Merge branch 'features/pca_jaxb_datasetrefs_JAL-3171_JAL-3063_JAL-1767' into develop

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

diff --git a/src/jalview/gui/Desktop.java b/src/jalview/gui/Desktop.java
index 569257f..bbdddbb 100644 (file)
--- a/src/jalview/gui/Desktop.java
+++ b/src/jalview/gui/Desktop.java
@@ -519,7 +519,7 @@ public class Desktop extends jalview.jbgui.GDesktop
   {
     final Desktop me = this;
     // Thread off the news reader, in case there are connection problems.
-    addDialogThread(new Runnable()
+    new Thread(new Runnable()
     {
       @Override
       public void run()
@@ -530,13 +530,13 @@ public class Desktop extends jalview.jbgui.GDesktop
         showNews.setVisible(true);
         Cache.log.debug("Completed news thread.");
       }
-    });
+    }).start();
   }
 
   public void getIdentifiersOrgData()
   {
     // Thread off the identifiers fetcher
-    addDialogThread(new Runnable()
+    new Thread(new Runnable()
     {
       @Override
       public void run()
@@ -553,7 +553,8 @@ public class Desktop extends jalview.jbgui.GDesktop
                   + e.getMessage());
         }
       }
-    });
+    }).start();
+    ;
   }
 
   @Override
@@ -1604,9 +1605,10 @@ public class Desktop extends jalview.jbgui.GDesktop
    *          DOCUMENT ME!
    */
   @Override
-  public void saveState_actionPerformed(ActionEvent e)
+  public void saveState_actionPerformed(boolean asCastor)
   {
-    JalviewFileChooser chooser = new JalviewFileChooser("jvp",
+    JalviewFileChooser chooser = new JalviewFileChooser(
+            asCastor ? "jvp" : "jvx",
             "Jalview Project");
 
     chooser.setFileView(new JalviewFileView());
@@ -1635,7 +1637,14 @@ public class Desktop extends jalview.jbgui.GDesktop
           // TODO prevent user from messing with the Desktop whilst we're saving
           try
           {
-            new Jalview2XML().saveState(choice);
+            if (asCastor)
+            {
+              new Jalview2XML().saveState(choice);
+            }
+            else
+            {
+              new jalview.project.Jalview2XML().saveState(choice);
+            }
           } catch (OutOfMemoryError oom)
           {
             new OOMWarning(
@@ -1677,13 +1686,19 @@ public class Desktop extends jalview.jbgui.GDesktop
    *          DOCUMENT ME!
    */
   @Override
-  public void loadState_actionPerformed(ActionEvent e)
-  {
+  public void loadState_actionPerformed(boolean asCastor)
+  {
+    final String[] suffix = asCastor ? new String[] { "jvp", "jar" }
+            : new String[]
+            { "jvx" };
+    final String[] desc = asCastor
+            ? new String[]
+            { "Jalview Project", "Jalview Project (old)" }
+            : new String[]
+            { "Jalview Project" };
     JalviewFileChooser chooser = new JalviewFileChooser(
-            Cache.getProperty("LAST_DIRECTORY"), new String[]
-            { "jvp", "jar" },
-            new String[]
-            { "Jalview Project", "Jalview Project (old)" },
+            Cache.getProperty("LAST_DIRECTORY"), suffix,
+            desc,
             "Jalview Project");
     chooser.setFileView(new JalviewFileView());
     chooser.setDialogTitle(MessageManager.getString("label.restore_state"));
@@ -1706,7 +1721,14 @@ public class Desktop extends jalview.jbgui.GDesktop
                   { choice }), choice.hashCode());
           try
           {
-            new Jalview2XML().loadJalviewAlign(choice);
+            if (asCastor)
+            {
+              new Jalview2XML().loadJalviewAlign(choice);
+            }
+            else
+            {
+              new jalview.project.Jalview2XML().loadJalviewAlign(choice);
+            }
           } catch (OutOfMemoryError oom)
           {
             new OOMWarning("Whilst loading project from " + choice, oom);