X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FPairwiseAlignPanel.java;h=22f1368e6494b80fa79bed80354f704c01253d2b;hb=af2dbf10bbcc54d9b9e4d398e9283b3c4a758e06;hp=e2c72694683d0a9b493465866684437df2c5d9e5;hpb=47168f025aefdaa044802bd5f8f510ffe43a4808;p=jalview.git

diff --git a/src/jalview/gui/PairwiseAlignPanel.java b/src/jalview/gui/PairwiseAlignPanel.java
index e2c7269..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.
  * 
@@ -20,13 +20,16 @@
  */
 package jalview.gui;
 
-import java.util.*;
-import java.awt.event.*;
-
-import jalview.analysis.*;
-import jalview.datamodel.*;
-import jalview.jbgui.*;
+import jalview.analysis.AlignSeq;
+import jalview.datamodel.Alignment;
+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;
 
 /**
  * DOCUMENT ME!
@@ -37,7 +40,7 @@ import jalview.util.MessageManager;
 public class PairwiseAlignPanel extends GPairwiseAlignPanel
 {
 
-  AlignViewport av;
+  AlignmentViewport av;
 
   Vector sequences;
 
@@ -47,7 +50,7 @@ public class PairwiseAlignPanel extends GPairwiseAlignPanel
    * @param av
    *          DOCUMENT ME!
    */
-  public PairwiseAlignPanel(AlignViewport av)
+  public PairwiseAlignPanel(AlignmentViewport av)
   {
     super();
     this.av = av;
@@ -97,13 +100,8 @@ public class PairwiseAlignPanel extends GPairwiseAlignPanel
         totscore = totscore + scores[i][j];
 
         textarea.append(as.getOutput());
-        seq = new Sequence(as.getS1().getName(), as.getAStr1(), as.getS1()
-                .getStart(), as.getS1().getEnd());
-        sequences.add(seq);
-
-        seq = new Sequence(as.getS2().getName(), as.getAStr2(), as.getS2()
-                .getStart(), as.getS2().getEnd());
-        sequences.add(seq);
+        sequences.add(as.getAlignedSeq1());
+        sequences.add(as.getAlignedSeq2());
       }
     }
 
@@ -151,7 +149,8 @@ public class PairwiseAlignPanel extends GPairwiseAlignPanel
     AlignFrame af = new AlignFrame(new Alignment(seq),
             AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
 
-    Desktop.addInternalFrame(af, MessageManager.getString("label.pairwise_aligned_sequences"),
+    Desktop.addInternalFrame(af,
+            MessageManager.getString("label.pairwise_aligned_sequences"),
             AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
   }
 }