X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FPairwiseAlignPanel.java;h=fedd8d210ffabb49735b7d6108bb68952b9fd9d8;hb=839949d19e1ba78e5d5d6e58fc827f417592d589;hp=5ca572c9e56f62cd2f3bd0d690faca5076c82828;hpb=a45774ee31d9f35d4eff46d54d7deab719afb092;p=jalview.git

diff --git a/src/jalview/gui/PairwiseAlignPanel.java b/src/jalview/gui/PairwiseAlignPanel.java
index 5ca572c..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 2.7)
- * Copyright (C) 2011 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * 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];