JAL-207 pairwise alignment sequence contexts propergation bugfix

[jalview.git] / src / jalview / gui / PairwiseAlignPanel.java

diff --git a/src/jalview/gui/PairwiseAlignPanel.java b/src/jalview/gui/PairwiseAlignPanel.java
index 82f0120..69b6ba6 100755 (executable)
--- a/src/jalview/gui/PairwiseAlignPanel.java
+++ b/src/jalview/gui/PairwiseAlignPanel.java
@@ -99,13 +99,8 @@ public class PairwiseAlignPanel extends GPairwiseAlignPanel
         totscore = totscore + scores[i][j];
 
         textarea.append(as.getOutput());
-        seq = new Sequence(as.getAlignedSeq1().getName(), as.getAStr1(), as
-                .getAlignedSeq1().getStart(), as.getAlignedSeq1().getEnd());
-        sequences.add(seq);
-
-        seq = new Sequence(as.getAlignedSeq2().getName(), as.getAStr2(), as
-                .getAlignedSeq2().getStart(), as.getAlignedSeq2().getEnd());
-        sequences.add(seq);
+        sequences.add(as.getAlignedSeq1());
+        sequences.add(as.getAlignedSeq1());
       }
     }