- int start, end;
- SequenceI[] seqs;
- boolean selview = (av.getSelectionGroup() != null)
- && (av.getSelectionGroup().getSize() > 1);
- AlignmentView seqStrings = av.getAlignmentView(selview);
- if (!selview)
- {
- start = 0;
- end = av.getAlignment().getWidth();
- seqs = av.getAlignment().getSequencesArray();
- }
- else
- {
- start = av.getSelectionGroup().getStartRes();
- end = av.getSelectionGroup().getEndRes() + 1;
- seqs = av.getSelectionGroup().getSequencesInOrder(
- av.getAlignment());
- }
-
- tree = new NJTree(seqs, seqStrings, type, pwtype, start, end);
+ ScoreModelI sm1 = ScoreModels.getInstance().getScoreModel(pwtype,
+ treeCanvas.ap);
+ ScoreModelI sm = sm1;
+ TreeBuilder njtree = type.equals(TreeBuilder.NEIGHBOUR_JOINING)
+ ? new NJTree(av, sm, SimilarityParams.Jalview)
+ : new AverageDistanceTree(av, sm, SimilarityParams.Jalview);
+ tree = new TreeModel(njtree);