numerous bugfixs (tree panel synchs) and DatastoreRegistry clas.

[jalview.git] / src / jalview / appletgui / AlignViewport.java

diff --git a/src/jalview/appletgui/AlignViewport.java b/src/jalview/appletgui/AlignViewport.java
index fd43a5d..ceb30d7 100755 (executable)
--- 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()