Merge branch 'develop' into Release_2_9_Branch

[jalview.git] / src / jalview / gui / VamsasApplication.java

diff --git a/src/jalview/gui/VamsasApplication.java b/src/jalview/gui/VamsasApplication.java
index 6daaf68..4630fd1 100644 (file)
--- a/src/jalview/gui/VamsasApplication.java
+++ b/src/jalview/gui/VamsasApplication.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2b1)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Copyright (C) 2015 The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -32,12 +32,12 @@ import jalview.structure.StructureSelectionManager;
 import jalview.structure.VamsasListener;
 import jalview.structure.VamsasSource;
 import jalview.util.MessageManager;
+import jalview.viewmodel.AlignmentViewport;
 
 import java.beans.PropertyChangeEvent;
 import java.beans.PropertyChangeListener;
 import java.io.File;
 import java.io.IOException;
-import java.util.Enumeration;
 import java.util.Hashtable;
 import java.util.IdentityHashMap;
 import java.util.Iterator;
@@ -156,7 +156,9 @@ public class VamsasApplication implements SelectionSource, VamsasSource
       {
         if (sess != null)
         {
-          throw new Error(MessageManager.getString("error.implementation_error_cannot_import_vamsas_doc"));
+          throw new Error(
+                  MessageManager
+                          .getString("error.implementation_error_cannot_import_vamsas_doc"));
         }
         try
         {
@@ -176,8 +178,10 @@ public class VamsasApplication implements SelectionSource, VamsasSource
                   .showInternalMessageDialog(
                           Desktop.desktop,
 
-                          MessageManager.getString("label.vamsas_doc_couldnt_be_opened_as_new_session"),
-                          MessageManager.getString("label.vamsas_document_import_failed"),
+                          MessageManager
+                                  .getString("label.vamsas_doc_couldnt_be_opened_as_new_session"),
+                          MessageManager
+                                  .getString("label.vamsas_document_import_failed"),
                           JOptionPane.ERROR_MESSAGE);
 
         }
@@ -263,7 +267,9 @@ public class VamsasApplication implements SelectionSource, VamsasSource
   {
     if (!inSession())
     {
-      throw new Error(MessageManager.getString("error.implementation_error_vamsas_operation_not_init"));
+      throw new Error(
+              MessageManager
+                      .getString("error.implementation_error_vamsas_operation_not_init"));
     }
     addDocumentUpdateHandler();
     addStoreDocumentHandler();
@@ -347,7 +353,11 @@ public class VamsasApplication implements SelectionSource, VamsasSource
   public void end_session(boolean promptUser)
   {
     if (!inSession())
-      throw new Error(MessageManager.getString("error.jalview_no_connected_vamsas_session"));
+    {
+      throw new Error(
+              MessageManager
+                      .getString("error.jalview_no_connected_vamsas_session"));
+    }
     Cache.log.info("Jalview disconnecting from the Vamsas Session.");
     try
     {
@@ -715,7 +725,9 @@ public class VamsasApplication implements SelectionSource, VamsasSource
         return;
       }
 
-      throw new Error(MessageManager.getString("error.implementation_error_cannot_recover_vamsas_object_mappings"));
+      throw new Error(
+              MessageManager
+                      .getString("error.implementation_error_cannot_recover_vamsas_object_mappings"));
     }
     jv2vobj.clear();
     Iterator el = _backup_jv2vobj.entrySet().iterator();
@@ -958,11 +970,14 @@ public class VamsasApplication implements SelectionSource, VamsasSource
 
           int i = -1;
 
-          public void mouseOver(SequenceI seq, int index,
+          @Override
+          public void mouseOverSequence(SequenceI seq, int index,
                   VamsasSource source)
           {
             if (jv2vobj == null)
+            {
               return;
+            }
             if (seq != last || i != index)
             {
               VorbaId v = (VorbaId) jv2vobj.get(seq);
@@ -998,7 +1013,7 @@ public class VamsasApplication implements SelectionSource, VamsasSource
               AlignmentI visal = null;
               if (source instanceof AlignViewport)
               {
-                visal = ((AlignViewport) source).getAlignment();
+                visal = ((AlignmentViewport) source).getAlignment();
               }
               SelectionMessage sm = null;
               if ((seqsel == null || seqsel.getSize() == 0)
@@ -1008,9 +1023,9 @@ public class VamsasApplication implements SelectionSource, VamsasSource
                 if (source instanceof AlignViewport)
                 {
                   // the empty selection.
-                  sm = new SelectionMessage("jalview", new String[]
-                  { ((AlignViewport) source).getSequenceSetId() }, null,
-                          true);
+                  sm = new SelectionMessage("jalview",
+                          new String[] { ((AlignmentViewport) source)
+                                  .getSequenceSetId() }, null, true);
                 }
                 else
                 {
@@ -1050,10 +1065,9 @@ public class VamsasApplication implements SelectionSource, VamsasSource
                   {
                     // gather selected columns outwith the sequence positions
                     // too
-                    Enumeration cols = colsel.getSelected().elements();
-                    while (cols.hasMoreElements())
+                    for (Object obj : colsel.getSelected())
                     {
-                      int ival = ((Integer) cols.nextElement()).intValue();
+                      int ival = ((Integer) obj).intValue();
                       Pos p = new Pos();
                       p.setI(ival + 1);
                       range.addPos(p);