private boolean isALeafTerm(OBOClassImpl oboClass) { return oboClass.getChildren().isEmpty(); } }
private boolean isARootTerm(OBOClassImpl oboClass) { return oboClass.getParents().isEmpty(); }
@SuppressWarnings("unchecked") private Set<String> getSynonyms(LinkedObject oboParent) { Set<String> parentSynonyms; if (oboParent instanceof OBOClassImpl) { OBOClassImpl parentOboClass = (OBOClassImpl) oboParent; parentSynonyms = synonymsToString(parentOboClass.getSynonyms()); } else { parentSynonyms = Collections.EMPTY_SET; } return parentSynonyms; }
String id = oboClass.getID(); String name = oboClass.getName(); Set<SynonymImpl> oboSynonyms = oboClass.getSynonyms(); Set<String> synonyms = synonymsToString(oboSynonyms); } else { for (Link link : oboClass.getParents()) { LinkedObject oboParent = link.getParent();
public OBOClass getOBOCellType() { if (cellTypeObj != null) { return cellTypeObj; } cellTypeObj = new OBOClassImpl("cell type", "IAX:0002"); cellTypeObj.setDefinition("IntAct cell type base object"); addLinkToRootFor(cellTypeObj); oboSession.addObject(cellTypeObj); return cellTypeObj; }
public OBOClass getOBOTissue() { if (tissueObj != null) { return tissueObj; } tissueObj = new OBOClassImpl("tissue", "IAX:0001"); tissueObj.setDefinition("IntAct tissue base object"); addLinkToRootFor(tissueObj); oboSession.addObject(tissueObj); return tissueObj; }
private OBOClass getRootObject() { if (rootObj != null) { return rootObj; } /* [Term] id: MI:0000 name: molecular interaction def: "Controlled vocabularies originally created for protein protein interactions, extended to other molecules interactions." [PMID:14755292] subset: Drugable subset: PSI-MI slim synonym: "mi" EXACT PSI-MI-short [] */ rootObj = new OBOClassImpl( "molecular interaction", "MI:0000" ); rootObj.setDefinition( "Controlled vocabularies originally created for protein protein interactions, extended to other molecules interactions." ); //[PMID:14755292]" Dbxref dbxref = new DbxrefImpl( "PMID", "14755292" ); dbxref.setType( Dbxref.DEFINITION ); rootObj.addDefDbxref( dbxref ); addPsimiShortSyn(rootObj, "mi"); return rootObj; }//end of method
OBOClass oboObj = new OBOClassImpl( dagObj.getFullName(), cvId);