Merge branch 'develop' into update_212_Dec_merge_with_21125_chamges

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

diff --git a/src/jalview/gui/VamsasApplication.java b/src/jalview/gui/VamsasApplication.java
index 8a8ba8d..1ad7caf 100644 (file)
--- a/src/jalview/gui/VamsasApplication.java
+++ b/src/jalview/gui/VamsasApplication.java
@@ -174,7 +174,7 @@ 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"),
@@ -453,7 +453,7 @@ 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)
     {
@@ -656,8 +656,7 @@ public class VamsasApplication implements SelectionSource, VamsasSource
                 {
                   Console.debug(
                           "Asking user if the vamsas session should be stored.");
-                  int reply = JvOptionPane.showInternalConfirmDialog(
-                          Desktop.desktop,
+                  int reply = JvOptionPane.showInternalConfirmDialog(Desktop.getDesktopPane(),
                           "The current VAMSAS session has unsaved data - do you want to save it ?",
                           "VAMSAS Session Shutdown",
                           JvOptionPane.YES_NO_OPTION,
@@ -666,7 +665,7 @@ public class VamsasApplication implements SelectionSource, VamsasSource
                   if (reply == JvOptionPane.YES_OPTION)
                   {
                     Console.debug("Prompting for vamsas store filename.");
-                    Desktop.instance.vamsasSave_actionPerformed(null);
+                    Desktop.getInstance().vamsasSave_actionPerformed(null);
                     Console.debug("Finished attempt at storing document.");
                   }
                   Console.debug(
@@ -760,7 +759,7 @@ public class VamsasApplication implements SelectionSource, VamsasSource
       {
         final IPickManager pm = vclient.getPickManager();
         final StructureSelectionManager ssm = StructureSelectionManager
-                .getStructureSelectionManager(Desktop.instance);
+           .getStructureSelectionManager(Desktop.getInstance());
         final VamsasApplication me = this;
         pm.registerMessageHandler(new IMessageHandler()
         {