X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FDesktop.java;h=7c08705e1cbcfd6023a74b8ed457f9da6920d002;hb=4d64932654de3f6ffe07db11d18f2d21f558c6e6;hp=7f36f7ffd13c34c8a506fe1c7e6376adc9de119b;hpb=1eb2c4e903341904671283699dc22bc611212b08;p=jalview.git

diff --git a/src/jalview/gui/Desktop.java b/src/jalview/gui/Desktop.java
index 7f36f7f..7c08705 100644
--- a/src/jalview/gui/Desktop.java
+++ b/src/jalview/gui/Desktop.java
@@ -24,6 +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.FileFormats;
 import jalview.io.FileLoader;
 import jalview.io.FormatAdapter;
 import jalview.io.IdentifyFile;
@@ -31,12 +36,16 @@ import jalview.io.JalviewFileChooser;
 import jalview.io.JalviewFileView;
 import jalview.jbgui.GSplitFrame;
 import jalview.jbgui.GStructureViewer;
+import jalview.project.Jalview2XML;
 import jalview.structure.StructureSelectionManager;
+import jalview.urls.IdOrgSettings;
 import jalview.util.ImageMaker;
 import jalview.util.MessageManager;
 import jalview.util.Platform;
+import jalview.util.UrlConstants;
 import jalview.viewmodel.AlignmentViewport;
 import jalview.ws.params.ParamManager;
+import jalview.ws.utils.UrlDownloadClient;
 
 import java.awt.BorderLayout;
 import java.awt.Color;
@@ -52,6 +61,14 @@ import java.awt.datatransfer.Clipboard;
 import java.awt.datatransfer.ClipboardOwner;
 import java.awt.datatransfer.DataFlavor;
 import java.awt.datatransfer.Transferable;
+import java.awt.desktop.AboutEvent;
+import java.awt.desktop.AboutHandler;
+import java.awt.desktop.PreferencesEvent;
+import java.awt.desktop.PreferencesHandler;
+import java.awt.desktop.QuitEvent;
+import java.awt.desktop.QuitHandler;
+import java.awt.desktop.QuitResponse;
+import java.awt.desktop.QuitStrategy;
 import java.awt.dnd.DnDConstants;
 import java.awt.dnd.DropTargetDragEvent;
 import java.awt.dnd.DropTargetDropEvent;
@@ -59,36 +76,44 @@ import java.awt.dnd.DropTargetEvent;
 import java.awt.dnd.DropTargetListener;
 import java.awt.event.ActionEvent;
 import java.awt.event.ActionListener;
-import java.awt.event.FocusEvent;
-import java.awt.event.FocusListener;
+import java.awt.event.InputEvent;
+import java.awt.event.KeyEvent;
 import java.awt.event.MouseAdapter;
 import java.awt.event.MouseEvent;
-import java.awt.event.MouseListener;
 import java.awt.event.WindowAdapter;
 import java.awt.event.WindowEvent;
 import java.beans.PropertyChangeEvent;
 import java.beans.PropertyChangeListener;
-import java.beans.PropertyVetoException;
 import java.io.BufferedInputStream;
 import java.io.File;
 import java.io.FileOutputStream;
+import java.io.FileWriter;
+import java.io.IOException;
 import java.net.URL;
 import java.util.ArrayList;
+import java.util.HashMap;
 import java.util.Hashtable;
 import java.util.List;
+import java.util.ListIterator;
 import java.util.StringTokenizer;
 import java.util.Vector;
 import java.util.concurrent.ExecutorService;
 import java.util.concurrent.Executors;
 import java.util.concurrent.Semaphore;
 
+import javax.swing.AbstractAction;
+import javax.swing.Action;
+import javax.swing.ActionMap;
+import javax.swing.Box;
+import javax.swing.BoxLayout;
 import javax.swing.DefaultDesktopManager;
 import javax.swing.DesktopManager;
+import javax.swing.InputMap;
 import javax.swing.JButton;
+import javax.swing.JCheckBox;
 import javax.swing.JComboBox;
 import javax.swing.JComponent;
 import javax.swing.JDesktopPane;
-import javax.swing.JFrame;
 import javax.swing.JInternalFrame;
 import javax.swing.JLabel;
 import javax.swing.JMenuItem;
@@ -96,12 +121,17 @@ 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;
+import javax.swing.event.InternalFrameAdapter;
+import javax.swing.event.InternalFrameEvent;
 import javax.swing.event.MenuEvent;
 import javax.swing.event.MenuListener;
 
+import org.stackoverflowusers.file.WindowsShortcut;
+
 /**
  * Jalview Desktop
  * 
@@ -109,10 +139,23 @@ import javax.swing.event.MenuListener;
  * @author $author$
  * @version $Revision: 1.155 $
  */
-public class Desktop extends jalview.jbgui.GDesktop implements
-        DropTargetListener, ClipboardOwner, IProgressIndicator,
+public class Desktop extends jalview.jbgui.GDesktop
+        implements DropTargetListener, ClipboardOwner, IProgressIndicator,
         jalview.api.StructureSelectionManagerProvider
 {
+  private static int DEFAULT_MIN_WIDTH = 300;
+
+  private static int DEFAULT_MIN_HEIGHT = 250;
+
+  private static int ALIGN_FRAME_DEFAULT_MIN_WIDTH = 600;
+
+  private static int ALIGN_FRAME_DEFAULT_MIN_HEIGHT = 70;
+
+  private static final String EXPERIMENTAL_FEATURES = "EXPERIMENTAL_FEATURES";
+
+  private static final String CONFIRM_KEYBOARD_QUIT = "CONFIRM_KEYBOARD_QUIT";
+
+  public static HashMap<String, FileWriter> savingFiles = new HashMap<>();
 
   private JalviewChangeSupport changeSupport = new JalviewChangeSupport();
 
@@ -123,6 +166,8 @@ public class Desktop extends jalview.jbgui.GDesktop implements
 
   private File projectFile;
 
+  private static boolean setAPQHandlers = false;
+
   /**
    * @param listener
    * @see jalview.gui.JalviewChangeSupport#addJalviewPropertyChangeListener(java.beans.PropertyChangeListener)
@@ -169,8 +214,6 @@ 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;
@@ -246,12 +289,14 @@ public class Desktop extends jalview.jbgui.GDesktop implements
     public void endDraggingFrame(JComponent f)
     {
       delegate.endDraggingFrame(f);
+      desktop.repaint();
     }
 
     @Override
     public void endResizingFrame(JComponent f)
     {
       delegate.endResizingFrame(f);
+      desktop.repaint();
     }
 
     @Override
@@ -313,33 +358,133 @@ public class Desktop extends jalview.jbgui.GDesktop implements
     instance = this;
     doVamsasClientCheck();
 
-    groovyShell = new JMenuItem();
-    groovyShell.setText(MessageManager.getString("label.groovy_console"));
-    groovyShell.addActionListener(new ActionListener()
+    doConfigureStructurePrefs();
+    setTitle("Jalview " + jalview.bin.Cache.getProperty("VERSION"));
+    /*
+    if (!Platform.isAMac())
+    {
+      // this.setDefaultCloseOperation(WindowConstants.EXIT_ON_CLOSE);
+    }
+    else
+    {
+     this.setDefaultCloseOperation(WindowConstants.DO_NOTHING_ON_CLOSE);
+    }
+    */
+
+    // flagging this test to avoid unnecessary reflection
+    if (!setAPQHandlers)
+    {
+      // see if the Quit, About and Preferences handlers are available
+      Class desktopClass = java.awt.Desktop.class;
+      java.awt.Desktop hdesktop = java.awt.Desktop.getDesktop();
+
+      try
+      {
+
+        if (desktopClass.getDeclaredMethod("setAboutHandler",
+                new Class[]
+                { AboutHandler.class }) != null)
+        {
+
+          hdesktop.setAboutHandler(new AboutHandler()
+          {
+            @Override
+            public void handleAbout(AboutEvent e)
+            {
+              aboutMenuItem_actionPerformed(null);
+            }
+          });
+
+        }
+
+        if (desktopClass.getDeclaredMethod("setPreferencesHandler",
+                new Class[]
+                { PreferencesHandler.class }) != null)
+        {
+
+          hdesktop.setPreferencesHandler(new PreferencesHandler()
+          {
+            @Override
+            public void handlePreferences(PreferencesEvent e)
+            {
+              preferences_actionPerformed(null);
+            }
+          });
+
+        }
+
+        if (desktopClass.getDeclaredMethod("setQuitHandler",
+                new Class[]
+                { QuitHandler.class }) != null)
+        {
+
+          hdesktop.setQuitHandler(new QuitHandler()
+          {
+            @Override
+            public void handleQuitRequestWith(QuitEvent e, QuitResponse r)
+            {
+              boolean confirmQuit = jalview.bin.Cache
+                      .getDefault(CONFIRM_KEYBOARD_QUIT, true);
+              int n;
+              if (confirmQuit)
+              {
+                n = JOptionPane.showConfirmDialog(null,
+                        MessageManager.getString("label.quit_jalview"),
+                        MessageManager.getString("action.quit"),
+                        JOptionPane.OK_CANCEL_OPTION,
+                        JOptionPane.PLAIN_MESSAGE, null);
+              }
+              else
+              {
+                n = JOptionPane.OK_OPTION;
+              }
+              if (n == JOptionPane.OK_OPTION)
+              {
+                System.out.println("Shortcut Quit confirmed by user");
+                quit();
+                r.performQuit(); // probably won't reach this line, but just in
+                                 // case
+              }
+              else
+              {
+                r.cancelQuit();
+                System.out.println("Shortcut Quit cancelled by user");
+              }
+            }
+          });
+          hdesktop.setQuitStrategy(QuitStrategy.CLOSE_ALL_WINDOWS);
+
+        }
+
+      } catch (NoSuchMethodException e)
+      {
+        System.out.println(
+                "NoSuchMethodException when looking for About, Preferences, Quit Handlers");
+        e.printStackTrace();
+      }
+
+      setAPQHandlers = true;
+    }
+
+    addWindowListener(new WindowAdapter()
     {
+
       @Override
-      public void actionPerformed(ActionEvent e)
+      public void windowClosing(WindowEvent ev)
       {
-        groovyShell_actionPerformed();
+        quit();
       }
     });
-    toolsMenu.add(groovyShell);
-    groovyShell.setVisible(true);
 
-    doConfigureStructurePrefs();
-    setTitle("Jalview " + jalview.bin.Cache.getProperty("VERSION"));
-    setDefaultCloseOperation(JFrame.EXIT_ON_CLOSE);
     boolean selmemusage = jalview.bin.Cache.getDefault("SHOW_MEMUSAGE",
             false);
-    boolean showjconsole = jalview.bin.Cache.getDefault(
-            "SHOW_JAVA_CONSOLE", false);
+
+    boolean showjconsole = jalview.bin.Cache.getDefault("SHOW_JAVA_CONSOLE",
+            false);
     desktop = new MyDesktopPane(selmemusage);
-    if (Platform.isAMac())
-    {
-      desktop.setDoubleBuffered(false);
-    }
     showMemusage.setSelected(selmemusage);
     desktop.setBackground(Color.white);
+
     getContentPane().setLayout(new BorderLayout());
     // alternate config - have scrollbars - see notes in JAL-153
     // JScrollPane sp = new JScrollPane();
@@ -351,7 +496,11 @@ public class Desktop extends jalview.jbgui.GDesktop implements
     // This line prevents Windows Look&Feel resizing all new windows to maximum
     // if previous window was maximised
     desktop.setDesktopManager(new MyDesktopManager(
-            new DefaultDesktopManager()));
+            (Platform.isWindows() ? new DefaultDesktopManager()
+                    : Platform.isAMac()
+                            ? new AquaInternalFrameManager(
+                                    desktop.getDesktopManager())
+                            : desktop.getDesktopManager())));
 
     Rectangle dims = getLastKnownDimensions("");
     if (dims != null)
@@ -361,26 +510,34 @@ public class Desktop extends jalview.jbgui.GDesktop implements
     else
     {
       Dimension screenSize = Toolkit.getDefaultToolkit().getScreenSize();
-      setBounds((screenSize.width - 900) / 2,
-              (screenSize.height - 650) / 2, 900, 650);
+      setBounds((screenSize.width - 900) / 2, (screenSize.height - 650) / 2,
+              900, 650);
     }
     jconsole = new Console(this, showjconsole);
     // add essential build information
-    jconsole.setHeader("Jalview Version: "
-            + jalview.bin.Cache.getProperty("VERSION") + "\n"
-            + "Jalview Installation: "
-            + jalview.bin.Cache.getDefault("INSTALLATION", "unknown")
-            + "\n" + "Build Date: "
-            + jalview.bin.Cache.getDefault("BUILD_DATE", "unknown") + "\n"
-            + "Java version: " + System.getProperty("java.version") + "\n"
-            + System.getProperty("os.arch") + " "
-            + System.getProperty("os.name") + " "
-            + System.getProperty("os.version"));
+    jconsole.setHeader(
+            "Jalview Version: " + jalview.bin.Cache.getProperty("VERSION")
+                    + "\n" + "Jalview Installation: "
+                    + jalview.bin.Cache.getDefault("INSTALLATION",
+                            "unknown")
+                    + "\n" + "Build Date: "
+                    + jalview.bin.Cache.getDefault("BUILD_DATE", "unknown")
+                    + "\n" + "Java version: "
+                    + System.getProperty("java.version") + "\n"
+                    + System.getProperty("os.arch") + " "
+                    + System.getProperty("os.name") + " "
+                    + System.getProperty("os.version"));
 
     showConsole(showjconsole);
 
     showNews.setVisible(false);
 
+    experimentalFeatures.setSelected(showExperimental());
+
+    getIdentifiersOrgData();
+
+    checkURLLinks();
+
     this.addWindowListener(new WindowAdapter()
     {
       @Override
@@ -396,32 +553,23 @@ public class Desktop extends jalview.jbgui.GDesktop implements
       @Override
       public void mousePressed(MouseEvent evt)
       {
-        if (evt.isPopupTrigger())
+        if (evt.isPopupTrigger()) // Mac
         {
           showPasteMenu(evt.getX(), evt.getY());
         }
       }
-    });
-    desktop.addMouseListener(ma);
-
-    this.addFocusListener(new FocusListener()
-    {
-
-      @Override
-      public void focusLost(FocusEvent e)
-      {
-        // TODO Auto-generated method stub
-
-      }
 
       @Override
-      public void focusGained(FocusEvent e)
+      public void mouseReleased(MouseEvent evt)
       {
-        Cache.log.debug("Relaying windows after focus gain");
-        // make sure that we sort windows properly after we gain focus
-        instance.relayerWindows();
+        if (evt.isPopupTrigger()) // Windows
+        {
+          showPasteMenu(evt.getX(), evt.getY());
+        }
       }
     });
+    desktop.addMouseListener(ma);
+
     this.setDropTarget(new java.awt.dnd.DropTarget(desktop, this));
     // Spawn a thread that shows the splashscreen
     SwingUtilities.invokeLater(new Runnable()
@@ -433,7 +581,6 @@ public class Desktop extends jalview.jbgui.GDesktop implements
       }
     });
 
-    // displayed.
     // Thread off a new instance of the file chooser - this reduces the time it
     // takes to open it later on.
     new Thread(new Runnable()
@@ -442,11 +589,9 @@ public class Desktop extends jalview.jbgui.GDesktop implements
       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"));
+        String fileFormat = Cache.getProperty("DEFAULT_FILE_FORMAT");
+        JalviewFileChooser.forRead(Cache.getProperty("LAST_DIRECTORY"),
+                fileFormat);
         Cache.log.debug("Filechooser init thread finished.");
       }
     }).start();
@@ -466,6 +611,19 @@ public class Desktop extends jalview.jbgui.GDesktop implements
             });
   }
 
+  /**
+   * Answers true if user preferences to enable experimental features is True
+   * (on), else false
+   * 
+   * @return
+   */
+  public boolean showExperimental()
+  {
+    String experimental = Cache.getDefault(EXPERIMENTAL_FEATURES,
+            Boolean.FALSE.toString());
+    return Boolean.valueOf(experimental).booleanValue();
+  }
+
   public void doConfigureStructurePrefs()
   {
     // configure services
@@ -473,12 +631,12 @@ public class Desktop extends jalview.jbgui.GDesktop implements
             .getStructureSelectionManager(this);
     if (jalview.bin.Cache.getDefault(Preferences.ADD_SS_ANN, true))
     {
-      ssm.setAddTempFacAnnot(jalview.bin.Cache.getDefault(
-              Preferences.ADD_TEMPFACT_ANN, true));
-      ssm.setProcessSecondaryStructure(jalview.bin.Cache.getDefault(
-              Preferences.STRUCT_FROM_PDB, true));
-      ssm.setSecStructServices(jalview.bin.Cache.getDefault(
-              Preferences.USE_RNAVIEW, true));
+      ssm.setAddTempFacAnnot(jalview.bin.Cache
+              .getDefault(Preferences.ADD_TEMPFACT_ANN, true));
+      ssm.setProcessSecondaryStructure(jalview.bin.Cache
+              .getDefault(Preferences.STRUCT_FROM_PDB, true));
+      ssm.setSecStructServices(
+              jalview.bin.Cache.getDefault(Preferences.USE_RNAVIEW, true));
     }
     else
     {
@@ -492,7 +650,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements
   {
     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()
@@ -503,7 +661,31 @@ public class Desktop extends jalview.jbgui.GDesktop implements
         showNews.setVisible(true);
         Cache.log.debug("Completed news thread.");
       }
-    });
+    }).start();
+  }
+
+  public void getIdentifiersOrgData()
+  {
+    // Thread off the identifiers fetcher
+    new Thread(new Runnable()
+    {
+      @Override
+      public void run()
+      {
+        Cache.log.debug("Downloading data from identifiers.org");
+        UrlDownloadClient client = new UrlDownloadClient();
+        try
+        {
+          client.download(IdOrgSettings.getUrl(),
+                  IdOrgSettings.getDownloadLocation());
+        } catch (IOException e)
+        {
+          Cache.log.debug("Exception downloading identifiers.org data"
+                  + e.getMessage());
+        }
+      }
+    }).start();
+    ;
   }
 
   @Override
@@ -526,7 +708,8 @@ public class Desktop extends jalview.jbgui.GDesktop implements
           {
             long now = System.currentTimeMillis();
             Desktop.instance.setProgressBar(
-                    MessageManager.getString("status.refreshing_news"), now);
+                    MessageManager.getString("status.refreshing_news"),
+                    now);
             jvnews.refreshNews();
             Desktop.instance.setProgressBar(null, now);
             jvnews.showNews();
@@ -550,25 +733,23 @@ public class Desktop extends jalview.jbgui.GDesktop implements
     Dimension screenSize = Toolkit.getDefaultToolkit().getScreenSize();
     String x = jalview.bin.Cache.getProperty(windowName + "SCREEN_X");
     String y = jalview.bin.Cache.getProperty(windowName + "SCREEN_Y");
-    String width = jalview.bin.Cache.getProperty(windowName
-            + "SCREEN_WIDTH");
-    String height = jalview.bin.Cache.getProperty(windowName
-            + "SCREEN_HEIGHT");
+    String width = jalview.bin.Cache
+            .getProperty(windowName + "SCREEN_WIDTH");
+    String height = jalview.bin.Cache
+            .getProperty(windowName + "SCREEN_HEIGHT");
     if ((x != null) && (y != null) && (width != null) && (height != null))
     {
-      int ix = Integer.parseInt(x), iy = Integer.parseInt(y), iw = Integer
-              .parseInt(width), ih = Integer.parseInt(height);
+      int ix = Integer.parseInt(x), iy = Integer.parseInt(y),
+              iw = Integer.parseInt(width), ih = Integer.parseInt(height);
       if (jalview.bin.Cache.getProperty("SCREENGEOMETRY_WIDTH") != null)
       {
         // attempt #1 - try to cope with change in screen geometry - this
         // version doesn't preserve original jv aspect ratio.
         // take ratio of current screen size vs original screen size.
-        double sw = ((1f * screenSize.width) / (1f * Integer
-                .parseInt(jalview.bin.Cache
-                        .getProperty("SCREENGEOMETRY_WIDTH"))));
-        double sh = ((1f * screenSize.height) / (1f * Integer
-                .parseInt(jalview.bin.Cache
-                        .getProperty("SCREENGEOMETRY_HEIGHT"))));
+        double sw = ((1f * screenSize.width) / (1f * Integer.parseInt(
+                jalview.bin.Cache.getProperty("SCREENGEOMETRY_WIDTH"))));
+        double sh = ((1f * screenSize.height) / (1f * Integer.parseInt(
+                jalview.bin.Cache.getProperty("SCREENGEOMETRY_HEIGHT"))));
         // rescale the bounds depending upon the current screen geometry.
         ix = (int) (ix * sw);
         iw = (int) (iw * sw);
@@ -576,19 +757,19 @@ public class Desktop extends jalview.jbgui.GDesktop implements
         ih = (int) (ih * sh);
         while (ix >= screenSize.width)
         {
-          jalview.bin.Cache.log
-                  .debug("Window geometry location recall error: shifting horizontal to within screenbounds.");
+          jalview.bin.Cache.log.debug(
+                  "Window geometry location recall error: shifting horizontal to within screenbounds.");
           ix -= screenSize.width;
         }
         while (iy >= screenSize.height)
         {
-          jalview.bin.Cache.log
-                  .debug("Window geometry location recall error: shifting vertical to within screenbounds.");
+          jalview.bin.Cache.log.debug(
+                  "Window geometry location recall error: shifting vertical to within screenbounds.");
           iy -= screenSize.height;
         }
-        jalview.bin.Cache.log.debug("Got last known dimensions for "
-                + windowName + ": x:" + ix + " y:" + iy + " width:" + iw
-                + " height:" + ih);
+        jalview.bin.Cache.log.debug(
+                "Got last known dimensions for " + windowName + ": x:" + ix
+                        + " y:" + iy + " width:" + iw + " height:" + ih);
       }
       // return dimensions for new instance
       return new Rectangle(ix, iy, iw, ih);
@@ -666,17 +847,16 @@ 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)
     {
-      System.out
-              .println("Unable to paste alignment from system clipboard:\n"
-                      + ex);
+      System.out.println(
+              "Unable to paste alignment from system clipboard:\n" + ex);
     }
   }
 
@@ -695,7 +875,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements
   public static synchronized void addInternalFrame(
           final JInternalFrame frame, String title, int w, int h)
   {
-    addInternalFrame(frame, title, true, w, h, true);
+    addInternalFrame(frame, title, true, w, h, true, false);
   }
 
   /**
@@ -717,7 +897,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements
           final JInternalFrame frame, String title, boolean makeVisible,
           int w, int h)
   {
-    addInternalFrame(frame, title, makeVisible, w, h, true);
+    addInternalFrame(frame, title, makeVisible, w, h, true, false);
   }
 
   /**
@@ -738,7 +918,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements
           final JInternalFrame frame, String title, int w, int h,
           boolean resizable)
   {
-    addInternalFrame(frame, title, true, w, h, resizable);
+    addInternalFrame(frame, title, true, w, h, resizable, false);
   }
 
   /**
@@ -757,10 +937,12 @@ public class Desktop extends jalview.jbgui.GDesktop implements
    *          height
    * @param resizable
    *          Allow resize
+   * @param ignoreMinSize
+   *          Do not set the default minimum size for frame
    */
   public static synchronized void addInternalFrame(
           final JInternalFrame frame, String title, boolean makeVisible,
-          int w, int h, boolean resizable)
+          int w, int h, boolean resizable, boolean ignoreMinSize)
   {
 
     // TODO: allow callers to determine X and Y position of frame (eg. via
@@ -777,61 +959,86 @@ public class Desktop extends jalview.jbgui.GDesktop implements
     // A HEADLESS STATE WHEN NO DESKTOP EXISTS. MUST RETURN
     // IF JALVIEW IS RUNNING HEADLESS
     // ///////////////////////////////////////////////
-    if (instance == null
-            || (System.getProperty("java.awt.headless") != null && System
-                    .getProperty("java.awt.headless").equals("true")))
+    if (instance == null || (System.getProperty("java.awt.headless") != null
+            && System.getProperty("java.awt.headless").equals("true")))
     {
       return;
     }
 
     openFrameCount++;
 
+    if (!ignoreMinSize)
+    {
+      frame.setMinimumSize(
+              new Dimension(DEFAULT_MIN_WIDTH, DEFAULT_MIN_HEIGHT));
+
+      // Set default dimension for Alignment Frame window.
+      // The Alignment Frame window could be added from a number of places,
+      // hence,
+      // I did this here in order not to miss out on any Alignment frame.
+      if (frame instanceof AlignFrame)
+      {
+        frame.setMinimumSize(new Dimension(ALIGN_FRAME_DEFAULT_MIN_WIDTH,
+                ALIGN_FRAME_DEFAULT_MIN_HEIGHT));
+      }
+    }
+
     frame.setVisible(makeVisible);
     frame.setClosable(true);
     frame.setResizable(resizable);
     frame.setMaximizable(resizable);
     frame.setIconifiable(resizable);
-    if (Platform.isAMac())
-    {
-      frame.setIconifiable(false);
-      frame.setFrameIcon(null);
-      // frame.setDesktopIcon(null);
-      frame.setDoubleBuffered(false);
-    }
+    frame.setOpaque(false);
+
     if (frame.getX() < 1 && frame.getY() < 1)
     {
-      frame.setLocation(xOffset * openFrameCount, yOffset
-              * ((openFrameCount - 1) % 10) + yOffset);
+      frame.setLocation(xOffset * openFrameCount,
+              yOffset * ((openFrameCount - 1) % 10) + yOffset);
     }
 
+    /*
+     * add an entry for the new frame in the Window menu 
+     * (and remove it when the frame is closed)
+     */
     final JMenuItem menuItem = new JMenuItem(title);
-    frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
+    frame.addInternalFrameListener(new InternalFrameAdapter()
     {
       @Override
-      public void internalFrameActivated(
-              javax.swing.event.InternalFrameEvent evt)
+      public void internalFrameActivated(InternalFrameEvent evt)
       {
         JInternalFrame itf = desktop.getSelectedFrame();
         if (itf != null)
         {
+          if (itf instanceof AlignFrame)
+          {
+            Jalview.setCurrentAlignFrame((AlignFrame) itf);
+          }
           itf.requestFocus();
         }
-
       }
 
       @Override
-      public void internalFrameClosed(
-              javax.swing.event.InternalFrameEvent evt)
+      public void internalFrameClosed(InternalFrameEvent evt)
       {
         PaintRefresher.RemoveComponent(frame);
-        openFrameCount--;
-        windowMenu.remove(menuItem);
-        JInternalFrame itf = desktop.getSelectedFrame();
-        if (itf != null)
+
+        /*
+         * defensive check to prevent frames being
+         * added half off the window
+         */
+        if (openFrameCount > 0)
         {
-          itf.requestFocus();
+          openFrameCount--;
+        }
+
+        /*
+         * ensure no reference to alignFrame retained by menu item listener
+         */
+        if (menuItem.getActionListeners().length > 0)
+        {
+          menuItem.removeActionListener(menuItem.getActionListeners()[0]);
         }
-        System.gc();
+        windowMenu.remove(menuItem);
       };
     });
 
@@ -850,51 +1057,13 @@ public class Desktop extends jalview.jbgui.GDesktop implements
         }
       }
     });
-    menuItem.addMouseListener(new MouseListener()
-    {
 
-      @Override
-      public void mouseReleased(MouseEvent e)
-      {
-      }
+    setKeyBindings(frame);
 
-      @Override
-      public void mousePressed(MouseEvent e)
-      {
-      }
-
-      @Override
-      public void mouseExited(MouseEvent e)
-      {
-        try
-        {
-          frame.setSelected(false);
-        } catch (PropertyVetoException e1)
-        {
-        }
-      }
-
-      @Override
-      public void mouseEntered(MouseEvent e)
-      {
-        try
-        {
-          frame.setSelected(true);
-        } catch (PropertyVetoException e1)
-        {
-        }
-      }
-
-      @Override
-      public void mouseClicked(MouseEvent e)
-      {
-
-      }
-    });
+    desktop.add(frame);
 
     windowMenu.add(menuItem);
 
-    desktop.add(frame);
     frame.toFront();
     try
     {
@@ -904,12 +1073,48 @@ public class Desktop extends jalview.jbgui.GDesktop implements
     {
     } catch (java.lang.ClassCastException cex)
     {
-      Cache.log
-              .warn("Squashed a possible GUI implementation error. If you can recreate this, please look at http://issues.jalview.org/browse/JAL-869",
-                      cex);
+      Cache.log.warn(
+              "Squashed a possible GUI implementation error. If you can recreate this, please look at http://issues.jalview.org/browse/JAL-869",
+              cex);
     }
   }
 
+  /**
+   * Add key bindings to a JInternalFrame so that Ctrl-W and Cmd-W will close
+   * the window
+   * 
+   * @param frame
+   */
+  private static void setKeyBindings(JInternalFrame frame)
+  {
+    @SuppressWarnings("serial")
+    final Action closeAction = new AbstractAction()
+    {
+      @Override
+      public void actionPerformed(ActionEvent e)
+      {
+        frame.dispose();
+      }
+    };
+
+    /*
+     * set up key bindings for Ctrl-W and Cmd-W, with the same (Close) action
+     */
+    KeyStroke ctrlWKey = KeyStroke.getKeyStroke(KeyEvent.VK_W,
+            InputEvent.CTRL_DOWN_MASK);
+    KeyStroke cmdWKey = KeyStroke.getKeyStroke(KeyEvent.VK_W,
+            Toolkit.getDefaultToolkit().getMenuShortcutKeyMask());
+
+    InputMap inputMap = frame
+            .getInputMap(JComponent.WHEN_IN_FOCUSED_WINDOW);
+    String ctrlW = ctrlWKey.toString();
+    inputMap.put(ctrlWKey, ctrlW);
+    inputMap.put(cmdWKey, ctrlW);
+
+    ActionMap actionMap = frame.getActionMap();
+    actionMap.put(ctrlW, closeAction);
+  }
+
   @Override
   public void lostOwnership(Clipboard clipboard, Transferable contents)
   {
@@ -951,54 +1156,19 @@ public class Desktop extends jalview.jbgui.GDesktop implements
   public void drop(DropTargetDropEvent evt)
   {
     boolean success = true;
+    // JAL-1552 - acceptDrop required before getTransferable call for
+    // Java's Transferable for native dnd
+    evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
     Transferable t = evt.getTransferable();
-    java.util.List files = null;
-    java.util.List protocols = null;
+    List<String> files = new ArrayList<>();
+    List<DataSourceType> protocols = new ArrayList<>();
 
     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;
     }
 
@@ -1009,13 +1179,14 @@ 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
@@ -1044,15 +1215,13 @@ public class Desktop extends jalview.jbgui.GDesktop implements
   @Override
   public void inputLocalFileMenuItem_actionPerformed(AlignViewport viewport)
   {
-    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"));
+    String fileFormat = Cache.getProperty("DEFAULT_FILE_FORMAT");
+    JalviewFileChooser chooser = JalviewFileChooser
+            .forRead(Cache.getProperty("LAST_DIRECTORY"), fileFormat);
 
     chooser.setFileView(new JalviewFileView());
-    chooser.setDialogTitle(MessageManager
-            .getString("label.open_local_file"));
+    chooser.setDialogTitle(
+            MessageManager.getString("label.open_local_file"));
     chooser.setToolTipText(MessageManager.getString("action.open"));
 
     int value = chooser.showOpenDialog(this);
@@ -1060,28 +1229,35 @@ 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
-              .getSelectedFile().getParent());
+      Cache.setProperty("LAST_DIRECTORY",
+              chooser.getSelectedFile().getParent());
 
-      String format = null;
-      if (chooser.getSelectedFormat() != null
-              && chooser.getSelectedFormat().equals("Jalview"))
-      {
-        format = "Jalview";
-      }
-      else
+      FileFormatI format = chooser.getSelectedFormat();
+
+      /*
+       * Call IdentifyFile to verify the file contains what its extension implies.
+       * Skip this step for dynamically added file formats, because
+       * IdentifyFile does not know how to recognise them.
+       */
+      if (FileFormats.getInstance().isIdentifiable(format))
       {
-        format = new IdentifyFile().identify(choice, FormatAdapter.FILE);
+        try
+        {
+          format = new IdentifyFile().identify(choice, DataSourceType.FILE);
+        } catch (FileFormatException e)
+        {
+          // format = null; //??
+        }
       }
 
       if (viewport != null)
       {
-        new FileLoader().LoadFile(viewport, choice, FormatAdapter.FILE,
+        new FileLoader().LoadFile(viewport, choice, DataSourceType.FILE,
                 format);
       }
       else
       {
-        new FileLoader().LoadFile(choice, FormatAdapter.FILE, format);
+        new FileLoader().LoadFile(choice, DataSourceType.FILE, format);
       }
     }
   }
@@ -1122,11 +1298,11 @@ public class Desktop extends jalview.jbgui.GDesktop implements
       }
     }
 
-    int reply = JOptionPane.showInternalConfirmDialog(desktop, panel,
+    int reply = JvOptionPane.showInternalConfirmDialog(desktop, panel,
             MessageManager.getString("label.input_alignment_from_url"),
-            JOptionPane.OK_CANCEL_OPTION);
+            JvOptionPane.OK_CANCEL_OPTION);
 
-    if (reply != JOptionPane.OK_OPTION)
+    if (reply != JvOptionPane.OK_OPTION)
     {
       return;
     }
@@ -1137,36 +1313,47 @@ 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 = null;
+      try
+      {
+        format = new IdentifyFile().identify(url, DataSourceType.URL);
+      } catch (FileFormatException e)
+      {
+        // TODO revise error handling, distinguish between
+        // URL not found and response not valid
+      }
 
-      if (format.equals("URL NOT FOUND"))
+      if (format == null)
       {
-        JOptionPane.showInternalMessageDialog(Desktop.desktop,
+        JvOptionPane.showInternalMessageDialog(Desktop.desktop,
                 MessageManager.formatMessage("label.couldnt_locate",
-                        new Object[] { url }), MessageManager
-                        .getString("label.url_not_found"),
-                JOptionPane.WARNING_MESSAGE);
+                        new Object[]
+                        { url }),
+                MessageManager.getString("label.url_not_found"),
+                JvOptionPane.WARNING_MESSAGE);
 
         return;
       }
 
       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);
       }
     }
   }
@@ -1185,8 +1372,8 @@ public class Desktop extends jalview.jbgui.GDesktop implements
     CutAndPasteTransfer cap = new CutAndPasteTransfer();
     cap.setForInput(viewPanel);
     Desktop.addInternalFrame(cap,
-            MessageManager.getString("label.cut_paste_alignmen_file"),
-            true, 600, 500);
+            MessageManager.getString("label.cut_paste_alignmen_file"), true,
+            600, 500);
   }
 
   /*
@@ -1195,13 +1382,15 @@ public class Desktop extends jalview.jbgui.GDesktop implements
   @Override
   public void quit()
   {
+    System.out.println("********** Desktop.quit()");
+    System.out.println(savingFiles.toString());
     Dimension screen = Toolkit.getDefaultToolkit().getScreenSize();
-    jalview.bin.Cache
-            .setProperty("SCREENGEOMETRY_WIDTH", screen.width + "");
-    jalview.bin.Cache.setProperty("SCREENGEOMETRY_HEIGHT", screen.height
-            + "");
-    storeLastKnownDimensions("", new Rectangle(getBounds().x,
-            getBounds().y, getWidth(), getHeight()));
+    jalview.bin.Cache.setProperty("SCREENGEOMETRY_WIDTH",
+            screen.width + "");
+    jalview.bin.Cache.setProperty("SCREENGEOMETRY_HEIGHT",
+            screen.height + "");
+    storeLastKnownDimensions("", new Rectangle(getBounds().x, getBounds().y,
+            getWidth(), getHeight()));
 
     if (jconsole != null)
     {
@@ -1218,6 +1407,13 @@ 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);
   }
 
@@ -1243,9 +1439,9 @@ public class Desktop extends jalview.jbgui.GDesktop implements
   public void aboutMenuItem_actionPerformed(ActionEvent e)
   {
     // StringBuffer message = getAboutMessage(false);
-    // JOptionPane.showInternalMessageDialog(Desktop.desktop,
+    // JvOptionPane.showInternalMessageDialog(Desktop.desktop,
     //
-    // message.toString(), "About Jalview", JOptionPane.INFORMATION_MESSAGE);
+    // message.toString(), "About Jalview", JvOptionPane.INFORMATION_MESSAGE);
     new Thread(new Runnable()
     {
       @Override
@@ -1263,7 +1459,8 @@ public class Desktop extends jalview.jbgui.GDesktop implements
     if (shortv)
     {
       message.append("<h1><strong>Version: "
-              + jalview.bin.Cache.getProperty("VERSION") + "</strong></h1>");
+              + jalview.bin.Cache.getProperty("VERSION")
+              + "</strong></h1>");
       message.append("<strong>Last Updated: <em>"
               + jalview.bin.Cache.getDefault("BUILD_DATE", "unknown")
               + "</em></strong>");
@@ -1278,8 +1475,8 @@ public class Desktop extends jalview.jbgui.GDesktop implements
               + jalview.bin.Cache.getDefault("BUILD_DATE", "unknown"));
     }
 
-    if (jalview.bin.Cache.getDefault("LATEST_VERSION", "Checking").equals(
-            "Checking"))
+    if (jalview.bin.Cache.getDefault("LATEST_VERSION", "Checking")
+            .equals("Checking"))
     {
       message.append("<br>...Checking latest version...</br>");
     }
@@ -1301,16 +1498,16 @@ public class Desktop extends jalview.jbgui.GDesktop implements
                       "..Checking..")
               + " is available for download from "
               + jalview.bin.Cache.getDefault("www.jalview.org",
-                      "http://www.jalview.org") + " !!");
+                      "http://www.jalview.org")
+              + " !!");
       if (red)
       {
         message.append("</div>");
       }
     }
-    message.append("<br>Authors:  "
-            + jalview.bin.Cache
-                    .getDefault("AUTHORFNAMES",
-                            "The Jalview Authors (See AUTHORS file for current list)")
+    message.append("<br>Authors:  " + jalview.bin.Cache.getDefault(
+            "AUTHORFNAMES",
+            "The Jalview Authors (See AUTHORS file for current list)")
             + "<br><br>Development managed by The Barton Group, University of Dundee, Scotland, UK.<br>"
             + "<br><br>For help, see the FAQ at <a href=\"http://www.jalview.org/faq\">www.jalview.org/faq</a> and/or join the jalview-discuss@jalview.org mailing list"
             + "<br><br>If  you use Jalview, please cite:"
@@ -1341,6 +1538,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements
   @Override
   public void closeAll_actionPerformed(ActionEvent e)
   {
+    // TODO show a progress bar while closing?
     JInternalFrame[] frames = desktop.getAllFrames();
     for (int i = 0; i < frames.length; i++)
     {
@@ -1351,6 +1549,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements
       {
       }
     }
+    Jalview.setCurrentAlignFrame(null);
     System.out.println("ALL CLOSED");
     if (v_client != null)
     {
@@ -1438,8 +1637,8 @@ public class Desktop extends jalview.jbgui.GDesktop implements
   {
     showConsole.setSelected(selected);
     // TODO: decide if we should update properties file
-    Cache.setProperty("SHOW_JAVA_CONSOLE", Boolean.valueOf(selected)
-            .toString());
+    Cache.setProperty("SHOW_JAVA_CONSOLE",
+            Boolean.valueOf(selected).toString());
     jconsole.setVisible(selected);
   }
 
@@ -1533,17 +1732,13 @@ public class Desktop extends jalview.jbgui.GDesktop implements
   }
 
   /**
-   * DOCUMENT ME!
-   * 
-   * @param e
-   *          DOCUMENT ME!
+   * Shows a file chooser dialog and writes out the current session as a Jalview
+   * project file
    */
   @Override
-  public void saveState_actionPerformed(ActionEvent e)
+  public void saveState_actionPerformed()
   {
-    JalviewFileChooser chooser = new JalviewFileChooser(
-            jalview.bin.Cache.getProperty("LAST_DIRECTORY"),
-            new String[] { "jvp" }, new String[] { "Jalview Project" },
+    JalviewFileChooser chooser = new JalviewFileChooser("jvp",
             "Jalview Project");
 
     chooser.setFileView(new JalviewFileView());
@@ -1564,8 +1759,8 @@ public class Desktop extends jalview.jbgui.GDesktop implements
         {
           // TODO: refactor to Jalview desktop session controller action.
           setProgressBar(MessageManager.formatMessage(
-                  "label.saving_jalview_project",
-                  new Object[] { choice.getName() }), choice.hashCode());
+                  "label.saving_jalview_project", new Object[]
+                  { choice.getName() }), choice.hashCode());
           jalview.bin.Cache.setProperty("LAST_DIRECTORY",
                   choice.getParent());
           // TODO catch and handle errors for savestate
@@ -1575,18 +1770,21 @@ public class Desktop extends jalview.jbgui.GDesktop implements
             new Jalview2XML().saveState(choice);
           } catch (OutOfMemoryError oom)
           {
-            new OOMWarning("Whilst saving current state to "
-                    + choice.getName(), oom);
+            new OOMWarning(
+                    "Whilst saving current state to " + choice.getName(),
+                    oom);
           } catch (Exception ex)
           {
             Cache.log.error(
                     "Problems whilst trying to save to " + choice.getName(),
                     ex);
-            JOptionPane.showMessageDialog(me, MessageManager.formatMessage(
-                    "label.error_whilst_saving_current_state_to",
-                    new Object[] { choice.getName() }), MessageManager
-                    .getString("label.couldnt_save_project"),
-                    JOptionPane.WARNING_MESSAGE);
+            JvOptionPane.showMessageDialog(me,
+                    MessageManager.formatMessage(
+                            "label.error_whilst_saving_current_state_to",
+                            new Object[]
+                            { choice.getName() }),
+                    MessageManager.getString("label.couldnt_save_project"),
+                    JvOptionPane.WARNING_MESSAGE);
           }
           setProgressBar(null, choice.hashCode());
         }
@@ -1605,18 +1803,19 @@ public class Desktop extends jalview.jbgui.GDesktop implements
   }
 
   /**
-   * DOCUMENT ME!
-   * 
-   * @param e
-   *          DOCUMENT ME!
+   * Shows a file chooser dialog and tries to read in the selected file as a
+   * Jalview project
    */
   @Override
-  public void loadState_actionPerformed(ActionEvent e)
+  public void loadState_actionPerformed()
   {
+    final String[] suffix = new String[] { "jvp", "jar" };
+    final String[] desc = new String[] { "Jalview Project",
+        "Jalview Project (old)" };
     JalviewFileChooser chooser = new JalviewFileChooser(
-            jalview.bin.Cache.getProperty("LAST_DIRECTORY"), new String[] {
-                "jvp", "jar" }, new String[] { "Jalview Project",
-                "Jalview Project (old)" }, "Jalview Project");
+            Cache.getProperty("LAST_DIRECTORY"), suffix,
+            desc,
+            "Jalview Project");
     chooser.setFileView(new JalviewFileView());
     chooser.setDialogTitle(MessageManager.getString("label.restore_state"));
 
@@ -1627,17 +1826,15 @@ public class Desktop extends jalview.jbgui.GDesktop implements
       final File selectedFile = chooser.getSelectedFile();
       setProjectFile(selectedFile);
       final String choice = selectedFile.getAbsolutePath();
-      jalview.bin.Cache.setProperty("LAST_DIRECTORY",
-              selectedFile.getParent());
+      Cache.setProperty("LAST_DIRECTORY", selectedFile.getParent());
       new Thread(new Runnable()
       {
         @Override
         public void run()
         {
-          setProgressBar(
-                  MessageManager.formatMessage(
-                          "label.loading_jalview_project",
-                          new Object[] { choice }), choice.hashCode());
+          setProgressBar(MessageManager.formatMessage(
+                  "label.loading_jalview_project", new Object[]
+                  { choice }), choice.hashCode());
           try
           {
             new Jalview2XML().loadJalviewAlign(choice);
@@ -1646,14 +1843,15 @@ public class Desktop extends jalview.jbgui.GDesktop implements
             new OOMWarning("Whilst loading project from " + choice, oom);
           } catch (Exception ex)
           {
-            Cache.log.error("Problems whilst loading project from "
-                    + choice, ex);
-            JOptionPane.showMessageDialog(Desktop.desktop, MessageManager
-                    .formatMessage(
+            Cache.log.error(
+                    "Problems whilst loading project from " + choice, ex);
+            JvOptionPane.showMessageDialog(Desktop.desktop,
+                    MessageManager.formatMessage(
                             "label.error_whilst_loading_project_from",
-                            new Object[] { choice }), MessageManager
-                    .getString("label.couldnt_load_project"),
-                    JOptionPane.WARNING_MESSAGE);
+                            new Object[]
+                            { choice }),
+                    MessageManager.getString("label.couldnt_load_project"),
+                    JvOptionPane.WARNING_MESSAGE);
           }
           setProgressBar(null, choice.hashCode());
         }
@@ -1669,14 +1867,15 @@ public class Desktop extends jalview.jbgui.GDesktop implements
 
   JPanel progressPanel;
 
-  ArrayList<JPanel> fileLoadingPanels = new ArrayList<JPanel>();
+  ArrayList<JPanel> fileLoadingPanels = new ArrayList<>();
 
   public void startLoading(final String fileName)
   {
     if (fileLoadingCount == 0)
     {
-      fileLoadingPanels.add(addProgressPanel(MessageManager.formatMessage(
-              "label.loading_file", new Object[] { fileName })));
+      fileLoadingPanels.add(addProgressPanel(MessageManager
+              .formatMessage("label.loading_file", new Object[]
+              { fileName })));
     }
     fileLoadingCount++;
   }
@@ -1697,8 +1896,8 @@ public class Desktop extends jalview.jbgui.GDesktop implements
 
     thisprogress.add(progressBar, BorderLayout.CENTER);
     progressPanel.add(thisprogress);
-    ((GridLayout) progressPanel.getLayout())
-            .setRows(((GridLayout) progressPanel.getLayout()).getRows() + 1);
+    ((GridLayout) progressPanel.getLayout()).setRows(
+            ((GridLayout) progressPanel.getLayout()).getRows() + 1);
     ++totalProgressCount;
     instance.validate();
     return thisprogress;
@@ -1760,7 +1959,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements
       // TODO: verify that frames are recoverable when in headless mode
       return null;
     }
-    List<AlignmentPanel> aps = new ArrayList<AlignmentPanel>();
+    List<AlignmentPanel> aps = new ArrayList<>();
     AlignFrame[] frames = getAlignFrames();
     if (frames == null)
     {
@@ -1795,16 +1994,15 @@ public class Desktop extends jalview.jbgui.GDesktop implements
    */
   public static AlignmentViewport[] getViewports(String sequenceSetId)
   {
-    List<AlignmentViewport> viewp = new ArrayList<AlignmentViewport>();
+    List<AlignmentViewport> viewp = new ArrayList<>();
     if (desktop != null)
     {
       AlignFrame[] frames = Desktop.getAlignFrames();
 
       for (AlignFrame afr : frames)
       {
-        if (sequenceSetId == null
-                || afr.getViewport().getSequenceSetId()
-                        .equals(sequenceSetId))
+        if (sequenceSetId == null || afr.getViewport().getSequenceSetId()
+                .equals(sequenceSetId))
         {
           if (afr.alignPanels != null)
           {
@@ -1836,7 +2034,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements
    * 
    * @param af
    */
-  public void explodeViews(AlignFrame af)
+  public static void explodeViews(AlignFrame af)
   {
     int size = af.alignPanels.size();
     if (size < 2)
@@ -1926,10 +2124,10 @@ public class Desktop extends jalview.jbgui.GDesktop implements
               jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
 
       chooser.setFileView(new JalviewFileView());
-      chooser.setDialogTitle(MessageManager
-              .getString("label.open_saved_vamsas_session"));
-      chooser.setToolTipText(MessageManager
-              .getString("label.select_vamsas_session_opened_as_new_vamsas_session"));
+      chooser.setDialogTitle(
+              MessageManager.getString("label.open_saved_vamsas_session"));
+      chooser.setToolTipText(MessageManager.getString(
+              "label.select_vamsas_session_opened_as_new_vamsas_session"));
 
       int value = chooser.showOpenDialog(this);
 
@@ -1938,22 +2136,21 @@ public class Desktop extends jalview.jbgui.GDesktop implements
         String fle = chooser.getSelectedFile().toString();
         if (!vamsasImport(chooser.getSelectedFile()))
         {
-          JOptionPane
-                  .showInternalMessageDialog(
-                          Desktop.desktop,
-                          MessageManager.formatMessage(
-                                  "label.couldnt_import_as_vamsas_session",
-                                  new Object[] { fle }),
-                          MessageManager
-                                  .getString("label.vamsas_document_import_failed"),
-                          JOptionPane.ERROR_MESSAGE);
+          JvOptionPane.showInternalMessageDialog(Desktop.desktop,
+                  MessageManager.formatMessage(
+                          "label.couldnt_import_as_vamsas_session",
+                          new Object[]
+                          { fle }),
+                  MessageManager
+                          .getString("label.vamsas_document_import_failed"),
+                  JvOptionPane.ERROR_MESSAGE);
         }
       }
     }
     else
     {
-      jalview.bin.Cache.log
-              .error("Implementation error - load session from a running session is not supported.");
+      jalview.bin.Cache.log.error(
+              "Implementation error - load session from a running session is not supported.");
     }
   }
 
@@ -1969,8 +2166,8 @@ public class Desktop extends jalview.jbgui.GDesktop implements
     if (v_client != null)
     {
 
-      jalview.bin.Cache.log
-              .error("Implementation error - load session from a running session is not supported.");
+      jalview.bin.Cache.log.error(
+              "Implementation error - load session from a running session is not supported.");
       return false;
     }
 
@@ -1995,7 +2192,8 @@ public class Desktop extends jalview.jbgui.GDesktop implements
     {
       jalview.bin.Cache.log.error(
               "Failed to create new vamsas session from contents of URL "
-                      + url, ex);
+                      + url,
+              ex);
       return false;
     }
     setupVamsasConnectedGui();
@@ -2014,22 +2212,22 @@ public class Desktop extends jalview.jbgui.GDesktop implements
     if (v_client != null)
     {
 
-      jalview.bin.Cache.log
-              .error("Implementation error - load session from a running session is not supported.");
+      jalview.bin.Cache.log.error(
+              "Implementation error - load session from a running session is not supported.");
       return false;
     }
 
     setProgressBar(MessageManager.formatMessage(
-            "status.importing_vamsas_session_from",
-            new Object[] { file.getName() }), file.hashCode());
+            "status.importing_vamsas_session_from", new Object[]
+            { file.getName() }), file.hashCode());
     try
     {
       v_client = new jalview.gui.VamsasApplication(this, file, null);
     } catch (Exception ex)
     {
       setProgressBar(MessageManager.formatMessage(
-              "status.importing_vamsas_session_from",
-              new Object[] { file.getName() }), file.hashCode());
+              "status.importing_vamsas_session_from", new Object[]
+              { file.getName() }), file.hashCode());
       jalview.bin.Cache.log.error(
               "New vamsas session from existing session file failed:", ex);
       return false;
@@ -2037,8 +2235,8 @@ public class Desktop extends jalview.jbgui.GDesktop implements
     setupVamsasConnectedGui();
     v_client.initial_update(); // TODO: thread ?
     setProgressBar(MessageManager.formatMessage(
-            "status.importing_vamsas_session_from",
-            new Object[] { file.getName() }), file.hashCode());
+            "status.importing_vamsas_session_from", new Object[]
+            { file.getName() }), file.hashCode());
     return v_client.inSession();
   }
 
@@ -2046,9 +2244,8 @@ public class Desktop extends jalview.jbgui.GDesktop implements
   {
     if (v_client != null)
     {
-      throw new Error(
-              MessageManager
-                      .getString("error.try_join_vamsas_session_another"));
+      throw new Error(MessageManager
+              .getString("error.try_join_vamsas_session_another"));
     }
     if (mysesid == null)
     {
@@ -2106,8 +2303,8 @@ public class Desktop extends jalview.jbgui.GDesktop implements
     vamsasSave.setVisible(false);
     vamsasStop.setVisible(false);
     vamsasImport.setVisible(true);
-    vamsasStart.setText(MessageManager
-            .getString("label.new_vamsas_session"));
+    vamsasStart
+            .setText(MessageManager.getString("label.new_vamsas_session"));
   }
 
   @Override
@@ -2131,21 +2328,22 @@ public class Desktop extends jalview.jbgui.GDesktop implements
         sess = VamsasApplication.getSessionList();
       } catch (Exception e)
       {
-        jalview.bin.Cache.log.warn(
-                "Problem getting current sessions list.", e);
+        jalview.bin.Cache.log.warn("Problem getting current sessions list.",
+                e);
         sess = null;
       }
       if (sess != null)
       {
-        jalview.bin.Cache.log.debug("Got current sessions list: "
-                + sess.length + " entries.");
+        jalview.bin.Cache.log.debug(
+                "Got current sessions list: " + sess.length + " entries.");
         VamsasStMenu.removeAll();
         for (int i = 0; i < sess.length; i++)
         {
           JMenuItem sessit = new JMenuItem();
           sessit.setText(sess[i]);
-          sessit.setToolTipText(MessageManager.formatMessage(
-                  "label.connect_to_session", new Object[] { sess[i] }));
+          sessit.setToolTipText(MessageManager
+                  .formatMessage("label.connect_to_session", new Object[]
+                  { sess[i] }));
           final Desktop dsktp = this;
           final String mysesid = sess[i];
           sessit.addActionListener(new ActionListener()
@@ -2197,10 +2395,9 @@ public class Desktop extends jalview.jbgui.GDesktop implements
   {
     if (v_client != null)
     {
-      JalviewFileChooser chooser = new JalviewFileChooser(
-              jalview.bin.Cache.getProperty("LAST_DIRECTORY"), new String[]
-              { "vdj" }, // TODO: VAMSAS DOCUMENT EXTENSION is VDJ
-              new String[] { "Vamsas Document" }, "Vamsas Document");
+      // TODO: VAMSAS DOCUMENT EXTENSION is VDJ
+      JalviewFileChooser chooser = new JalviewFileChooser("vdj",
+              "Vamsas Document");
 
       chooser.setFileView(new JalviewFileView());
       chooser.setDialogTitle(MessageManager
@@ -2211,10 +2408,10 @@ public class Desktop extends jalview.jbgui.GDesktop implements
       if (value == JalviewFileChooser.APPROVE_OPTION)
       {
         java.io.File choice = chooser.getSelectedFile();
-        JPanel progpanel = addProgressPanel(MessageManager.formatMessage(
-                "label.saving_vamsas_doc",
-                new Object[] { choice.getName() }));
-        jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice.getParent());
+        JPanel progpanel = addProgressPanel(MessageManager
+                .formatMessage("label.saving_vamsas_doc", new Object[]
+                { choice.getName() }));
+        Cache.setProperty("LAST_DIRECTORY", choice.getParent());
         String warnmsg = null;
         String warnttl = null;
         try
@@ -2224,23 +2421,23 @@ public class Desktop extends jalview.jbgui.GDesktop implements
         {
           warnttl = "Serious Problem saving Vamsas Document";
           warnmsg = ex.toString();
-          jalview.bin.Cache.log.error("Error Whilst saving document to "
-                  + choice, ex);
+          jalview.bin.Cache.log
+                  .error("Error Whilst saving document to " + choice, ex);
 
         } catch (Exception ex)
         {
           warnttl = "Problem saving Vamsas Document.";
           warnmsg = ex.toString();
-          jalview.bin.Cache.log.warn("Exception Whilst saving document to "
-                  + choice, ex);
+          jalview.bin.Cache.log.warn(
+                  "Exception Whilst saving document to " + choice, ex);
 
         }
         removeProgressPanel(progpanel);
         if (warnmsg != null)
         {
-          JOptionPane.showInternalMessageDialog(Desktop.desktop,
+          JvOptionPane.showInternalMessageDialog(Desktop.desktop,
 
-          warnmsg, warnttl, JOptionPane.ERROR_MESSAGE);
+                  warnmsg, warnttl, JvOptionPane.ERROR_MESSAGE);
         }
       }
     }
@@ -2256,7 +2453,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements
    */
   public void setVamsasUpdate(boolean b)
   {
-    jalview.bin.Cache.log.debug("Setting gui for Vamsas update "
+    Cache.log.debug("Setting gui for Vamsas update "
             + (b ? "in progress" : "finished"));
 
     if (vamUpdate != null)
@@ -2265,8 +2462,8 @@ public class Desktop extends jalview.jbgui.GDesktop implements
     }
     if (b)
     {
-      vamUpdate = this.addProgressPanel(MessageManager
-              .getString("label.updating_vamsas_session"));
+      vamUpdate = this.addProgressPanel(
+              MessageManager.getString("label.updating_vamsas_session"));
     }
     vamsasStart.setVisible(!b);
     vamsasStop.setVisible(!b);
@@ -2291,6 +2488,85 @@ public class Desktop extends jalview.jbgui.GDesktop implements
     new Thread(jvq).start();
   }
 
+  public void checkURLLinks()
+  {
+    // Thread off the URL link checker
+    addDialogThread(new Runnable()
+    {
+      @Override
+      public void run()
+      {
+        if (Cache.getDefault("CHECKURLLINKS", true))
+        {
+          // check what the actual links are - if it's just the default don't
+          // bother with the warning
+          List<String> links = Preferences.sequenceUrlLinks
+                  .getLinksForMenu();
+
+          // only need to check links if there is one with a
+          // SEQUENCE_ID which is not the default EMBL_EBI link
+          ListIterator<String> li = links.listIterator();
+          boolean check = false;
+          List<JLabel> urls = new ArrayList<>();
+          while (li.hasNext())
+          {
+            String link = li.next();
+            if (link.contains(jalview.util.UrlConstants.SEQUENCE_ID)
+                    && !UrlConstants.isDefaultString(link))
+            {
+              check = true;
+              int barPos = link.indexOf("|");
+              String urlMsg = barPos == -1 ? link
+                      : link.substring(0, barPos) + ": "
+                              + link.substring(barPos + 1);
+              urls.add(new JLabel(urlMsg));
+            }
+          }
+          if (!check)
+          {
+            return;
+          }
+
+          // ask user to check in case URL links use old style tokens
+          // ($SEQUENCE_ID$ for sequence id _or_ accession id)
+          JPanel msgPanel = new JPanel();
+          msgPanel.setLayout(new BoxLayout(msgPanel, BoxLayout.PAGE_AXIS));
+          msgPanel.add(Box.createVerticalGlue());
+          JLabel msg = new JLabel(MessageManager
+                  .getString("label.SEQUENCE_ID_for_DB_ACCESSION1"));
+          JLabel msg2 = new JLabel(MessageManager
+                  .getString("label.SEQUENCE_ID_for_DB_ACCESSION2"));
+          msgPanel.add(msg);
+          for (JLabel url : urls)
+          {
+            msgPanel.add(url);
+          }
+          msgPanel.add(msg2);
+
+          final JCheckBox jcb = new JCheckBox(
+                  MessageManager.getString("label.do_not_display_again"));
+          jcb.addActionListener(new ActionListener()
+          {
+            @Override
+            public void actionPerformed(ActionEvent e)
+            {
+              // update Cache settings for "don't show this again"
+              boolean showWarningAgain = !jcb.isSelected();
+              Cache.setProperty("CHECKURLLINKS",
+                      Boolean.valueOf(showWarningAgain).toString());
+            }
+          });
+          msgPanel.add(jcb);
+
+          JvOptionPane.showMessageDialog(Desktop.desktop, msgPanel,
+                  MessageManager
+                          .getString("label.SEQUENCE_ID_no_longer_used"),
+                  JvOptionPane.WARNING_MESSAGE);
+        }
+      }
+    });
+  }
+
   /**
    * Proxy class for JDesktopPane which optionally displays the current memory
    * usage and highlights the desktop area with a red bar if free memory runs
@@ -2325,6 +2601,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements
         Thread worker = new Thread(this);
         worker.start();
       }
+      repaint();
     }
 
     public boolean isShowMemoryUsage()
@@ -2378,28 +2655,17 @@ public class Desktop extends jalview.jbgui.GDesktop implements
         FontMetrics fm = g.getFontMetrics();
         if (fm != null)
         {
-          g.drawString(MessageManager.formatMessage(
-                  "label.memory_stats",
-                  new Object[] { df.format(totalFreeMemory),
-                      df.format(maxMemory), df.format(percentUsage) }), 10,
-                  getHeight() - fm.getHeight());
+          g.drawString(MessageManager.formatMessage("label.memory_stats",
+                  new Object[]
+                  { df.format(totalFreeMemory), df.format(maxMemory),
+                      df.format(percentUsage) }),
+                  10, getHeight() - fm.getHeight());
         }
       }
     }
   }
 
   /**
-   * fixes stacking order after a modal dialog to ensure windows that should be
-   * on top actually are
-   */
-  public void relayerWindows()
-  {
-
-  }
-
-  protected JMenuItem groovyShell;
-
-  /**
    * Accessor method to quickly get all the AlignmentFrames loaded.
    * 
    * @return an array of AlignFrame, or null if none found
@@ -2409,7 +2675,7 @@ 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();
@@ -2418,7 +2684,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements
     {
       return null;
     }
-    List<AlignFrame> avp = new ArrayList<AlignFrame>();
+    List<AlignFrame> avp = new ArrayList<>();
     // REVERSE ORDER
     for (int i = frames.length - 1; i > -1; i--)
     {
@@ -2463,7 +2729,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements
     {
       return null;
     }
-    List<GStructureViewer> avp = new ArrayList<GStructureViewer>();
+    List<GStructureViewer> avp = new ArrayList<>();
     // REVERSE ORDER
     for (int i = frames.length - 1; i > -1; i--)
     {
@@ -2484,6 +2750,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements
   /**
    * Add Groovy Support to Jalview
    */
+  @Override
   public void groovyShell_actionPerformed()
   {
     try
@@ -2492,11 +2759,11 @@ public class Desktop extends jalview.jbgui.GDesktop implements
     } catch (Exception ex)
     {
       jalview.bin.Cache.log.error("Groovy Shell Creation failed.", ex);
-      JOptionPane.showInternalMessageDialog(Desktop.desktop,
+      JvOptionPane.showInternalMessageDialog(Desktop.desktop,
 
-      MessageManager.getString("label.couldnt_create_groovy_shell"),
+              MessageManager.getString("label.couldnt_create_groovy_shell"),
               MessageManager.getString("label.groovy_support_failed"),
-              JOptionPane.ERROR_MESSAGE);
+              JvOptionPane.ERROR_MESSAGE);
     }
   }
 
@@ -2505,50 +2772,79 @@ public class Desktop extends jalview.jbgui.GDesktop implements
    */
   void openGroovyConsole()
   {
-    groovyConsole = new groovy.ui.Console();
+    if (groovyConsole == null)
+    {
+      groovyConsole = new groovy.ui.Console();
+      groovyConsole.setVariable("Jalview", this);
+      groovyConsole.run();
 
-    /*
-     * bind groovy variable 'Jalview' to the Desktop object
-     */
-    groovyConsole.setVariable("Jalview", this);
+      /*
+       * 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);
+        }
+      });
+    }
 
     /*
-     * start the console
+     * show Groovy console window (after close and reopen)
      */
-    groovyConsole.run();
+    ((Window) groovyConsole.getFrame()).setVisible(true);
 
     /*
-     * Allow only one console at a time, so that the AlignFrame menu option
-     * 'Calculate | Run Groovy script' is unambiguous.
-     * Disable 'new console', and enable 'Run script', when the console is 
-     * opened, and the reverse when it is closed
+     * if we got this far, enable 'Run Groovy' in AlignFrame menus
+     * and disable opening a second console
      */
-    Window window = (Window) groovyConsole.getFrame();
-    window.addWindowListener(new WindowAdapter()
+    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 windowClosed(WindowEvent e)
+      public void actionPerformed(ActionEvent e)
       {
-        groovyShell.setEnabled(true);
-        enableExecuteGroovy(false);
+        quit();
       }
     });
-
-    /*
-     * if we got this far, enable 'Run Groovy' in AlignFrame menus
-     * and disable opening a second console
-     */
-    groovyShell.setEnabled(false);
-    enableExecuteGroovy(true);
   }
 
   /**
    * 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)
     {
@@ -2576,8 +2872,8 @@ public class Desktop extends jalview.jbgui.GDesktop implements
   {
     if (progressBars == null)
     {
-      progressBars = new Hashtable<Long, JPanel>();
-      progressBarHandlers = new Hashtable<Long, IProgressIndicatorHandler>();
+      progressBars = new Hashtable<>();
+      progressBarHandlers = new Hashtable<>();
     }
 
     if (progressBars.get(new Long(id)) != null)
@@ -2608,9 +2904,8 @@ public class Desktop extends jalview.jbgui.GDesktop implements
     if (progressBarHandlers == null
             || !progressBars.containsKey(new Long(id)))
     {
-      throw new Error(
-              MessageManager
-                      .getString("error.call_setprogressbar_before_registering_handler"));
+      throw new Error(MessageManager.getString(
+              "error.call_setprogressbar_before_registering_handler"));
     }
     progressBarHandlers.put(new Long(id), handler);
     final JPanel progressPanel = progressBars.get(new Long(id));
@@ -2626,10 +2921,10 @@ public class Desktop extends jalview.jbgui.GDesktop implements
         public void actionPerformed(ActionEvent e)
         {
           handler.cancelActivity(id);
-          us.setProgressBar(MessageManager.formatMessage(
-                  "label.cancelled_params",
-                  new Object[] { ((JLabel) progressPanel.getComponent(0))
-                          .getText() }), id);
+          us.setProgressBar(MessageManager
+                  .formatMessage("label.cancelled_params", new Object[]
+                  { ((JLabel) progressPanel.getComponent(0)).getText() }),
+                  id);
         }
       });
       progressPanel.add(cancel, BorderLayout.EAST);
@@ -2662,7 +2957,8 @@ public class Desktop extends jalview.jbgui.GDesktop implements
   {
     if (desktop != null)
     {
-      AlignmentPanel[] aps = getAlignmentPanels(viewport.getSequenceSetId());
+      AlignmentPanel[] aps = getAlignmentPanels(
+              viewport.getSequenceSetId());
       for (int panel = 0; aps != null && panel < aps.length; panel++)
       {
         if (aps[panel] != null && aps[panel].av == viewport)
@@ -2731,13 +3027,8 @@ public class Desktop extends jalview.jbgui.GDesktop implements
 
     if (Cache.getDefault("SHOW_JWS2_SERVICES", true))
     {
-      if (jalview.ws.jws2.Jws2Discoverer.getDiscoverer().isRunning())
-      {
-        jalview.ws.jws2.Jws2Discoverer.getDiscoverer().setAborted(true);
-      }
-      t2 = jalview.ws.jws2.Jws2Discoverer.getDiscoverer().startDiscoverer(
-              changeSupport);
-
+      t2 = jalview.ws.jws2.Jws2Discoverer.getDiscoverer()
+              .startDiscoverer(changeSupport);
     }
     Thread t3 = null;
     {
@@ -2753,8 +3044,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements
         } catch (Exception e)
         {
         }
-        alive = (t1 != null && t1.isAlive())
-                || (t2 != null && t2.isAlive())
+        alive = (t1 != null && t1.isAlive()) || (t2 != null && t2.isAlive())
                 || (t3 != null && t3.isAlive())
                 || (t0 != null && t0.isAlive());
       }
@@ -2809,20 +3099,16 @@ public class Desktop extends jalview.jbgui.GDesktop implements
                  * 
                  * jd.waitForInput();
                  */
-                JOptionPane
-                        .showConfirmDialog(
-                                Desktop.desktop,
-                                new JLabel(
-                                        "<html><table width=\"450\"><tr><td>"
-                                                + ermsg
-                                                + "</td></tr></table>"
-                                                + "<p>It may be that you have invalid JABA URLs<br/>in your web service preferences,"
-                                                + "<br>or as a command-line argument, or mis-configured HTTP proxy settings.</p>"
-                                                + "<p>Check the <em>Connections</em> and <em>Web services</em> tab<br/>of the"
-                                                + " Tools->Preferences dialog box to change them.</p></html>"),
-                                "Web Service Configuration Problem",
-                                JOptionPane.DEFAULT_OPTION,
-                                JOptionPane.ERROR_MESSAGE);
+                JvOptionPane.showConfirmDialog(Desktop.desktop,
+                        new JLabel("<html><table width=\"450\"><tr><td>"
+                                + ermsg + "</td></tr></table>"
+                                + "<p>It may be that you have invalid JABA URLs<br/>in your web service preferences,"
+                                + "<br>or as a command-line argument, or mis-configured HTTP proxy settings.</p>"
+                                + "<p>Check the <em>Connections</em> and <em>Web services</em> tab<br/>of the"
+                                + " Tools->Preferences dialog box to change them.</p></html>"),
+                        "Web Service Configuration Problem",
+                        JvOptionPane.DEFAULT_OPTION,
+                        JvOptionPane.ERROR_MESSAGE);
                 serviceChangedDialog = null;
 
               }
@@ -2831,8 +3117,8 @@ public class Desktop extends jalview.jbgui.GDesktop implements
         }
         else
         {
-          Cache.log
-                  .error("Errors reported by JABA discovery service. Check web services preferences.\n"
+          Cache.log.error(
+                  "Errors reported by JABA discovery service. Check web services preferences.\n"
                           + ermsg);
         }
       }
@@ -2872,18 +3158,18 @@ public class Desktop extends jalview.jbgui.GDesktop implements
         {
           if (progress != null)
           {
-            progress.setProgressBar(MessageManager.formatMessage(
-                    "status.opening_params", new Object[] { url }), this
-                    .hashCode());
+            progress.setProgressBar(MessageManager
+                    .formatMessage("status.opening_params", new Object[]
+                    { url }), this.hashCode());
           }
           jalview.util.BrowserLauncher.openURL(url);
         } catch (Exception ex)
         {
-          JOptionPane.showInternalMessageDialog(Desktop.desktop,
+          JvOptionPane.showInternalMessageDialog(Desktop.desktop,
                   MessageManager
                           .getString("label.web_browser_not_found_unix"),
                   MessageManager.getString("label.web_browser_not_found"),
-                  JOptionPane.WARNING_MESSAGE);
+                  JvOptionPane.WARNING_MESSAGE);
 
           ex.printStackTrace();
         }
@@ -2930,8 +3216,8 @@ public class Desktop extends jalview.jbgui.GDesktop implements
           }
           else
           {
-            System.err.println("Couldn't handle string " + url
-                    + " as a URL.");
+            System.err.println(
+                    "Couldn't handle string " + url + " as a URL.");
           }
         }
         // ignore any exceptions due to dud links.
@@ -3007,10 +3293,11 @@ public class Desktop extends jalview.jbgui.GDesktop implements
   {
     invalidate();
     File of;
-    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", null, 0, false);
+    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", null, 0, false);
     try
     {
       paintAll(im.getGraphics());
@@ -3123,9 +3410,9 @@ public class Desktop extends jalview.jbgui.GDesktop implements
     AlignFrame myBottomFrame = (AlignFrame) source.getBottomFrame();
     myTopFrame.viewport.setExplodedGeometry(new Rectangle(source.getX(),
             source.getY(), myTopFrame.getWidth(), myTopFrame.getHeight()));
-    myBottomFrame.viewport.setExplodedGeometry(new Rectangle(source.getX(),
-            source.getY(), myBottomFrame.getWidth(), myBottomFrame
-                    .getHeight()));
+    myBottomFrame.viewport
+            .setExplodedGeometry(new Rectangle(source.getX(), source.getY(),
+                    myBottomFrame.getWidth(), myBottomFrame.getHeight()));
     myTopFrame.viewport.setGatherViewsHere(true);
     myBottomFrame.viewport.setGatherViewsHere(true);
     String topViewId = myTopFrame.viewport.getSequenceSetId();
@@ -3150,10 +3437,10 @@ public class Desktop extends jalview.jbgui.GDesktop implements
             gatherThis = true;
             topPanel.av.setGatherViewsHere(false);
             bottomPanel.av.setGatherViewsHere(false);
-            topPanel.av.setExplodedGeometry(new Rectangle(sf.getLocation(),
-                    topFrame.getSize()));
-            bottomPanel.av.setExplodedGeometry(new Rectangle(sf
-                    .getLocation(), bottomFrame.getSize()));
+            topPanel.av.setExplodedGeometry(
+                    new Rectangle(sf.getLocation(), topFrame.getSize()));
+            bottomPanel.av.setExplodedGeometry(
+                    new Rectangle(sf.getLocation(), bottomFrame.getSize()));
             myTopFrame.addAlignmentPanel(topPanel, false);
             myBottomFrame.addAlignmentPanel(bottomPanel, false);
           }
@@ -3172,22 +3459,258 @@ 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)
+  /**
+   * handles the payload of a drag and drop event.
+   * 
+   * TODO refactor to desktop utilities class
+   * 
+   * @param files
+   *          - Data source strings extracted from the drop event
+   * @param protocols
+   *          - protocol for each data source extracted from the drop event
+   * @param evt
+   *          - the drop event
+   * @param t
+   *          - the payload from the drop event
+   * @throws Exception
+   */
+  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"), urlFlavour = null;
+    try
+    {
+      urlFlavour = new DataFlavor(
+              "application/x-java-url; class=java.net.URL");
+    } catch (ClassNotFoundException cfe)
+    {
+      Cache.log.debug("Couldn't instantiate the URL dataflavor.", cfe);
+    }
+
+    if (urlFlavour != null && t.isDataFlavorSupported(urlFlavour))
+    {
+
+      try
+      {
+        java.net.URL url = (URL) t.getTransferData(urlFlavour);
+        // nb: java 8 osx bug https://bugs.openjdk.java.net/browse/JDK-8156099
+        // means url may be null.
+        if (url != null)
+        {
+          protocols.add(DataSourceType.URL);
+          files.add(url.toString());
+          Cache.log.debug("Drop handled as URL dataflavor "
+                  + files.get(files.size() - 1));
+          return;
+        }
+        else
+        {
+          if (Platform.isAMac())
+          {
+            System.err.println(
+                    "Please ignore plist error - occurs due to problem with java 8 on OSX");
+          }
+          ;
+        }
+      } catch (Throwable ex)
+      {
+        Cache.log.debug("URL drop handler failed.", ex);
+      }
+    }
+    if (t.isDataFlavorSupported(DataFlavor.javaFileListFlavor))
+    {
+      // Works on Windows and MacOSX
+      Cache.log.debug("Drop handled as javaFileListFlavor");
+      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
+        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
+        DataFlavor textDf = new DataFlavor(
+                "text/plain;class=java.lang.String");
+        if (t.isDataFlavorSupported(textDf))
+        {
+          data = (String) t.getTransferData(textDf);
+        }
+
+        Cache.log.debug("Plain text drop content returned "
+                + (data == null ? "Null - failed" : data));
+
+      }
+      if (data != null)
+      {
+        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)
+        {
+
+          if (t.getTransferDataFlavors() != null
+                  && t.getTransferDataFlavors().length > 0)
+          {
+            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());
+              Object df = t.getTransferData(fl);
+              if (df != null)
+              {
+                Cache.log.debug("Retrieves: " + df);
+              }
+              else
+              {
+                Cache.log.debug("Retrieved nothing");
+              }
+            }
+          }
+          else
+          {
+            Cache.log.debug("Couldn't resolve dataflavor for drop: "
+                    + t.toString());
+          }
+        }
+      }
+    }
+    if (Platform.isWindows())
+
+    {
+      Cache.log.debug("Scanning dropped content for Windows Link Files");
+
+      // resolve any .lnk files in the file drop
+      for (int f = 0; f < files.size(); f++)
+      {
+        String source = files.get(f).toLowerCase();
+        if (protocols.get(f).equals(DataSourceType.FILE)
+                && (source.endsWith(".lnk") || source.endsWith(".url")
+                        || source.endsWith(".site")))
+        {
+          try
+          {
+            File lf = new File(files.get(f));
+            // process link file to get a URL
+            Cache.log.debug("Found potential link file: " + lf);
+            WindowsShortcut wscfile = new WindowsShortcut(lf);
+            String fullname = wscfile.getRealFilename();
+            protocols.set(f, FormatAdapter.checkProtocol(fullname));
+            files.set(f, fullname);
+            Cache.log.debug("Parsed real filename " + fullname
+                    + " to extract protocol: " + protocols.get(f));
+          } catch (Exception ex)
+          {
+            Cache.log.error(
+                    "Couldn't parse " + files.get(f) + " as a link file.",
+                    ex);
+          }
+        }
+      }
+    }
   }
 
-  public static groovy.ui.Console getGroovyConsole()
+  /**
+   * Sets the Preferences property for experimental features to True or False
+   * depending on the state of the controlling menu item
+   */
+  @Override
+  protected void showExperimental_actionPerformed(boolean selected)
   {
-    return groovyConsole;
+    Cache.setProperty(EXPERIMENTAL_FEATURES, Boolean.toString(selected));
   }
 
+  /**
+   * Answers a (possibly empty) list of any structure viewer frames (currently
+   * for either Jmol or Chimera) which are currently open. This may optionally
+   * be restricted to viewers of a specified class, or viewers linked to a
+   * specified alignment panel.
+   * 
+   * @param apanel
+   *          if not null, only return viewers linked to this panel
+   * @param structureViewerClass
+   *          if not null, only return viewers of this class
+   * @return
+   */
+  public List<StructureViewerBase> getStructureViewers(
+          AlignmentPanel apanel,
+          Class<? extends StructureViewerBase> structureViewerClass)
+  {
+    List<StructureViewerBase> result = new ArrayList<>();
+    JInternalFrame[] frames = Desktop.instance.getAllFrames();
+
+    for (JInternalFrame frame : frames)
+    {
+      if (frame instanceof StructureViewerBase)
+      {
+        if (structureViewerClass == null
+                || structureViewerClass.isInstance(frame))
+        {
+          if (apanel == null
+                  || ((StructureViewerBase) frame).isLinkedWith(apanel))
+          {
+            result.add((StructureViewerBase) frame);
+          }
+        }
+      }
+    }
+    return result;
+  }
 }