X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fgui%2FDesktop.java;h=1f8983f0e8360876ba5f52ca8a1091272bd02d11;hb=45cdda84387bfd8b7383573f9788dd0dd6e70ecd;hp=e4535ff6ccbc7f1542150f8313fb14876b7cfba4;hpb=57dd16688caa6dacaeaf465bab3ee8b6126e1a51;p=jalview.git

diff --git a/src/jalview/gui/Desktop.java b/src/jalview/gui/Desktop.java
index e4535ff..d2f3841 100644
--- a/src/jalview/gui/Desktop.java
+++ b/src/jalview/gui/Desktop.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
- * Copyright (C) 2015 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -22,21 +22,38 @@ package jalview.gui;
 
 import jalview.api.AlignViewportI;
 import jalview.api.AlignmentViewPanel;
+import jalview.api.StructureSelectionManagerProvider;
+import jalview.bin.ApplicationSingletonProvider;
+import jalview.bin.ApplicationSingletonProvider.ApplicationSingletonI;
 import jalview.bin.Cache;
 import jalview.bin.Jalview;
+import jalview.gui.ImageExporter.ImageWriterI;
+import jalview.io.BackupFiles;
+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;
 import jalview.io.JalviewFileChooser;
 import jalview.io.JalviewFileView;
+import jalview.jbgui.GDesktop;
 import jalview.jbgui.GSplitFrame;
 import jalview.jbgui.GStructureViewer;
+import jalview.project.Jalview2XML;
 import jalview.structure.StructureSelectionManager;
-import jalview.util.ImageMaker;
+import jalview.urls.IdOrgSettings;
+import jalview.util.BrowserLauncher;
+import jalview.util.ImageMaker.TYPE;
 import jalview.util.MessageManager;
 import jalview.util.Platform;
+import jalview.util.UrlConstants;
 import jalview.viewmodel.AlignmentViewport;
+import jalview.ws.jws1.Discoverer;
 import jalview.ws.params.ParamManager;
+import jalview.ws.utils.UrlDownloadClient;
 
 import java.awt.BorderLayout;
 import java.awt.Color;
@@ -47,6 +64,7 @@ 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;
@@ -58,33 +76,38 @@ 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.lang.reflect.Constructor;
+import java.io.IOException;
 import java.net.URL;
 import java.util.ArrayList;
 import java.util.Hashtable;
 import java.util.List;
-import java.util.StringTokenizer;
+import java.util.ListIterator;
 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;
@@ -92,16 +115,21 @@ import javax.swing.JFrame;
 import javax.swing.JInternalFrame;
 import javax.swing.JLabel;
 import javax.swing.JMenuItem;
-import javax.swing.JOptionPane;
 import javax.swing.JPanel;
 import javax.swing.JPopupMenu;
 import javax.swing.JProgressBar;
+import javax.swing.JTextField;
+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
  * 
@@ -109,17 +137,28 @@ import javax.swing.event.MenuListener;
  * @author $author$
  * @version $Revision: 1.155 $
  */
-public class Desktop extends jalview.jbgui.GDesktop implements
-        DropTargetListener, ClipboardOwner, IProgressIndicator,
-        jalview.api.StructureSelectionManagerProvider
+@SuppressWarnings("serial")
+public class Desktop extends GDesktop
+        implements DropTargetListener, ClipboardOwner, IProgressIndicator,
+        StructureSelectionManagerProvider, ApplicationSingletonI
 {
 
+  private final static int DEFAULT_MIN_WIDTH = 300;
+
+  private final static int DEFAULT_MIN_HEIGHT = 250;
+
+  private final static int ALIGN_FRAME_DEFAULT_MIN_WIDTH = 600;
+
+  private final static int ALIGN_FRAME_DEFAULT_MIN_HEIGHT = 70;
+
+  private final static String EXPERIMENTAL_FEATURES = "EXPERIMENTAL_FEATURES";
+
   private JalviewChangeSupport changeSupport = new JalviewChangeSupport();
 
   /**
    * news reader - null if it was never started.
    */
-  private BlogReader jvnews = null;
+  BlogReader jvnews = null;
 
   private File projectFile;
 
@@ -158,10 +197,17 @@ public class Desktop extends jalview.jbgui.GDesktop implements
             listener);
   }
 
-  /** Singleton Desktop instance */
-  public static Desktop instance;
+  public static MyDesktopPane getDesktopPane()
+  {
+    Desktop desktop = Desktop.getInstance();
+    return desktop == null ? null : desktop.desktopPane;
+  }
 
-  public static MyDesktopPane desktop;
+  public static StructureSelectionManager getStructureSelectionManager()
+  {
+    return StructureSelectionManager
+            .getStructureSelectionManager(getInstance());
+  }
 
   static int openFrameCount = 0;
 
@@ -169,15 +215,29 @@ public class Desktop extends jalview.jbgui.GDesktop implements
 
   static final int yOffset = 30;
 
-  private static AlignFrame currentAlignFrame;
+  public Discoverer discoverer;
 
-  public static jalview.ws.jws1.Discoverer discoverer;
+  public Object[] jalviewClipboard;
 
-  public static Object[] jalviewClipboard;
+  public boolean internalCopy = false;
 
-  public static boolean internalCopy = false;
+  private static int fileLoadingCount = 0;
 
-  static int fileLoadingCount = 0;
+  public JInternalFrame conservationSlider;
+
+  public JInternalFrame PIDSlider;
+
+  /**
+   * just an instance (for testng, probably); no actual frames
+   * 
+   * This flag, when set true, allows a headless-like operation, with a Desktop
+   * object but no actual frames. Though not headless, this option disallows
+   * dialogs to run in test environments.
+   * 
+   * It is set by invoking the Desktop(true) constructor.
+   * 
+   */
+  boolean instanceOnly;
 
   class MyDesktopManager implements DesktopManager
   {
@@ -189,6 +249,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements
       this.delegate = delegate;
     }
 
+    @Override
     public void activateFrame(JInternalFrame f)
     {
       try
@@ -197,35 +258,41 @@ public class Desktop extends jalview.jbgui.GDesktop implements
       } catch (NullPointerException npe)
       {
         Point p = getMousePosition();
-        instance.showPasteMenu(p.x, p.y);
+        showPasteMenu(p.x, p.y);
       }
     }
 
+    @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 +302,39 @@ public class Desktop extends jalview.jbgui.GDesktop implements
       delegate.dragFrame(f, newX, newY);
     }
 
+    @Override
     public void endDraggingFrame(JComponent f)
     {
       delegate.endDraggingFrame(f);
+      desktopPane.repaint();
     }
 
+    @Override
     public void endResizingFrame(JComponent f)
     {
       delegate.endResizingFrame(f);
+      desktopPane.repaint();
     }
 
+    @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 +351,7 @@ 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)
     {
@@ -286,153 +362,238 @@ public class Desktop extends jalview.jbgui.GDesktop implements
 
   }
 
+  public MyDesktopPane desktopPane;
+
   /**
-   * Creates a new Desktop object.
+   * Answers an 'application scope' singleton instance of this class. Separate
+   * SwingJS 'applets' running in the same browser page will each have a
+   * distinct instance of Desktop.
+   * 
+   * @return
    */
-  public Desktop()
+  public static Desktop getInstance()
   {
-    /**
-     * A note to implementors. It is ESSENTIAL that any activities that might
-     * block are spawned off as threads rather than waited for during this
-     * constructor.
-     */
-    instance = this;
-    doVamsasClientCheck();
-    doGroovyCheck();
-    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);
-    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();
-    // sp.getViewport().setView(desktop);
-    // getContentPane().add(sp, BorderLayout.CENTER);
-    getContentPane().add(desktop, BorderLayout.CENTER);
-    desktop.setDragMode(JDesktopPane.OUTLINE_DRAG_MODE);
-
-    // This line prevents Windows Look&Feel resizing all new windows to maximum
-    // if previous window was maximised
-    desktop.setDesktopManager(new MyDesktopManager(
-            new DefaultDesktopManager()));
-
-    Rectangle dims = getLastKnownDimensions("");
-    if (dims != null)
-    {
-      setBounds(dims);
-    }
-    else
+    return Jalview.isHeadlessMode() ? null
+            : (Desktop) ApplicationSingletonProvider
+                    .getInstance(Desktop.class);
+  }
+
+  /**
+   * For TestNG, this constructor can be utilized to allow the creation of a
+   * singleton Desktop instance without the formation of frames and, especially,
+   * not involving dialogs. Cache.log is also initialized for some tests that
+   * require it despite there being no Desktop.
+   * 
+   * @param forInstance
+   */
+  public Desktop(boolean forInstance)
+  {
+    ApplicationSingletonProvider.setInstance(Desktop.class, this);
+    Cache.initLogger();
+    instanceOnly = true;
+  }
+  
+  /**
+   * Private constructor enforces singleton pattern. It is called by reflection
+   * from ApplicationSingletonProvider.getInstance().
+   */
+  @SuppressWarnings("unused")
+  private Desktop()
+  {
+    Cache.initLogger();
+    try
     {
-      Dimension screenSize = Toolkit.getDefaultToolkit().getScreenSize();
-      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"));
+      /**
+       * A note to implementors. It is ESSENTIAL that any activities that might
+       * block are spawned off as threads rather than waited for during this
+       * constructor.
+       */
+      if (!Platform.isJS())
+      {
+        doVamsasClientCheck();
+      }
 
-    showConsole(showjconsole);
+      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);
+      desktopPane = new MyDesktopPane(selmemusage);
 
-    showNews.setVisible(false);
+      showMemusage.setSelected(selmemusage);
+      desktopPane.setBackground(Color.white);
+      getContentPane().setLayout(new BorderLayout());
+      // alternate config - have scrollbars - see notes in JAL-153
+      // JScrollPane sp = new JScrollPane();
+      // sp.getViewport().setView(desktop);
+      // getContentPane().add(sp, BorderLayout.CENTER);
 
-    this.addWindowListener(new WindowAdapter()
-    {
-      public void windowClosing(WindowEvent evt)
+      // BH 2018 - just an experiment to try unclipped JInternalFrames.
+      if (Platform.isJS())
       {
-        quit();
+        getRootPane().putClientProperty("swingjs.overflow.hidden", "false");
       }
-    });
 
-    MouseAdapter ma;
-    this.addMouseListener(ma = new MouseAdapter()
-    {
-      public void mousePressed(MouseEvent evt)
+      getContentPane().add(desktopPane, BorderLayout.CENTER);
+      desktopPane.setDragMode(JDesktopPane.OUTLINE_DRAG_MODE);
+
+      // This line prevents Windows Look&Feel resizing all new windows to
+      // maximum
+      // if previous window was maximised
+      desktopPane.setDesktopManager(new MyDesktopManager(
+              (Platform.isWindowsAndNotJS() ? new DefaultDesktopManager()
+                      : Platform.isAMacAndNotJS()
+                              ? new AquaInternalFrameManager(
+                                      desktopPane.getDesktopManager())
+                              : desktopPane.getDesktopManager())));
+
+      Rectangle dims = getLastKnownDimensions("");
+      if (dims != null)
       {
-        if (SwingUtilities.isRightMouseButton(evt))
-        {
-          showPasteMenu(evt.getX(), evt.getY());
-        }
+        setBounds(dims);
+      }
+      else
+      {
+        Dimension screenSize = Toolkit.getDefaultToolkit().getScreenSize();
+        int xPos = Math.max(5, (screenSize.width - 900) / 2);
+        int yPos = Math.max(5, (screenSize.height - 650) / 2);
+        setBounds(xPos, yPos, 900, 650);
       }
-    });
-    desktop.addMouseListener(ma);
 
-    this.addFocusListener(new FocusListener()
-    {
+      // Note that this next syntax, checking for Platform.isJS and also
+      // escaping the code using @j2sIgnore, serves two purposes. It gives
+      // us an easily findable tag, Platform.isJS(), to places in the code where
+      // there is something different about the SwingJS implementation. Second,
+      // it deletes the unneeded Java-only code form the JavaScript version
+      // completely (@j2sIgnore), since it will never be used there.
 
-      @Override
-      public void focusLost(FocusEvent e)
+      if (!Platform.isJS())
+      /**
+       * Java only
+       * 
+       * @j2sIgnore
+       */
       {
-        // TODO Auto-generated method stub
 
-      }
+        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"));
+
+        showConsole(showjconsole);
+
+        showNews.setVisible(false);
+
+        experimentalFeatures.setSelected(showExperimental());
+
+        getIdentifiersOrgData();
+
+        checkURLLinks();
+
+        // Spawn a thread that shows the splashscreen
+
+        SwingUtilities.invokeLater(new Runnable()
+        {
+          @Override
+          public void run()
+          {
+            new SplashScreen();
+          }
+        });
+
+        // Thread off a new instance of the file chooser - this reduces the time
+        // it
+        // takes to open it later on.
+        new Thread(new Runnable()
+        {
+          @Override
+          public void run()
+          {
+            Cache.log.debug("Filechooser init thread started.");
+            String fileFormat = Cache.getProperty("DEFAULT_FILE_FORMAT");
+            JalviewFileChooser.forRead(Cache.getProperty("LAST_DIRECTORY"),
+                    fileFormat);
+            Cache.log.debug("Filechooser init thread finished.");
+          }
+        }).start();
+        // Add the service change listener
+        changeSupport.addJalviewPropertyChangeListener("services",
+                new PropertyChangeListener()
+                {
+
+                  @Override
+                  public void propertyChange(PropertyChangeEvent evt)
+                  {
+                    Cache.log.debug("Firing service changed event for "
+                            + evt.getNewValue());
+                    JalviewServicesChanged(evt);
+                  }
+
+                });
 
-      @Override
-      public void focusGained(FocusEvent e)
-      {
-        Cache.log.debug("Relaying windows after focus gain");
-        // make sure that we sort windows properly after we gain focus
-        instance.relayerWindows();
       }
-    });
-    this.setDropTarget(new java.awt.dnd.DropTarget(desktop, this));
-    // Spawn a thread that shows the splashscreen
-    SwingUtilities.invokeLater(new Runnable()
-    {
-      public void run()
+
+      this.setDropTarget(new java.awt.dnd.DropTarget(desktopPane, this));
+
+      this.addWindowListener(new WindowAdapter()
       {
-        new SplashScreen();
-      }
-    });
+        @Override
+        public void windowClosing(WindowEvent evt)
+        {
+          quit();
+        }
+      });
 
-    // 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()
-    {
-      public void run()
+      MouseAdapter ma;
+      this.addMouseListener(ma = new MouseAdapter()
       {
-        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"));
-        Cache.log.debug("Filechooser init thread finished.");
-      }
-    }).start();
-    // Add the service change listener
-    changeSupport.addJalviewPropertyChangeListener("services",
-            new PropertyChangeListener()
-            {
+        @Override
+        public void mousePressed(MouseEvent evt)
+        {
+          if (evt.isPopupTrigger()) // Mac
+          {
+            showPasteMenu(evt.getX(), evt.getY());
+          }
+        }
 
-              @Override
-              public void propertyChange(PropertyChangeEvent evt)
-              {
-                Cache.log.debug("Firing service changed event for "
-                        + evt.getNewValue());
-                JalviewServicesChanged(evt);
-              }
+        @Override
+        public void mouseReleased(MouseEvent evt)
+        {
+          if (evt.isPopupTrigger()) // Windows
+          {
+            showPasteMenu(evt.getX(), evt.getY());
+          }
+        }
+      });
+      desktopPane.addMouseListener(ma);
+    } catch (Throwable t)
+    {
+      t.printStackTrace();
+    }
+  }
 
-            });
+  /**
+   * 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()
@@ -442,12 +603,12 @@ 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
     {
@@ -461,18 +622,41 @@ 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()
       {
         Cache.log.debug("Starting news thread.");
-
         jvnews = new BlogReader(me);
         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
+        {
+          UrlDownloadClient.download(IdOrgSettings.getUrl(),
+                  IdOrgSettings.getDownloadLocation());
+        } catch (IOException e)
+        {
+          Cache.log.debug("Exception downloading identifiers.org data"
+                  + e.getMessage());
+        }
+      }
+    }).start();
+    
   }
 
   @Override
@@ -481,27 +665,25 @@ public class Desktop extends jalview.jbgui.GDesktop implements
     showNews(showNews.isSelected());
   }
 
-  void showNews(boolean visible)
+  protected void showNews(boolean visible)
   {
+    Cache.log.debug((visible ? "Showing" : "Hiding") + " news.");
+    showNews.setSelected(visible);
+    if (visible && !jvnews.isVisible())
     {
-      Cache.log.debug((visible ? "Showing" : "Hiding") + " news.");
-      showNews.setSelected(visible);
-      if (visible && !jvnews.isVisible())
+      new Thread(new Runnable()
       {
-        new Thread(new Runnable()
+        @Override
+        public void run()
         {
-          @Override
-          public void run()
-          {
-            long now = System.currentTimeMillis();
-            Desktop.instance.setProgressBar(
-                    MessageManager.getString("status.refreshing_news"), now);
-            jvnews.refreshNews();
-            Desktop.instance.setProgressBar(null, now);
-            jvnews.showNews();
-          }
-        }).start();
-      }
+          long now = System.currentTimeMillis();
+          setProgressBar(
+                  MessageManager.getString("status.refreshing_news"), now);
+          jvnews.refreshNews();
+          setProgressBar(null, now);
+          jvnews.showNews();
+        }
+      }).start();
     }
   }
 
@@ -519,25 +701,23 @@ 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);
@@ -545,19 +725,19 @@ 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);
@@ -567,7 +747,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements
 
   private void doVamsasClientCheck()
   {
-    if (jalview.bin.Cache.vamsasJarsPresent())
+    if (Cache.vamsasJarsPresent())
     {
       setupVamsasDisconnectedGui();
       VamsasMenu.setVisible(true);
@@ -579,16 +759,19 @@ 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)
@@ -602,13 +785,14 @@ public class Desktop extends jalview.jbgui.GDesktop implements
     }
   }
 
-  void showPasteMenu(int x, int y)
+  protected void showPasteMenu(int x, int y)
   {
     JPopupMenu popup = new JPopupMenu();
     JMenuItem item = new JMenuItem(
             MessageManager.getString("label.paste_new_window"));
     item.addActionListener(new ActionListener()
     {
+      @Override
       public void actionPerformed(ActionEvent evt)
       {
         paste();
@@ -631,17 +815,16 @@ 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);
     }
   }
 
@@ -660,7 +843,7 @@ 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);
   }
 
   /**
@@ -682,7 +865,7 @@ 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);
   }
 
   /**
@@ -703,7 +886,7 @@ 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);
   }
 
   /**
@@ -722,19 +905,22 @@ 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
     // bounds object).
     // TODO: consider fixing method to update entries in the window submenu with
     // the current window title
 
     frame.setTitle(title);
-    if (frame.getWidth() < 1 || frame.getHeight() < 1)
+    if (w > 0 && (frame.getWidth() < 1 || frame.getHeight() < 1))
     {
       frame.setSize(w, h);
     }
@@ -742,64 +928,92 @@ 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 (Jalview.isHeadlessMode() || Desktop.getInstance().instanceOnly)
     {
       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);
-    }
-    if (frame.getX() < 1 && frame.getY() < 1)
+    frame.setOpaque(Platform.isJS());
+
+    boolean isEmbedded = (Platform.getDimIfEmbedded(frame, -1, -1) != null);
+    if (!isEmbedded && frame.getX() < 1 && frame.getY() < 1)
     {
-      frame.setLocation(xOffset * openFrameCount, yOffset
-              * ((openFrameCount - 1) % 10) + yOffset);
+      frame.setLocation(xOffset * openFrameCount,
+              yOffset * ((openFrameCount - 1) % 10) + yOffset);
     }
 
-    final JMenuItem menuItem = new JMenuItem(title);
-    frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
+    /*
+     * add an entry for the new frame in the Window menu 
+     * (and remove it when the frame is closed)
+     */
+    JMenuItem menuItem = new JMenuItem(title);
+    frame.addInternalFrameListener(new InternalFrameAdapter()
     {
-      public void internalFrameActivated(
-              javax.swing.event.InternalFrameEvent evt)
+      @Override
+      public void internalFrameActivated(InternalFrameEvent evt)
       {
-        JInternalFrame itf = desktop.getSelectedFrame();
+        JInternalFrame itf = getDesktopPane().getSelectedFrame();
         if (itf != null)
         {
+          if (itf instanceof AlignFrame)
+          {
+            Jalview.setCurrentAlignFrame((AlignFrame) itf);
+          }
           itf.requestFocus();
         }
-
       }
 
-      public void internalFrameClosed(
-              javax.swing.event.InternalFrameEvent evt)
+      @Override
+      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--;
         }
-        System.gc();
-      };
+
+        /*
+         * ensure no reference to alignFrame retained by menu item listener
+         */
+        if (menuItem.getActionListeners().length > 0)
+        {
+          menuItem.removeActionListener(menuItem.getActionListeners()[0]);
+        }
+        Desktop.getInstance().windowMenu.remove(menuItem);
+      }
     });
 
     menuItem.addActionListener(new ActionListener()
     {
+      @Override
       public void actionPerformed(ActionEvent e)
       {
         try
@@ -808,55 +1022,17 @@ public class Desktop extends jalview.jbgui.GDesktop implements
           frame.setIcon(false);
         } catch (java.beans.PropertyVetoException ex)
         {
-
+          // System.err.println(ex.toString());
         }
       }
     });
-    menuItem.addMouseListener(new MouseListener()
-    {
-
-      @Override
-      public void mouseReleased(MouseEvent e)
-      {
-      }
 
-      @Override
-      public void mousePressed(MouseEvent e)
-      {
-      }
-
-      @Override
-      public void mouseExited(MouseEvent e)
-      {
-        try
-        {
-          frame.setSelected(false);
-        } catch (PropertyVetoException e1)
-        {
-        }
-      }
+    setKeyBindings(frame);
 
-      @Override
-      public void mouseEntered(MouseEvent e)
-      {
-        try
-        {
-          frame.setSelected(true);
-        } catch (PropertyVetoException e1)
-        {
-        }
-      }
+    getDesktopPane().add(frame);
 
-      @Override
-      public void mouseClicked(MouseEvent e)
-      {
+    Desktop.getInstance().windowMenu.add(menuItem);
 
-      }
-    });
-
-    windowMenu.add(menuItem);
-
-    desktop.add(frame);
     frame.toFront();
     try
     {
@@ -866,30 +1042,69 @@ 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)
+  {
+    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)
   {
     if (!internalCopy)
     {
-      Desktop.jalviewClipboard = null;
+      Desktop.getInstance().jalviewClipboard = null;
     }
 
     internalCopy = false;
   }
 
+  @Override
   public void dragEnter(DropTargetDragEvent evt)
   {
   }
 
+  @Override
   public void dragExit(DropTargetEvent evt)
   {
   }
 
+  @Override
   public void dragOver(DropTargetDragEvent evt)
   {
   }
@@ -905,57 +1120,23 @@ public class Desktop extends jalview.jbgui.GDesktop implements
    * @param evt
    *          DOCUMENT ME!
    */
+  @Override
   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<Object> 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;
     }
 
@@ -965,22 +1146,28 @@ 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;
-
-          if (file.endsWith(".jar"))
+          // BH 2018 File or String
+          Object file = files.get(i);
+          String fileName = file.toString();
+          DataSourceType protocol = (protocols == null)
+                  ? DataSourceType.FILE
+                  : protocols.get(i);
+          FileFormatI format = null;
+
+          if (fileName.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);
+          if (file instanceof File)
+          {
+            Platform.cacheFileData((File) file);
+          }
+          new FileLoader().loadFile(null, file, protocol, format);
 
         }
       } catch (Exception ex)
@@ -1001,60 +1188,53 @@ 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, true);
 
     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);
-
-    if (value == JalviewFileChooser.APPROVE_OPTION)
+    chooser.setResponseHandler(0, new Runnable()
     {
-      String choice = chooser.getSelectedFile().getPath();
-      jalview.bin.Cache.setProperty("LAST_DIRECTORY", chooser
-              .getSelectedFile().getParent());
-
-      String format = null;
-      if (chooser.getSelectedFormat() != null
-              && chooser.getSelectedFormat().equals("Jalview"))
-      {
-        format = "Jalview";
-      }
-      else
+      @Override
+      public void run()
       {
-        format = new IdentifyFile().Identify(choice, FormatAdapter.FILE);
-      }
+        File selectedFile = chooser.getSelectedFile();
+        Cache.setProperty("LAST_DIRECTORY", selectedFile.getParent());
 
-      if (viewport != null)
-      {
-        new FileLoader().LoadFile(viewport, choice, FormatAdapter.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);
+        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))
+        {
+          try
+          {
+            format = new IdentifyFile().identify(selectedFile,
+                    DataSourceType.FILE);
+          } catch (FileFormatException e)
+          {
+            // format = null; //??
+          }
+        }
+
+        new FileLoader().loadFile(viewport, selectedFile,
+                DataSourceType.FILE, format);
       }
-    }
+    });
+    chooser.showOpenDialog(this);
   }
 
   /**
-   * DOCUMENT ME!
+   * Shows a dialog for input of a URL at which to retrieve alignment data
    * 
-   * @param e
-   *          DOCUMENT ME!
+   * @param viewport
    */
   @Override
   public void inputURLMenuItem_actionPerformed(AlignViewport viewport)
@@ -1063,76 +1243,114 @@ public class Desktop extends jalview.jbgui.GDesktop implements
     // for viewing
     JLabel label = new JLabel(
             MessageManager.getString("label.input_file_url"));
-    final JComboBox history = new JComboBox();
 
     JPanel panel = new JPanel(new GridLayout(2, 1));
     panel.add(label);
-    panel.add(history);
-    history.setPreferredSize(new Dimension(400, 20));
-    history.setEditable(true);
-    history.addItem("http://www.");
-
-    String historyItems = jalview.bin.Cache.getProperty("RECENT_URL");
-
-    StringTokenizer st;
-
-    if (historyItems != null)
-    {
-      st = new StringTokenizer(historyItems, "\t");
-
-      while (st.hasMoreTokens())
-      {
-        history.addItem(st.nextElement());
-      }
-    }
-
-    int reply = JOptionPane.showInternalConfirmDialog(desktop, panel,
-            MessageManager.getString("label.input_alignment_from_url"),
-            JOptionPane.OK_CANCEL_OPTION);
 
-    if (reply != JOptionPane.OK_OPTION)
+    /*
+     * the URL to fetch is
+     * Java: an editable combobox with history
+     * JS: (pending JAL-3038) a plain text field
+     */
+    JComponent history;
+    String urlBase = "http://www.";
+    if (Platform.isJS())
     {
-      return;
+      history = new JTextField(urlBase, 35);
     }
-
-    String url = history.getSelectedItem().toString();
-
-    if (url.toLowerCase().endsWith(".jar"))
+    else
+    /**
+     * Java only
+     * 
+     * @j2sIgnore
+     */
     {
-      if (viewport != null)
-      {
-        new FileLoader().LoadFile(viewport, url, FormatAdapter.URL,
-                "Jalview");
-      }
-      else
+      JComboBox<String> asCombo = new JComboBox<>();
+      asCombo.setPreferredSize(new Dimension(400, 20));
+      asCombo.setEditable(true);
+      asCombo.addItem(urlBase);
+      String historyItems = Cache.getProperty("RECENT_URL");
+      if (historyItems != null)
       {
-        new FileLoader().LoadFile(url, FormatAdapter.URL, "Jalview");
+        for (String token : historyItems.split("\\t"))
+        {
+          asCombo.addItem(token);
+        }
       }
+      history = asCombo;
     }
-    else
-    {
-      String format = new IdentifyFile().Identify(url, FormatAdapter.URL);
+    panel.add(history);
 
-      if (format.equals("URL NOT FOUND"))
+    Object[] options = new Object[] { MessageManager.getString("action.ok"),
+        MessageManager.getString("action.cancel") };
+    Runnable action = new Runnable()
+    {
+      @Override
+      public void run()
       {
-        JOptionPane.showInternalMessageDialog(Desktop.desktop,
-                MessageManager.formatMessage("label.couldnt_locate",
-                        new Object[] { url }), MessageManager
-                        .getString("label.url_not_found"),
-                JOptionPane.WARNING_MESSAGE);
+        @SuppressWarnings("unchecked")
+        String url = (history instanceof JTextField
+                ? ((JTextField) history).getText()
+                : ((JComboBox<String>) history).getSelectedItem()
+                        .toString());
 
-        return;
-      }
+        if (url.toLowerCase().endsWith(".jar"))
+        {
+          if (viewport != null)
+          {
+            new FileLoader().loadFile(viewport, url, DataSourceType.URL,
+                    FileFormat.Jalview);
+          }
+          else
+          {
+            new FileLoader().loadFile(url, DataSourceType.URL,
+                    FileFormat.Jalview);
+          }
+        }
+        else
+        {
+          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 (viewport != null)
-      {
-        new FileLoader().LoadFile(viewport, url, FormatAdapter.URL, format);
-      }
-      else
-      {
-        new FileLoader().LoadFile(url, FormatAdapter.URL, format);
+          if (format == null)
+          {
+            String msg = MessageManager
+                    .formatMessage("label.couldnt_locate", url);
+            JvOptionPane.showInternalMessageDialog(Desktop.getDesktopPane(),
+                    msg,
+                    MessageManager.getString("label.url_not_found"),
+                    JvOptionPane.WARNING_MESSAGE);
+
+            return;
+          }
+
+          if (viewport != null)
+          {
+            new FileLoader().loadFile(viewport, url, DataSourceType.URL,
+                    format);
+          }
+          else
+          {
+            new FileLoader().loadFile(url, DataSourceType.URL, format);
+          }
+        }
       }
-    }
+    };
+    String dialogOption = MessageManager
+            .getString("label.input_alignment_from_url");
+    JvOptionPane.newOptionDialog(getDesktopPane())
+            .setResponseHandler(0, action)
+            .showInternalDialog(panel, dialogOption,
+                    JvOptionPane.YES_NO_CANCEL_OPTION,
+                    JvOptionPane.PLAIN_MESSAGE, null, options,
+                    MessageManager.getString("action.ok"));
   }
 
   /**
@@ -1149,8 +1367,8 @@ 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);
   }
 
   /*
@@ -1160,12 +1378,12 @@ public class Desktop extends jalview.jbgui.GDesktop implements
   public void quit()
   {
     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)
     {
@@ -1182,6 +1400,13 @@ 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);
   }
 
@@ -1207,11 +1432,12 @@ 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.getDesktop(),
     //
-    // message.toString(), "About Jalview", JOptionPane.INFORMATION_MESSAGE);
+    // message.toString(), "About Jalview", JvOptionPane.INFORMATION_MESSAGE);
     new Thread(new Runnable()
     {
+      @Override
       public void run()
       {
         new SplashScreen(true);
@@ -1226,7 +1452,8 @@ 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>");
@@ -1241,8 +1468,8 @@ 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>");
     }
@@ -1264,16 +1491,16 @@ 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:"
@@ -1285,26 +1512,41 @@ public class Desktop extends jalview.jbgui.GDesktop implements
   }
 
   /**
-   * DOCUMENT ME!
-   * 
-   * @param e
-   *          DOCUMENT ME!
+   * Action on requesting Help documentation
    */
   @Override
-  public void documentationMenuItem_actionPerformed(ActionEvent e)
+  public void documentationMenuItem_actionPerformed()
   {
     try
     {
-      Help.showHelpWindow();
+      if (Platform.isJS())
+      {
+        BrowserLauncher.openURL("http://www.jalview.org/help.html");
+      }
+      else
+      /**
+       * Java only
+       * 
+       * @j2sIgnore
+       */
+      {
+        Help.showHelpWindow();
+      }
     } catch (Exception ex)
     {
+      System.err.println("Error opening help: " + ex.getMessage());
     }
   }
 
   @Override
   public void closeAll_actionPerformed(ActionEvent e)
   {
-    JInternalFrame[] frames = desktop.getAllFrames();
+    if (desktopPane == null)
+    {
+      return;
+    }
+    // TODO show a progress bar while closing?
+    JInternalFrame[] frames = desktopPane.getAllFrames();
     for (int i = 0; i < frames.length; i++)
     {
       try
@@ -1314,6 +1556,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements
       {
       }
     }
+    Jalview.setCurrentAlignFrame(null);
     System.out.println("ALL CLOSED");
     if (v_client != null)
     {
@@ -1324,12 +1567,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements
      * reset state of singleton objects as appropriate (clear down session state
      * when all windows are closed)
      */
-    StructureSelectionManager ssm = StructureSelectionManager
-            .getStructureSelectionManager(this);
-    if (ssm != null)
-    {
-      ssm.resetAll();
-    }
+    getStructureSelectionManager().resetAll();
   }
 
   @Override
@@ -1374,7 +1612,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements
   @Override
   protected void showMemusage_actionPerformed(ActionEvent e)
   {
-    desktop.showMemoryUsage(showMemusage.isSelected());
+    getDesktopPane().showMemoryUsage(showMemusage.isSelected());
   }
 
   /*
@@ -1399,16 +1637,19 @@ public class Desktop extends jalview.jbgui.GDesktop implements
    */
   void showConsole(boolean selected)
   {
-    showConsole.setSelected(selected);
     // TODO: decide if we should update properties file
-    Cache.setProperty("SHOW_JAVA_CONSOLE", Boolean.valueOf(selected)
-            .toString());
-    jconsole.setVisible(selected);
+    if (jconsole != null) // BH 2018
+    {
+      showConsole.setSelected(selected);
+      Cache.setProperty("SHOW_JAVA_CONSOLE",
+              Boolean.valueOf(selected).toString());
+      jconsole.setVisible(selected);
+    }
   }
 
   void reorderAssociatedWindows(boolean minimize, boolean close)
   {
-    JInternalFrame[] frames = desktop.getAllFrames();
+    JInternalFrame[] frames = getDesktopPane().getAllFrames();
     if (frames == null || frames.length < 1)
     {
       return;
@@ -1496,67 +1737,103 @@ public class Desktop extends jalview.jbgui.GDesktop implements
   }
 
   /**
-   * DOCUMENT ME!
-   * 
-   * @param e
-   *          DOCUMENT ME!
+   * Prompts the user to choose a file and then saves the Jalview state 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" },
-            "Jalview Project");
+    saveState_actionPerformed(false);
+  }
 
-    chooser.setFileView(new JalviewFileView());
-    chooser.setDialogTitle(MessageManager.getString("label.save_state"));
+  public void saveState_actionPerformed(boolean saveAs)
+  {
+    java.io.File projectFile = getProjectFile();
+    // autoSave indicates we already have a file and don't need to ask
+    boolean autoSave = projectFile != null && !saveAs
+            && BackupFiles.getEnabled();
 
-    int value = chooser.showSaveDialog(this);
+    // System.out.println("autoSave="+autoSave+", projectFile='"+projectFile+"',
+    // saveAs="+saveAs+", Backups
+    // "+(BackupFiles.getEnabled()?"enabled":"disabled"));
 
-    if (value == JalviewFileChooser.APPROVE_OPTION)
+    boolean approveSave = false;
+    if (!autoSave)
     {
-      final Desktop me = this;
-      final java.io.File choice = chooser.getSelectedFile();
-      setProjectFile(choice);
+      JalviewFileChooser chooser = new JalviewFileChooser("jvp",
+              "Jalview Project");
+
+      chooser.setFileView(new JalviewFileView());
+      chooser.setDialogTitle(MessageManager.getString("label.save_state"));
+
+      int value = chooser.showSaveDialog(this);
+
+      if (value == JalviewFileChooser.APPROVE_OPTION)
+      {
+        projectFile = chooser.getSelectedFile();
+        setProjectFile(projectFile);
+        approveSave = true;
+      }
+    }
 
+    if (approveSave || autoSave)
+    {
+      final Desktop me = this;
+      final java.io.File chosenFile = projectFile;
       new Thread(new Runnable()
       {
+        @Override
         public void run()
         {
           // 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[]
+                  { chosenFile.getName() }), chosenFile.hashCode());
           jalview.bin.Cache.setProperty("LAST_DIRECTORY",
-                  choice.getParent());
+                  chosenFile.getParent());
           // TODO catch and handle errors for savestate
           // TODO prevent user from messing with the Desktop whilst we're saving
           try
           {
-            new Jalview2XML().saveState(choice);
+        	boolean doBackup = BackupFiles.getEnabled();
+            BackupFiles backupfiles = doBackup ? new BackupFiles(chosenFile) : null;
+
+            new Jalview2XML().saveState(doBackup ? backupfiles.getTempFile() : chosenFile);
+
+            if (doBackup)
+            {
+              backupfiles.setWriteSuccess(true);
+              backupfiles.rollBackupsAndRenameTempFile();
+            }
           } catch (OutOfMemoryError oom)
           {
             new OOMWarning("Whilst saving current state to "
-                    + choice.getName(), oom);
+                    + chosenFile.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);
+            Cache.log.error("Problems whilst trying to save to "
+                    + chosenFile.getName(), ex);
+            JvOptionPane.showMessageDialog(me,
+                    MessageManager.formatMessage(
+                            "label.error_whilst_saving_current_state_to",
+                            new Object[]
+                            { chosenFile.getName() }),
+                    MessageManager.getString("label.couldnt_save_project"),
+                    JvOptionPane.WARNING_MESSAGE);
           }
-          setProgressBar(null, choice.hashCode());
+          setProgressBar(null, chosenFile.hashCode());
         }
       }).start();
-    }
+      }
+  }
+
+  @Override
+  public void saveAsState_actionPerformed(ActionEvent e)
+  {
+    saveState_actionPerformed(true);
   }
 
-  private void setProjectFile(File choice)
+  protected void setProjectFile(File choice)
   {
     this.projectFile = choice;
   }
@@ -1567,59 +1844,59 @@ 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", true, true); // last two booleans: allFiles,
+                                            // allowBackupFiles
     chooser.setFileView(new JalviewFileView());
     chooser.setDialogTitle(MessageManager.getString("label.restore_state"));
-
-    int value = chooser.showOpenDialog(this);
-
-    if (value == JalviewFileChooser.APPROVE_OPTION)
+    chooser.setResponseHandler(0, new Runnable()
     {
-      final File selectedFile = chooser.getSelectedFile();
-      setProjectFile(selectedFile);
-      final String choice = selectedFile.getAbsolutePath();
-      jalview.bin.Cache.setProperty("LAST_DIRECTORY",
-              selectedFile.getParent());
-      new Thread(new Runnable()
+      @Override
+      public void run()
       {
-        public void run()
+        File selectedFile = chooser.getSelectedFile();
+        setProjectFile(selectedFile);
+        String choice = selectedFile.getAbsolutePath();
+        Cache.setProperty("LAST_DIRECTORY", selectedFile.getParent());
+        new Thread(new Runnable()
         {
-          setProgressBar(
-                  MessageManager.formatMessage(
-                          "label.loading_jalview_project",
-                          new Object[] { choice }), choice.hashCode());
-          try
-          {
-            new Jalview2XML().loadJalviewAlign(choice);
-          } catch (OutOfMemoryError oom)
-          {
-            new OOMWarning("Whilst loading project from " + choice, oom);
-          } catch (Exception ex)
+          @Override
+          public void run()
           {
-            Cache.log.error("Problems whilst loading project from "
-                    + choice, ex);
-            JOptionPane.showMessageDialog(Desktop.desktop, MessageManager
-                    .formatMessage(
-                            "label.error_whilst_loading_project_from",
-                            new Object[] { choice }), MessageManager
-                    .getString("label.couldnt_load_project"),
-                    JOptionPane.WARNING_MESSAGE);
+        	try 
+            {
+              new Jalview2XML().loadJalviewAlign(choice);
+            } catch (OutOfMemoryError oom)
+	        {
+	          new OOMWarning("Whilst loading project from " + choice, oom);
+	        } catch (Exception ex)
+	        {
+	          Cache.log.error(
+	                  "Problems whilst loading project from " + choice, ex);
+              JvOptionPane.showMessageDialog(Desktop.getDesktopPane(),
+	                  MessageManager.formatMessage(
+	                          "label.error_whilst_loading_project_from",
+	                        new Object[]
+	                            { choice }),
+	                  MessageManager.getString("label.couldnt_load_project"),
+	                  JvOptionPane.WARNING_MESSAGE);
+	        }
           }
-          setProgressBar(null, choice.hashCode());
-        }
-      }).start();
-    }
+        }).start();
+      }
+    });
+    
+    chooser.showOpenDialog(this);
   }
 
   @Override
@@ -1630,14 +1907,15 @@ 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)
+  public void startLoading(final Object 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++;
   }
@@ -1648,7 +1926,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements
     {
       progressPanel = new JPanel(new GridLayout(1, 1));
       totalProgressCount = 0;
-      instance.getContentPane().add(progressPanel, BorderLayout.SOUTH);
+      getContentPane().add(progressPanel, BorderLayout.SOUTH);
     }
     JPanel thisprogress = new JPanel(new BorderLayout(10, 5));
     JProgressBar progressBar = new JProgressBar();
@@ -1658,10 +1936,10 @@ 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();
+    validate();
     return thisprogress;
   }
 
@@ -1715,13 +1993,13 @@ public class Desktop extends jalview.jbgui.GDesktop implements
    */
   public static AlignmentPanel[] getAlignmentPanels(String alignmentId)
   {
-    if (Desktop.desktop == null)
+    if (Desktop.getDesktopPane() == null)
     {
       // no frames created and in headless mode
       // 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)
     {
@@ -1756,16 +2034,15 @@ public class Desktop extends jalview.jbgui.GDesktop implements
    */
   public static AlignmentViewport[] getViewports(String sequenceSetId)
   {
-    List<AlignmentViewport> viewp = new ArrayList<AlignmentViewport>();
-    if (desktop != null)
+    List<AlignmentViewport> viewp = new ArrayList<>();
+    if (getDesktopPane() != 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)
           {
@@ -1797,7 +2074,7 @@ 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)
@@ -1834,9 +2111,9 @@ public class Desktop extends jalview.jbgui.GDesktop implements
 
   /**
    * Gather expanded views (separate AlignFrame's) with the same sequence set
-   * identifier back in to this frame as additional views, and close the
-   * expanded views. Note the expanded frames may themselves have multiple
-   * views. We take the lot.
+   * identifier back in to this frame as additional views, and close the expanded
+   * views. Note the expanded frames may themselves have multiple views. We take
+   * the lot.
    * 
    * @param source
    */
@@ -1844,7 +2121,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements
   {
     source.viewport.setGatherViewsHere(true);
     source.viewport.setExplodedGeometry(source.getBounds());
-    JInternalFrame[] frames = desktop.getAllFrames();
+    JInternalFrame[] frames = getAllFrames();
     String viewId = source.viewport.getSequenceSetId();
 
     for (int t = 0; t < frames.length; t++)
@@ -1880,6 +2157,8 @@ public class Desktop extends jalview.jbgui.GDesktop implements
   @Override
   public void vamsasImport_actionPerformed(ActionEvent e)
   {
+    // TODO: JAL-3048 not needed for Jalview-JS
+
     if (v_client == null)
     {
       // Load and try to start a session.
@@ -1887,10 +2166,10 @@ 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);
 
@@ -1899,22 +2178,21 @@ 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.getDesktopPane(),
+                  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.");
     }
   }
 
@@ -1930,8 +2208,8 @@ 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;
     }
 
@@ -1956,7 +2234,8 @@ 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();
@@ -1975,22 +2254,22 @@ 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;
@@ -1998,8 +2277,8 @@ 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();
   }
 
@@ -2007,9 +2286,8 @@ 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)
     {
@@ -2067,8 +2345,8 @@ 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
@@ -2092,26 +2370,28 @@ 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()
           {
 
+            @Override
             public void actionPerformed(ActionEvent e)
             {
               if (dsktp.v_client == null)
@@ -2119,6 +2399,7 @@ 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);
@@ -2129,7 +2410,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements
                 });
                 rthr.start();
               }
-            };
+            }
           });
           VamsasStMenu.add(sessit);
         }
@@ -2154,12 +2435,13 @@ public class Desktop extends jalview.jbgui.GDesktop implements
   @Override
   public void vamsasSave_actionPerformed(ActionEvent e)
   {
+    // TODO: JAL-3048 not needed for Jalview-JS
+
     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
@@ -2170,10 +2452,10 @@ 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
@@ -2183,23 +2465,23 @@ 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.getDesktopPane(),
 
-          warnmsg, warnttl, JOptionPane.ERROR_MESSAGE);
+                  warnmsg, warnttl, JvOptionPane.ERROR_MESSAGE);
         }
       }
     }
@@ -2215,7 +2497,7 @@ 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)
@@ -2224,8 +2506,8 @@ 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);
@@ -2234,7 +2516,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements
 
   public JInternalFrame[] getAllFrames()
   {
-    return desktop.getAllFrames();
+    return desktopPane.getAllFrames();
   }
 
   /**
@@ -2250,16 +2532,94 @@ 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(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(desktopPane, 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
-   * low.
+   * usage and highlights the desktop area with a red bar if free memory runs low.
    * 
    * @author AMW
    */
-  public class MyDesktopPane extends JDesktopPane implements Runnable
+  public class MyDesktopPane extends JDesktopPane
+          implements Runnable
   {
-
     private static final float ONE_MB = 1048576f;
 
     boolean showMemoryUsage = false;
@@ -2284,6 +2644,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements
         Thread worker = new Thread(this);
         worker.start();
       }
+      repaint();
     }
 
     public boolean isShowMemoryUsage()
@@ -2291,6 +2652,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements
       return showMemoryUsage;
     }
 
+    @Override
     public void run()
     {
       df = java.text.NumberFormat.getNumberInstance();
@@ -2336,46 +2698,17 @@ 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;
-
-  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.
    * 
    * @return an array of AlignFrame, or null if none found
@@ -2384,17 +2717,17 @@ public class Desktop extends jalview.jbgui.GDesktop implements
   {
     if (Jalview.isHeadlessMode())
     {
-      // Desktop.desktop is null in headless mode
-      return new AlignFrame[] { currentAlignFrame };
+      // Desktop.getDesktop() is null in headless mode
+      return new AlignFrame[] { Jalview.getCurrentAlignFrame() };
     }
 
-    JInternalFrame[] frames = Desktop.desktop.getAllFrames();
+    JInternalFrame[] frames = Desktop.getDesktopPane().getAllFrames();
 
     if (frames == null)
     {
       return null;
     }
-    List<AlignFrame> avp = new ArrayList<AlignFrame>();
+    List<AlignFrame> avp = new ArrayList<>();
     // REVERSE ORDER
     for (int i = frames.length - 1; i > -1; i--)
     {
@@ -2433,13 +2766,13 @@ public class Desktop extends jalview.jbgui.GDesktop implements
    */
   public GStructureViewer[] getJmols()
   {
-    JInternalFrame[] frames = Desktop.desktop.getAllFrames();
+    JInternalFrame[] frames = Desktop.getDesktopPane().getAllFrames();
 
     if (frames == null)
     {
       return null;
     }
-    List<GStructureViewer> avp = new ArrayList<GStructureViewer>();
+    List<GStructureViewer> avp = new ArrayList<>();
     // REVERSE ORDER
     for (int i = frames.length - 1; i > -1; i--)
     {
@@ -2460,34 +2793,108 @@ public class Desktop extends jalview.jbgui.GDesktop implements
   /**
    * Add Groovy Support to Jalview
    */
+  @Override
   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);
-      JOptionPane.showInternalMessageDialog(Desktop.desktop,
+      JvOptionPane.showInternalMessageDialog(desktopPane,
 
-      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);
+    }
+  }
+
+  /**
+   * Open the Groovy console
+   */
+  private 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);
+      }
     }
   }
 
@@ -2503,12 +2910,15 @@ 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)
   {
+	    Platform.timeCheck("Desktop " + message, Platform.TIME_MARK);     
+
     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)
@@ -2532,15 +2942,15 @@ 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)
   {
     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));
@@ -2552,13 +2962,14 @@ public class Desktop extends jalview.jbgui.GDesktop implements
       cancel.addActionListener(new ActionListener()
       {
 
+        @Override
         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);
@@ -2580,18 +2991,18 @@ public class Desktop extends jalview.jbgui.GDesktop implements
   }
 
   /**
-   * This will return the first AlignFrame holding the given viewport instance.
-   * It will break if there are more than one AlignFrames viewing a particular
-   * av.
+   * This will return the first AlignFrame holding the given viewport instance. It
+   * will break if there are more than one AlignFrames viewing a particular av.
    * 
    * @param viewport
    * @return alignFrame for viewport
    */
   public static AlignFrame getAlignFrameFor(AlignViewportI viewport)
   {
-    if (desktop != null)
+    if (getDesktopPane() != 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)
@@ -2649,8 +3060,8 @@ public class Desktop extends jalview.jbgui.GDesktop implements
       // todo: changesupport handlers need to be transferred
       if (discoverer == null)
       {
-        discoverer = new jalview.ws.jws1.Discoverer();
-        // register PCS handler for desktop.
+        discoverer = Discoverer.getInstance();
+        // register PCS handler for getDesktop().
         discoverer.addPropertyChangeListener(changeSupport);
       }
       // JAL-940 - disabled JWS1 service configuration - always start discoverer
@@ -2660,13 +3071,8 @@ 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.getInstance()
+              .startDiscoverer(changeSupport);
     }
     Thread t3 = null;
     {
@@ -2682,8 +3088,7 @@ 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());
       }
@@ -2699,7 +3104,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements
   {
     if (evt.getNewValue() == null || evt.getNewValue() instanceof Vector)
     {
-      final String ermsg = jalview.ws.jws2.Jws2Discoverer.getDiscoverer()
+      final String ermsg = jalview.ws.jws2.Jws2Discoverer.getInstance()
               .getErrorMessages();
       if (ermsg != null)
       {
@@ -2710,6 +3115,7 @@ 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()
               {
 
@@ -2737,20 +3143,16 @@ 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.getDesktopPane(),
+                        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;
 
               }
@@ -2759,15 +3161,15 @@ 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);
         }
       }
     }
   }
 
-  private Runnable serviceChangedDialog = null;
+  Runnable serviceChangedDialog = null;
 
   /**
    * start a thread to open a URL in the configured browser. Pops up a warning
@@ -2778,7 +3180,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements
    */
   public static void showUrl(final String url)
   {
-    showUrl(url, Desktop.instance);
+    showUrl(url, Desktop.getInstance());
   }
 
   /**
@@ -2793,24 +3195,25 @@ public class Desktop extends jalview.jbgui.GDesktop implements
   {
     new Thread(new Runnable()
     {
+      @Override
       public void run()
       {
         try
         {
           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);
+          BrowserLauncher.openURL(url);
         } catch (Exception ex)
         {
-          JOptionPane.showInternalMessageDialog(Desktop.desktop,
+          JvOptionPane.showInternalMessageDialog(Desktop.getDesktopPane(),
                   MessageManager
                           .getString("label.web_browser_not_found_unix"),
                   MessageManager.getString("label.web_browser_not_found"),
-                  JOptionPane.WARNING_MESSAGE);
+                  JvOptionPane.WARNING_MESSAGE);
 
           ex.printStackTrace();
         }
@@ -2822,15 +3225,16 @@ public class Desktop extends jalview.jbgui.GDesktop implements
     }).start();
   }
 
-  public static WsParamSetManager wsparamManager = null;
+  private WsParamSetManager wsparamManager = null;
 
   public static ParamManager getUserParameterStore()
   {
-    if (wsparamManager == null)
+    Desktop d = Desktop.getInstance();
+    if (d.wsparamManager == null)
     {
-      wsparamManager = new WsParamSetManager();
+      d.wsparamManager = new WsParamSetManager();
     }
-    return wsparamManager;
+    return d.wsparamManager;
   }
 
   /**
@@ -2857,8 +3261,8 @@ 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.
@@ -2875,12 +3279,16 @@ public class Desktop extends jalview.jbgui.GDesktop implements
   /**
    * flag indicating if dialogExecutor should try to acquire a permit
    */
-  private volatile boolean dialogPause = true;
+  volatile boolean dialogPause = true;
 
   /**
    * pause the queue
    */
-  private java.util.concurrent.Semaphore block = new Semaphore(0);
+  java.util.concurrent.Semaphore block = new Semaphore(0);
+
+  private groovy.ui.Console groovyConsole;
+
+  public StructureViewer lastTargetedView;
 
   /**
    * add another dialog thread to the queue
@@ -2891,6 +3299,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements
   {
     dialogExecutor.submit(new Runnable()
     {
+      @Override
       public void run()
       {
         if (dialogPause)
@@ -2901,9 +3310,10 @@ public class Desktop extends jalview.jbgui.GDesktop implements
           } catch (InterruptedException x)
           {
           }
-          ;
         }
-        if (instance == null)
+        System.out.println("Desktop headless or instanceonly" + instanceOnly
+                + " " + Jalview.isHeadlessMode());
+        if (instanceOnly || Jalview.isHeadlessMode())
         {
           return;
         }
@@ -2926,33 +3336,45 @@ public class Desktop extends jalview.jbgui.GDesktop implements
     block.release();
   }
 
+  /**
+   * Outputs an image of the desktop to file in EPS format, after prompting the
+   * user for choice of Text or Lineart character rendering (unless a preference
+   * has been set). The file name is generated as
+   * 
+   * <pre>
+   * Jalview_snapshot_nnnnn.eps where nnnnn is the current timestamp in milliseconds
+   * </pre>
+   */
   @Override
   protected void snapShotWindow_actionPerformed(ActionEvent e)
   {
+    // currently the menu option to do this is not shown
     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");
-    try
-    {
-      paintAll(im.getGraphics());
-      im.writeImage();
-    } catch (Exception q)
+
+    int width = getWidth();
+    int height = getHeight();
+    File of = new File(
+            "Jalview_snapshot_" + System.currentTimeMillis() + ".eps");
+    ImageWriterI writer = new ImageWriterI()
     {
-      Cache.log.error("Couldn't write snapshot to " + of.getAbsolutePath(),
-              q);
-      return;
-    }
-    Cache.log.info("Successfully written snapshot to file "
-            + of.getAbsolutePath());
+      @Override
+      public void exportImage(Graphics g) throws Exception
+      {
+        paintAll(g);
+        Cache.log.info("Successfully written snapshot to file "
+                + of.getAbsolutePath());
+      }
+    };
+    String title = "View of desktop";
+    ImageExporter exporter = new ImageExporter(writer, null, TYPE.EPS,
+            title);
+    exporter.doExport(of, this, width, height, title);
   }
 
   /**
    * Explode the views in the given SplitFrame into separate SplitFrame windows.
-   * This respects (remembers) any previous 'exploded geometry' i.e. the size
-   * and location last time the view was expanded (if any). However it does not
+   * This respects (remembers) any previous 'exploded geometry' i.e. the size and
+   * location last time the view was expanded (if any). However it does not
    * remember the split pane divider location - this is set to match the
    * 'exploding' frame.
    * 
@@ -3047,15 +3469,15 @@ 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();
     String bottomViewId = myBottomFrame.viewport.getSequenceSetId();
 
-    JInternalFrame[] frames = desktop.getAllFrames();
+    JInternalFrame[] frames = desktopPane.getAllFrames();
     for (JInternalFrame frame : frames)
     {
       if (frame instanceof SplitFrame && frame != source)
@@ -3074,10 +3496,10 @@ 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);
           }
@@ -3096,17 +3518,281 @@ 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 groovy.ui.Console getGroovyConsole()
+  {
+    Desktop desktop = Desktop.getInstance();
+    return desktop == null ? null : desktop.groovyConsole;
+  }
+
+  /**
+   * 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
+   */
+  @SuppressWarnings("unchecked")
+  public static void transferFromDropTarget(List<Object> files,
+          List<DataSourceType> protocols, DropTargetDropEvent evt,
+          Transferable t) throws Exception
+  {
+
+    // BH 2018 changed List<String> to List<Object> to allow for File from SwingJS
+
+    // DataFlavor[] flavors = t.getTransferDataFlavors();
+    // for (int i = 0; i < flavors.length; i++) {
+    // if (flavors[i].isFlavorJavaFileListType()) {
+    // evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
+    // List<File> list = (List<File>) t.getTransferData(flavors[i]);
+    // for (int j = 0; j < list.size(); j++) {
+    // File file = (File) list.get(j);
+    // byte[] data = getDroppedFileBytes(file);
+    // fileName.setText(file.getName() + " - " + data.length + " " +
+    // evt.getLocation());
+    // JTextArea target = (JTextArea) ((DropTarget) evt.getSource()).getComponent();
+    // target.setText(new String(data));
+    // }
+    // dtde.dropComplete(true);
+    // return;
+    // }
+    //
+
+    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.isAMacAndNotJS())
+          {
+            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<Object>) t
+              .getTransferData(DataFlavor.javaFileListFlavor))
+      {
+        files.add(file);
+        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.isWindowsAndNotJS())
+    {
+      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).toString().toLowerCase();
+        if (protocols.get(f).equals(DataSourceType.FILE)
+                && (source.endsWith(".lnk") || source.endsWith(".url")
+                        || source.endsWith(".site")))
+        {
+          try
+          {
+            Object obj = files.get(f);
+            File lf = (obj instanceof File ? (File) obj
+                    : new File((String) obj));
+            // 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 AlignFrame getCurrentAlignFrame()
+  /**
+   * 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 currentAlignFrame;
+    Cache.setProperty(EXPERIMENTAL_FEATURES, Boolean.toString(selected));
   }
 
-  public static void setCurrentAlignFrame(AlignFrame currentAlignFrame)
+  /**
+   * 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)
   {
-    Desktop.currentAlignFrame = currentAlignFrame;
+    List<StructureViewerBase> result = new ArrayList<>();
+    JInternalFrame[] frames = 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;
   }
 
 }