本文整理汇总了Java中org.pathvisio.core.model.Pathway类的典型用法代码示例。如果您正苦于以下问题:Java Pathway类的具体用法?Java Pathway怎么用?Java Pathway使用的例子?那么恭喜您, 这里精选的类代码示例或许可以为您提供帮助。
Pathway类属于org.pathvisio.core.model包,在下文中一共展示了Pathway类的15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: loadGexCache
import org.pathvisio.core.model.Pathway; //导入依赖的package包/类
/**
* Load the Gex cache for the current pathway. Only starts loading
* when an expression dataset is available and a pathway is open.
*/
public void loadGexCache() {
final CachedData gex = gexManager.getCachedData();
final Pathway p = swingEngine.getEngine().getActivePathway();
if(p != null && gex != null) {
try
{
gex.clearCache();
gex.setMapper (swingEngine.getGdbManager().getCurrentGdb());
gex.preSeed(p.getDataNodeXrefs());
gex.preSeed(p.getLineXrefs());
swingEngine.getEngine().getActiveVPathway().redraw();
}
catch (DataException e)
{
Logger.log.error ("Exception while caching expression data ", e);
}
}
}
示例2: fromModel
import org.pathvisio.core.model.Pathway; //导入依赖的package包/类
/**
* Maps the contents of a pathway to this VPathway
*/
public void fromModel(Pathway aData)
{
Logger.log.trace("Create view structure");
data = aData;
for (PathwayElement o : data.getDataObjects())
{
fromModelElement(o);
}
// data.fireObjectModifiedEvent(new PathwayEvent(null,
// PathwayEvent.MODIFIED_GENERAL));
fireVPathwayEvent(new VPathwayEvent(this, VPathwayEventType.MODEL_LOADED));
data.addListener(this);
undoManager.setPathway(data);
addScheduled();
Logger.log.trace("Done creating view structure");
}
示例3: addElements
import org.pathvisio.core.model.Pathway; //导入依赖的package包/类
public PathwayElement[] addElements(Pathway p, double mx, double my) {
PathwayElement e = PathwayElement.createPathwayElement(ObjectType.SHAPE);
e.setShapeType(type);
e.setMCenterX(mx);
e.setMCenterY(my);
e.setMWidth(1);
e.setMHeight(1);
e.setRotation(0);
e.setGraphId(p.getUniqueGraphId());
addElement(e, p);
//brace
// gdata.setOrientation(OrientationType.RIGHT);
return new PathwayElement[] { e };
}
示例4: exportPathway
import org.pathvisio.core.model.Pathway; //导入依赖的package包/类
/**
* Exports given pathway to file. This function doesn't act on the active pathway.
* @param pathway pathway to export
* @param file file to write to.
* @returns a list of warnings that occurred during export, or an empty list if there were none.
*/
public List<String> exportPathway(File file, Pathway pathway, String exporterName) throws ConverterException
{
Logger.log.trace("Exporting pathway to " + file);
Set<PathwayExporter> set = getPathwayExporters(file);
try {
for ( PathwayExporter pExporter : set){
if (pExporter.getName().equals(exporterName))
{
// System.out.println(pExporter.getName());
pExporter.doExport(file, pathway);
return pExporter.getWarnings();
}
}
} catch (Exception e) {
// TODO Auto-generated catch block
e.printStackTrace();
}
return null;
}
示例5: usesOldEnsembl
import org.pathvisio.core.model.Pathway; //导入依赖的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6: convertEnsembl
import org.pathvisio.core.model.Pathway; //导入依赖的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7: applicationEvent
import org.pathvisio.core.model.Pathway; //导入依赖的package包/类
public void applicationEvent(ApplicationEvent e)
{
switch (e.getType())
{
case PATHWAY_OPENED:
{
Pathway pwy = swingEngine.getEngine().getActivePathway();
if (usesOldEnsembl(pwy))
{
int result = JOptionPane.showConfirmDialog(
swingEngine.getFrame(),
"This Pathway uses the old style references to Ensembl.\nDo you want" +
"to update this pathway?\n\n" +
"This update is required if you want to use the latest gene databases.",
"Update pathway?", JOptionPane.YES_NO_OPTION);
if (result == JOptionPane.YES_OPTION)
{
convertEnsembl(pwy);
}
}
}
}
}
示例8: savePathway
import org.pathvisio.core.model.Pathway; //导入依赖的package包/类
public boolean savePathway()
{
Pathway pathway = engine.getActivePathway();
boolean result = true;
// Overwrite the existing xml file.
// If the target file is read-only, let the user select a new pathway
if (pathway.getSourceFile() != null && pathway.getSourceFile().canWrite())
{
try {
engine.savePathway(pathway.getSourceFile());
} catch (ConverterException e) {
handleConverterException(e.getMessage(), null, e);
}
}
else {
result = savePathwayAs();
}
return result;
}
示例9: canDiscardPathway
import org.pathvisio.core.model.Pathway; //导入依赖的package包/类
/**
* Call this when the user is about to perform an
* action that could lead to discarding the current pathway.
* (For example when creating a new pathway)
*
* Checks if there are any unsaved changes, and
* asks the user if they want to save those changes.
*
* @return true if the user allows discarding the pathway, possibly after saving.
*/
public boolean canDiscardPathway()
{
Pathway pathway = engine.getActivePathway();
// checking not necessary if there is no pathway or if pathway is not changed.
if (pathway == null || !pathway.hasChanged()) return true;
int result = JOptionPane.showConfirmDialog
(frame, "Save changes?",
"Your pathway has changed. Do you want to save?",
JOptionPane.YES_NO_CANCEL_OPTION,
JOptionPane.QUESTION_MESSAGE);
if (result == JOptionPane.CANCEL_OPTION) // cancel
{
return false;
}
else if (result == JOptionPane.YES_OPTION) // yes
{
// return false if save is cancelled.
return (savePathway());
}
// yes or no
return true;
}
示例10: parsePathwayInfoGpml
import org.pathvisio.core.model.Pathway; //导入依赖的package包/类
/**
* conversion only GPML vocabulary
*/
public static Resource parsePathwayInfoGpml(Pathway p, String wpId, String revision, Model model) {
Resource pwyRes = model.createResource(Utils.WP_RDF_URL + "/Pathway/" + wpId + "_r" + revision.trim().replaceAll(" ", "_"));
// Required Attributes
pwyRes.addLiteral(Gpml.ORGANISM, p.getMappInfo().getOrganism());
pwyRes.addLiteral(Gpml.BOARD_HEIGHT, p.getMappInfo().getMBoardHeight());
pwyRes.addLiteral(Gpml.BOARD_WIDTH, p.getMappInfo().getMBoardWidth());
pwyRes.addLiteral(Gpml.NAME, p.getMappInfo().getMapInfoName());
// Optional Attributes
if(p.getMappInfo().getVersion() != null) pwyRes.addLiteral(Gpml.VERSION, p.getMappInfo().getVersion());
if(p.getMappInfo().getCopyright() != null) pwyRes.addLiteral(Gpml.LICENSE, p.getMappInfo().getCopyright());
if(p.getMappInfo().getAuthor() != null) pwyRes.addLiteral(Gpml.AUTHOR, p.getMappInfo().getAuthor());
if(p.getMappInfo().getEmail() != null) pwyRes.addLiteral(Gpml.EMAIL, p.getMappInfo().getEmail());
if(p.getMappInfo().getMaintainer() != null) pwyRes.addLiteral(Gpml.MAINTAINER, p.getMappInfo().getMaintainer());
if(p.getMappInfo().getLastModified() != null) pwyRes.addLiteral(Gpml.LAST_MODIFIED, p.getMappInfo().getLastModified());
if(p.getMappInfo().getMapInfoDataSource() != null) pwyRes.addLiteral(Gpml.DATA_SOURCE, p.getMappInfo().getMapInfoDataSource());
for(String s : p.getMappInfo().getBiopaxRefs()) {
pwyRes.addLiteral(Gpml.BIOPAX_REF, s);
}
return pwyRes;
}
示例11: convertGpml
import org.pathvisio.core.model.Pathway; //导入依赖的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12: test
import org.pathvisio.core.model.Pathway; //导入依赖的package包/类
@Test
public void test() throws ConverterException, IOException {
client.login(props.getProperty("username"), props.getProperty("password"));
String id = "WP4";
WSPathway p = client.getPathway(id);
Pathway pathway = new Pathway();
pathway.readFromXml(IOUtils.toInputStream(p.getGpml(), "UTF-8"), true);
PathwayElement pel = PathwayElement.createPathwayElement(ObjectType.DATANODE);
pel.setGraphId(pathway.getUniqueGraphId());
pel.setDataNodeType(DataNodeType.GENEPRODUCT);
pel.setMCenterX(65);
pel.setMCenterY(65);
pel.setMHeight(20);
pel.setMWidth(80);
pel.setTextLabel("Test");
pel.setElementID("12334");
pathway.add(pel);
String newRevision = client.updatePathway(p.getId(), pathway, "add data node test", Integer.parseInt(p.getRevision()));
assertTrue(Integer.parseInt(newRevision) > Integer.parseInt(p.getRevision()));
}
示例13: scanPathway
import org.pathvisio.core.model.Pathway; //导入依赖的package包/类
protected Result scanPathway(File pathwayFile) throws BotException {
try {
Pathway p = new Pathway();
p.readFromXml(pathwayFile, true);
String comment = null;
for(Comment c : p.getMappInfo().getComments()) {
if(COMMENT_DESCRIPTION.equals(c.getSource())) {
comment = c.getComment();
break;
}
}
boolean hasDescr = comment != null && !"".equals(comment);
WSPathwayInfo wsp = getCache().getPathwayInfo(pathwayFile);
return new DescriptionResult(wsp, hasDescr);
} catch(Exception e) {
throw new BotException(e);
}
}
示例14: scanPathway
import org.pathvisio.core.model.Pathway; //导入依赖的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15: scanPathway
import org.pathvisio.core.model.Pathway; //导入依赖的package包/类
@Override
protected Result scanPathway(File pathwayFile) throws BotException {
try {
Pathway p = new Pathway();
p.readFromXml(pathwayFile, true);
boolean hasRef = false;
for(BiopaxNode bpe : p.getBiopaxElementManager().getElements()) {
if(bpe instanceof PublicationXref) {
hasRef = true;
break;
}
}
WSPathwayInfo wsp = getCache().getPathwayInfo(pathwayFile);
return new LiteratureResult(wsp, hasRef);
} catch(Exception e) {
throw new BotException(e);
}
}