X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FVamsasApplication.java;h=13f6692f13a6a10bcc997fc7819f72fdb43e3875;hb=ad20cd92225f2ee8c251d39b00b90555d382a616;hp=cd9a529581b0d4aee1fedab16cbcaa25e88d3c58;hpb=caf13e6a9dc82023cd8648420201e5ad60ce0393;p=jalview.git

diff --git a/src/jalview/gui/VamsasApplication.java b/src/jalview/gui/VamsasApplication.java
index cd9a529..13f6692 100644
--- a/src/jalview/gui/VamsasApplication.java
+++ b/src/jalview/gui/VamsasApplication.java
@@ -1,13 +1,13 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
+ * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
  * 
  * This file is part of Jalview.
  * 
  * Jalview is free software: you can redistribute it and/or
  * modify it under the terms of the GNU General Public License 
  * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
- * 
+ *  
  * Jalview is distributed in the hope that it will be useful, but 
  * WITHOUT ANY WARRANTY; without even the implied warranty 
  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
@@ -45,7 +45,6 @@ import uk.ac.vamsas.client.ClientHandle;
 import uk.ac.vamsas.client.IClient;
 import uk.ac.vamsas.client.IClientDocument;
 import uk.ac.vamsas.client.InvalidSessionDocumentException;
-import uk.ac.vamsas.client.NoDefaultSessionException;
 import uk.ac.vamsas.client.UserHandle;
 import uk.ac.vamsas.client.VorbaId;
 import uk.ac.vamsas.client.picking.IMessageHandler;
@@ -62,7 +61,7 @@ import uk.ac.vamsas.objects.core.Seg;
  * @author jimp
  * 
  */
-public class VamsasApplication implements SelectionSource,VamsasSource
+public class VamsasApplication implements SelectionSource, VamsasSource
 {
   IClient vclient = null;
 
@@ -756,7 +755,7 @@ public class VamsasApplication implements SelectionSource,VamsasSource
       {
         final IPickManager pm = vclient.getPickManager();
         final StructureSelectionManager ssm = StructureSelectionManager
-                .getStructureSelectionManager();
+                .getStructureSelectionManager(Desktop.instance);
         final VamsasApplication me = this;
         pm.registerMessageHandler(new IMessageHandler()
         {
@@ -958,7 +957,8 @@ public class VamsasApplication implements SelectionSource,VamsasSource
 
           int i = -1;
 
-          public void mouseOver(SequenceI seq, int index, VamsasSource source)
+          public void mouseOver(SequenceI seq, int index,
+                  VamsasSource source)
           {
             if (jv2vobj == null)
               return;
@@ -1021,10 +1021,8 @@ public class VamsasApplication implements SelectionSource,VamsasSource
               {
                 String[] vobj = new String[seqsel.getSize()];
                 int o = 0;
-                Enumeration sels = seqsel.getSequences(null).elements();
-                while (sels.hasMoreElements())
+                for (SequenceI sel : seqsel.getSequences(null))
                 {
-                  SequenceI sel = (SequenceI) sels.nextElement();
                   VorbaId v = (VorbaId) jv2vobj.get(sel);
                   if (v != null)
                   {