public void onMODIdentifierUpdate(CvTerm cv, String oldMOD) { if (oldMOD == null){ cvChangeLogger.log(Level.INFO, "The MOD identifier " + cv.getMODIdentifier() + " has been added to the cv term " + cv.toString()); } else if (cv.getMIIdentifier() == null){ cvChangeLogger.log(Level.INFO, "The MOD identifier "+ oldMOD+ " has been removed from the cv term " + cv.toString()); } else { cvChangeLogger.log(Level.INFO, "The MOD identifier "+oldMOD+" has been updated with " + cv.getMODIdentifier() + " in the cv term " + cv.toString()); } }
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()); } }
CvTerm database1 = externalIdentifier1.getDatabase(); String mi = database1.getMIIdentifier(); String mod = database1.getMODIdentifier(); String par = database1.getPARIdentifier();
else if (cv.getMODIdentifier() != null){ writer.write(CvTerm.PSI_MOD); writer.write(MitabUtils.XREF_SEPARATOR); writer.write("\""); writer.write(cv.getMODIdentifier()); writer.write("\"");
hashcode = 31*hashcode + cv1.getMIIdentifier().hashCode(); else if (cv1.getMODIdentifier() != null){ hashcode = 31*hashcode + cv1.getMODIdentifier().hashCode();
hashcode = 31*hashcode + cv1.getMIIdentifier().hashCode(); else if (cv1.getMODIdentifier() != null){ hashcode = 31*hashcode + cv1.getMODIdentifier().hashCode();
/** * 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; } }
CvTerm database1 = externalIdentifier1.getDatabase(); String mi = database1.getMIIdentifier(); String mod = database1.getMODIdentifier(); String par = database1.getPARIdentifier();
String mod1 = cvTerm1.getMODIdentifier(); String mod2 = cvTerm2.getMODIdentifier(); String par1 = cvTerm1.getPARIdentifier(); String par2 = cvTerm2.getPARIdentifier();
String mod1 = database1.getMODIdentifier(); String mod2 = database2.getMODIdentifier(); if (mod1 != null && mod2 != null){ comp = mi1.compareTo(mi2);
String mod1 = database1.getMODIdentifier(); String mod2 = database2.getMODIdentifier(); if (mod1 != null && mod2 != null){ comp = mod1.equals(mod2);
String mod1 = cvTerm1.getMODIdentifier(); String mod2 = cvTerm2.getMODIdentifier(); String par1 = cvTerm1.getPARIdentifier(); String par2 = cvTerm2.getPARIdentifier();
String mod1 = cvTerm1.getMODIdentifier(); String mod2 = cvTerm2.getMODIdentifier(); String par1 = cvTerm1.getPARIdentifier(); String par2 = cvTerm2.getPARIdentifier();
if (feature.getType().getMODIdentifier() != null){ final OntologyAccess access = ontologyManager.getOntologyAccess("MOD"); final OntologyTermI dbTerms = access.getTermForAccession(feature.getType().getMODIdentifier());
hasId = true; else if (object.getMODIdentifier() != null){ MIJsonUtils.writeProperty("id", JSONValue.escape(object.getMODIdentifier()), writer); hasId = true;
CvTerm type = feature.getType(); if (type.getMODIdentifier() != null){ return "ptms";