X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAlignViewport.java;h=ceb30d713f4db2e20f2f890bf88688332fc740de;hb=f2287ae5b61b6bf36ee90bd6bbf38d44331bf273;hp=fd43a5d41cc07b56c7d42b7556c8eefaf8f34d5e;hpb=b57fe83e78a9fb160a4765099880827b82222c53;p=jalview.git

diff --git a/src/jalview/appletgui/AlignViewport.java b/src/jalview/appletgui/AlignViewport.java
index fd43a5d..ceb30d7 100755
--- a/src/jalview/appletgui/AlignViewport.java
+++ b/src/jalview/appletgui/AlignViewport.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
- * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1)
+ * Copyright (C) 2009 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
@@ -198,6 +198,11 @@ public class AlignViewport
           upperCasebold = true;
         }
       }
+      param = applet.getParameter("sortByTree");
+      if (param != null)
+      {
+        sortByTree=Boolean.valueOf(param).booleanValue();
+      }
 
     }
 
@@ -1514,6 +1519,11 @@ public class AlignViewport
   public boolean showUnconserved=false;
 
   /**
+   * when set, alignment should be reordered according to a newly opened tree
+   */
+  public boolean sortByTree=false;
+
+  /**
    * @return the showUnconserved
    */
   public boolean getShowunconserved()