/** * add a new uniprot cross reference with qualifier identity to the list of cross references of the protein * @param prot : the protein * @param uniprotAc : the uniprot accession * @param factory : the Intact factory (not used) */ private void addUniprotCrossReferenceTo(ProteinImpl prot, String uniprotAc, DaoFactory factory){ InteractorXref ref = createIdentityInteractorXrefForUniprotAc(uniprotAc); if (ref != null){ log.info("cross reference to uniprot "+ uniprotAc +" added to the cross references of " + prot.getAc()); //factory.getXrefDao(InteractorXref.class).persist( ref ); prot.addXref(ref); } }
public boolean isProteinEligible(ProteinImpl protein) { // Skip proteins annotated no-uniprot-update if (false == needsUniprotUpdate(protein)) { getOut().println(protein.getAc() + " " + protein.getShortLabel() + " is not from UniProt, skip it."); return false; } return isInvolvedWithBinaryInteractions(protein); }
public boolean isProteinEligible(ProteinImpl protein) { // Skip proteins annotated no-uniprot-update if (false == needsUniprotUpdate(protein)) { getOut().println(protein.getAc() + " " + protein.getShortLabel() + " is not from UniProt, skip it."); return false; } return isHighConfidence(protein); }
public boolean isProteinEligible(ProteinImpl protein) { // Skip proteins annotated no-uniprot-update if (false == needsUniprotUpdate(protein)) { getOut().println(protein.getAc() + " " + protein.getShortLabel() + " is not from UniProt, skip it."); return false; } return isHighConfidence(protein); }
getOut().println("ERROR: The splice variant having the AC(" + protein.getAc() + ") doesn't have it's master AC."); } else { master = IntactContext.getCurrentInstance().getDataContext().getDaoFactory().getProteinDao().getByAc(masterAc); protein.getAc() + ") having the AC(" + masterAc + ")"); } else {
getOut().println("ERROR: The splice variant having the AC(" + protein.getAc() + ") doesn't have it's master AC."); } else { master = IntactContext.getCurrentInstance().getDataContext().getDaoFactory().getProteinDao().getByAc(masterAc); protein.getAc() + ") having the AC(" + masterAc + ")"); } else {
getOut().println(protein.getAc() + " " + protein.getShortLabel() + " is not from UniProt, skip it."); continue; // process next AC getOut().println("ERROR: The splice variant having the AC(" + protein.getAc() + ") doesn't have it's master AC."); } else { master = IntactContext.getCurrentInstance().getDataContext().getDaoFactory().getProteinDao().getByAc(masterAc); protein.getAc() + ") having the AC(" + masterAc + ")"); } else {
this.context.clean(); String accession = prot.getAc(); Collection<InteractorXref> refs = prot.getXrefs(); String sequence = prot.getSequence();
String accession = prot.getAc(); String shortLabel = prot.getShortLabel(); log.info("Protein AC = " + accession + " shortLabel = " + shortLabel);
String accession = prot.getAc(); String shortLabel = prot.getShortLabel(); log.info("Protein AC = " + accession + " shortLabel = " + shortLabel);