public LinkedHashMap<String, ProteinSequence> getProteinSequences() throws Exception { LinkedHashMap<String, ProteinSequence> proteinSequenceList = new LinkedHashMap<String, ProteinSequence>(); ArrayList<Element> elementList = XMLHelper.selectElements(geneidDoc.getDocumentElement(), "prediction/gene/protein"); logger.info("{} hits", elementList.size()); for (Element proteinElement : elementList) { Element geneElement = (Element) proteinElement.getParentNode(); String sequence = proteinElement.getTextContent().replaceAll("\\W",""); ProteinSequence proteinSequence = new ProteinSequence(sequence); String idGene = geneElement.getAttribute("idGene"); proteinSequence.setAccession(new AccessionID(idGene)); proteinSequenceList.put(idGene, proteinSequence); } return proteinSequenceList; }
seq.setAccession(new AccessionID(id));
pseq.setAccession(acc); msa.addAlignedSequence(pseq);
proteinSequence.setAccession(new AccessionID(cdsSequence.getAccession().getID())); proteinSequence.setParentDNASequence(cdsSequence, 1, cdsSequence.getLength()); proteinSequenceList.add(proteinSequence);
proteinSequence.setAccession(new AccessionID(cdsSequence.getAccession().getID())); proteinSequence.setParentDNASequence(cdsSequence, 1, cdsSequence.getLength()); proteinSequenceList.add(proteinSequence);
/** * Get the protein sequence with user defined TranscriptEngine * @param engine * @return */ public ProteinSequence getProteinSequence(TranscriptionEngine engine) { DNASequence dnaCodingSequence = getDNACodingSequence(); RNASequence rnaCodingSequence = dnaCodingSequence.getRNASequence(engine); ProteinSequence proteinSequence = rnaCodingSequence.getProteinSequence(engine); proteinSequence.setAccession(new AccessionID(this.getAccession().getID())); return proteinSequence; }
/** * Get the protein sequence with user defined TranscriptEngine * @param engine * @return */ public ProteinSequence getProteinSequence(TranscriptionEngine engine) { DNASequence dnaCodingSequence = getDNACodingSequence(); RNASequence rnaCodingSequence = dnaCodingSequence.getRNASequence(engine); ProteinSequence proteinSequence = rnaCodingSequence.getProteinSequence(engine); proteinSequence.setAccession(new AccessionID(this.getAccession().getID())); return proteinSequence; }