@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")));
}
