X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FVamsasApplication.java;h=b789040bb688dcb0ab3ae076c46553def82c1a4c;hb=5c33de4092732a61c2bc4ab3cb76b773752ad37a;hp=c48c86f460191618f91640d95bab082ae32c2410;hpb=153dd62dc91da13ae732600e6ea55ddbe15eab39;p=jalview.git

diff --git a/src/jalview/gui/VamsasApplication.java b/src/jalview/gui/VamsasApplication.java
index c48c86f..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;
 
@@ -222,14 +225,12 @@ public class VamsasApplication implements SelectionSource
     } catch (Error e)
     {
       Cache.log
-              .warn(
-                      "Probable SERIOUS VAMSAS client incompatibility - carrying on regardless",
+              .warn("Probable SERIOUS VAMSAS client incompatibility - carrying on regardless",
                       e);
     } catch (Exception e)
     {
       Cache.log
-              .warn(
-                      "Probable VAMSAS client incompatibility - carrying on regardless",
+              .warn("Probable VAMSAS client incompatibility - carrying on regardless",
                       e);
     }
   }
@@ -241,8 +242,8 @@ public class VamsasApplication implements SelectionSource
    */
   private ClientHandle getJalviewHandle()
   {
-    return new ClientHandle("jalview.bin.Jalview", jalview.bin.Cache
-            .getProperty("VERSION"));
+    return new ClientHandle("jalview.bin.Jalview",
+            jalview.bin.Cache.getProperty("VERSION"));
   }
 
   /**
@@ -305,8 +306,7 @@ public class VamsasApplication implements SelectionSource
     } catch (Exception e)
     {
       Cache.log
-              .warn(
-                      "Exception whilst refreshing jalview windows after a vamsas document update.",
+              .warn("Exception whilst refreshing jalview windows after a vamsas document update.",
                       e);
     }
   }
@@ -758,8 +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;
@@ -791,8 +791,8 @@ public class VamsasApplication implements SelectionSource
                 // Cache.log.debug("Handling Mouse over "+mm.getVorbaID()+"
                 // bound to "+jvobj+" at "+mm.getPosition());
                 // position is character position in aligned sequence
-                ssm.mouseOverVamsasSequence((SequenceI) jvobj, mm
-                        .getPosition());
+                ssm.mouseOverVamsasSequence((SequenceI) jvobj,
+                        mm.getPosition(), me);
               }
             }
             if (message instanceof uk.ac.vamsas.client.picking.SelectionMessage)
@@ -960,7 +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;
@@ -1023,10 +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)
                   {
@@ -1064,8 +1063,8 @@ public class VamsasApplication implements SelectionSource
                   }
                   else
                   {
-                    int[] intervals = colsel.getVisibleContigs(seqsel
-                            .getStartRes(), seqsel.getEndRes() + 1);
+                    int[] intervals = colsel.getVisibleContigs(
+                            seqsel.getStartRes(), seqsel.getEndRes() + 1);
                     for (int iv = 0; iv < intervals.length; iv += 2)
                     {
                       Seg s = new Seg();