public static CvTerm createIdentityQualifier(CvTerm psiMi){ CvTerm identity = new DefaultCvTerm(Xref.IDENTITY); Xref psiMiXref = new DefaultXref(psiMi, Xref.IDENTITY_MI, identity); identity.getIdentifiers().add(psiMiXref); return identity; } }
public static CvTerm createPsiMiDatabase(CvTerm identity){ CvTerm psiMi = new DefaultCvTerm(CvTerm.PSI_MI); Xref psiMiXref = new DefaultXref(psiMi, CvTerm.PSI_MI_MI, identity); psiMi.getIdentifiers().add(psiMiXref); return psiMi; }
public static CvTerm createPsiMiDatabase(){ CvTerm psiMi = new DefaultCvTerm(CvTerm.PSI_MI); Xref psiMiXref = new DefaultXref(psiMi, CvTerm.PSI_MI_MI, createIdentityQualifier(psiMi)); psiMi.getIdentifiers().add(psiMiXref); return psiMi; }
public static CvTerm createIdentityQualifier(){ CvTerm identity = new DefaultCvTerm(Xref.IDENTITY); Xref psiMiXref = new DefaultXref(createPsiMiDatabase(identity), Xref.IDENTITY_MI, identity); identity.getIdentifiers().add(psiMiXref); return identity; }
return AFTER; else if (!cvTerm1.getIdentifiers().isEmpty() && !cvTerm2.getIdentifiers().isEmpty()){ return this.identifierCollectionComparator.compare(cvTerm1.getIdentifiers(), cvTerm2.getIdentifiers()); else if (!cvTerm1.getIdentifiers().isEmpty()){ return BEFORE; else if (!cvTerm2.getIdentifiers().isEmpty()){ return AFTER;
public static Xref getPsiMiReference(CvTerm term){ if (term == null){ return null; } else if (term.getMIIdentifier() == null){ return null; } else{ return XrefUtils.collectFirstIdentifierWithDatabaseAndId(term.getIdentifiers(), CvTerm.PSI_MI_MI, CvTerm.PSI_MI, term.getMIIdentifier()); } }
public static Xref getPsiModReference(CvTerm term){ if (term == null){ return null; } else if (term.getMODIdentifier() == null){ return null; } else{ return XrefUtils.collectFirstIdentifierWithDatabaseAndId(term.getIdentifiers(), CvTerm.PSI_MOD_MI, CvTerm.PSI_MOD, term.getMODIdentifier()); } }
public static Xref getPsiParReference(CvTerm term){ if (term == null){ return null; } else if (term.getPARIdentifier() == null){ return null; } else{ return XrefUtils.collectFirstIdentifierWithDatabaseAndId(term.getIdentifiers(), null, CvTerm.PSI_PAR, term.getPARIdentifier()); } }
/*** * This method will copy properties of cv term source in cv term target and will override all the other properties of Target cv term. * @param source : the cv term source to copy from * @param target : the cv term target to copy to */ public static void copyAndOverrideCvTermProperties(CvTerm source, CvTerm target){ if (source != null && target != null){ target.setShortName(source.getShortName()); target.setFullName(source.getFullName()); // copy collections target.getAnnotations().clear(); target.getAnnotations().addAll(source.getAnnotations()); target.getXrefs().clear(); target.getXrefs().addAll(source.getXrefs()); target.getIdentifiers().clear(); target.getIdentifiers().addAll(source.getIdentifiers()); target.getSynonyms().clear(); target.getSynonyms().addAll(source.getSynonyms()); } }
return par1.equals(par2); else if (!cvTerm1.getIdentifiers().isEmpty() && !cvTerm2.getIdentifiers().isEmpty()){ Iterator<Xref> iterator1 = cvTerm1.getIdentifiers().iterator(); Xref altid1 = iterator1.next(); for (Xref altid2 : cvTerm2.getIdentifiers()){ if (DefaultExternalIdentifierComparator.areEquals(altid1, altid2)){ return true;
else if (!cv.getIdentifiers().isEmpty()) { writeIdentifier(cv.getIdentifiers().iterator().next());
hashcode = 31*hashcode + cv1.getPARIdentifier().hashCode(); else if (!cv1.getIdentifiers().isEmpty()){ List<Xref> list1 = new ArrayList<Xref>(cv1.getIdentifiers()); Collections.sort(list1, unambiguousCvTermComparator.getIdentifierComparator()); for (Xref ref : list1){
hashcode = 31*hashcode + cv1.getPARIdentifier().hashCode(); else if (!cv1.getIdentifiers().isEmpty()){ List<Xref> list1 = new ArrayList<Xref>(cv1.getIdentifiers()); Collections.sort(list1, unambiguousCvTermComparator.getIdentifierComparator()); for (Xref ref : list1){
/** * Gets the unique identifier of a CvObject. If it has PSI MI Identifier (miIdentifier) return it, otherwise returns the MOD identifier, * If no MOD identifier, returns the PAR identifier. * if no PAR identifier, returns the first identifier in the list of identifiers. * * @param cvObject The object to get the identifier from. * @return The identifier. Will be null if no miIdentifier or identity xref is found. * @since 1.8.0 */ public static String getBestIdentifier(CvTerm cvObject) { if (cvObject == null) return null; // try the PSI MI first if (cvObject.getMIIdentifier() != null) { return cvObject.getMIIdentifier(); } // try the PSI MOD second else if (cvObject.getMODIdentifier() != null) { return cvObject.getMODIdentifier(); } // try the PSI PAR third else if (cvObject.getPARIdentifier() != null) { return cvObject.getPARIdentifier(); } else if (!cvObject.getIdentifiers().isEmpty()) { return cvObject.getIdentifiers().iterator().next().getId(); } else{ return null; } }
if (!cvTerm1.getIdentifiers().isEmpty() || !cvTerm2.getIdentifiers().isEmpty()){ int comp = getIdentifierCollectionComparator().compare(cvTerm1.getIdentifiers(), cvTerm2.getIdentifiers()); if (comp != 0){ return comp;
if (!tissue.getIdentifiers().isEmpty()){ Collection<psidev.psi.mi.jami.model.Xref> brendaRef = XrefUtils.collectAllXrefsHavingDatabase(tissue.getIdentifiers(), RuleUtils.BRENDA_MI_REF, RuleUtils.BRENDA); Collection<psidev.psi.mi.jami.model.Xref> tissueRef = XrefUtils.collectAllXrefsHavingDatabase(tissue.getIdentifiers(), RuleUtils.TISSUE_LIST_MI_REF, RuleUtils.TISSUE_LIST); return Collections.singletonList( new ValidatorMessage( "The tissue " + tissue.getShortName() + " has "+tissue.getIdentifiers().size()+" identifier(s) but none of them is a BRENDA or Tissue List cross reference with a qualifier 'identity' and it is strongly recommended.'", MessageLevel.WARN, context,
CvTerm cellType = organism.getCellType(); if (!cellType.getIdentifiers().isEmpty() || !cellType.getXrefs().isEmpty()){ Collection<psidev.psi.mi.jami.model.Xref> cabriReferences = XrefUtils.collectAllXrefsHavingDatabase(cellType.getIdentifiers(), RuleUtils.CABRI_MI_REF, RuleUtils.CABRI); Collection<psidev.psi.mi.jami.model.Xref> cellReferences = XrefUtils.collectAllXrefsHavingDatabase(cellType.getIdentifiers(), RuleUtils.CELL_ONTOLOGY_MI_REF, RuleUtils.CELL_ONTOLOGY); Collection<psidev.psi.mi.jami.model.Xref> allPubmeds = XrefUtils.collectAllXrefsHavingDatabaseAndQualifier(cellType.getXrefs(), psidev.psi.mi.jami.model.Xref.PUBMED_MI, psidev.psi.mi.jami.model.Xref.PUBMED, psidev.psi.mi.jami.model.Xref.PRIMARY_MI, psidev.psi.mi.jami.model.Xref.PRIMARY);
hasId = true; else if (!object.getIdentifiers().isEmpty()){ MIJsonUtils.writeProperty("id", JSONValue.escape(object.getIdentifiers().iterator().next().getId()), writer); hasId = true;