedGraphId();
		line.getMStart().setGraphRef(e1.getGraphId());
		line.getMEnd().setGraphRef(e2.getGraphId());
		client.updatePathway(pwId, pathway, "junit test - connecting line",
				Integer.parseInt(wsp.getRevision()));

		//Run the bot, it should remove the tag
		Bot bot = createConnectorBot();
		Collection<Result> results = bot.scan();
		BotReport report = bot.createReport(results);
		bot.applyCurationTags(results, report);

		//Check if the pathway is tagged
		WSCurationTag[] tags = client.getCurationTags(wsp.getId());
		boolean found = false;
		for(WSCurationTag t : tags) {
			if(t.getName().equals(ConnectorBot.CURATIONTAG)) {
				found = true;
				break;
			}
		}
		assertFalse("Should have removed connector tag", found);
	} catch (Exception e) {
		e.printStackTrace();
		fail(e.getMessage());
	}
}
 

import org.pathvisio.core.model.Pathway; //导入方法依赖的package包/类
/**
 * Test if override mechanism works properly.
 */
public void overrideConnectorTag(String pwId) {
	try {
		WSPathway wsp = client.getPathway(pwId);
		Pathway pathway = WikiPathwaysClient.toPathway(wsp);

		//Reset the line
		for(PathwayElement pwe : new ArrayList<PathwayElement>(pathway.getDataObjects())) {
			switch(pwe.getObjectType()) {
			case DATANODE:
			case LINE:
				pathway.remove(pwe);
				break;
			}
		}
		PathwayElement line = PathwayElement.createPathwayElement(ObjectType.LINE);
		pathway.add(line);
		client.updatePathway(pwId, pathway, "junit test", Integer.parseInt(wsp.getRevision()));

		//Re-add the tag
		addConnectorTag(pwId);

		//Manually remove the tag, it shouldn't be re-added
		client.removeCurationTag(pwId, ConnectorBot.CURATIONTAG);

		//Try to re-add the tag, it should fail
		//Run the bot, it should tag the created pathway
		Bot bot = createConnectorBot();
		Collection<Result> results = bot.scan();
		BotReport report = bot.createReport(results);
		bot.applyCurationTags(results, report);

		WSCurationTag[] tags = client.getCurationTags(pwId);
		boolean found = false;
		for(WSCurationTag t : tags) {
			if(t.getName().equals(ConnectorBot.CURATIONTAG)) {
				found = true;
				break;
			}
		}
		assertFalse("Should not have added connector tag", found);

		//Change the number of unconnected lines, the tag should be added again
		PathwayElement line2 = PathwayElement.createPathwayElement(ObjectType.LINE);
		pathway.add(line2);

		wsp = client.getPathway(pwId);
		client.updatePathway(pwId, pathway, "junit test", Integer.parseInt(wsp.getRevision()));

		addConnectorTag(pwId);
	} catch(Exception e) {
		e.printStackTrace();
		fail(e.getMessage());
	}
}