X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FPairwiseAlignPanel.java;h=b85cb94a9dc9952fe37c0a0d1598a0c03923fa28;hb=4ea7364b143ad06a38fb9ce4c39e565ebe1ee9fb;hp=c771693d4837ab9ed80110cfc436a28336b501ba;hpb=1ecf6419aba86993b3c223bf5ec0fa79427baf85;p=jalview.git

diff --git a/src/jalview/gui/PairwiseAlignPanel.java b/src/jalview/gui/PairwiseAlignPanel.java
index c771693..b85cb94 100755
--- a/src/jalview/gui/PairwiseAlignPanel.java
+++ b/src/jalview/gui/PairwiseAlignPanel.java
@@ -28,7 +28,6 @@ public class PairwiseAlignPanel extends GPairwiseAlignPanel
           {
             acount++;
             AlignSeq as = new AlignSeq(av.getSelection().sequenceAt(i),av.getSelection().sequenceAt(j),"pep");
-            //tf.status.setText("Aligning " + as.getS1().getName() + " and " + as.getS2().getName() + " (" + acount + "/" + (count*(count-1)/2) + ")");
 
             as.calcScoreMatrix();
             as.traceAlignment();
@@ -37,8 +36,9 @@ public class PairwiseAlignPanel extends GPairwiseAlignPanel
             totscore = totscore + scores[i][j];
 
             textarea.append(as.getOutput());
-            sequences.add( as.getS1() );
-            sequences.add( as.getS2() );
+            sequences.add( new Sequence( as.getS1().getName(), as.getAStr1()) );
+            sequences.add( new Sequence( as.getS2().getName(), as.getAStr2()) );
+
 
           }
         }