X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FDesktop.java;h=22a52035dcbe2a30d508faa9a1896bfb9f1bea6e;hb=4a5137b64f7ec23db2a09290bfcd392984a52150;hp=d3b8afc948f58c4a1f190e22c7a31525f3218618;hpb=cd2f8500d0130b3e695086259912bac873a3c9e8;p=jalview.git

diff --git a/src/jalview/gui/Desktop.java b/src/jalview/gui/Desktop.java
index d3b8afc..22a5203 100644
--- a/src/jalview/gui/Desktop.java
+++ b/src/jalview/gui/Desktop.java
@@ -24,8 +24,11 @@ import jalview.api.AlignViewportI;
 import jalview.api.AlignmentViewPanel;
 import jalview.bin.Cache;
 import jalview.bin.Jalview;
+import jalview.io.DataSourceType;
+import jalview.io.FileFormat;
+import jalview.io.FileFormatException;
+import jalview.io.FileFormatI;
 import jalview.io.FileLoader;
-import jalview.io.FormatAdapter;
 import jalview.io.IdentifyFile;
 import jalview.io.JalviewFileChooser;
 import jalview.io.JalviewFileView;
@@ -47,6 +50,7 @@ import java.awt.GridLayout;
 import java.awt.Point;
 import java.awt.Rectangle;
 import java.awt.Toolkit;
+import java.awt.Window;
 import java.awt.datatransfer.Clipboard;
 import java.awt.datatransfer.ClipboardOwner;
 import java.awt.datatransfer.DataFlavor;
@@ -60,6 +64,7 @@ import java.awt.event.ActionEvent;
 import java.awt.event.ActionListener;
 import java.awt.event.FocusEvent;
 import java.awt.event.FocusListener;
+import java.awt.event.KeyEvent;
 import java.awt.event.MouseAdapter;
 import java.awt.event.MouseEvent;
 import java.awt.event.MouseListener;
@@ -71,7 +76,6 @@ import java.beans.PropertyVetoException;
 import java.io.BufferedInputStream;
 import java.io.File;
 import java.io.FileOutputStream;
-import java.lang.reflect.Constructor;
 import java.net.URL;
 import java.util.ArrayList;
 import java.util.Hashtable;
@@ -82,6 +86,7 @@ import java.util.concurrent.ExecutorService;
 import java.util.concurrent.Executors;
 import java.util.concurrent.Semaphore;
 
+import javax.swing.AbstractAction;
 import javax.swing.DefaultDesktopManager;
 import javax.swing.DesktopManager;
 import javax.swing.JButton;
@@ -96,6 +101,7 @@ import javax.swing.JOptionPane;
 import javax.swing.JPanel;
 import javax.swing.JPopupMenu;
 import javax.swing.JProgressBar;
+import javax.swing.KeyStroke;
 import javax.swing.SwingUtilities;
 import javax.swing.event.HyperlinkEvent;
 import javax.swing.event.HyperlinkEvent.EventType;
@@ -169,8 +175,6 @@ public class Desktop extends jalview.jbgui.GDesktop implements
 
   static final int yOffset = 30;
 
-  private static AlignFrame currentAlignFrame;
-
   public static jalview.ws.jws1.Discoverer discoverer;
 
   public static Object[] jalviewClipboard;
@@ -189,6 +193,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements
       this.delegate = delegate;
     }
 
+    @Override
     public void activateFrame(JInternalFrame f)
     {
       try
@@ -201,31 +206,37 @@ public class Desktop extends jalview.jbgui.GDesktop implements
       }
     }
 
+    @Override
     public void beginDraggingFrame(JComponent f)
     {
       delegate.beginDraggingFrame(f);
     }
 
+    @Override
     public void beginResizingFrame(JComponent f, int direction)
     {
       delegate.beginResizingFrame(f, direction);
     }
 
+    @Override
     public void closeFrame(JInternalFrame f)
     {
       delegate.closeFrame(f);
     }
 
+    @Override
     public void deactivateFrame(JInternalFrame f)
     {
       delegate.deactivateFrame(f);
     }
 
+    @Override
     public void deiconifyFrame(JInternalFrame f)
     {
       delegate.deiconifyFrame(f);
     }
 
+    @Override
     public void dragFrame(JComponent f, int newX, int newY)
     {
       if (newY < 0)
@@ -235,31 +246,37 @@ public class Desktop extends jalview.jbgui.GDesktop implements
       delegate.dragFrame(f, newX, newY);
     }
 
+    @Override
     public void endDraggingFrame(JComponent f)
     {
       delegate.endDraggingFrame(f);
     }
 
+    @Override
     public void endResizingFrame(JComponent f)
     {
       delegate.endResizingFrame(f);
     }
 
+    @Override
     public void iconifyFrame(JInternalFrame f)
     {
       delegate.iconifyFrame(f);
     }
 
+    @Override
     public void maximizeFrame(JInternalFrame f)
     {
       delegate.maximizeFrame(f);
     }
 
+    @Override
     public void minimizeFrame(JInternalFrame f)
     {
       delegate.minimizeFrame(f);
     }
 
+    @Override
     public void openFrame(JInternalFrame f)
     {
       delegate.openFrame(f);
@@ -276,6 +293,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements
       delegate.resizeFrame(f, newX, newY, newWidth, newHeight);
     }
 
+    @Override
     public void setBoundsForFrame(JComponent f, int newX, int newY,
             int newWidth, int newHeight)
     {
@@ -298,7 +316,20 @@ public class Desktop extends jalview.jbgui.GDesktop implements
      */
     instance = this;
     doVamsasClientCheck();
-    doGroovyCheck();
+
+    groovyShell = new JMenuItem();
+    groovyShell.setText(MessageManager.getString("label.groovy_console"));
+    groovyShell.addActionListener(new ActionListener()
+    {
+      @Override
+      public void actionPerformed(ActionEvent e)
+      {
+        groovyShell_actionPerformed();
+      }
+    });
+    toolsMenu.add(groovyShell);
+    groovyShell.setVisible(true);
+
     doConfigureStructurePrefs();
     setTitle("Jalview " + jalview.bin.Cache.getProperty("VERSION"));
     setDefaultCloseOperation(JFrame.EXIT_ON_CLOSE);
@@ -356,6 +387,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements
 
     this.addWindowListener(new WindowAdapter()
     {
+      @Override
       public void windowClosing(WindowEvent evt)
       {
         quit();
@@ -365,9 +397,10 @@ public class Desktop extends jalview.jbgui.GDesktop implements
     MouseAdapter ma;
     this.addMouseListener(ma = new MouseAdapter()
     {
+      @Override
       public void mousePressed(MouseEvent evt)
       {
-        if (SwingUtilities.isRightMouseButton(evt))
+        if (evt.isPopupTrigger())
         {
           showPasteMenu(evt.getX(), evt.getY());
         }
@@ -397,6 +430,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements
     // Spawn a thread that shows the splashscreen
     SwingUtilities.invokeLater(new Runnable()
     {
+      @Override
       public void run()
       {
         new SplashScreen();
@@ -408,14 +442,16 @@ public class Desktop extends jalview.jbgui.GDesktop implements
     // takes to open it later on.
     new Thread(new Runnable()
     {
+      @Override
       public void run()
       {
         Cache.log.debug("Filechooser init thread started.");
-        new JalviewFileChooser(
-                jalview.bin.Cache.getProperty("LAST_DIRECTORY"),
-                jalview.io.AppletFormatAdapter.READABLE_EXTENSIONS,
-                jalview.io.AppletFormatAdapter.READABLE_FNAMES,
-                jalview.bin.Cache.getProperty("DEFAULT_FILE_FORMAT"));
+        FileFormat fileFormat = FileFormat.valueOf(Cache
+                .getProperty("DEFAULT_FILE_FORMAT"));
+        new JalviewFileChooser(Cache.getProperty("LAST_DIRECTORY"),
+        // jalview.io.AppletFormatAdapter.READABLE_EXTENSIONS,
+        // jalview.io.AppletFormatAdapter.READABLE_FNAMES,
+                fileFormat);
         Cache.log.debug("Filechooser init thread finished.");
       }
     }).start();
@@ -579,16 +615,19 @@ public class Desktop extends jalview.jbgui.GDesktop implements
         // reselected again.
         boolean refresh = true;
 
+        @Override
         public void menuCanceled(MenuEvent e)
         {
           refresh = true;
         }
 
+        @Override
         public void menuDeselected(MenuEvent e)
         {
           refresh = true;
         }
 
+        @Override
         public void menuSelected(MenuEvent e)
         {
           if (refresh)
@@ -609,6 +648,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements
             MessageManager.getString("label.paste_new_window"));
     item.addActionListener(new ActionListener()
     {
+      @Override
       public void actionPerformed(ActionEvent evt)
       {
         paste();
@@ -631,10 +671,10 @@ public class Desktop extends jalview.jbgui.GDesktop implements
         String file = (String) contents
                 .getTransferData(DataFlavor.stringFlavor);
 
-        String format = new IdentifyFile().Identify(file,
-                FormatAdapter.PASTE);
+        FileFormatI format = new IdentifyFile().identify(file,
+                DataSourceType.PASTE);
 
-        new FileLoader().LoadFile(file, FormatAdapter.PASTE, format);
+        new FileLoader().LoadFile(file, DataSourceType.PASTE, format);
 
       }
     } catch (Exception ex)
@@ -772,6 +812,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements
     final JMenuItem menuItem = new JMenuItem(title);
     frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
     {
+      @Override
       public void internalFrameActivated(
               javax.swing.event.InternalFrameEvent evt)
       {
@@ -783,6 +824,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements
 
       }
 
+      @Override
       public void internalFrameClosed(
               javax.swing.event.InternalFrameEvent evt)
       {
@@ -800,6 +842,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements
 
     menuItem.addActionListener(new ActionListener()
     {
+      @Override
       public void actionPerformed(ActionEvent e)
       {
         try
@@ -872,6 +915,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements
     }
   }
 
+  @Override
   public void lostOwnership(Clipboard clipboard, Transferable contents)
   {
     if (!internalCopy)
@@ -882,14 +926,17 @@ public class Desktop extends jalview.jbgui.GDesktop implements
     internalCopy = false;
   }
 
+  @Override
   public void dragEnter(DropTargetDragEvent evt)
   {
   }
 
+  @Override
   public void dragExit(DropTargetEvent evt)
   {
   }
 
+  @Override
   public void dragOver(DropTargetDragEvent evt)
   {
   }
@@ -905,57 +952,20 @@ public class Desktop extends jalview.jbgui.GDesktop implements
    * @param evt
    *          DOCUMENT ME!
    */
+  @Override
   public void drop(DropTargetDropEvent evt)
   {
     boolean success = true;
     Transferable t = evt.getTransferable();
-    java.util.List files = null;
-    java.util.List protocols = null;
+    List<String> files = new ArrayList<String>();
+    List<DataSourceType> protocols = new ArrayList<DataSourceType>();
 
     try
     {
-      DataFlavor uriListFlavor = new DataFlavor(
-              "text/uri-list;class=java.lang.String");
-      if (t.isDataFlavorSupported(DataFlavor.javaFileListFlavor))
-      {
-        // Works on Windows and MacOSX
-        evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
-        files = (java.util.List) t
-                .getTransferData(DataFlavor.javaFileListFlavor);
-      }
-      else if (t.isDataFlavorSupported(uriListFlavor))
-      {
-        // This is used by Unix drag system
-        evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
-        String data = (String) t.getTransferData(uriListFlavor);
-        files = new java.util.ArrayList(1);
-        protocols = new java.util.ArrayList(1);
-        for (java.util.StringTokenizer st = new java.util.StringTokenizer(
-                data, "\r\n"); st.hasMoreTokens();)
-        {
-          String s = st.nextToken();
-          if (s.startsWith("#"))
-          {
-            // the line is a comment (as per the RFC 2483)
-            continue;
-          }
-          java.net.URI uri = new java.net.URI(s);
-          if (uri.getScheme().toLowerCase().startsWith("http"))
-          {
-            protocols.add(FormatAdapter.URL);
-            files.add(uri.toString());
-          }
-          else
-          {
-            // otherwise preserve old behaviour: catch all for file objects
-            java.io.File file = new java.io.File(uri);
-            protocols.add(FormatAdapter.FILE);
-            files.add(file.toString());
-          }
-        }
-      }
+      Desktop.transferFromDropTarget(files, protocols, evt, t);
     } catch (Exception e)
     {
+      e.printStackTrace();
       success = false;
     }
 
@@ -966,18 +976,18 @@ public class Desktop extends jalview.jbgui.GDesktop implements
         for (int i = 0; i < files.size(); i++)
         {
           String file = files.get(i).toString();
-          String protocol = (protocols == null) ? FormatAdapter.FILE
-                  : (String) protocols.get(i);
-          String format = null;
+          DataSourceType protocol = (protocols == null) ? DataSourceType.FILE
+                  : protocols.get(i);
+          FileFormatI format = null;
 
           if (file.endsWith(".jar"))
           {
-            format = "Jalview";
+            format = FileFormat.Jalview;
 
           }
           else
           {
-            format = new IdentifyFile().Identify(file, protocol);
+            format = new IdentifyFile().identify(file, protocol);
           }
 
           new FileLoader().LoadFile(file, protocol, format);
@@ -1001,11 +1011,13 @@ public class Desktop extends jalview.jbgui.GDesktop implements
   @Override
   public void inputLocalFileMenuItem_actionPerformed(AlignViewport viewport)
   {
+    FileFormat fileFormat = FileFormat.valueOf(Cache
+            .getProperty("DEFAULT_FILE_FORMAT"));
     JalviewFileChooser chooser = new JalviewFileChooser(
-            jalview.bin.Cache.getProperty("LAST_DIRECTORY"),
-            jalview.io.AppletFormatAdapter.READABLE_EXTENSIONS,
-            jalview.io.AppletFormatAdapter.READABLE_FNAMES,
-            jalview.bin.Cache.getProperty("DEFAULT_FILE_FORMAT"));
+            Cache.getProperty("LAST_DIRECTORY"),
+            // AppletFormatAdapter.READABLE_EXTENSIONS,
+            // AppletFormatAdapter.READABLE_FNAMES,
+            fileFormat);
 
     chooser.setFileView(new JalviewFileView());
     chooser.setDialogTitle(MessageManager
@@ -1017,35 +1029,34 @@ public class Desktop extends jalview.jbgui.GDesktop implements
     if (value == JalviewFileChooser.APPROVE_OPTION)
     {
       String choice = chooser.getSelectedFile().getPath();
-      jalview.bin.Cache.setProperty("LAST_DIRECTORY", chooser
+      Cache.setProperty("LAST_DIRECTORY", chooser
               .getSelectedFile().getParent());
 
-      String format = null;
+      FileFormatI format = null;
       if (chooser.getSelectedFormat() != null
-              && chooser.getSelectedFormat().equals("Jalview"))
+              && chooser.getSelectedFormat() == FileFormat.Jalview)
       {
-        format = "Jalview";
+        format = FileFormat.Jalview;
       }
       else
       {
-        format = new IdentifyFile().Identify(choice, FormatAdapter.FILE);
+        try
+        {
+          format = new IdentifyFile().identify(choice, DataSourceType.FILE);
+        } catch (FileFormatException e)
+        {
+          // format is null
+        }
       }
 
       if (viewport != null)
       {
-        new FileLoader().LoadFile(viewport, choice, FormatAdapter.FILE,
+        new FileLoader().LoadFile(viewport, choice, DataSourceType.FILE,
                 format);
-        // viewport.setShowSequenceFeatures(JSONFile.isSeqFeaturesEnabled());
-        // AlignFrame af = viewport.getAlignPanel().alignFrame;
-        // if (af != null)
-        // {
-        // af.changeColour(JSONFile.getColourScheme());
-        // af.setMenusForViewport();
-        // }
       }
       else
       {
-        new FileLoader().LoadFile(choice, FormatAdapter.FILE, format);
+        new FileLoader().LoadFile(choice, DataSourceType.FILE, format);
       }
     }
   }
@@ -1055,9 +1066,11 @@ public class Desktop extends jalview.jbgui.GDesktop implements
    * 
    * @param e
    *          DOCUMENT ME!
+   * @throws FileFormatException
    */
   @Override
   public void inputURLMenuItem_actionPerformed(AlignViewport viewport)
+          throws FileFormatException
   {
     // This construct allows us to have a wider textfield
     // for viewing
@@ -1101,17 +1114,19 @@ public class Desktop extends jalview.jbgui.GDesktop implements
     {
       if (viewport != null)
       {
-        new FileLoader().LoadFile(viewport, url, FormatAdapter.URL,
-                "Jalview");
+        new FileLoader().LoadFile(viewport, url, DataSourceType.URL,
+                FileFormat.Jalview);
       }
       else
       {
-        new FileLoader().LoadFile(url, FormatAdapter.URL, "Jalview");
+        new FileLoader().LoadFile(url, DataSourceType.URL,
+                FileFormat.Jalview);
       }
     }
     else
     {
-      String format = new IdentifyFile().Identify(url, FormatAdapter.URL);
+      FileFormatI format = new IdentifyFile().identify(url,
+              DataSourceType.URL);
 
       if (format.equals("URL NOT FOUND"))
       {
@@ -1126,11 +1141,12 @@ public class Desktop extends jalview.jbgui.GDesktop implements
 
       if (viewport != null)
       {
-        new FileLoader().LoadFile(viewport, url, FormatAdapter.URL, format);
+        new FileLoader()
+                .LoadFile(viewport, url, DataSourceType.URL, format);
       }
       else
       {
-        new FileLoader().LoadFile(url, FormatAdapter.URL, format);
+        new FileLoader().LoadFile(url, DataSourceType.URL, format);
       }
     }
   }
@@ -1182,6 +1198,13 @@ public class Desktop extends jalview.jbgui.GDesktop implements
       dialogExecutor.shutdownNow();
     }
     closeAll_actionPerformed(null);
+
+    if (groovyConsole != null)
+    {
+      // suppress a possible repeat prompt to save script
+      groovyConsole.setDirty(false);
+      groovyConsole.exit();
+    }
     System.exit(0);
   }
 
@@ -1212,6 +1235,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements
     // message.toString(), "About Jalview", JOptionPane.INFORMATION_MESSAGE);
     new Thread(new Runnable()
     {
+      @Override
       public void run()
       {
         new SplashScreen(true);
@@ -1522,6 +1546,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements
 
       new Thread(new Runnable()
       {
+        @Override
         public void run()
         {
           // TODO: refactor to Jalview desktop session controller action.
@@ -1593,6 +1618,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements
               selectedFile.getParent());
       new Thread(new Runnable()
       {
+        @Override
         public void run()
         {
           setProgressBar(
@@ -2112,6 +2138,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements
           sessit.addActionListener(new ActionListener()
           {
 
+            @Override
             public void actionPerformed(ActionEvent e)
             {
               if (dsktp.v_client == null)
@@ -2119,6 +2146,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements
                 Thread rthr = new Thread(new Runnable()
                 {
 
+                  @Override
                   public void run()
                   {
                     dsktp.v_client = new VamsasApplication(dsktp, mysesid);
@@ -2291,6 +2319,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements
       return showMemoryUsage;
     }
 
+    @Override
     public void run()
     {
       df = java.text.NumberFormat.getNumberInstance();
@@ -2357,24 +2386,6 @@ public class Desktop extends jalview.jbgui.GDesktop implements
 
   protected JMenuItem groovyShell;
 
-  public void doGroovyCheck()
-  {
-    if (jalview.bin.Cache.groovyJarsPresent())
-    {
-      groovyShell = new JMenuItem();
-      groovyShell.setText(MessageManager.getString("label.groovy_console"));
-      groovyShell.addActionListener(new ActionListener()
-      {
-        public void actionPerformed(ActionEvent e)
-        {
-          groovyShell_actionPerformed();
-        }
-      });
-      toolsMenu.add(groovyShell);
-      groovyShell.setVisible(true);
-    }
-  }
-
   /**
    * Accessor method to quickly get all the AlignmentFrames loaded.
    * 
@@ -2385,7 +2396,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements
     if (Jalview.isHeadlessMode())
     {
       // Desktop.desktop is null in headless mode
-      return new AlignFrame[] { currentAlignFrame };
+      return new AlignFrame[] { Jalview.currentAlignFrame };
     }
 
     JInternalFrame[] frames = Desktop.desktop.getAllFrames();
@@ -2462,24 +2473,9 @@ public class Desktop extends jalview.jbgui.GDesktop implements
    */
   public void groovyShell_actionPerformed()
   {
-    // use reflection to avoid creating compilation dependency.
-    if (!jalview.bin.Cache.groovyJarsPresent())
-    {
-      throw new Error(
-              MessageManager
-                      .getString("error.implementation_error_cannot_create_groovyshell"));
-    }
     try
     {
-      Class<?> gcClass = Desktop.class.getClassLoader().loadClass(
-              "groovy.ui.Console");
-      Constructor<?> gccons = gcClass.getConstructor();
-      java.lang.reflect.Method setvar = gcClass.getMethod("setVariable",
-              new Class[] { String.class, Object.class });
-      java.lang.reflect.Method run = gcClass.getMethod("run");
-      Object gc = gccons.newInstance();
-      setvar.invoke(gc, new Object[] { "Jalview", this });
-      run.invoke(gc);
+      openGroovyConsole();
     } catch (Exception ex)
     {
       jalview.bin.Cache.log.error("Groovy Shell Creation failed.", ex);
@@ -2492,6 +2488,94 @@ public class Desktop extends jalview.jbgui.GDesktop implements
   }
 
   /**
+   * Open the Groovy console
+   */
+  void openGroovyConsole()
+  {
+    if (groovyConsole == null)
+    {
+      groovyConsole = new groovy.ui.Console();
+      groovyConsole.setVariable("Jalview", this);
+      groovyConsole.run();
+
+      /*
+       * We allow only one console at a time, so that AlignFrame menu option
+       * 'Calculate | Run Groovy script' is unambiguous.
+       * Disable 'Groovy Console', and enable 'Run script', when the console is 
+       * opened, and the reverse when it is closed
+       */
+      Window window = (Window) groovyConsole.getFrame();
+      window.addWindowListener(new WindowAdapter()
+      {
+        @Override
+        public void windowClosed(WindowEvent e)
+        {
+          /*
+           * rebind CMD-Q from Groovy Console to Jalview Quit
+           */
+          addQuitHandler();
+          enableExecuteGroovy(false);
+        }
+      });
+    }
+
+    /*
+     * show Groovy console window (after close and reopen)
+     */
+    ((Window) groovyConsole.getFrame()).setVisible(true);
+
+    /*
+     * if we got this far, enable 'Run Groovy' in AlignFrame menus
+     * and disable opening a second console
+     */
+    enableExecuteGroovy(true);
+  }
+
+  /**
+   * Bind Ctrl/Cmd-Q to Quit - for reset as Groovy Console takes over this
+   * binding when opened
+   */
+  protected void addQuitHandler()
+  {
+    getRootPane().getInputMap(JComponent.WHEN_IN_FOCUSED_WINDOW).put(
+            KeyStroke.getKeyStroke(KeyEvent.VK_Q, Toolkit
+                    .getDefaultToolkit().getMenuShortcutKeyMask()),
+            "Quit");
+    getRootPane().getActionMap().put("Quit", new AbstractAction()
+    {
+      @Override
+      public void actionPerformed(ActionEvent e)
+      {
+        quit();
+      }
+    });
+  }
+
+  /**
+   * Enable or disable 'Run Groovy script' in AlignFrame calculate menus
+   * 
+   * @param enabled
+   *          true if Groovy console is open
+   */
+  public void enableExecuteGroovy(boolean enabled)
+  {
+    /*
+     * disable opening a second Groovy console
+     * (or re-enable when the console is closed)
+     */
+    groovyShell.setEnabled(!enabled);
+
+    AlignFrame[] alignFrames = getAlignFrames();
+    if (alignFrames != null)
+    {
+      for (AlignFrame af : alignFrames)
+      {
+        af.setGroovyEnabled(enabled);
+      }
+    }
+  }
+
+  /**
    * Progress bars managed by the IProgressIndicator method.
    */
   private Hashtable<Long, JPanel> progressBars;
@@ -2503,6 +2587,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements
    * 
    * @see jalview.gui.IProgressIndicator#setProgressBar(java.lang.String, long)
    */
+  @Override
   public void setProgressBar(String message, long id)
   {
     if (progressBars == null)
@@ -2532,6 +2617,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements
    * @see jalview.gui.IProgressIndicator#registerHandler(long,
    * jalview.gui.IProgressIndicatorHandler)
    */
+  @Override
   public void registerHandler(final long id,
           final IProgressIndicatorHandler handler)
   {
@@ -2552,6 +2638,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements
       cancel.addActionListener(new ActionListener()
       {
 
+        @Override
         public void actionPerformed(ActionEvent e)
         {
           handler.cancelActivity(id);
@@ -2710,6 +2797,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements
             // only run if we aren't already displaying one of these.
             addDialogThread(serviceChangedDialog = new Runnable()
             {
+              @Override
               public void run()
               {
 
@@ -2793,6 +2881,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements
   {
     new Thread(new Runnable()
     {
+      @Override
       public void run()
       {
         try
@@ -2882,6 +2971,8 @@ public class Desktop extends jalview.jbgui.GDesktop implements
    */
   private java.util.concurrent.Semaphore block = new Semaphore(0);
 
+  private static groovy.ui.Console groovyConsole;
+
   /**
    * add another dialog thread to the queue
    * 
@@ -2891,6 +2982,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements
   {
     dialogExecutor.submit(new Runnable()
     {
+      @Override
       public void run()
       {
         if (dialogPause)
@@ -2934,7 +3026,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements
     ImageMaker im = new jalview.util.ImageMaker(this, ImageMaker.TYPE.EPS,
             "View of Desktop", getWidth(), getHeight(), of = new File(
                     "Jalview_snapshot" + System.currentTimeMillis()
-                            + ".eps"), "View of desktop");
+                            + ".eps"), "View of desktop", null, 0, false);
     try
     {
       paintAll(im.getGraphics());
@@ -3096,17 +3188,110 @@ public class Desktop extends jalview.jbgui.GDesktop implements
      * The dust settles...give focus to the tab we did this from.
      */
     myTopFrame.setDisplayedView(myTopFrame.alignPanel);
-
   }
 
-  public static AlignFrame getCurrentAlignFrame()
+  public static groovy.ui.Console getGroovyConsole()
   {
-    return currentAlignFrame;
+    return groovyConsole;
   }
 
-  public static void setCurrentAlignFrame(AlignFrame currentAlignFrame)
+  public static void transferFromDropTarget(List<String> files,
+          List<DataSourceType> protocols, DropTargetDropEvent evt,
+          Transferable t)
+          throws Exception
   {
-    Desktop.currentAlignFrame = currentAlignFrame;
-  }
 
+    DataFlavor uriListFlavor = new DataFlavor(
+            "text/uri-list;class=java.lang.String");
+    if (t.isDataFlavorSupported(DataFlavor.javaFileListFlavor))
+    {
+      // Works on Windows and MacOSX
+      Cache.log.debug("Drop handled as javaFileListFlavor");
+      evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
+      for (Object file : (List) t
+              .getTransferData(DataFlavor.javaFileListFlavor))
+      {
+        files.add(((File)file).toString());
+        protocols.add(DataSourceType.FILE);
+      }
+    }
+    else
+    {
+      // Unix like behaviour
+      boolean added = false;
+      String data = null;
+      if (t.isDataFlavorSupported(uriListFlavor))
+      {
+        Cache.log.debug("Drop handled as uriListFlavor");
+        // This is used by Unix drag system
+        evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
+        data = (String) t.getTransferData(uriListFlavor);
+      }
+      if (data == null)
+      {
+        // fallback to text: workaround - on OSX where there's a JVM bug
+        Cache.log.debug("standard URIListFlavor failed. Trying text");
+        // try text fallback
+        data = (String) t.getTransferData(new DataFlavor(
+                "text/plain;class=java.lang.String"));
+        if (Cache.log.isDebugEnabled())
+        {
+          Cache.log.debug("fallback returned " + data);
+        }
+      }
+      while (protocols.size() < files.size())
+      {
+        Cache.log.debug("Adding missing FILE protocol for "
+                + files.get(protocols.size()));
+        protocols.add(DataSourceType.FILE);
+      }
+      for (java.util.StringTokenizer st = new java.util.StringTokenizer(
+              data, "\r\n"); st.hasMoreTokens();)
+      {
+        added = true;
+        String s = st.nextToken();
+        if (s.startsWith("#"))
+        {
+          // the line is a comment (as per the RFC 2483)
+          continue;
+        }
+        java.net.URI uri = new java.net.URI(s);
+        if (uri.getScheme().toLowerCase().startsWith("http"))
+        {
+          protocols.add(DataSourceType.URL);
+          files.add(uri.toString());
+        }
+        else
+        {
+          // otherwise preserve old behaviour: catch all for file objects
+          java.io.File file = new java.io.File(uri);
+          protocols.add(DataSourceType.FILE);
+          files.add(file.toString());
+        }
+      }
+      if (Cache.log.isDebugEnabled())
+      {
+        if (data == null || !added)
+        {
+          Cache.log
+                  .debug("Couldn't resolve drop data. Here are the supported flavors:");
+          for (DataFlavor fl : t.getTransferDataFlavors())
+          {
+            Cache.log.debug("Supported transfer dataflavor: "
+                    + fl.toString());
+            evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
+            Object df = t.getTransferData(fl);
+            if (df != null)
+            {
+              Cache.log.debug("Retrieves: " + df);
+            }
+            else
+            {
+              Cache.log.debug("Retrieved nothing");
+            }
+          }
+        }
+      }
+    }
+  }
 }