if (sq != dsq)
{ // make this dataset sequence sq's dataset sequence
sq.setDatasetSequence(dsq);
+ // and update the current dataset alignment
+ if (ds==null) {
+ if (dseqs!=null) {
+ if (!dseqs.contains(dsq))
+ {
+ dseqs.add(dsq);
+ }
+ } else {
+ if (ds.findIndex(dsq)<0)
+ {
+ ds.addSequence(dsq);
+ }
+ }
+ }
}
}
}
* sb.append(newres.substring(newres.length() - sq.getEnd() -
* dsq.getEnd())); dsq.setEnd(sq.getEnd()); }
*/
- dsq.setSequence(sb.toString());
+ dsq.setSequence(newres);
}
// TODO: merges will never happen if we 'know' we have the real dataset
// sequence - this should be detected when id==dssid