X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FPairwiseAlignPanel.java;h=7574802ba17dd3f6c9581b369ab988beea8a60b5;hb=ff2d6b48be7f17742defac9c965c70d7944d773b;hp=9afc70b2e54081427cc582eda8bbe9d0ad06c7bd;hpb=7ab5d6b0ba5fec1ea4a4239e79c476d841622485;p=jalview.git

diff --git a/src/jalview/appletgui/PairwiseAlignPanel.java b/src/jalview/appletgui/PairwiseAlignPanel.java
index 9afc70b..7574802 100644
--- a/src/jalview/appletgui/PairwiseAlignPanel.java
+++ b/src/jalview/appletgui/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.
  * 
@@ -20,15 +20,21 @@
  */
 package jalview.appletgui;
 
-import java.util.*;
-
-import java.awt.*;
-import java.awt.event.*;
-
-import jalview.analysis.*;
-import jalview.datamodel.*;
+import jalview.analysis.AlignSeq;
+import jalview.datamodel.Alignment;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceI;
 import jalview.util.MessageManager;
 
+import java.awt.BorderLayout;
+import java.awt.Button;
+import java.awt.Panel;
+import java.awt.ScrollPane;
+import java.awt.TextArea;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.util.Vector;
+
 public class PairwiseAlignPanel extends Panel implements ActionListener
 {
   Vector sequences = new Vector();
@@ -89,13 +95,8 @@ public class PairwiseAlignPanel extends Panel implements ActionListener
         totscore = totscore + scores[i][j];
 
         textarea.append(as.getOutput());
-        seq = new Sequence(as.getS1().getName(), as.getAStr1(), as.getS1()
-                .getStart(), as.getS1().getEnd());
-        sequences.addElement(seq);
-
-        seq = new Sequence(as.getS2().getName(), as.getAStr2(), as.getS2()
-                .getStart(), as.getS2().getEnd());
-        sequences.addElement(seq);
+        sequences.add(as.getAlignedSeq1());
+        sequences.add(as.getAlignedSeq1());
       }
     }