Multiple Views

[jalview.git] / src / jalview / gui / PairwiseAlignPanel.java

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