X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FPairwiseAlignPanel.java;h=fedd8d210ffabb49735b7d6108bb68952b9fd9d8;hb=27e20b88d0c73ced06e9c20a6e0fa14e27fed179;hp=844345494f4ab3f584a51748b7f1691f60839e1c;hpb=d423f22792e47dbc800ae220a58677f988971d06;p=jalview.git

diff --git a/src/jalview/gui/PairwiseAlignPanel.java b/src/jalview/gui/PairwiseAlignPanel.java
index 8443454..fedd8d2 100755
--- a/src/jalview/gui/PairwiseAlignPanel.java
+++ b/src/jalview/gui/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.
  * 
@@ -56,14 +56,14 @@ public class PairwiseAlignPanel extends GPairwiseAlignPanel
 
     if (av.getSelectionGroup() == null)
     {
-      seqs = av.alignment.getSequencesArray();
+      seqs = av.getAlignment().getSequencesArray();
     }
     else
     {
-      seqs = av.getSelectionGroup().getSequencesInOrder(av.alignment);
+      seqs = av.getSelectionGroup().getSequencesInOrder(av.getAlignment());
     }
 
-    String type = (av.alignment.isNucleotide()) ? AlignSeq.DNA
+    String type = (av.getAlignment().isNucleotide()) ? AlignSeq.DNA
             : AlignSeq.PEP;
 
     float[][] scores = new float[seqs.length][seqs.length];