package jalview.gui;
import jalview.analysis.AlignmentSorter;
+import jalview.analysis.AverageDistanceTree;
import jalview.analysis.NJTree;
+import jalview.analysis.TreeBuilder;
+import jalview.analysis.TreeModel;
import jalview.api.analysis.ScoreModelI;
import jalview.api.analysis.SimilarityParamsI;
import jalview.api.analysis.ViewBasedAnalysisI;
TreeCanvas treeCanvas;
- NJTree tree;
+ TreeModel tree;
AlignViewport av;
{
if (odata == null)
{
- tree = new NJTree(av.getAlignment().getSequencesArray(), newtree);
+ tree = new TreeModel(av.getAlignment().getSequencesArray(),
+ newtree);
}
else
{
- tree = new NJTree(av.getAlignment().getSequencesArray(), odata,
- newtree);
+ tree = new TreeModel(av.getAlignment().getSequencesArray(),
+ odata, newtree);
}
if (!tree.hasOriginalSequenceData())
{
else
{
ScoreModelI sm = configureScoreModel();
- tree = new NJTree(av, treeType, sm, similarityParams);
+ TreeBuilder njtree = treeType.equals(TreeBuilder.NEIGHBOUR_JOINING) ? new NJTree(
+ av, sm, similarityParams) : new AverageDistanceTree(av, sm,
+ similarityParams);
+ tree = new TreeModel(njtree);
showDistances(true);
}
*
* @return DOCUMENT ME!
*/
- public NJTree getTree()
+ public TreeModel getTree()
{
return tree;
}