X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FPairwiseAlignPanel.java;h=292b970bb38bb8ddd2ff702730ea277a645ea6c9;hb=5bd245162908974e3c96329da6a803598341bae1;hp=69b6ba634b5e687ba5da95b528e0ba79f1304473;hpb=8c240f48e7e8c991aef02203f1b05b86ab963178;p=jalview.git

diff --git a/src/jalview/gui/PairwiseAlignPanel.java b/src/jalview/gui/PairwiseAlignPanel.java
index 69b6ba6..292b970 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.
  * 
@@ -25,7 +25,9 @@ import jalview.datamodel.Alignment;
 import jalview.datamodel.Sequence;
 import jalview.datamodel.SequenceI;
 import jalview.jbgui.GPairwiseAlignPanel;
+import jalview.util.Format;
 import jalview.util.MessageManager;
+import jalview.viewmodel.AlignmentViewport;
 
 import java.awt.event.ActionEvent;
 import java.util.Vector;
@@ -39,7 +41,7 @@ import java.util.Vector;
 public class PairwiseAlignPanel extends GPairwiseAlignPanel
 {
 
-  AlignViewport av;
+  AlignmentViewport av;
 
   Vector sequences;
 
@@ -49,7 +51,7 @@ public class PairwiseAlignPanel extends GPairwiseAlignPanel
    * @param av
    *          DOCUMENT ME!
    */
-  public PairwiseAlignPanel(AlignViewport av)
+  public PairwiseAlignPanel(AlignmentViewport av)
   {
     super();
     this.av = av;
@@ -100,7 +102,7 @@ public class PairwiseAlignPanel extends GPairwiseAlignPanel
 
         textarea.append(as.getOutput());
         sequences.add(as.getAlignedSeq1());
-        sequences.add(as.getAlignedSeq1());
+        sequences.add(as.getAlignedSeq2());
       }
     }
 
@@ -111,8 +113,8 @@ public class PairwiseAlignPanel extends GPairwiseAlignPanel
 
       for (int i = 0; i < count; i++)
       {
-        jalview.util.Format.print(System.out, "%s \n", ("" + i) + " "
-                + seqs[i].getName());
+        Format.print(System.out, "%s \n",
+                ("" + i) + " " + seqs[i].getName());
       }
 
       System.out.println("\n");
@@ -121,8 +123,7 @@ public class PairwiseAlignPanel extends GPairwiseAlignPanel
       {
         for (int j = 0; j < i; j++)
         {
-          jalview.util.Format.print(System.out, "%7.3f", scores[i][j]
-                  / totscore);
+          Format.printDouble(System.out, "%7.3f", scores[i][j] / totscore);
         }
       }