Output new alignment bug fixed

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