- 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());
- }
- ScoreModelI sm = ScoreModels.getInstance().forName(pwtype);
- sm = configureScoreModel(sm);
- tree = new NJTree(seqs, seqStrings, type, pwtype, sm, start, end);
+ ScoreModelI sm = ScoreModels.getInstance()
+ .getScoreModel(scoreModelName, getTreeCanvas().getAssociatedPanel());
+ TreeBuilder njtree = treeType.equals(TreeBuilder.NEIGHBOUR_JOINING)
+ ? new NJTree(getViewport(), sm, similarityParams)
+ : new AverageDistanceTree(getViewport(), sm, similarityParams);
+ tree = new TreeModel(njtree);