else
{
match = align.findName(seqId, true);
+ if (match == null && newseqs != null)
+ {
+ for (SequenceI m : newseqs)
+ {
+ if (seqId.equals(m.getName()))
+ {
+ return m;
+ }
+ }
+ }
}
if (match==null && newseqs!=null)
matcher.addAll(Arrays.asList(new SequenceI[]
{ match }));
}
+ // add dummy sequence to the newseqs list
+ newseqs.add(match);
}
return match;
}