{
Sequence ds = new Sequence(snew.getName(),
AlignSeq.extractGaps("-. ",
- snew.getSequence()),
+ snew.getSequenceAsString()),
snew.getStart(),
snew.getEnd());
for (int i = 0; i < sequences.size(); i++)
{
Sequence seq = (Sequence) sequences.elementAt(i);
- seq.setSequence( seq.getSequence().replace('.', gc) );
- seq.setSequence( seq.getSequence().replace('-', gc) );
- seq.setSequence( seq.getSequence().replace(' ', gc) );
+ seq.setSequence( seq.getSequenceAsString().replace('.', gc) );
+ seq.setSequence( seq.getSequenceAsString().replace('-', gc) );
+ seq.setSequence( seq.getSequenceAsString().replace(' ', gc) );
}
}
seqs[i] = new Sequence(currentSeq.getName(),
AlignSeq.extractGaps(
jalview.util.Comparison.GapChars,
- currentSeq.getSequence()
+ currentSeq.getSequenceAsString()
),
currentSeq.getStart(),
currentSeq.getEnd());