X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FTreePanel.java;h=6ce68b3383874aed94b20e7158f434055e76cc80;hb=cf994d96657bbc96e6d2bf6f294e4ec6608debcf;hp=5bedf36d9bf9e4447f4ceef5aeb6a30d8285c115;hpb=7a2f4e9ee4119f0369743e7996bcebbb6ab46f9e;p=jalview.git

diff --git a/src/jalview/gui/TreePanel.java b/src/jalview/gui/TreePanel.java
index 5bedf36..6ce68b3 100755
--- a/src/jalview/gui/TreePanel.java
+++ b/src/jalview/gui/TreePanel.java
@@ -313,8 +313,26 @@ public class TreePanel extends GTreePanel
           seqs = av.getSelectionGroup().getSequencesInOrder(
                   av.getAlignment());
         }
-
-        tree = new NJTree(seqs, seqStrings, type, pwtype, start, end);
+        ScoreModelI sm = ResidueProperties.getScoreModel(pwtype);
+        if (sm instanceof ViewBasedAnalysisI)
+        {
+          try
+          {
+            sm = sm.getClass().newInstance();
+            ((ViewBasedAnalysisI) sm)
+                    .configureFromAlignmentView(treeCanvas.ap);
+          } catch (Exception q)
+          {
+            Cache.log.error("Couldn't create a scoremodel instance for "
+                    + sm.getName());
+          }
+          tree = new NJTree(seqs, seqStrings, type, pwtype, sm, start, end);
+        }
+        else
+        {
+          tree = new NJTree(seqs, seqStrings, type, pwtype, null, start,
+                  end);
+        }
         showDistances(true);
       }