X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FPairwiseAlignPanel.java;h=0d3b0f3ce8232be8ca4477f5caef038b12b11921;hb=577f505f54fe343e89f581461e780ea8308c20ec;hp=b85cb94a9dc9952fe37c0a0d1598a0c03923fa28;hpb=ad69965c1fc78b90245919ad711682e5dc333dc1;p=jalview.git

diff --git a/src/jalview/gui/PairwiseAlignPanel.java b/src/jalview/gui/PairwiseAlignPanel.java
index b85cb94..0d3b0f3 100755
--- a/src/jalview/gui/PairwiseAlignPanel.java
+++ b/src/jalview/gui/PairwiseAlignPanel.java
@@ -19,7 +19,7 @@ public class PairwiseAlignPanel extends GPairwiseAlignPanel
       this.av = av;
       float scores[][] = new float[av.getAlignment().getHeight()][av.getAlignment().getHeight()];
       double totscore = 0;
-      int count = av.getSelection().size();
+      int count = av.getSelectionGroup().getSize();
 
       int acount = 0;
         for (int i = 1; i < count; i++)
@@ -27,7 +27,8 @@ public class PairwiseAlignPanel extends GPairwiseAlignPanel
           for (int j = 0; j < i; j++)
           {
             acount++;
-            AlignSeq as = new AlignSeq(av.getSelection().sequenceAt(i),av.getSelection().sequenceAt(j),"pep");
+            AlignSeq as = new AlignSeq(av.getSelectionGroup().getSequenceAt(i),
+                                       av.getSelectionGroup().getSequenceAt(j),"pep");
 
             as.calcScoreMatrix();
             as.traceAlignment();