Merge branch 'feature/JAL-3169cancelOverwrite' into trialMerge

Conflicts:
	src/jalview/io/JalviewFileChooser.java

diff --cc src/jalview/io/JalviewFileChooser.java
index b7eeaab,6b0eba8..2419bef
--- 1/src/jalview/io/JalviewFileChooser.java
--- 2/src/jalview/io/JalviewFileChooser.java
+++ b/src/jalview/io/JalviewFileChooser.java
@@@ -62,10 -58,7 +62,10 @@@ import javax.swing.plaf.basic.BasicFile
   *
   */
  public class JalviewFileChooser extends JFileChooser
-         implements PropertyChangeListener, DialogRunnerI
++        implements PropertyChangeListener, DialogRunnerI<JalviewFileChooser>
  {
 +  DialogRunner<JalviewFileChooser> runner = new DialogRunner<>(this);
 +  
    /**
     * Factory method to return a file chooser that offers readable alignment file
     * formats
@@@ -331,16 -293,33 +331,35 @@@
      return selfile;
    }
  
-   Component saveparent;
-   RunResponse overwriteCheck = new RunResponse(
-           JalviewFileChooser.APPROVE_OPTION)
+   @Override
+   public int showSaveDialog(Component parent) throws HeadlessException
    {
-     @Override
-     public void run()
+     this.setAccessory(null);
++    // Java 9,10,11 on OSX - clear selected file so name isn't auto populated
+     this.setSelectedFile(null);
++
+     return super.showSaveDialog(parent);
+   }
+ 
+   /**
+    * If doing a Save, and an existing file is chosen or entered, prompt for
+    * confirmation of overwrite. Proceed if Yes, else leave the file chooser
+    * open.
+    * 
+    * @see https://stackoverflow.com/questions/8581215/jfilechooser-and-checking-for-overwrite
+    */
+   @Override
+   public void approveSelection()
+   {
+     if (getDialogType() != SAVE_DIALOG)
      {
+       super.approveSelection();
+       return;
+     }
+ 
      ourselectedFile = getSelectedFile();
  
-     if (getSelectedFile() == null)
+     if (ourselectedFile == null)
      {
        // Workaround for Java 9,10 on OSX - no selected file, but there is a
        // filename typed in
@@@ -360,89 -342,36 +382,36 @@@
      }
      if (ourselectedFile == null)
      {
-       returned = new Response(JalviewFileChooser.CANCEL_OPTION);
        return;
      }
-       // JBP Note - this code was executed regardless of 'SAVE' being pressed
-       // need to see if there were side effects
-       if (getFileFilter() instanceof JalviewFileFilter)
-       {
-         JalviewFileFilter jvf = (JalviewFileFilter) getFileFilter();
  
-         if (!jvf.accept(getSelectedFile()))
-         {
-           String withExtension = getSelectedFile() + "."
-                   + jvf.getAcceptableExtension();
-           setSelectedFile(new File(withExtension));
-         }
-       }
-       // All good, so we continue to save
-       returned = new Response(JalviewFileChooser.APPROVE_OPTION);
+     if (getFileFilter() instanceof JalviewFileFilter)
+     {
+       JalviewFileFilter jvf = (JalviewFileFilter) getFileFilter();
  
-       // TODO: ENSURE THAT FILES SAVED WITH A ':' IN THE NAME ARE REFUSED AND THE
-       // USER PROMPTED FOR A NEW FILENAME
-       /**
-        * @j2sNative
-        */
+       if (!jvf.accept(ourselectedFile))
        {
-         if (getSelectedFile().exists())
-         {
-           // JAL-3048 - may not need to raise this for browser saves
- 
-           // yes/no cancel
-           int confirm = JvOptionPane.showConfirmDialog(saveparent,
-                   MessageManager.getString("label.overwrite_existing_file"),
-                   MessageManager.getString("label.file_already_exists"),
-                   JvOptionPane.YES_NO_OPTION);
- 
-           if (confirm != JvOptionPane.YES_OPTION)
-           {
-             returned = new Response(JalviewFileChooser.CANCEL_OPTION);
-           }
-         }
+         String withExtension = getSelectedFile().getName() + "."
+                 + jvf.getAcceptableExtension();
+         ourselectedFile = (new File(getCurrentDirectory(), withExtension));
+         setSelectedFile(ourselectedFile);
        }
-     };
-   };
- 
-   /**
-    * Overridden for JalviewJS compatibility: only one thread in Javascript, 
-    * so we can't wait for user choice in another thread and then perform the 
-    * desired action
-    */
-   @Override
-   public int showSaveDialog(Component parent) throws HeadlessException
-   {
-     this.setAccessory(null);
- 
-     /*
-      * Save dialog is opened until user picks a file format 
-      */
-     if (!runner.isRegistered(overwriteCheck))
-     {
-       // first call for this instance
-       runner.firstResponse(overwriteCheck);
      }
-     else
-     {
-       // reset response flags
-       runner.resetResponses();
-     }
- 
-     setDialogType(SAVE_DIALOG);
-     
-     // Java 9,10,11 on OSX - clear selected file so name isn't auto populated
-     this.setSelectedFile(null);
-  
-     saveparent = parent;
  
-     int value = showDialog(parent, MessageManager.getString("action.save"));
-     /**
-      * @j2sNative
-      */
+     if (ourselectedFile.exists())
 -      {
 -        int confirm = JvOptionPane.showConfirmDialog(this,
 -                MessageManager.getString("label.overwrite_existing_file"),
 -                MessageManager.getString("label.file_already_exists"),
 -                JvOptionPane.YES_NO_OPTION);
 +    {
-       runner.firstRun(value);
++      int confirm = JvOptionPane.showConfirmDialog(this,
++              MessageManager.getString("label.overwrite_existing_file"),
++              MessageManager.getString("label.file_already_exists"),
++              JvOptionPane.YES_NO_OPTION);
+ 
 -        if (confirm != JvOptionPane.YES_OPTION)
 -        {
 -          return;
 -        }
++      if (confirm != JvOptionPane.YES_OPTION)
++      {
++        return;
+       }
 +    }
-     return value;
+ 
+     super.approveSelection();
    }
  
    void recentListSelectionChanged(Object selection)