@Override protected void processResults() throws ServiceException { String seqs[] = getOutputs().get("sequences").split(">"); String seq1 = seqs[0].substring(seqs[0].indexOf('\n')).replace("\n", "").trim(); String seq2 = seqs[1].substring(seqs[1].indexOf('\n')).replace("\n", "").trim(); try { if (isAa()) { setAlignedSequence1( ProteinTools.createGappedProteinSequence(seq1, getSequence1().getName())); setAlignedSequence2( ProteinTools.createGappedProteinSequence(seq2, getSequence2().getName())); } else { setAlignedSequence1(DNATools.createGappedDNASequence(seq1, getSequence1().getName())); setAlignedSequence2(DNATools.createGappedDNASequence(seq2, getSequence2().getName())); } } catch (IllegalSymbolException e) { e.printStackTrace(); throw new AlignServiceException(getService(), getUrl(), e); } setScore(Double.parseDouble(getOutputs().get("score"))); }