X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=inline;f=src%2Fjalview%2Fappletgui%2FPairwiseAlignPanel.java;h=a1fb5ea186d80f63a78197cd067c4f224a1cc5c0;hb=ff7e72d6df848ca0694d25bde0e9616e8df1d18e;hp=7a47d0241d16beece72e43a4a2f8f7b93c118bb6;hpb=d423f22792e47dbc800ae220a58677f988971d06;p=jalview.git

diff --git a/src/jalview/appletgui/PairwiseAlignPanel.java b/src/jalview/appletgui/PairwiseAlignPanel.java
index 7a47d02..a1fb5ea 100755
--- a/src/jalview/appletgui/PairwiseAlignPanel.java
+++ b/src/jalview/appletgui/PairwiseAlignPanel.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
  * 
  * This file is part of Jalview.
  * 
@@ -48,17 +48,17 @@ public class PairwiseAlignPanel extends Panel implements ActionListener
 
     if (ap.av.getSelectionGroup() == null)
     {
-      seqs = ap.av.alignment.getSequencesArray();
+      seqs = ap.av.getAlignment().getSequencesArray();
     }
     else
     {
-      seqs = ap.av.getSelectionGroup().getSequencesInOrder(ap.av.alignment);
+      seqs = ap.av.getSelectionGroup().getSequencesInOrder(ap.av.getAlignment());
     }
 
     float scores[][] = new float[seqs.length][seqs.length];
     double totscore = 0;
     int count = ap.av.getSelectionGroup().getSize();
-    String type = (ap.av.alignment.isNucleotide()) ? AlignSeq.DNA
+    String type = (ap.av.getAlignment().isNucleotide()) ? AlignSeq.DNA
             : AlignSeq.PEP;
     Sequence seq;