/**
* This method is used to dump all human pathway diagrams into a specified directory.
*
* @param dir
* @throws Exception
*/
public void dumpHumanPathwayDiagrams(File dir) throws Exception {
Collection<?> diagrams = adaptor.fetchInstancesByClass(ReactomeJavaConstants.PathwayDiagram);
SchemaClass cls = adaptor.fetchSchema().getClassByName(ReactomeJavaConstants.PathwayDiagram);
SchemaAttribute att = cls.getAttribute(ReactomeJavaConstants.representedPathway);
adaptor.loadInstanceAttributeValues(diagrams, att);
// Group all human pathways
for (Iterator<?> it = diagrams.iterator(); it.hasNext(); ) {
GKInstance diagram = (GKInstance) it.next();
GKInstance pathway =
(GKInstance) diagram.getAttributeValue(ReactomeJavaConstants.representedPathway);
GKInstance species = (GKInstance) pathway.getAttributeValue(ReactomeJavaConstants.species);
if (species == null) continue;
if (species.getDBID().equals(48887L)) {
String fileName = getFileName(pathway);
File file = new File(dir, fileName);
convertReactomeToGPML(pathway, file.getAbsolutePath());
}
}
}
