Merge develop to Release_2_8_3_Branch

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

diff --git a/src/jalview/gui/VamsasApplication.java b/src/jalview/gui/VamsasApplication.java
index 3671b39..6444667 100644 (file)
--- a/src/jalview/gui/VamsasApplication.java
+++ b/src/jalview/gui/VamsasApplication.java
@@ -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;
@@ -347,7 +347,9 @@ 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"));
+    }
     Cache.log.info("Jalview disconnecting from the Vamsas Session.");
     try
     {
@@ -958,11 +960,14 @@ 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 +1003,7 @@ 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)
@@ -1009,7 +1014,7 @@ public class VamsasApplication implements SelectionSource, VamsasSource
                 {
                   // the empty selection.
                   sm = new SelectionMessage("jalview", new String[]
-                  { ((AlignViewport) source).getSequenceSetId() }, null,
+                  { ((AlignmentViewport) source).getSequenceSetId() }, null,
                           true);
                 }
                 else
@@ -1050,10 +1055,9 @@ 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);