X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FVamsasApplication.java;h=b789040bb688dcb0ab3ae076c46553def82c1a4c;hb=47168f025aefdaa044802bd5f8f510ffe43a4808;hp=efd94de08b633823ace20430cba4ff1886c3bc87;hpb=8a6fa9ea9900d0f106529c3f6283e7f9d76dd2cb;p=jalview.git

diff --git a/src/jalview/gui/VamsasApplication.java b/src/jalview/gui/VamsasApplication.java
index efd94de..b789040 100644
--- a/src/jalview/gui/VamsasApplication.java
+++ b/src/jalview/gui/VamsasApplication.java
@@ -1,19 +1,22 @@
 /*
- * 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 2.8.2)
+ * Copyright (C) 2014 The Jalview Authors
  * 
  * 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.
- * 
+ * 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 
  * PURPOSE.  See the GNU General Public License for more details.
  * 
- * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
  */
 package jalview.gui;
 
@@ -27,6 +30,7 @@ import jalview.structure.SelectionListener;
 import jalview.structure.SelectionSource;
 import jalview.structure.StructureSelectionManager;
 import jalview.structure.VamsasListener;
+import jalview.structure.VamsasSource;
 
 import java.beans.PropertyChangeEvent;
 import java.beans.PropertyChangeListener;
@@ -44,7 +48,6 @@ 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;
@@ -61,7 +64,7 @@ import uk.ac.vamsas.objects.core.Seg;
  * @author jimp
  * 
  */
-public class VamsasApplication implements SelectionSource
+public class VamsasApplication implements SelectionSource, VamsasSource
 {
   IClient vclient = null;
 
@@ -755,8 +758,8 @@ public class VamsasApplication implements SelectionSource
       {
         final IPickManager pm = vclient.getPickManager();
         final StructureSelectionManager ssm = StructureSelectionManager
-                .getStructureSelectionManager();
-        final SelectionSource me = this;
+                .getStructureSelectionManager(Desktop.instance);
+        final VamsasApplication me = this;
         pm.registerMessageHandler(new IMessageHandler()
         {
           String last = null;
@@ -789,7 +792,7 @@ public class VamsasApplication implements SelectionSource
                 // bound to "+jvobj+" at "+mm.getPosition());
                 // position is character position in aligned sequence
                 ssm.mouseOverVamsasSequence((SequenceI) jvobj,
-                        mm.getPosition());
+                        mm.getPosition(), me);
               }
             }
             if (message instanceof uk.ac.vamsas.client.picking.SelectionMessage)
@@ -957,7 +960,8 @@ public class VamsasApplication implements SelectionSource
 
           int i = -1;
 
-          public void mouseOver(SequenceI seq, int index)
+          public void mouseOver(SequenceI seq, int index,
+                  VamsasSource source)
           {
             if (jv2vobj == null)
               return;
@@ -1020,10 +1024,8 @@ public class VamsasApplication implements SelectionSource
               {
                 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)
                   {