From cf64def09a8b741483854ddd8c034d0aefff15b4 Mon Sep 17 00:00:00 2001
From: gmungoc <g.m.carstairs@dundee.ac.uk>
Date: Tue, 18 Sep 2018 16:03:09 +0100
Subject: [PATCH] JAL-3063 temporary extra menu option to save/load project as
 JAXB

---
 src/jalview/gui/AlignFrame.java |    4 +++-
 src/jalview/gui/Desktop.java    |   41 +++++++++++++++++++++++++++++----------
 src/jalview/jbgui/GDesktop.java |   28 ++++++++++++++++++++++----
 3 files changed, 58 insertions(+), 15 deletions(-)

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index a2336a0..1f1fac0 100644
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -5399,7 +5399,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    */
   public List<? extends AlignmentViewPanel> getAlignPanels()
   {
-    return alignPanels == null ? Arrays.asList(alignPanel) : alignPanels;
+    // alignPanels is never null
+    // return alignPanels == null ? Arrays.asList(alignPanel) : alignPanels;
+    return alignPanels;
   }
 
   /**
diff --git a/src/jalview/gui/Desktop.java b/src/jalview/gui/Desktop.java
index 8d9e366..bbdddbb 100644
--- a/src/jalview/gui/Desktop.java
+++ b/src/jalview/gui/Desktop.java
@@ -1605,9 +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());
@@ -1636,7 +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(
@@ -1678,13 +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"));
@@ -1707,7 +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);
diff --git a/src/jalview/jbgui/GDesktop.java b/src/jalview/jbgui/GDesktop.java
index a4afb74..290c4a4 100755
--- a/src/jalview/jbgui/GDesktop.java
+++ b/src/jalview/jbgui/GDesktop.java
@@ -245,7 +245,16 @@ public class GDesktop extends JFrame
       @Override
       public void actionPerformed(ActionEvent e)
       {
-        saveState_actionPerformed(e);
+        saveState_actionPerformed(true);
+      }
+    });
+    JMenuItem saveAsJaxb = new JMenuItem("Save Project as JAXB");
+    saveAsJaxb.addActionListener(new ActionListener()
+    {
+      @Override
+      public void actionPerformed(ActionEvent e)
+      {
+        saveState_actionPerformed(false);
       }
     });
     loadState.setText(MessageManager.getString("action.load_project"));
@@ -254,7 +263,16 @@ public class GDesktop extends JFrame
       @Override
       public void actionPerformed(ActionEvent e)
       {
-        loadState_actionPerformed(e);
+        loadState_actionPerformed(true);
+      }
+    });
+    JMenuItem loadAsJaxb = new JMenuItem("Load Project as JAXB");
+    loadAsJaxb.addActionListener(new ActionListener()
+    {
+      @Override
+      public void actionPerformed(ActionEvent e)
+      {
+        loadState_actionPerformed(false);
       }
     });
     inputMenu.setText(MessageManager.getString("label.input_alignment"));
@@ -424,7 +442,9 @@ public class GDesktop extends JFrame
     FileMenu.add(inputSequence);
     FileMenu.addSeparator();
     FileMenu.add(saveState);
+    FileMenu.add(saveAsJaxb);
     FileMenu.add(loadState);
+    FileMenu.add(loadAsJaxb);
     FileMenu.addSeparator();
     FileMenu.add(quit);
     HelpMenu.add(aboutMenuItem);
@@ -586,7 +606,7 @@ public class GDesktop extends JFrame
    * @param e
    *          DOCUMENT ME!
    */
-  public void saveState_actionPerformed(ActionEvent e)
+  public void saveState_actionPerformed(boolean asCastor)
   {
   }
 
@@ -596,7 +616,7 @@ public class GDesktop extends JFrame
    * @param e
    *          DOCUMENT ME!
    */
-  public void loadState_actionPerformed(ActionEvent e)
+  public void loadState_actionPerformed(boolean asCastor)
   {
   }
 
-- 
1.7.10.2