name = id.substring(id.indexOf(";") + 1) + "_" + ++i;
}
+ if (QuerySeqPosition==-1)
+ QuerySeqPosition = ids.size();
ids.addElement(name);
-
noSeqs++;
}
else
") has an unexpected number of columns");
}
- if (newSeq.getName().startsWith("QUERY") &&
+ if ((newSeq.getName().startsWith("QUERY") || newSeq.getName().startsWith("align;"))&&
(QuerySeqPosition == -1))
{
QuerySeqPosition = seqs.size();