JAL-3210 Improvements to eclipse detection. New src tree and SwingJS updated from...

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

diff --git a/src/jalview/gui/VamsasApplication.java b/src/jalview/gui/VamsasApplication.java
index c094b1c..ef814d3 100644 (file)
--- a/src/jalview/gui/VamsasApplication.java
+++ b/src/jalview/gui/VamsasApplication.java
@@ -173,7 +173,7 @@ public class VamsasApplication implements SelectionSource, VamsasSource
           }
         } catch (InvalidSessionDocumentException e)
         {
-          JvOptionPane.showInternalMessageDialog(Desktop.desktop,
+          JvOptionPane.showInternalMessageDialog(Desktop.getDesktopPane(),
 
                   MessageManager.getString(
                           "label.vamsas_doc_couldnt_be_opened_as_new_session"),
@@ -455,7 +455,7 @@ public class VamsasApplication implements SelectionSource, VamsasSource
     VamsasAppDatastore vds = new VamsasAppDatastore(doc, vobj2jv, jv2vobj,
             baseProvEntry(), alRedoState);
     // wander through frames
-    JInternalFrame[] frames = Desktop.desktop.getAllFrames();
+    JInternalFrame[] frames = Desktop.getDesktopPane().getAllFrames();
 
     if (frames == null)
     {
@@ -660,7 +660,7 @@ public class VamsasApplication implements SelectionSource, VamsasSource
                   Cache.log.debug(
                           "Asking user if the vamsas session should be stored.");
                   int reply = JvOptionPane.showInternalConfirmDialog(
-                          Desktop.desktop,
+                          Desktop.getDesktopPane(),
                           "The current VAMSAS session has unsaved data - do you want to save it ?",
                           "VAMSAS Session Shutdown",
                           JvOptionPane.YES_NO_OPTION,
@@ -669,7 +669,7 @@ public class VamsasApplication implements SelectionSource, VamsasSource
                   if (reply == JvOptionPane.YES_OPTION)
                   {
                     Cache.log.debug("Prompting for vamsas store filename.");
-                    Desktop.instance.vamsasSave_actionPerformed(null);
+                    Desktop.getInstance().vamsasSave_actionPerformed(null);
                     Cache.log
                             .debug("Finished attempt at storing document.");
                   }
@@ -688,7 +688,7 @@ public class VamsasApplication implements SelectionSource, VamsasSource
 
   public void disableGui(boolean b)
   {
-    Desktop.instance.setVamsasUpdate(b);
+    Desktop.getInstance().setVamsasUpdate(b);
   }
 
   Hashtable _backup_vobj2jv;
@@ -761,10 +761,10 @@ public class VamsasApplication implements SelectionSource, VamsasSource
       }
       try
       {
-        final IPickManager pm = vclient.getPickManager();
-        final StructureSelectionManager ssm = StructureSelectionManager
-                .getStructureSelectionManager(Desktop.instance);
-        final VamsasApplication me = this;
+        IPickManager pm = vclient.getPickManager();
+        StructureSelectionManager ssm = Desktop
+                .getStructureSelectionManager();
+        VamsasApplication me = this;
         pm.registerMessageHandler(new IMessageHandler()
         {
           String last = null;
@@ -830,7 +830,6 @@ public class VamsasApplication implements SelectionSource, VamsasSource
                 {
                   type = jvobjs[o].getClass();
                 }
-                ;
                 if (type != jvobjs[o].getClass())
                 {
                   send = false;
@@ -954,7 +953,6 @@ public class VamsasApplication implements SelectionSource, VamsasSource
               {
                 jvobjs[c] = null;
               }
-              ;
               jvobjs = null;
               return;
             }