private static NucleotideSequenceXref stripUniqueIdentifierAndTrimForNucleotideSeq(String id) { if (id == null || id.isEmpty()) { throw new IllegalStateException("Found an identifier in a fasta file which is null or empty???"); } else { id = id.trim(); Matcher matcher = DEFLINE_ID_PATTERN.matcher(id); if (matcher.find()) { return new NucleotideSequenceXref(null, matcher.group(1), id); } else { return new NucleotideSequenceXref(null, id, id); } } }
NucleotideSequence nucleotideSequenceTest = xref.getNucleotideSequence(); Long startGetNucleotideSequence = System.currentTimeMillis(); Long sequenceId = xref.getNucleotideSequence().getId(); final Query query = entityManager.createQuery(
public void addCrossReference(NucleotideSequenceXref xref) { if (xref == null) { throw new IllegalArgumentException("The xref argument cannot be null."); } xrefs.add(xref); xref.setNucleotideSequence(this); }
Set<NucleotideSequenceXref> nsXrefs = ns.getCrossReferences() ; for (NucleotideSequenceXref nsXref: nsXrefs) { LOGGER.debug("Nucleotide xref identifier: " + nsXref.getIdentifier());
String nucleotideSequenceXrefId = nucleotideSequenceXref.getIdentifier();
String nucleotideSequenceXrefId = nucleotideSequenceXref.getIdentifier();
private static NucleotideSequenceXref stripUniqueIdentifierAndTrimForNucleotideSeq(String id) { if (id == null || id.isEmpty()) { throw new IllegalStateException("Found an identifier in a fasta file which is null or empty???"); } else { id = id.trim(); Matcher matcher = DEFLINE_ID_PATTERN.matcher(id); if (matcher.find()) { return new NucleotideSequenceXref(null, matcher.group(1), matcher.group(2)); } else { return new NucleotideSequenceXref(id); } } }
String nucleotideSequenceXrefId = nucleotideSequenceXref.getIdentifier();
String nucleotideSequenceXrefId = nucleotideSequenceXref.getIdentifier();