(JAL-969) refactored alignmentViewport base class to own package and pulled up most...

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

diff --git a/src/jalview/appletgui/TreePanel.java b/src/jalview/appletgui/TreePanel.java
index 29e5654..aa57908 100644 (file)
--- a/src/jalview/appletgui/TreePanel.java
+++ b/src/jalview/appletgui/TreePanel.java
@@ -186,11 +186,11 @@ public class TreePanel extends EmbmenuFrame implements ActionListener,
       {
         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);
         }
 
@@ -204,14 +204,14 @@ public class TreePanel extends EmbmenuFrame implements ActionListener,
         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);