X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FVamsasApplication.java;h=ef814d3bd291ad925d3c099527f316514b2ab4e8;hb=a83adb45bdf9554e270921b4baad94defd314b36;hp=ac72e936279e7cb8a8f1a321cab084b226ef0c46;hpb=4c1ab51e2c08f85ba8c38486adf4a6ce0b0f25c3;p=jalview.git

diff --git a/src/jalview/gui/VamsasApplication.java b/src/jalview/gui/VamsasApplication.java
index ac72e93..ef814d3 100644
--- 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)
     {
@@ -484,8 +484,8 @@ public class VamsasApplication implements SelectionSource, VamsasSource
               errorsDuringUpdate = true;
               Cache.log.error("Exception synchronizing " + af.getTitle()
                       + " "
-                      + (af.getViewport().viewName == null ? ""
-                              : " view " + af.getViewport().viewName)
+                      + (af.getViewport().getViewName() == null ? ""
+                              : " view " + af.getViewport().getViewName())
                       + " to document.", e);
               stored = false;
             }
@@ -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;
             }
@@ -1076,7 +1074,7 @@ public class VamsasApplication implements SelectionSource, VamsasSource
                   {
                     Iterator<int[]> intervals = hidden
                             .getVisContigsIterator(seqsel.getStartRes(),
-                                    seqsel.getEndRes() + 1);
+                                    seqsel.getEndRes() + 1, false);
                     while (intervals.hasNext())
                     {
                       int[] region = intervals.next();