X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FPairwiseAlignPanel.java;h=fedd8d210ffabb49735b7d6108bb68952b9fd9d8;hb=d053a3c980cf4318b9a19a255f9fc870e74de989;hp=95d38d5b1db6b4b0c638a159c2274abad3ae88d2;hpb=34286266321abbbab6d462c39f500650f9c860c9;p=jalview.git

diff --git a/src/jalview/gui/PairwiseAlignPanel.java b/src/jalview/gui/PairwiseAlignPanel.java
index 95d38d5..fedd8d2 100755
--- a/src/jalview/gui/PairwiseAlignPanel.java
+++ b/src/jalview/gui/PairwiseAlignPanel.java
@@ -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];