{
if (odata == null)
{
- tree = new NJTree(av.alignment.getSequencesArray(), newtree);
+ tree = new NJTree(av.getAlignment().getSequencesArray(), newtree);
}
else
{
- tree = new NJTree(av.alignment.getSequencesArray(), odata,
+ tree = new NJTree(av.getAlignment().getSequencesArray(), odata,
newtree);
}
if (!tree.hasOriginalSequenceData())
if (av.getSelectionGroup() == null)
{
start = 0;
- end = av.alignment.getWidth();
- seqs = av.alignment.getSequencesArray();
+ end = av.getAlignment().getWidth();
+ seqs = av.getAlignment().getSequencesArray();
}
else
{
start = av.getSelectionGroup().getStartRes();
end = av.getSelectionGroup().getEndRes() + 1;
- seqs = av.getSelectionGroup().getSequencesInOrder(av.alignment);
+ seqs = av.getSelectionGroup().getSequencesInOrder(av.getAlignment());
}
tree = new NJTree(seqs, seqStrings, type, pwtype, start, end);
AlignmentSorter.sortByTree(av.getAlignment(), tree);
CommandI undo;
undo=new OrderCommand("Tree Sort", oldOrder,
- av.alignment);
+ av.getAlignment());
ap.paintAlignment(true);
return undo;