if (ap.av.getSelectionGroup() == null)
{
- seqs = ap.av.alignment.getSequencesArray();
+ seqs = ap.av.getAlignment().getSequencesArray();
}
else
{
- seqs = ap.av.getSelectionGroup().getSequencesInOrder(ap.av.alignment);
+ seqs = ap.av.getSelectionGroup().getSequencesInOrder(ap.av.getAlignment());
}
float scores[][] = new float[seqs.length][seqs.length];
double totscore = 0;
int count = ap.av.getSelectionGroup().getSize();
- String type = (ap.av.alignment.isNucleotide()) ? AlignSeq.DNA
+ String type = (ap.av.getAlignment().isNucleotide()) ? AlignSeq.DNA
: AlignSeq.PEP;
Sequence seq;