本文整理汇总了Java中org.pathvisio.core.model.Pathway.getDataObjects方法的典型用法代码示例。如果您正苦于以下问题:Java Pathway.getDataObjects方法的具体用法?Java Pathway.getDataObjects怎么用?Java Pathway.getDataObjects使用的例子?那么恭喜您, 这里精选的方法代码示例或许可以为您提供帮助。您也可以进一步了解该方法所在类org.pathvisio.core.model.Pathway
的用法示例。
在下文中一共展示了Pathway.getDataObjects方法的9个代码示例,这些例子默认根据受欢迎程度排序。您可以为喜欢或者感觉有用的代码点赞,您的评价将有助于系统推荐出更棒的Java代码示例。
示例1: usesOldEnsembl
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;
}
示例2: convertEnsembl
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));
}
}
}
示例3: convertGpml
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);
}
}
}
示例4: scanPathway
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);
}
}
示例5: pathwayFromTransferable
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;
}
示例6: testCopyPaste
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()));
}
示例7: main
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());
}
}
示例8: removeConnectorTag
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());
}
}
示例9: overrideConnectorTag
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());
}
}