fix for viewing user plots when the sequence has been flipped

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@10108 ee4ac58c-ac51-4696-9907-e4b3aa274f04

uk/ac/sanger/artemis/plot/UserDataAlgorithm.java

@@ -20,7 +20,7 @@
  * along with this program; if not, write to the Free Software
  * Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA  02111-1307, USA.
  *
- * $Header: //tmp/pathsoft/artemis/uk/ac/sanger/artemis/plot/UserDataAlgorithm.java,v 1.6 2008-10-30 17:18:28 tjc Exp $
+ * $Header: //tmp/pathsoft/artemis/uk/ac/sanger/artemis/plot/UserDataAlgorithm.java,v 1.7 2009-03-16 14:09:51 tjc Exp $
  */
 
 package uk.ac.sanger.artemis.plot;
@@ -40,7 +40,7 @@ import java.util.regex.Pattern;
  *  set in the constructor.
  *
  *  @author Kim Rutherford <kmr@sanger.ac.uk>
- *  @version $Id: UserDataAlgorithm.java,v 1.6 2008-10-30 17:18:28 tjc Exp $
+ *  @version $Id: UserDataAlgorithm.java,v 1.7 2009-03-16 14:09:51 tjc Exp $
  **/
 
 public class UserDataAlgorithm extends BaseAlgorithm
@@ -171,6 +171,14 @@ public class UserDataAlgorithm extends BaseAlgorithm
   {
     final int value_count = getValueCount ();
 
+    if(getStrand ().getDirection() == Bases.REVERSE)
+    {
+      int tstart = start;
+      int tend   = end;
+      end   = getStrand().getBases().getComplementPosition(tstart);
+      start = getStrand().getBases().getComplementPosition(tend);
+    }
+    
     for (int i = 0 ; i < value_count ; ++i) 
     {
       values [i] = 0;