JAL-2089 patch broken merge to master for Release 2.10.0b1

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

diff --git a/src/jalview/gui/VamsasApplication.java b/src/jalview/gui/VamsasApplication.java
index 6444667..afb6df4 100644 (file)
--- a/src/jalview/gui/VamsasApplication.java
+++ b/src/jalview/gui/VamsasApplication.java
@@ -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();
@@ -315,6 +321,7 @@ public class VamsasApplication implements SelectionSource, VamsasSource
     Thread udthread = new Thread(new Runnable()
     {
 
+      @Override
       public void run()
       {
         Cache.log.info("Jalview updating to the Vamsas Session.");
@@ -348,7 +355,9 @@ public class VamsasApplication implements SelectionSource, VamsasSource
   {
     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
@@ -631,6 +640,7 @@ public class VamsasApplication implements SelectionSource, VamsasSource
     final VamsasApplication client = this;
     vclient.addDocumentUpdateHandler(new PropertyChangeListener()
     {
+      @Override
       public void propertyChange(PropertyChangeEvent evt)
       {
         Cache.log.debug("Dealing with document update event.");
@@ -648,6 +658,7 @@ public class VamsasApplication implements SelectionSource, VamsasSource
             uk.ac.vamsas.client.Events.DOCUMENT_REQUESTTOCLOSE,
             new PropertyChangeListener()
             {
+              @Override
               public void propertyChange(PropertyChangeEvent evt)
               {
                 if (client.promptUser)
@@ -717,7 +728,9 @@ 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();
@@ -764,6 +777,7 @@ public class VamsasApplication implements SelectionSource, VamsasSource
         {
           String last = null;
 
+          @Override
           public void handleMessage(Message message)
           {
             if (vobj2jv == null)
@@ -988,6 +1002,7 @@ public class VamsasApplication implements SelectionSource, VamsasSource
         selecter = new SelectionListener()
         {
 
+          @Override
           public void selection(SequenceGroup seqsel,
                   ColumnSelection colsel, SelectionSource source)
           {
@@ -1013,9 +1028,9 @@ public class VamsasApplication implements SelectionSource, VamsasSource
                 if (source instanceof AlignViewport)
                 {
                   // the empty selection.
-                  sm = new SelectionMessage("jalview", new String[]
-                  { ((AlignmentViewport) source).getSequenceSetId() }, null,
-                          true);
+                  sm = new SelectionMessage("jalview",
+                          new String[] { ((AlignmentViewport) source)
+                                  .getSequenceSetId() }, null, true);
                 }
                 else
                 {
@@ -1055,11 +1070,10 @@ public class VamsasApplication implements SelectionSource, VamsasSource
                   {
                     // gather selected columns outwith the sequence positions
                     // too
-                    for (Object obj : colsel.getSelected())
+                    for (Integer ival : colsel.getSelected())
                     {
-                      int ival = ((Integer) obj).intValue();
                       Pos p = new Pos();
-                      p.setI(ival + 1);
+                      p.setI(ival.intValue() + 1);
                       range.addPos(p);
                     }
                   }