X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FPairwiseAlignPanel.java;h=248a54c4ba013bb37b28942ab6bd2b654341e975;hb=2e22e46f5f79840fd368858faa191e1be5f6095c;hp=ba961eec82002c5f167a0fa447dcfe4c607397a5;hpb=621a628afc1f6ee7a2778b9d0ae2729b88fe5bfd;p=jalview.git

diff --git a/src/jalview/gui/PairwiseAlignPanel.java b/src/jalview/gui/PairwiseAlignPanel.java
index ba961ee..248a54c 100755
--- a/src/jalview/gui/PairwiseAlignPanel.java
+++ b/src/jalview/gui/PairwiseAlignPanel.java
@@ -1,6 +1,6 @@
 /*
  * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
  *
  * This program is free software; you can redistribute it and/or
  * modify it under the terms of the GNU General Public License
@@ -54,7 +54,7 @@ public class PairwiseAlignPanel extends GPairwiseAlignPanel
         sequences = new Vector();
 
         SequenceI [] seqs;
-        String []  seqStrings = av.getSelectionAsString();
+        String []  seqStrings = av.getViewAsString(true);
 
         if(av.getSelectionGroup()==null)
         {
@@ -150,8 +150,11 @@ public class PairwiseAlignPanel extends GPairwiseAlignPanel
             seq[i] = (Sequence) sequences.elementAt(i);
         }
 
-        AlignFrame af = new AlignFrame(new Alignment(seq));
+        AlignFrame af = new AlignFrame(new Alignment(seq),
+                                           AlignFrame.DEFAULT_WIDTH,
+                                           AlignFrame.DEFAULT_HEIGHT);
+
         Desktop.addInternalFrame(af, "Pairwise Aligned Sequences",
-            AlignFrame.NEW_WINDOW_WIDTH, AlignFrame.NEW_WINDOW_HEIGHT);
+            AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
     }
 }