JAL-629 Add a timeout to modal dialogs for command line warning
[jalview.git] / src / jalview / gui / JvOptionPane.java
index bf15b86..0a7c49e 100644 (file)
  * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  * The Jalview Authors are detailed in the 'AUTHORS' file.
  */
-
 package jalview.gui;
 
-import jalview.util.Platform;
-import jalview.util.dialogrunner.DialogRunnerI;
-
+import java.awt.AWTEvent;
+import java.awt.ActiveEvent;
 import java.awt.Component;
+import java.awt.Container;
+import java.awt.Dialog.ModalityType;
+import java.awt.EventQueue;
 import java.awt.HeadlessException;
+import java.awt.MenuComponent;
+import java.awt.Toolkit;
+import java.awt.Window;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.awt.event.KeyEvent;
+import java.awt.event.MouseAdapter;
+import java.awt.event.MouseMotionAdapter;
 import java.beans.PropertyChangeEvent;
 import java.beans.PropertyChangeListener;
+import java.beans.PropertyVetoException;
+import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.HashMap;
 import java.util.List;
 import java.util.Map;
+import java.util.concurrent.ExecutorService;
+import java.util.concurrent.Executors;
 
 import javax.swing.Icon;
+import javax.swing.JButton;
+import javax.swing.JDialog;
+import javax.swing.JFrame;
+import javax.swing.JInternalFrame;
+import javax.swing.JLayeredPane;
+import javax.swing.JMenu;
+import javax.swing.JMenuBar;
 import javax.swing.JOptionPane;
 import javax.swing.JPanel;
+import javax.swing.JRootPane;
+import javax.swing.SwingUtilities;
+import javax.swing.UIManager;
+import javax.swing.event.InternalFrameEvent;
+import javax.swing.event.InternalFrameListener;
+
+import jalview.bin.Console;
+import jalview.util.ChannelProperties;
+import jalview.util.MessageManager;
+import jalview.util.Platform;
+import jalview.util.dialogrunner.DialogRunnerI;
 
-public class JvOptionPane extends JOptionPane implements DialogRunnerI,
-    PropertyChangeListener
+public class JvOptionPane extends JOptionPane
+        implements DialogRunnerI, PropertyChangeListener
 {
   private static final long serialVersionUID = -3019167117756785229L;
 
@@ -46,19 +77,34 @@ public class JvOptionPane extends JOptionPane implements DialogRunnerI,
 
   private static boolean interactiveMode = true;
 
+  public static final Runnable NULLCALLABLE = () -> {
+  };
+
   private Component parentComponent;
 
+  private ExecutorService executor = Executors.newCachedThreadPool();
+
+  private JDialog dialog = null;
+
   private Map<Object, Runnable> callbacks = new HashMap<>();
 
+  private int timeout = -1;
+
+  public void setTimeout(int i)
+  {
+    timeout = i;
+  }
+
   /*
-   * JalviewJS reports user choice in the dialog as the selected
-   * option (text); this list allows conversion to index (int)
+   * JalviewJS reports user choice in the dialog as the selected option (text);
+   * this list allows conversion to index (int)
    */
   List<Object> ourOptions;
-  
+
   public JvOptionPane(final Component parent)
   {
     this.parentComponent = Platform.isJS() ? this : parent;
+    this.setIcon(null);
   }
 
   public static int showConfirmDialog(Component parentComponent,
@@ -91,7 +137,7 @@ public class JvOptionPane extends JOptionPane implements DialogRunnerI,
     switch (optionType)
     {
     case JvOptionPane.YES_NO_CANCEL_OPTION:
-      // FeatureRenderer amendFeatures  ?? TODO ??
+      // FeatureRenderer amendFeatures ?? TODO ??
       // Chimera close
       // PromptUserConfig
       // $FALL-THROUGH$
@@ -164,8 +210,10 @@ public class JvOptionPane extends JOptionPane implements DialogRunnerI,
           Object message)
   {
     // JvOptionPaneTest only;
-    return isInteractiveMode() ? JOptionPane.showInternalConfirmDialog(
-            parentComponent, message) : (int) getMockResponse();
+    return isInteractiveMode()
+            ? JOptionPane.showInternalConfirmDialog(parentComponent,
+                    message)
+            : (int) getMockResponse();
   }
 
   /**
@@ -399,7 +447,6 @@ public class JvOptionPane extends JOptionPane implements DialogRunnerI,
     JOptionPane.showMessageDialog(parentComponent, message);
   }
 
-
   /**
    * Adds title and messageType
    * 
@@ -506,6 +553,7 @@ public class JvOptionPane extends JOptionPane implements DialogRunnerI,
 
     return JOptionPane.showInputDialog(message, initialSelectionValue);
   }
+
   /**
    * centered on parent
    * 
@@ -535,15 +583,14 @@ public class JvOptionPane extends JOptionPane implements DialogRunnerI,
   public static String showInputDialog(Component parentComponent,
           String message, String initialSelectionValue)
   {
-    
+
     // AnnotationPanel
-    
+
     return isInteractiveMode()
             ? JOptionPane.showInputDialog(parentComponent, message,
                     initialSelectionValue)
             : getMockResponse().toString();
   }
-  
 
   /**
    * input with initial selection
@@ -556,9 +603,9 @@ public class JvOptionPane extends JOptionPane implements DialogRunnerI,
   public static String showInputDialog(Component parentComponent,
           Object message, Object initialSelectionValue)
   {
-    
+
     // AnnotationPanel
-    
+
     return isInteractiveMode()
             ? JOptionPane.showInputDialog(parentComponent, message,
                     initialSelectionValue)
@@ -581,13 +628,14 @@ public class JvOptionPane extends JOptionPane implements DialogRunnerI,
 
     // test only
 
-    return isInteractiveMode() ? JOptionPane
-            .showInputDialog(parentComponent, message, title, messageType)
+    return isInteractiveMode()
+            ? JOptionPane.showInputDialog(parentComponent, message, title,
+                    messageType)
             : getMockResponse().toString();
   }
 
   /**
-   * Customized input option 
+   * Customized input option
    * 
    * @param parentComponent
    * @param message
@@ -604,9 +652,9 @@ public class JvOptionPane extends JOptionPane implements DialogRunnerI,
           Object[] selectionValues, Object initialSelectionValue)
           throws HeadlessException
   {
-    
+
     // test only
-    
+
     return isInteractiveMode()
             ? JOptionPane.showInputDialog(parentComponent, message, title,
                     messageType, icon, selectionValues,
@@ -614,8 +662,6 @@ public class JvOptionPane extends JOptionPane implements DialogRunnerI,
             : getMockResponse().toString();
   }
 
-  
-  
   /**
    * internal version
    * 
@@ -627,13 +673,12 @@ public class JvOptionPane extends JOptionPane implements DialogRunnerI,
           String message)
   {
     // test only
-    
+
     return isInteractiveMode()
             ? JOptionPane.showInternalInputDialog(parentComponent, message)
             : getMockResponse().toString();
   }
 
-  
   /**
    * internal with title and messageType
    * 
@@ -646,9 +691,9 @@ public class JvOptionPane extends JOptionPane implements DialogRunnerI,
   public static String showInternalInputDialog(Component parentComponent,
           String message, String title, int messageType)
   {
-    
+
     // AlignFrame tabbedPane_mousePressed
-    
+
     return isInteractiveMode()
             ? JOptionPane.showInternalInputDialog(parentComponent,
                     getPrefix(messageType) + message, title, messageType)
@@ -672,7 +717,7 @@ public class JvOptionPane extends JOptionPane implements DialogRunnerI,
           Object[] selectionValues, Object initialSelectionValue)
   {
     // test only
-    
+
     return isInteractiveMode()
             ? JOptionPane.showInternalInputDialog(parentComponent, message,
                     title, messageType, icon, selectionValues,
@@ -680,13 +725,12 @@ public class JvOptionPane extends JOptionPane implements DialogRunnerI,
             : getMockResponse().toString();
   }
 
-  
   ///////////// end of options ///////////////
-  
-  
+
   private static void outputMessage(Object message)
   {
-    System.out.println(">>> JOption Message : " + message.toString());
+    jalview.bin.Console
+            .outPrintln(">>> JOption Message : " + message.toString());
   }
 
   public static Object getMockResponse()
@@ -717,8 +761,8 @@ public class JvOptionPane extends JOptionPane implements DialogRunnerI,
 
   private static String getPrefix(int messageType)
   {
-    String prefix = ""; 
-    
+    String prefix = "";
+
     // JavaScript only
     if (Platform.isJS())
     {
@@ -751,19 +795,39 @@ public class JvOptionPane extends JOptionPane implements DialogRunnerI,
    * @param string2
    * @return
    */
+  public static JvOptionPane newOptionDialog()
+  {
+    return new JvOptionPane(null);
+  }
+
   public static JvOptionPane newOptionDialog(Component parentComponent)
   {
     return new JvOptionPane(parentComponent);
   }
 
-  public void showDialog(
-          String message, String title, int optionType, int messageType,
-          Icon icon, Object[] options, Object initialValue)
+  public void showDialog(String message, String title, int optionType,
+          int messageType, Icon icon, Object[] options, Object initialValue)
   {
+    showDialog(message, title, optionType, messageType, icon, options,
+            initialValue, true);
+  }
 
+  public void showDialog(Object message, String title, int optionType,
+          int messageType, Icon icon, Object[] options, Object initialValue,
+          boolean modal)
+  {
+    showDialog(message, title, optionType, messageType, icon, options,
+            initialValue, modal, null);
+  }
+
+  public void showDialog(Object message, String title, int optionType,
+          int messageType, Icon icon, Object[] options, Object initialValue,
+          boolean modal, JButton[] buttons)
+  {
     if (!isInteractiveMode())
     {
       handleResponse(getMockResponse());
+      return;
     }
     // two uses:
     //
@@ -779,28 +843,260 @@ public class JvOptionPane extends JOptionPane implements DialogRunnerI,
     //
     // 2) UserDefinedColors warning about saving over a name already defined
     //
-    
+
     ourOptions = Arrays.asList(options);
-    
-    int response = JOptionPane.showOptionDialog(parentComponent, message, title,
-            optionType, messageType, icon, options, initialValue);
-    
-    /*
-     * In Java, the response is returned to this thread and handled here;
-     * (for Javascript, see propertyChange)
-     */
-    if (!Platform.isJS())
-    /**
-     * Java only
-     * 
-     * @j2sIgnore
-     */
+
+    if (modal)
     {
-      handleResponse(response);
+      boolean useButtons = false;
+      Object initialValueButton = null;
+      NOTNULL: if (buttons != null)
+      {
+        if (buttons.length != options.length)
+        {
+          jalview.bin.Console.error(
+                  "Supplied buttons array not the same length as supplied options array.");
+          break NOTNULL;
+        }
+
+        // run through buttons for initialValue first so can set a final
+        // timeoutThreadF
+        Thread timeoutThread = null;
+        for (int i = 0; i < options.length; i++)
+        {
+          Object o = options[i];
+          JButton jb = buttons[i];
+          if (o.equals(initialValue))
+          {
+            initialValueButton = jb;
+            if (timeout > 0 && initialValueButton != null
+                    && initialValueButton instanceof JButton)
+            {
+              Runnable timeoutClose = () -> {
+                try
+                {
+                  Thread.sleep(timeout);
+                } catch (InterruptedException e)
+                {
+                  Console.debug(
+                          "Dialog timeout interrupted.  Probably a button pressed.");
+                }
+                jb.doClick();
+              };
+              timeoutThread = new Thread(timeoutClose);
+            }
+          }
+        }
+        final Thread timeoutThreadF = timeoutThread;
+        timeoutThreadF.start();
+
+        int[] buttonActions = { JOptionPane.YES_OPTION,
+            JOptionPane.NO_OPTION, JOptionPane.CANCEL_OPTION };
+        for (int i = 0; i < options.length; i++)
+        {
+          Object o = options[i];
+          jalview.bin.Console.debug(
+                  "Setting button " + i + " to '" + o.toString() + "'");
+          JButton jb = buttons[i];
+
+          int buttonAction = buttonActions[i];
+          Runnable action = callbacks.get(buttonAction);
+          jb.setText((String) o);
+          jb.addActionListener(new ActionListener()
+          {
+            @Override
+            public void actionPerformed(ActionEvent e)
+            {
+              if (timeoutThreadF != null)
+              {
+                timeoutThreadF.interrupt();
+              }
+
+              Object obj = e.getSource();
+              if (obj == null || !(obj instanceof Component))
+              {
+                jalview.bin.Console.debug(
+                        "Could not find Component source of event object "
+                                + obj);
+                return;
+              }
+              Object joptionpaneObject = SwingUtilities.getAncestorOfClass(
+                      JOptionPane.class, (Component) obj);
+              if (joptionpaneObject == null
+                      || !(joptionpaneObject instanceof JOptionPane))
+              {
+                jalview.bin.Console.debug(
+                        "Could not find JOptionPane ancestor of event object "
+                                + obj);
+                return;
+              }
+              JOptionPane joptionpane = (JOptionPane) joptionpaneObject;
+              joptionpane.setValue(buttonAction);
+              if (action != null)
+                new Thread(action).start();
+              joptionpane.transferFocusBackward();
+              joptionpane.setVisible(false);
+              // put focus and raise parent window if possible, unless cancel or
+              // no button pressed
+              boolean raiseParent = (parentComponent != null);
+              if (buttonAction == JOptionPane.CANCEL_OPTION)
+                raiseParent = false;
+              if (optionType == JOptionPane.YES_NO_OPTION
+                      && buttonAction == JOptionPane.NO_OPTION)
+                raiseParent = false;
+              if (raiseParent)
+              {
+                parentComponent.requestFocus();
+                if (parentComponent instanceof JInternalFrame)
+                {
+                  JInternalFrame jif = (JInternalFrame) parentComponent;
+                  jif.show();
+                  jif.moveToFront();
+                  jif.grabFocus();
+                }
+                else if (parentComponent instanceof Window)
+                {
+                  Window w = (Window) parentComponent;
+                  w.toFront();
+                  w.requestFocus();
+                }
+              }
+              joptionpane.setVisible(false);
+            }
+          });
+
+        }
+        useButtons = true;
+      }
+      // use a JOptionPane as usual
+      int response = JOptionPane.showOptionDialog(parentComponent, message,
+              title, optionType, messageType, icon,
+              useButtons ? buttons : options,
+              useButtons ? initialValueButton : initialValue);
+
+      /*
+       * In Java, the response is returned to this thread and handled here; (for
+       * Javascript, see propertyChange)
+       */
+      if (!Platform.isJS())
+      /**
+       * Java only
+       * 
+       * @j2sIgnore
+       */
+      {
+        handleResponse(response);
+      }
+    }
+    else
+    {
+      /*
+       * This is java similar to the swingjs handling, with the callbacks attached to
+       * the button press of the dialog. This means we can use a non-modal JDialog for
+       * the confirmation without blocking the GUI.
+       */
+      JOptionPane joptionpane = new JOptionPane();
+      // Make button options
+      int[] buttonActions = { JvOptionPane.YES_OPTION,
+          JvOptionPane.NO_OPTION, JvOptionPane.CANCEL_OPTION };
+
+      // we need the strings to make the buttons with actionEventListener
+      if (options == null)
+      {
+        ArrayList<String> options_default = new ArrayList<>();
+        options_default
+                .add(UIManager.getString("OptionPane.yesButtonText"));
+        if (optionType == JvOptionPane.YES_NO_OPTION
+                || optionType == JvOptionPane.YES_NO_CANCEL_OPTION)
+        {
+          options_default
+                  .add(UIManager.getString("OptionPane.noButtonText"));
+        }
+        if (optionType == JvOptionPane.YES_NO_CANCEL_OPTION)
+        {
+          options_default
+                  .add(UIManager.getString("OptionPane.cancelButtonText"));
+        }
+        options = options_default.toArray();
+      }
+
+      ArrayList<JButton> options_btns = new ArrayList<>();
+      Object initialValue_btn = null;
+      if (!Platform.isJS()) // JalviewJS already uses callback, don't need to
+                            // add them here
+      {
+        for (int i = 0; i < options.length && i < 3; i++)
+        {
+          Object o = options[i];
+          int buttonAction = buttonActions[i];
+          Runnable action = callbacks.get(buttonAction);
+          JButton jb = new JButton();
+          jb.setText((String) o);
+          jb.addActionListener(new ActionListener()
+          {
+
+            @Override
+            public void actionPerformed(ActionEvent e)
+            {
+              joptionpane.setValue(buttonAction);
+              if (action != null)
+                new Thread(action).start();
+              // joptionpane.transferFocusBackward();
+              joptionpane.transferFocusBackward();
+              joptionpane.setVisible(false);
+              // put focus and raise parent window if possible, unless cancel
+              // button pressed
+              boolean raiseParent = (parentComponent != null);
+              if (buttonAction == JvOptionPane.CANCEL_OPTION)
+                raiseParent = false;
+              if (optionType == JvOptionPane.YES_NO_OPTION
+                      && buttonAction == JvOptionPane.NO_OPTION)
+                raiseParent = false;
+              if (raiseParent)
+              {
+                parentComponent.requestFocus();
+                if (parentComponent instanceof JInternalFrame)
+                {
+                  JInternalFrame jif = (JInternalFrame) parentComponent;
+                  jif.show();
+                  jif.moveToFront();
+                  jif.grabFocus();
+                }
+                else if (parentComponent instanceof Window)
+                {
+                  Window w = (Window) parentComponent;
+                  w.toFront();
+                  w.requestFocus();
+                }
+              }
+              joptionpane.setVisible(false);
+            }
+          });
+          options_btns.add(jb);
+          if (o.equals(initialValue))
+            initialValue_btn = jb;
+        }
+      }
+      joptionpane.setMessage(message);
+      joptionpane.setMessageType(messageType);
+      joptionpane.setOptionType(optionType);
+      joptionpane.setIcon(icon);
+      joptionpane.setOptions(
+              Platform.isJS() ? options : options_btns.toArray());
+      joptionpane.setInitialValue(
+              Platform.isJS() ? initialValue : initialValue_btn);
+
+      JDialog dialog = joptionpane.createDialog(parentComponent, title);
+      dialog.setIconImages(ChannelProperties.getIconList());
+      dialog.setModalityType(modal ? ModalityType.APPLICATION_MODAL
+              : ModalityType.MODELESS);
+      dialog.setDefaultCloseOperation(JDialog.DISPOSE_ON_CLOSE);
+      dialog.setVisible(true);
+      setDialog(dialog);
     }
   }
 
-  public void showInternalDialog(JPanel mainPanel, String title,
+  public void showInternalDialog(Object mainPanel, String title,
           int yesNoCancelOption, int questionMessage, Icon icon,
           Object[] options, String initresponse)
   {
@@ -808,21 +1104,93 @@ public class JvOptionPane extends JOptionPane implements DialogRunnerI,
     {
       handleResponse(getMockResponse());
     }
-    
+
+    // need to set these separately so we can set the title bar icon later
+    this.setOptionType(yesNoCancelOption);
+    this.setMessageType(questionMessage);
+    this.setIcon(icon);
+    this.setInitialValue(initresponse);
+    this.setOptions(options);
+    this.setMessage(mainPanel);
+
     ourOptions = Arrays.asList(options);
-    int response;
-    if (parentComponent != this) 
+    if (parentComponent != this
+            && !(parentComponent == null && Desktop.instance == null))
     {
-      response = JOptionPane.showInternalOptionDialog(parentComponent, mainPanel,
-              title, yesNoCancelOption, questionMessage, icon, options,
-              initresponse);
+      // note the parent goes back to a JRootPane so is probably
+      // Desktop.getDesktop()
+      JInternalFrame jif = this.createInternalFrame(
+              parentComponent != null ? parentComponent : Desktop.instance,
+              title);
+      // connect to the alignFrame using a map in Desktop
+      if (parentComponent instanceof AlignFrame)
+      {
+        Desktop.addModal((AlignFrame) parentComponent, jif);
+      }
+      jif.setFrameIcon(null);
+      jif.addInternalFrameListener(new InternalFrameListener()
+      {
+        @Override
+        public void internalFrameActivated(InternalFrameEvent arg0)
+        {
+        }
+
+        @Override
+        public void internalFrameClosed(InternalFrameEvent arg0)
+        {
+          JvOptionPane.this.internalDialogHandleResponse();
+        }
+
+        @Override
+        public void internalFrameClosing(InternalFrameEvent arg0)
+        {
+        }
+
+        @Override
+        public void internalFrameDeactivated(InternalFrameEvent arg0)
+        {
+        }
+
+        @Override
+        public void internalFrameDeiconified(InternalFrameEvent arg0)
+        {
+        }
+
+        @Override
+        public void internalFrameIconified(InternalFrameEvent arg0)
+        {
+        }
+
+        @Override
+        public void internalFrameOpened(InternalFrameEvent arg0)
+        {
+        }
+      });
+      jif.setVisible(true);
+      startModal(jif);
+      return;
     }
     else
     {
-      response = JOptionPane.showOptionDialog(parentComponent, mainPanel, title,
-              yesNoCancelOption, questionMessage, icon, options,
-              initresponse);
+      JDialog dialog = this.createDialog(parentComponent, title);
+      dialog.setIconImages(ChannelProperties.getIconList());
+      dialog.setVisible(true); // blocking
+      this.internalDialogHandleResponse();
+      return;
     }
+  }
+
+  private void internalDialogHandleResponse()
+  {
+    Object value = this.getValue();
+    if (value == null
+            || (value instanceof Integer && (Integer) value == -1))
+    {
+      return;
+    }
+    String responseString = value.toString();
+    int response = ourOptions.indexOf(responseString);
+
     if (!Platform.isJS())
     /**
      * Java only
@@ -833,18 +1201,153 @@ public class JvOptionPane extends JOptionPane implements DialogRunnerI,
       handleResponse(response);
     }
   }
-    
+
+  /*
+   * @Override public JvOptionPane setResponseHandler(Object response, Runnable
+   * action) { callbacks.put(response, new Callable<Void>() {
+   * 
+   * @Override public Void call() { action.run(); return null; } }); return this;
+   * }
+   */
   @Override
   public JvOptionPane setResponseHandler(Object response, Runnable action)
   {
-       callbacks.put(response,  action);
+    if (action == null)
+    {
+      action = NULLCALLABLE;
+    }
+    callbacks.put(response, action);
     return this;
   }
 
+  public void setDialog(JDialog d)
+  {
+    dialog = d;
+  }
+
+  public JDialog getDialog()
+  {
+    return dialog;
+  }
+
   /**
-   * JalviewJS signals option selection by a property change event
-   * for the option e.g. "OK".  This methods responds to that by
-   * running the response action that corresponds to that option.
+   * showDialogOnTop will create a dialog that (attempts to) come to top of OS
+   * desktop windows
+   */
+  public static int showDialogOnTop(String label, String actionString,
+          int JOPTIONPANE_OPTION, int JOPTIONPANE_MESSAGETYPE)
+  {
+    return showDialogOnTop(null, label, actionString, JOPTIONPANE_OPTION,
+            JOPTIONPANE_MESSAGETYPE);
+  }
+
+  public static int showDialogOnTop(Component dialogParentComponent,
+          String label, String actionString, int JOPTIONPANE_OPTION,
+          int JOPTIONPANE_MESSAGETYPE)
+  {
+    if (!isInteractiveMode())
+    {
+      return (int) getMockResponse();
+    }
+    // Ensure Jalview window is brought to front (primarily for Quit
+    // confirmation window to be visible)
+
+    // This method of raising the Jalview window is broken in java
+    // jalviewDesktop.setVisible(true);
+    // jalviewDesktop.toFront();
+
+    // A better hack which works is to create a new JFrame parent with
+    // setAlwaysOnTop(true)
+    JFrame dialogParent = new JFrame();
+    if (dialogParentComponent == null)
+    {
+      dialogParent.setIconImages(ChannelProperties.getIconList());
+      dialogParent.setAlwaysOnTop(true);
+    }
+
+    int answer = JOptionPane.showConfirmDialog(
+            dialogParentComponent == null ? dialogParent
+                    : dialogParentComponent,
+            label, actionString, JOPTIONPANE_OPTION,
+            JOPTIONPANE_MESSAGETYPE);
+
+    if (dialogParentComponent == null)
+    {
+      dialogParent.setAlwaysOnTop(false);
+      dialogParent.dispose();
+    }
+
+    return answer;
+  }
+
+  public void showDialogOnTopAsync(String label, String actionString,
+          int JOPTIONPANE_OPTION, int JOPTIONPANE_MESSAGETYPE, Icon icon,
+          Object[] options, Object initialValue, boolean modal)
+  {
+    JFrame frame = new JFrame();
+    frame.setIconImages(ChannelProperties.getIconList());
+    showDialogOnTopAsync(frame, label, actionString, JOPTIONPANE_OPTION,
+            JOPTIONPANE_MESSAGETYPE, icon, options, initialValue, modal);
+  }
+
+  public void showDialogOnTopAsync(JFrame dialogParent, Object label,
+          String actionString, int JOPTIONPANE_OPTION,
+          int JOPTIONPANE_MESSAGETYPE, Icon icon, Object[] options,
+          Object initialValue, boolean modal)
+  {
+    showDialogOnTopAsync(dialogParent, label, actionString,
+            JOPTIONPANE_OPTION, JOPTIONPANE_MESSAGETYPE, icon, options,
+            initialValue, modal, null);
+  }
+
+  public void showDialogOnTopAsync(JFrame dialogParent, Object label,
+          String actionString, int JOPTIONPANE_OPTION,
+          int JOPTIONPANE_MESSAGETYPE, Icon icon, Object[] options,
+          Object initialValue, boolean modal, JButton[] buttons)
+  {
+    showDialogOnTopAsync(dialogParent, label, actionString,
+            JOPTIONPANE_OPTION, JOPTIONPANE_MESSAGETYPE, icon, options,
+            initialValue, modal, buttons, true);
+  }
+
+  public void showDialogOnTopAsync(JFrame dialogParent, Object label,
+          String actionString, int JOPTIONPANE_OPTION,
+          int JOPTIONPANE_MESSAGETYPE, Icon icon, Object[] options,
+          Object initialValue, boolean modal, JButton[] buttons,
+          boolean dispose)
+  {
+    if (!isInteractiveMode())
+    {
+      handleResponse(getMockResponse());
+      return;
+    }
+    // Ensure Jalview window is brought to front (primarily for Quit
+    // confirmation window to be visible)
+
+    // This method of raising the Jalview window is broken in java
+    // jalviewDesktop.setVisible(true);
+    // jalviewDesktop.toFront();
+
+    // A better hack which works is to create a new JFrame parent with
+    // setAlwaysOnTop(true)
+    dialogParent.setAlwaysOnTop(true);
+    parentComponent = dialogParent;
+
+    showDialog(label, actionString, JOPTIONPANE_OPTION,
+            JOPTIONPANE_MESSAGETYPE, icon, options, initialValue, modal,
+            buttons);
+
+    if (dispose)
+    {
+      dialogParent.setAlwaysOnTop(false);
+      dialogParent.dispose();
+    }
+  }
+
+  /**
+   * JalviewJS signals option selection by a property change event for the
+   * option e.g. "OK". This methods responds to that by running the response
+   * action that corresponds to that option.
    * 
    * @param evt
    */
@@ -852,7 +1355,7 @@ public class JvOptionPane extends JOptionPane implements DialogRunnerI,
   public void propertyChange(PropertyChangeEvent evt)
   {
     Object newValue = evt.getNewValue();
-       int ourOption = ourOptions.indexOf(newValue);
+    int ourOption = ourOptions.indexOf(newValue);
     if (ourOption >= 0)
     {
       handleResponse(ourOption);
@@ -868,8 +1371,8 @@ public class JvOptionPane extends JOptionPane implements DialogRunnerI,
   public void handleResponse(Object response)
   {
     /*
-        * this test is for NaN in Chrome
-        */
+     * this test is for NaN in Chrome
+     */
     if (response != null && !response.equals(response))
     {
       return;
@@ -877,7 +1380,368 @@ public class JvOptionPane extends JOptionPane implements DialogRunnerI,
     Runnable action = callbacks.get(response);
     if (action != null)
     {
-      action.run();
+      try
+      {
+        new Thread(action).start();
+        // action.call();
+      } catch (Exception e)
+      {
+        e.printStackTrace();
+      }
+      if (parentComponent != null)
+        parentComponent.requestFocus();
+    }
+  }
+
+  /**
+   * Create a non-modal confirm dialog
+   */
+  public JDialog createDialog(Component parentComponent, Object message,
+          String title, int optionType, int messageType, Icon icon,
+          Object[] options, Object initialValue, boolean modal)
+  {
+    return createDialog(parentComponent, message, title, optionType,
+            messageType, icon, options, initialValue, modal, null);
+  }
+
+  public JDialog createDialog(Component parentComponent, Object message,
+          String title, int optionType, int messageType, Icon icon,
+          Object[] options, Object initialValue, boolean modal,
+          JButton[] buttons)
+  {
+    if (!isInteractiveMode())
+    {
+      handleResponse(getMockResponse());
+      return null;
+    }
+    JButton[] optionsButtons = null;
+    Object initialValueButton = null;
+    JOptionPane joptionpane = new JOptionPane();
+    // Make button options
+    int[] buttonActions = { JOptionPane.YES_OPTION, JOptionPane.NO_OPTION,
+        JOptionPane.CANCEL_OPTION };
+
+    // we need the strings to make the buttons with actionEventListener
+    if (options == null)
+    {
+      ArrayList<String> options_default = new ArrayList<>();
+      options_default.add(UIManager.getString("OptionPane.yesButtonText"));
+      if (optionType == JOptionPane.YES_NO_OPTION
+              || optionType == JOptionPane.YES_NO_CANCEL_OPTION)
+      {
+        options_default.add(UIManager.getString("OptionPane.noButtonText"));
+      }
+      if (optionType == JOptionPane.YES_NO_CANCEL_OPTION)
+      {
+        options_default
+                .add(UIManager.getString("OptionPane.cancelButtonText"));
+      }
+      options = options_default.toArray();
+    }
+    if (!Platform.isJS()) // JalviewJS already uses callback, don't need to
+                          // add them here
+    {
+      if (((optionType == JOptionPane.YES_OPTION
+              || optionType == JOptionPane.NO_OPTION
+              || optionType == JOptionPane.CANCEL_OPTION
+              || optionType == JOptionPane.OK_OPTION
+              || optionType == JOptionPane.DEFAULT_OPTION)
+              && options.length < 1)
+              || ((optionType == JOptionPane.YES_NO_OPTION
+                      || optionType == JOptionPane.OK_CANCEL_OPTION)
+                      && options.length < 2)
+              || (optionType == JOptionPane.YES_NO_CANCEL_OPTION
+                      && options.length < 3))
+      {
+        jalview.bin.Console
+                .debug("JvOptionPane: not enough options for dialog type");
+      }
+      optionsButtons = new JButton[options.length];
+      for (int i = 0; i < options.length && i < 3; i++)
+      {
+        Object o = options[i];
+        int buttonAction = buttonActions[i];
+        Runnable action = callbacks.get(buttonAction);
+        JButton jb;
+        if (buttons != null && buttons.length > i && buttons[i] != null)
+        {
+          jb = buttons[i];
+        }
+        else
+        {
+          jb = new JButton();
+        }
+        jb.setText((String) o);
+        jb.addActionListener(new ActionListener()
+        {
+          @Override
+          public void actionPerformed(ActionEvent e)
+          {
+            joptionpane.setValue(buttonAction);
+            if (action != null)
+              new Thread(action).start();
+            // joptionpane.transferFocusBackward();
+            joptionpane.transferFocusBackward();
+            joptionpane.setVisible(false);
+            // put focus and raise parent window if possible, unless cancel
+            // button pressed
+            boolean raiseParent = (parentComponent != null);
+            if (buttonAction == JOptionPane.CANCEL_OPTION)
+              raiseParent = false;
+            if (optionType == JOptionPane.YES_NO_OPTION
+                    && buttonAction == JOptionPane.NO_OPTION)
+              raiseParent = false;
+            if (raiseParent)
+            {
+              parentComponent.requestFocus();
+              if (parentComponent instanceof JInternalFrame)
+              {
+                JInternalFrame jif = (JInternalFrame) parentComponent;
+                jif.show();
+                jif.moveToFront();
+                jif.grabFocus();
+              }
+              else if (parentComponent instanceof Window)
+              {
+                Window w = (Window) parentComponent;
+                w.toFront();
+                w.requestFocus();
+              }
+            }
+            joptionpane.setVisible(false);
+          }
+        });
+        optionsButtons[i] = jb;
+        if (o.equals(initialValue))
+          initialValueButton = jb;
+      }
+    }
+    joptionpane.setMessage(message);
+    joptionpane.setMessageType(messageType);
+    joptionpane.setOptionType(optionType);
+    joptionpane.setIcon(icon);
+    joptionpane.setOptions(Platform.isJS() ? options : optionsButtons);
+    joptionpane.setInitialValue(
+            Platform.isJS() ? initialValue : initialValueButton);
+
+    JDialog dialog = joptionpane.createDialog(parentComponent, title);
+    dialog.setIconImages(ChannelProperties.getIconList());
+    dialog.setModalityType(
+            modal ? ModalityType.APPLICATION_MODAL : ModalityType.MODELESS);
+    dialog.setDefaultCloseOperation(JDialog.DISPOSE_ON_CLOSE);
+    setDialog(dialog);
+    return dialog;
+  }
+
+  /**
+   * Utility to programmatically click a button on a JOptionPane (as a JFrame)
+   * 
+   * returns true if button was found
+   */
+  public static boolean clickButton(JFrame frame, int buttonType)
+  {
+
+    return false;
+  }
+
+  /**
+   * This helper method makes the JInternalFrame wait until it is notified by an
+   * InternalFrameClosing event. This method also adds the given JOptionPane to
+   * the JInternalFrame and sizes it according to the JInternalFrame's preferred
+   * size.
+   *
+   * @param f
+   *          The JInternalFrame to make modal.
+   */
+  private static void startModal(JInternalFrame f)
+  {
+    // We need to add an additional glasspane-like component directly
+    // below the frame, which intercepts all mouse events that are not
+    // directed at the frame itself.
+    JPanel modalInterceptor = new JPanel();
+    modalInterceptor.setOpaque(false);
+    JLayeredPane lp = JLayeredPane.getLayeredPaneAbove(f);
+    lp.setLayer(modalInterceptor, JLayeredPane.MODAL_LAYER.intValue());
+    modalInterceptor.setBounds(0, 0, lp.getWidth(), lp.getHeight());
+    modalInterceptor.addMouseListener(new MouseAdapter()
+    {
+    });
+    modalInterceptor.addMouseMotionListener(new MouseMotionAdapter()
+    {
+    });
+    lp.add(modalInterceptor);
+    f.toFront();
+
+    // disable the main menu bar if in Linux
+    JMenuBar menubar = null;
+    if (Platform.isLinux())
+    {
+      JRootPane rootpane = Desktop.getDesktop().getRootPane();
+      menubar = rootpane.getJMenuBar();
+    }
+
+    // We need to explicitly dispatch events when we are blocking the event
+    // dispatch thread.
+    EventQueue queue = Toolkit.getDefaultToolkit().getSystemEventQueue();
+    try
+    {
+      if (menubar != null)
+      {
+        // don't allow clicks on main menu on linux due to a hanging bug.
+        // see JAL-4214.
+        setMenusEnabled(menubar, false);
+      }
+
+      while (!f.isClosed())
+      {
+        if (EventQueue.isDispatchThread())
+        {
+          // The getNextEventMethod() issues wait() when no
+          // event is available, so we don't need do explicitly wait().
+          AWTEvent ev = queue.getNextEvent();
+          // This mimics EventQueue.dispatchEvent(). We can't use
+          // EventQueue.dispatchEvent() directly, because it is
+          // protected, unfortunately.
+          if (ev instanceof ActiveEvent)
+          {
+            ((ActiveEvent) ev).dispatch();
+          }
+          else if (ev instanceof KeyEvent && ((KeyEvent) ev).isControlDown()
+                  && menubar != null)
+          {
+            // temporarily enable menus to send Ctrl+? KeyEvents
+            setMenusEnabled(menubar, true);
+            ((Component) ev.getSource()).dispatchEvent(ev);
+            setMenusEnabled(menubar, false);
+          }
+          else if (ev.getSource() instanceof MenuComponent)
+          {
+            ((MenuComponent) ev.getSource()).dispatchEvent(ev);
+          }
+          else if (ev.getSource() instanceof Component)
+          {
+            ((Component) ev.getSource()).dispatchEvent(ev);
+          }
+          // Other events are ignored as per spec in
+          // EventQueue.dispatchEvent
+        }
+        else
+        {
+          // Give other threads a chance to become active.
+          Thread.yield();
+        }
+      }
+    } catch (InterruptedException ex)
+    {
+      // If we get interrupted, then leave the modal state.
+    } finally
+    {
+      // re-enable the main menu bar
+      if (menubar != null)
+      {
+        setMenusEnabled(menubar, true);
+      }
+
+      // Clean up the modal interceptor.
+      lp.remove(modalInterceptor);
+
+      // unpaint the frame
+      f.setVisible(false);
+
+      // close the frame
+      try
+      {
+        f.setClosed(true);
+      } catch (PropertyVetoException e)
+      {
+        f.doDefaultCloseAction();
+      }
+
+      // Remove the internal frame from its parent, so it is no longer
+      // lurking around and clogging memory.
+      Container parent = f.getParent();
+      if (parent != null)
+      {
+        parent.remove(f);
+      }
+    }
+  }
+
+  public static JvOptionPane frameDialog(Object message, String title,
+          int messageType, String[] buttonsTextS, String defaultButtonS,
+          List<Runnable> handlers, boolean modal)
+  {
+    JFrame parent = new JFrame();
+    JvOptionPane jvop = JvOptionPane.newOptionDialog();
+    final String[] buttonsText;
+    final String defaultButton;
+    if (buttonsTextS == null)
+    {
+      String ok = MessageManager.getString("action.ok");
+      buttonsText = new String[] { ok };
+      defaultButton = ok;
     }
+    else
+    {
+      buttonsText = buttonsTextS;
+      defaultButton = defaultButtonS;
+    }
+    JButton[] buttons = new JButton[buttonsText.length];
+    for (int i = 0; i < buttonsText.length; i++)
+    {
+      buttons[i] = new JButton();
+      buttons[i].setText(buttonsText[i]);
+      Console.debug("DISABLING BUTTON " + buttons[i].getText());
+      buttons[i].setEnabled(false);
+      buttons[i].setVisible(false);
+    }
+
+    int dialogType = -1;
+    if (buttonsText.length == 1)
+    {
+      dialogType = JOptionPane.OK_OPTION;
+    }
+    else if (buttonsText.length == 2)
+    {
+      dialogType = JOptionPane.YES_NO_OPTION;
+    }
+    else
+    {
+      dialogType = JOptionPane.YES_NO_CANCEL_OPTION;
+    }
+    jvop.setResponseHandler(JOptionPane.YES_OPTION,
+            (handlers != null && handlers.size() > 0) ? handlers.get(0)
+                    : NULLCALLABLE);
+    if (dialogType == JOptionPane.YES_NO_OPTION
+            || dialogType == JOptionPane.YES_NO_CANCEL_OPTION)
+    {
+      jvop.setResponseHandler(JOptionPane.NO_OPTION,
+              (handlers != null && handlers.size() > 1) ? handlers.get(1)
+                      : NULLCALLABLE);
+    }
+    if (dialogType == JOptionPane.YES_NO_CANCEL_OPTION)
+    {
+      jvop.setResponseHandler(JOptionPane.CANCEL_OPTION,
+              (handlers != null && handlers.size() > 2) ? handlers.get(2)
+                      : NULLCALLABLE);
+    }
+
+    final int dt = dialogType;
+    new Thread(() -> {
+      jvop.showDialog(message, title, dt, messageType, null, buttonsText,
+              defaultButton, modal, buttons);
+    }).start();
+
+    return jvop;
   }
+
+  private static void setMenusEnabled(JMenuBar menubar, boolean b)
+  {
+    for (int i = 0; i < menubar.getMenuCount(); i++)
+    {
+      JMenu menu = menubar.getMenu(i);
+      menu.setEnabled(b);
+    }
+  }
+
 }