JAL-838 move two callers off Comparison.PID and deprecate it

[jalview.git] / src / jalview / gui / TreePanel.java

diff --git a/src/jalview/gui/TreePanel.java b/src/jalview/gui/TreePanel.java
index 9ac2872..1e98535 100755 (executable)
--- a/src/jalview/gui/TreePanel.java
+++ b/src/jalview/gui/TreePanel.java
@@ -21,7 +21,10 @@
 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;
@@ -81,7 +84,7 @@ public class TreePanel extends GTreePanel
 
   TreeCanvas treeCanvas;
 
-  NJTree tree;
+  TreeModel tree;
 
   AlignViewport av;
 
@@ -267,12 +270,13 @@ public class TreePanel extends GTreePanel
       {
         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())
         {
@@ -282,7 +286,10 @@ public class TreePanel extends GTreePanel
       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);
       }
 
@@ -326,7 +333,7 @@ public class TreePanel extends GTreePanel
    * 
    * @return DOCUMENT ME!
    */
-  public NJTree getTree()
+  public TreeModel getTree()
   {
     return tree;
   }