X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FPairwiseAlignPanel.java;h=22f1368e6494b80fa79bed80354f704c01253d2b;hb=49665d43dbcc49a55d7d44fbf58a7c27ab0ae860;hp=69b6ba634b5e687ba5da95b528e0ba79f1304473;hpb=8c240f48e7e8c991aef02203f1b05b86ab963178;p=jalview.git

diff --git a/src/jalview/gui/PairwiseAlignPanel.java b/src/jalview/gui/PairwiseAlignPanel.java
index 69b6ba6..22f1368 100755
--- a/src/jalview/gui/PairwiseAlignPanel.java
+++ b/src/jalview/gui/PairwiseAlignPanel.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -26,6 +26,7 @@ import jalview.datamodel.Sequence;
 import jalview.datamodel.SequenceI;
 import jalview.jbgui.GPairwiseAlignPanel;
 import jalview.util.MessageManager;
+import jalview.viewmodel.AlignmentViewport;
 
 import java.awt.event.ActionEvent;
 import java.util.Vector;
@@ -39,7 +40,7 @@ import java.util.Vector;
 public class PairwiseAlignPanel extends GPairwiseAlignPanel
 {
 
-  AlignViewport av;
+  AlignmentViewport av;
 
   Vector sequences;
 
@@ -49,7 +50,7 @@ public class PairwiseAlignPanel extends GPairwiseAlignPanel
    * @param av
    *          DOCUMENT ME!
    */
-  public PairwiseAlignPanel(AlignViewport av)
+  public PairwiseAlignPanel(AlignmentViewport av)
   {
     super();
     this.av = av;
@@ -100,7 +101,7 @@ public class PairwiseAlignPanel extends GPairwiseAlignPanel
 
         textarea.append(as.getOutput());
         sequences.add(as.getAlignedSeq1());
-        sequences.add(as.getAlignedSeq1());
+        sequences.add(as.getAlignedSeq2());
       }
     }