X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FTreePanel.java;h=602ded6549fdf35d3ab6f1e09de1c844342ef55d;hb=839949d19e1ba78e5d5d6e58fc827f417592d589;hp=a266412113e1f5f54a8c262534beeab7efcc7eef;hpb=797df64fa2a0a30773d0f48f5494d4155e5a8be3;p=jalview.git

diff --git a/src/jalview/gui/TreePanel.java b/src/jalview/gui/TreePanel.java
index a266412..602ded6 100755
--- a/src/jalview/gui/TreePanel.java
+++ b/src/jalview/gui/TreePanel.java
@@ -255,11 +255,11 @@ public class TreePanel extends GTreePanel
       {
         if (odata == null)
         {
-          tree = new NJTree(av.alignment.getSequencesArray(), newtree);
+          tree = new NJTree(av.getAlignment().getSequencesArray(), newtree);
         }
         else
         {
-          tree = new NJTree(av.alignment.getSequencesArray(), odata,
+          tree = new NJTree(av.getAlignment().getSequencesArray(), odata,
                   newtree);
         }
         if (!tree.hasOriginalSequenceData())
@@ -276,14 +276,14 @@ public class TreePanel extends GTreePanel
         if (av.getSelectionGroup() == null)
         {
           start = 0;
-          end = av.alignment.getWidth();
-          seqs = av.alignment.getSequencesArray();
+          end = av.getAlignment().getWidth();
+          seqs = av.getAlignment().getSequencesArray();
         }
         else
         {
           start = av.getSelectionGroup().getStartRes();
           end = av.getSelectionGroup().getEndRes() + 1;
-          seqs = av.getSelectionGroup().getSequencesInOrder(av.alignment);
+          seqs = av.getSelectionGroup().getSequencesInOrder(av.getAlignment());
         }
 
         tree = new NJTree(seqs, seqStrings, type, pwtype, start, end);
@@ -570,7 +570,7 @@ public class TreePanel extends GTreePanel
     AlignmentSorter.sortByTree(av.getAlignment(), tree);
     CommandI undo;
     undo=new OrderCommand("Tree Sort", oldOrder,
-          av.alignment);
+          av.getAlignment());
 
     ap.paintAlignment(true);    
     return undo;