/** * Extract the ensembl gene accession from this uniprotProtein * @param protein : the protein * @return the ensembl gene accession (if any) of this protein, null otherwise */ public static String extractENSEMBLGeneAccessionFrom(UniprotProtein protein){ if (protein != null){ String ensemblGene = extractENSEMBLGeneAccessionFrom(protein.getCrossReferences()); return ensemblGene; } return null; }
/** * Get the uniprot cross references of the uniprot entry matching this accession and extract the ensembl gene accession if any * @param uniprotAccession : the uniprot accession * @return the ensembl gene accession (if any) of this protein, null otherwise * @throws StrategyException */ public static String extractENSEMBLGeneAccessionFrom(String uniprotAccession) throws StrategyException{ UniprotProtein entry = getUniprotProteinFor(uniprotAccession); if (entry != null){ String ensemblGene = extractENSEMBLGeneAccessionFrom(entry.getCrossReferences()); return ensemblGene; } else { throw new StrategyException("We couldn't find an Uniprot entry which matches this accession number " + uniprotAccession); } }
protein.getCrossReferences().add( new UniprotXref( ac, db, desc ) ); protein.getCrossReferences().add( new UniprotXref( geneName, "HUGE" ) ); String syn = synonym.getValue(); if ( syn.startsWith( "KIAA" ) ) { protein.getCrossReferences().add( new UniprotXref( syn, "HUGE" ) );
String ensemblGene = extractENSEMBLGeneAccessionFrom(tremblEntry.getCrossReferences()); blastContext.setEnsemblGene(ensemblGene);
String ensemblGene = extractENSEMBLGeneAccessionFrom(tremblEntry.getCrossReferences()); blastContext.setEnsemblGene(ensemblGene);
String ensemblGene = extractENSEMBLGeneAccessionFrom(tremblEntry.getCrossReferences()); blastContext.setEnsemblGene(ensemblGene);
String ensemblGene = extractENSEMBLGeneAccessionFrom(tremblEntry.getCrossReferences()); blastContext.setEnsemblGene(ensemblGene);