@XmlElement(name = "sequence") private Sequence getSequenceObject() { return new Sequence(getSequence(), getMd5()); }
private List<String> getNucleicAcidLine(NucleotideSequence nucleotideSeq) { String seqId = getNucleotideId(); int end = nucleotideSeq.getSequence().length(); GFF3Feature nucleicAcidFeature = new GFF3Feature(seqId, "provided_by_user", "nucleic_acid", 1, end, "+"); nucleicAcidFeature.addAttribute(GFF3Feature.ID_ATTR, getNucleotideId()); nucleicAcidFeature.addAttribute(GFF3Feature.NAME_ATTR, getNucleotideId()); nucleicAcidFeature.addAttribute(GFF3Feature.MD5_ATTR, nucleotideSeq.getMd5()); return nucleicAcidFeature.getGFF3FeatureLine(); }
private List<String> getNucleicAcidLine(NucleotideSequence nucleotideSeq) { String seqId = getNucleotideId(); int end = nucleotideSeq.getSequence().length(); GFF3Feature nucleicAcidFeature = new GFF3Feature(seqId, "provided_by_user", "nucleic_acid", 1, end, "+"); nucleicAcidFeature.addAttribute(GFF3Feature.ID_ATTR, getNucleotideId()); nucleicAcidFeature.addAttribute(GFF3Feature.NAME_ATTR, getNucleotideId()); nucleicAcidFeature.addAttribute(GFF3Feature.MD5_ATTR, nucleotideSeq.getMd5()); return nucleicAcidFeature.getGFF3FeatureLine(); }
if (concatenatedNucSeqIdentifiersStr.length() > 0) { setNucleotideId(concatenatedNucSeqIdentifiersStr); super.gffWriter.write("##sequence-region " + concatenatedNucSeqIdentifiersStr + " 1 " + nucleotideSequence.getSequence().length()); super.gffWriter.write(getNucleicAcidLine(nucleotideSequence));
if (concatenatedNucSeqIdentifiersStr.length() > 0) { setNucleotideId(concatenatedNucSeqIdentifiersStr); super.gffWriter.write("##sequence-region " + concatenatedNucSeqIdentifiersStr + " 1 " + nucleotideSequence.getSequence().length()); super.gffWriter.write(getNucleicAcidLine(nucleotideSequence));
if (concatenatedNucSeqIdentifiersStr.length() > 0) { setNucleotideId(concatenatedNucSeqIdentifiersStr); super.gffWriter.write("##sequence-region " + concatenatedNucSeqIdentifiersStr + " 1 " + nucleotideSequence.getSequence().length()); super.gffWriter.write(getNucleicAcidLine(nucleotideSequence));
if (concatenatedNucSeqIdentifiersStr.length() > 0) { setNucleotideId(concatenatedNucSeqIdentifiersStr); super.gffWriter.write("##sequence-region " + concatenatedNucSeqIdentifiersStr + " 1 " + nucleotideSequence.getSequence().length()); super.gffWriter.write(getNucleicAcidLine(nucleotideSequence));