X-Git-Url: http://source.jalview.org/gitweb/?p=jalview.git;a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FDesktop.java;h=3ad5384d626547c262784e60354403d4036d489a;hp=6e155ebb2bddacbe4b0f18533f7c11b2a77c92f4;hb=dda7fb15c035fe454eae0fe85c29c0df922ec271;hpb=37fa20fdbf571bf7fbf080595a3529c9c469ee37

diff --git a/src/jalview/gui/Desktop.java b/src/jalview/gui/Desktop.java
index 6e155eb..3ad5384 100644
--- a/src/jalview/gui/Desktop.java
+++ b/src/jalview/gui/Desktop.java
@@ -20,42 +20,12 @@
  */
 package jalview.gui;
 
-import static jalview.util.UrlConstants.SEQUENCE_ID;
-
-import jalview.api.AlignViewportI;
-import jalview.api.AlignmentViewPanel;
-import jalview.bin.Cache;
-import jalview.bin.Jalview;
-import jalview.gui.ImageExporter.ImageWriterI;
-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.GSplitFrame;
-import jalview.jbgui.GStructureViewer;
-import jalview.structure.StructureSelectionManager;
-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.util.dialogrunner.RunResponse;
-import jalview.viewmodel.AlignmentViewport;
-import jalview.ws.params.ParamManager;
-import jalview.ws.utils.UrlDownloadClient;
-
 import java.awt.BorderLayout;
 import java.awt.Color;
 import java.awt.Dimension;
 import java.awt.FontMetrics;
 import java.awt.Graphics;
+import java.awt.Graphics2D;
 import java.awt.GridLayout;
 import java.awt.Point;
 import java.awt.Rectangle;
@@ -78,18 +48,21 @@ import java.awt.event.MouseAdapter;
 import java.awt.event.MouseEvent;
 import java.awt.event.WindowAdapter;
 import java.awt.event.WindowEvent;
+import java.awt.geom.AffineTransform;
 import java.beans.PropertyChangeEvent;
 import java.beans.PropertyChangeListener;
-import java.io.BufferedInputStream;
 import java.io.File;
-import java.io.FileOutputStream;
+import java.io.FileWriter;
 import java.io.IOException;
+import java.lang.reflect.Field;
 import java.net.URL;
 import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.HashMap;
 import java.util.Hashtable;
 import java.util.List;
 import java.util.ListIterator;
-import java.util.StringTokenizer;
+import java.util.Locale;
 import java.util.Vector;
 import java.util.concurrent.ExecutorService;
 import java.util.concurrent.Executors;
@@ -108,24 +81,54 @@ import javax.swing.JCheckBox;
 import javax.swing.JComboBox;
 import javax.swing.JComponent;
 import javax.swing.JDesktopPane;
-import javax.swing.JFrame;
 import javax.swing.JInternalFrame;
 import javax.swing.JLabel;
 import javax.swing.JMenuItem;
 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;
 
+import jalview.api.AlignViewportI;
+import jalview.api.AlignmentViewPanel;
+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.GSplitFrame;
+import jalview.jbgui.GStructureViewer;
+import jalview.project.Jalview2XML;
+import jalview.structure.StructureSelectionManager;
+import jalview.urls.IdOrgSettings;
+import jalview.util.BrowserLauncher;
+import jalview.util.ChannelProperties;
+import jalview.util.ImageMaker.TYPE;
+import jalview.util.MessageManager;
+import jalview.util.Platform;
+import jalview.util.ShortcutKeyMaskExWrapper;
+import jalview.util.UrlConstants;
+import jalview.viewmodel.AlignmentViewport;
+import jalview.ws.params.ParamManager;
+import jalview.ws.utils.UrlDownloadClient;
+
 /**
  * Jalview Desktop
  * 
@@ -137,6 +140,38 @@ public class Desktop extends jalview.jbgui.GDesktop
         implements DropTargetListener, ClipboardOwner, IProgressIndicator,
         jalview.api.StructureSelectionManagerProvider
 {
+  private static final String CITATION;
+  static
+  {
+    URL bg_logo_url = ChannelProperties.getImageURL(
+            "bg_logo." + String.valueOf(SplashScreen.logoSize));
+    URL uod_logo_url = ChannelProperties.getImageURL(
+            "uod_banner." + String.valueOf(SplashScreen.logoSize));
+    boolean logo = (bg_logo_url != null || uod_logo_url != null);
+    StringBuilder sb = new StringBuilder();
+    sb.append(
+            "<br><br>Jalview is free software released under GPLv3.<br><br>Development is managed by The Barton Group, University of Dundee, Scotland, UK.");
+    if (logo)
+    {
+      sb.append("<br>");
+    }
+    sb.append(bg_logo_url == null ? ""
+            : "<img alt=\"Barton Group logo\" src=\""
+                    + bg_logo_url.toString() + "\">");
+    sb.append(uod_logo_url == null ? ""
+            : "&nbsp;<img alt=\"University of Dundee shield\" src=\""
+                    + uod_logo_url.toString() + "\">");
+    sb.append(
+            "<br><br>For help, see <a href=\"https://www.jalview.org/faq\">www.jalview.org/faq</a> and join <a href=\"https://discourse.jalview.org\">discourse.jalview.org</a>");
+    sb.append("<br><br>If  you use Jalview, please cite:"
+            + "<br>Waterhouse, A.M., Procter, J.B., Martin, D.M.A, Clamp, M. and Barton, G. J. (2009)"
+            + "<br>Jalview Version 2 - a multiple sequence alignment editor and analysis workbench"
+            + "<br>Bioinformatics <a href=\"https://doi.org/10.1093/bioinformatics/btp033\">doi: 10.1093/bioinformatics/btp033</a>");
+    CITATION = sb.toString();
+  }
+
+  private static final String DEFAULT_AUTHORS = "The Jalview Authors (See AUTHORS file for current list)";
+
   private static int DEFAULT_MIN_WIDTH = 300;
 
   private static int DEFAULT_MIN_HEIGHT = 250;
@@ -147,8 +182,14 @@ public class Desktop extends jalview.jbgui.GDesktop
 
   private static final String EXPERIMENTAL_FEATURES = "EXPERIMENTAL_FEATURES";
 
+  public static final String CONFIRM_KEYBOARD_QUIT = "CONFIRM_KEYBOARD_QUIT";
+
+  public static HashMap<String, FileWriter> savingFiles = new HashMap<String, FileWriter>();
+
   private JalviewChangeSupport changeSupport = new JalviewChangeSupport();
 
+  public static boolean nosplash = false;
+
   /**
    * news reader - null if it was never started.
    */
@@ -345,39 +386,103 @@ public class Desktop extends jalview.jbgui.GDesktop
    */
   public Desktop()
   {
+    super();
     /**
-     * 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.
+     * 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;
-    if (!Jalview.isJS())
+
+    doConfigureStructurePrefs();
+    setTitle(ChannelProperties.getProperty("app_name") + " "
+            + Cache.getProperty("VERSION"));
+
+    /**
+     * Set taskbar "grouped windows" name for linux desktops (works in GNOME and
+     * KDE). This uses sun.awt.X11.XToolkit.awtAppClassName which is not
+     * officially documented or guaranteed to exist, so we access it via
+     * reflection. There appear to be unfathomable criteria about what this
+     * string can contain, and it if doesn't meet those criteria then "java"
+     * (KDE) or "jalview-bin-Jalview" (GNOME) is used. "Jalview", "Jalview
+     * Develop" and "Jalview Test" seem okay, but "Jalview non-release" does
+     * not. The reflection access may generate a warning: WARNING: An illegal
+     * reflective access operation has occurred WARNING: Illegal reflective
+     * access by jalview.gui.Desktop () to field
+     * sun.awt.X11.XToolkit.awtAppClassName which I don't think can be avoided.
+     */
+    if (Platform.isLinux())
     {
-      doVamsasClientCheck();
+      try
+      {
+        Toolkit xToolkit = Toolkit.getDefaultToolkit();
+        Field[] declaredFields = xToolkit.getClass().getDeclaredFields();
+        Field awtAppClassNameField = null;
+
+        if (Arrays.stream(declaredFields)
+                .anyMatch(f -> f.getName().equals("awtAppClassName")))
+        {
+          awtAppClassNameField = xToolkit.getClass()
+                  .getDeclaredField("awtAppClassName");
+        }
+
+        String title = ChannelProperties.getProperty("app_name");
+        if (awtAppClassNameField != null)
+        {
+          awtAppClassNameField.setAccessible(true);
+          awtAppClassNameField.set(xToolkit, title);
+        }
+        else
+        {
+          jalview.bin.Console.debug("XToolkit: awtAppClassName not found");
+        }
+      } catch (Exception e)
+      {
+        jalview.bin.Console.debug("Error setting awtAppClassName");
+        jalview.bin.Console.trace(Cache.getStackTraceString(e));
+      }
     }
 
-    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);
+    setIconImages(ChannelProperties.getIconList());
+
+    addWindowListener(new WindowAdapter()
+    {
+
+      @Override
+      public void windowClosing(WindowEvent ev)
+      {
+        quit();
+      }
+    });
+
+    boolean selmemusage = Cache.getDefault("SHOW_MEMUSAGE", false);
+
+    boolean showjconsole = Cache.getDefault("SHOW_JAVA_CONSOLE", false);
     desktop = new MyDesktopPane(selmemusage);
+
     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);
+
+    // BH 2018 - just an experiment to try unclipped JInternalFrames.
+    if (Platform.isJS())
+    {
+      getRootPane().putClientProperty("swingjs.overflow.hidden", "false");
+    }
+
     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(
-            (Platform.isWindows() ? new DefaultDesktopManager()
-                    : Platform.isAMac()
+            (Platform.isWindowsAndNotJS() ? new DefaultDesktopManager()
+                    : Platform.isAMacAndNotJS()
                             ? new AquaInternalFrameManager(
                                     desktop.getDesktopManager())
                             : desktop.getDesktopManager())));
@@ -394,24 +499,16 @@ public class Desktop extends jalview.jbgui.GDesktop
       int yPos = Math.max(5, (screenSize.height - 650) / 2);
       setBounds(xPos, yPos, 900, 650);
     }
-    
-    boolean doFullLoad = /** @j2sNative ! */true;
-    
-    if (doFullLoad) {
-      
-      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"));
 
+    if (!Platform.isJS())
+    /**
+     * Java only
+     * 
+     * @j2sIgnore
+     */
+    {
+      jconsole = new Console(this, showjconsole);
+      jconsole.setHeader(Cache.getVersionDetailsForConsole());
       showConsole(showjconsole);
 
       showNews.setVisible(false);
@@ -423,28 +520,31 @@ public class Desktop extends jalview.jbgui.GDesktop
       checkURLLinks();
 
       // Spawn a thread that shows the splashscreen
-
-      SwingUtilities.invokeLater(new Runnable()
+      if (!nosplash)
       {
-        @Override
-        public void run()
+        SwingUtilities.invokeLater(new Runnable()
         {
-          new SplashScreen();
-        }
-      });
+          @Override
+          public void run()
+          {
+            new SplashScreen(true);
+          }
+        });
+      }
 
-      // Thread off a new instance of the file chooser - this reduces the time it
+      // 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.");
+          jalview.bin.Console.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.");
+          jalview.bin.Console.debug("Filechooser init thread finished.");
         }
       }).start();
       // Add the service change listener
@@ -455,14 +555,13 @@ public class Desktop extends jalview.jbgui.GDesktop
                 @Override
                 public void propertyChange(PropertyChangeEvent evt)
                 {
-                  Cache.log.debug("Firing service changed event for "
-                          + evt.getNewValue());
+                  jalview.bin.Console
+                          .debug("Firing service changed event for "
+                                  + evt.getNewValue());
                   JalviewServicesChanged(evt);
                 }
-
               });
-
-    } 
+    }
 
     this.setDropTarget(new java.awt.dnd.DropTarget(desktop, this));
 
@@ -497,7 +596,6 @@ public class Desktop extends jalview.jbgui.GDesktop
       }
     });
     desktop.addMouseListener(ma);
-
   }
 
   /**
@@ -518,14 +616,15 @@ public class Desktop extends jalview.jbgui.GDesktop
     // configure services
     StructureSelectionManager ssm = StructureSelectionManager
             .getStructureSelectionManager(this);
-    if (jalview.bin.Cache.getDefault(Preferences.ADD_SS_ANN, true))
+    if (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.setAddTempFacAnnot(
+              Cache.getDefault(Preferences.ADD_TEMPFACT_ANN, true));
+      ssm.setProcessSecondaryStructure(
+              Cache.getDefault(Preferences.STRUCT_FROM_PDB, true));
+      // JAL-3915 - RNAView is no longer an option so this has no effect
       ssm.setSecStructServices(
-              jalview.bin.Cache.getDefault(Preferences.USE_RNAVIEW, true));
+              Cache.getDefault(Preferences.USE_RNAVIEW, false));
     }
     else
     {
@@ -539,40 +638,44 @@ public class Desktop extends jalview.jbgui.GDesktop
   {
     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.");
+        jalview.bin.Console.debug("Starting news thread.");
         jvnews = new BlogReader(me);
         showNews.setVisible(true);
-        Cache.log.debug("Completed news thread.");
+        jalview.bin.Console.debug("Completed news thread.");
       }
-    });
+    }).start();
   }
 
   public void getIdentifiersOrgData()
   {
-    // Thread off the identifiers fetcher
-    addDialogThread(new Runnable()
-    {
-      @Override
-      public void run()
+    if (Cache.getProperty("NOIDENTIFIERSSERVICE") == null)
+    {// Thread off the identifiers fetcher
+      new Thread(new Runnable()
       {
-        Cache.log.debug("Downloading data from identifiers.org");
-        UrlDownloadClient client = new UrlDownloadClient();
-        try
-        {
-          client.download(IdOrgSettings.getUrl(),
-                  IdOrgSettings.getDownloadLocation());
-        } catch (IOException e)
+        @Override
+        public void run()
         {
-          Cache.log.debug("Exception downloading identifiers.org data"
-                  + e.getMessage());
+          jalview.bin.Console
+                  .debug("Downloading data from identifiers.org");
+          try
+          {
+            UrlDownloadClient.download(IdOrgSettings.getUrl(),
+                    IdOrgSettings.getDownloadLocation());
+          } catch (IOException e)
+          {
+            jalview.bin.Console
+                    .debug("Exception downloading identifiers.org data"
+                            + e.getMessage());
+          }
         }
-      }
-    });
+      }).start();
+      ;
+    }
   }
 
   @Override
@@ -583,7 +686,7 @@ public class Desktop extends jalview.jbgui.GDesktop
 
   void showNews(boolean visible)
   {
-    Cache.log.debug((visible ? "Showing" : "Hiding") + " news.");
+    jalview.bin.Console.debug((visible ? "Showing" : "Hiding") + " news.");
     showNews.setSelected(visible);
     if (visible && !jvnews.isVisible())
     {
@@ -615,25 +718,23 @@ public class Desktop extends jalview.jbgui.GDesktop
   {
     // TODO: lock aspect ratio for scaling desktop Bug #0058199
     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 x = Cache.getProperty(windowName + "SCREEN_X");
+    String y = Cache.getProperty(windowName + "SCREEN_Y");
+    String width = Cache.getProperty(windowName + "SCREEN_WIDTH");
+    String height = 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);
-      if (jalview.bin.Cache.getProperty("SCREENGEOMETRY_WIDTH") != null)
+      if (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(Cache.getProperty("SCREENGEOMETRY_WIDTH"))));
+        double sh = ((1f * screenSize.height) / (1f * Integer
+                .parseInt(Cache.getProperty("SCREENGEOMETRY_HEIGHT"))));
         // rescale the bounds depending upon the current screen geometry.
         ix = (int) (ix * sw);
         iw = (int) (iw * sw);
@@ -641,17 +742,17 @@ public class Desktop extends jalview.jbgui.GDesktop
         ih = (int) (ih * sh);
         while (ix >= screenSize.width)
         {
-          jalview.bin.Cache.log.debug(
+          jalview.bin.Console.debug(
                   "Window geometry location recall error: shifting horizontal to within screenbounds.");
           ix -= screenSize.width;
         }
         while (iy >= screenSize.height)
         {
-          jalview.bin.Cache.log.debug(
+          jalview.bin.Console.debug(
                   "Window geometry location recall error: shifting vertical to within screenbounds.");
           iy -= screenSize.height;
         }
-        jalview.bin.Cache.log.debug(
+        jalview.bin.Console.debug(
                 "Got last known dimensions for " + windowName + ": x:" + ix
                         + " y:" + iy + " width:" + iw + " height:" + ih);
       }
@@ -661,46 +762,6 @@ public class Desktop extends jalview.jbgui.GDesktop
     return null;
   }
 
-  private void doVamsasClientCheck()
-  {
-    if (Cache.vamsasJarsPresent())
-    {
-      setupVamsasDisconnectedGui();
-      VamsasMenu.setVisible(true);
-      final Desktop us = this;
-      VamsasMenu.addMenuListener(new MenuListener()
-      {
-        // this listener remembers when the menu was first selected, and
-        // doesn't rebuild the session list until it has been cleared and
-        // 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)
-          {
-            us.buildVamsasStMenu();
-            refresh = false;
-          }
-        }
-      });
-      vamsasStart.setVisible(true);
-    }
-  }
-
   void showPasteMenu(int x, int y)
   {
     JPopupMenu popup = new JPopupMenu();
@@ -872,8 +933,7 @@ public class Desktop extends jalview.jbgui.GDesktop
     frame.setResizable(resizable);
     frame.setMaximizable(resizable);
     frame.setIconifiable(resizable);
-    frame.setOpaque(/** @j2sNative true || */
-            false);
+    frame.setOpaque(Platform.isJS());
 
     if (frame.getX() < 1 && frame.getY() < 1)
     {
@@ -882,8 +942,8 @@ public class Desktop extends jalview.jbgui.GDesktop
     }
 
     /*
-     * add an entry for the new frame in the Window menu 
-     * (and remove it when the frame is closed)
+     * add an entry for the new frame in the Window menu (and remove it when the
+     * frame is closed)
      */
     final JMenuItem menuItem = new JMenuItem(title);
     frame.addInternalFrameListener(new InternalFrameAdapter()
@@ -908,8 +968,7 @@ public class Desktop extends jalview.jbgui.GDesktop
         PaintRefresher.RemoveComponent(frame);
 
         /*
-         * defensive check to prevent frames being
-         * added half off the window
+         * defensive check to prevent frames being added half off the window
          */
         if (openFrameCount > 0)
         {
@@ -924,7 +983,7 @@ public class Desktop extends jalview.jbgui.GDesktop
           menuItem.removeActionListener(menuItem.getActionListeners()[0]);
         }
         windowMenu.remove(menuItem);
-      };
+      }
     });
 
     menuItem.addActionListener(new ActionListener()
@@ -938,7 +997,7 @@ public class Desktop extends jalview.jbgui.GDesktop
           frame.setIcon(false);
         } catch (java.beans.PropertyVetoException ex)
         {
-          // System.err.println(ex.toString());
+
         }
       }
     });
@@ -958,15 +1017,15 @@ public class Desktop extends jalview.jbgui.GDesktop
     {
     } 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",
+      jalview.bin.Console.warn(
+              "Squashed a possible GUI implementation error. If you can recreate this, please look at https://issues.jalview.org/browse/JAL-869",
               cex);
     }
   }
 
   /**
-   * Add key bindings to a JInternalFrame so that Ctrl-W and Cmd-W will close the
-   * window
+   * Add key bindings to a JInternalFrame so that Ctrl-W and Cmd-W will close
+   * the window
    * 
    * @param frame
    */
@@ -988,7 +1047,7 @@ public class Desktop extends jalview.jbgui.GDesktop
     KeyStroke ctrlWKey = KeyStroke.getKeyStroke(KeyEvent.VK_W,
             InputEvent.CTRL_DOWN_MASK);
     KeyStroke cmdWKey = KeyStroke.getKeyStroke(KeyEvent.VK_W,
-            Toolkit.getDefaultToolkit().getMenuShortcutKeyMask());
+            ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx());
 
     InputMap inputMap = frame
             .getInputMap(JComponent.WHEN_IN_FOCUSED_WINDOW);
@@ -1080,7 +1139,10 @@ public class Desktop extends jalview.jbgui.GDesktop
           {
             format = new IdentifyFile().identify(file, protocol);
           }
-
+          if (file instanceof File)
+          {
+            Platform.cacheFileData((File) file);
+          }
           new FileLoader().LoadFile(null, file, protocol, format);
 
         }
@@ -1103,17 +1165,17 @@ public class Desktop extends jalview.jbgui.GDesktop
   public void inputLocalFileMenuItem_actionPerformed(AlignViewport viewport)
   {
     String fileFormat = Cache.getProperty("DEFAULT_FILE_FORMAT");
-    JalviewFileChooser chooser = JalviewFileChooser
-            .forRead(Cache.getProperty("LAST_DIRECTORY"), fileFormat);
+    JalviewFileChooser chooser = JalviewFileChooser.forRead(
+            Cache.getProperty("LAST_DIRECTORY"), fileFormat,
+            BackupFiles.getEnabled());
 
     chooser.setFileView(new JalviewFileView());
     chooser.setDialogTitle(
             MessageManager.getString("label.open_local_file"));
     chooser.setToolTipText(MessageManager.getString("action.open"));
 
-    chooser.response(new RunResponse(JalviewFileChooser.APPROVE_OPTION)
+    chooser.setResponseHandler(0, new Runnable()
     {
-
       @Override
       public void run()
       {
@@ -1124,8 +1186,8 @@ public class Desktop extends jalview.jbgui.GDesktop
 
         /*
          * 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.
+         * Skip this step for dynamically added file formats, because IdentifyFile does
+         * not know how to recognise them.
          */
         if (FileFormats.getInstance().isIdentifiable(format))
         {
@@ -1142,14 +1204,14 @@ public class Desktop extends jalview.jbgui.GDesktop
         new FileLoader().LoadFile(viewport, selectedFile,
                 DataSourceType.FILE, format);
       }
-    }).openDialog(this);
+    });
+    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)
@@ -1159,46 +1221,110 @@ public class Desktop extends jalview.jbgui.GDesktop
     JLabel label = new JLabel(
             MessageManager.getString("label.input_file_url"));
 
-    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)
+    /*
+     * the URL to fetch is input in Java: an editable combobox with history JS:
+     * (pending JAL-3038) a plain text field
+     */
+    JComponent history;
+    String urlBase = "https://www.";
+    if (Platform.isJS())
     {
-      st = new StringTokenizer(historyItems, "\t");
-
-      while (st.hasMoreTokens())
+      history = new JTextField(urlBase, 35);
+    }
+    else
+    /**
+     * Java only
+     * 
+     * @j2sIgnore
+     */
+    {
+      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)
       {
-        history.addItem(st.nextElement());
+        for (String token : historyItems.split("\\t"))
+        {
+          asCombo.addItem(token);
+        }
       }
+      history = asCombo;
     }
+    panel.add(history);
+
+    Object[] options = new Object[] { MessageManager.getString("action.ok"),
+        MessageManager.getString("action.cancel") };
+    Runnable action = new Runnable()
+    {
+      @Override
+      public void run()
+      {
+        @SuppressWarnings("unchecked")
+        String url = (history instanceof JTextField
+                ? ((JTextField) history).getText()
+                : ((JComboBox<String>) history).getEditor().getItem()
+                        .toString().trim());
 
-    // BH 2018 -- providing a callback for SwingJS
-    // dialogOption is just a simple way to provide
-    // context for the modal-like response.
-    // The only requirement is that desktop implement
-    // PropertyChangeListener, which is used already in Java
-    // for changes in input value and such within the dialogs.
+        if (url.toLowerCase(Locale.ROOT).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
+          }
 
-    String dialogOption = "label.input_alignment_from_url";
-    desktop.dialogData = new Object[] { dialogOption, viewport, history };
-    desktop.onDialogReturn(JvOptionPane.showInternalConfirmDialog(desktop,
-            panel, MessageManager.getString(dialogOption),
-            JvOptionPane.OK_CANCEL_OPTION));
+          if (format == null)
+          {
+            String msg = MessageManager
+                    .formatMessage("label.couldnt_locate", url);
+            JvOptionPane.showInternalMessageDialog(Desktop.desktop, msg,
+                    MessageManager.getString("label.url_not_found"),
+                    JvOptionPane.WARNING_MESSAGE);
 
-    // no code may follow this, as SwingJS will not block
-    // callback in JavaScript comes via a property change event,
-    // thus going into desktop.onDialogReturn(int) just the same as
-    // in Java.
+            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(desktop).setResponseHandler(0, action)
+            .showInternalDialog(panel, dialogOption,
+                    JvOptionPane.YES_NO_CANCEL_OPTION,
+                    JvOptionPane.PLAIN_MESSAGE, null, options,
+                    MessageManager.getString("action.ok"));
   }
 
   /**
@@ -1226,10 +1352,8 @@ public class Desktop extends jalview.jbgui.GDesktop
   public void quit()
   {
     Dimension screen = Toolkit.getDefaultToolkit().getScreenSize();
-    jalview.bin.Cache.setProperty("SCREENGEOMETRY_WIDTH",
-            screen.width + "");
-    jalview.bin.Cache.setProperty("SCREENGEOMETRY_HEIGHT",
-            screen.height + "");
+    Cache.setProperty("SCREENGEOMETRY_WIDTH", screen.width + "");
+    Cache.setProperty("SCREENGEOMETRY_HEIGHT", screen.height + "");
     storeLastKnownDimensions("", new Rectangle(getBounds().x, getBounds().y,
             getWidth(), getHeight()));
 
@@ -1260,14 +1384,14 @@ public class Desktop extends jalview.jbgui.GDesktop
 
   private void storeLastKnownDimensions(String string, Rectangle jc)
   {
-    jalview.bin.Cache.log.debug("Storing last known dimensions for "
-            + string + ": x:" + jc.x + " y:" + jc.y + " width:" + jc.width
+    jalview.bin.Console.debug("Storing last known dimensions for " + string
+            + ": x:" + jc.x + " y:" + jc.y + " width:" + jc.width
             + " height:" + jc.height);
 
-    jalview.bin.Cache.setProperty(string + "SCREEN_X", jc.x + "");
-    jalview.bin.Cache.setProperty(string + "SCREEN_Y", jc.y + "");
-    jalview.bin.Cache.setProperty(string + "SCREEN_WIDTH", jc.width + "");
-    jalview.bin.Cache.setProperty(string + "SCREEN_HEIGHT", jc.height + "");
+    Cache.setProperty(string + "SCREEN_X", jc.x + "");
+    Cache.setProperty(string + "SCREEN_Y", jc.y + "");
+    Cache.setProperty(string + "SCREEN_WIDTH", jc.width + "");
+    Cache.setProperty(string + "SCREEN_HEIGHT", jc.height + "");
   }
 
   /**
@@ -1279,53 +1403,44 @@ public class Desktop extends jalview.jbgui.GDesktop
   @Override
   public void aboutMenuItem_actionPerformed(ActionEvent e)
   {
-    // StringBuffer message = getAboutMessage(false);
-    // JvOptionPane.showInternalMessageDialog(Desktop.desktop,
-    //
-    // message.toString(), "About Jalview", JvOptionPane.INFORMATION_MESSAGE);
     new Thread(new Runnable()
     {
       @Override
       public void run()
       {
-        new SplashScreen(true);
+        new SplashScreen(false);
       }
     }).start();
   }
 
-  public StringBuffer getAboutMessage(boolean shortv)
+  /**
+   * Returns the html text for the About screen, including any available version
+   * number, build details, author details and citation reference, but without
+   * the enclosing {@code html} tags
+   * 
+   * @return
+   */
+  public String getAboutMessage()
   {
-    StringBuffer message = new StringBuffer();
-    message.append("<html>");
-    if (shortv)
-    {
-      message.append("<h1><strong>Version: "
-              + jalview.bin.Cache.getProperty("VERSION")
-              + "</strong></h1>");
-      message.append("<strong>Last Updated: <em>"
-              + jalview.bin.Cache.getDefault("BUILD_DATE", "unknown")
-              + "</em></strong>");
-
-    }
-    else
-    {
+    StringBuilder message = new StringBuilder(1024);
+    message.append("<div style=\"font-family: sans-serif;\">")
+            .append("<h1><strong>Version: ")
+            .append(Cache.getProperty("VERSION")).append("</strong></h1>")
+            .append("<strong>Built: <em>")
+            .append(Cache.getDefault("BUILD_DATE", "unknown"))
+            .append("</em> from ").append(Cache.getBuildDetailsForSplash())
+            .append("</strong>");
 
-      message.append("<strong>Version "
-              + jalview.bin.Cache.getProperty("VERSION")
-              + "; last updated: "
-              + jalview.bin.Cache.getDefault("BUILD_DATE", "unknown"));
-    }
-
-    if (jalview.bin.Cache.getDefault("LATEST_VERSION", "Checking")
-            .equals("Checking"))
+    String latestVersion = Cache.getDefault("LATEST_VERSION", "Checking");
+    if (latestVersion.equals("Checking"))
     {
-      message.append("<br>...Checking latest version...</br>");
+      // JBP removed this message for 2.11: May be reinstated in future version
+      // message.append("<br>...Checking latest version...</br>");
     }
-    else if (!jalview.bin.Cache.getDefault("LATEST_VERSION", "Checking")
-            .equals(jalview.bin.Cache.getProperty("VERSION")))
+    else if (!latestVersion.equals(Cache.getProperty("VERSION")))
     {
       boolean red = false;
-      if (jalview.bin.Cache.getProperty("VERSION").toLowerCase()
+      if (Cache.getProperty("VERSION").toLowerCase(Locale.ROOT)
               .indexOf("automated build") == -1)
       {
         red = true;
@@ -1334,29 +1449,24 @@ public class Desktop extends jalview.jbgui.GDesktop
         message.append("<div style=\"color: #FF0000;font-style: bold;\">");
       }
 
-      message.append("<br>!! Version "
-              + jalview.bin.Cache.getDefault("LATEST_VERSION",
-                      "..Checking..")
-              + " is available for download from "
-              + jalview.bin.Cache.getDefault("www.jalview.org",
-                      "http://www.jalview.org")
-              + " !!");
+      message.append("<br>!! Version ")
+              .append(Cache.getDefault("LATEST_VERSION", "..Checking.."))
+              .append(" is available for download from ")
+              .append(Cache.getDefault("www.jalview.org",
+                      "https://www.jalview.org"))
+              .append(" !!");
       if (red)
       {
         message.append("</div>");
       }
     }
-    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:"
-            + "<br>Waterhouse, A.M., Procter, J.B., Martin, D.M.A, Clamp, M. and Barton, G. J. (2009)"
-            + "<br>Jalview Version 2 - a multiple sequence alignment editor and analysis workbench"
-            + "<br>Bioinformatics doi: 10.1093/bioinformatics/btp033"
-            + "</html>");
-    return message;
+    message.append("<br>Authors:  ");
+    message.append(Cache.getDefault("AUTHORFNAMES", DEFAULT_AUTHORS));
+    message.append(CITATION);
+
+    message.append("</div>");
+
+    return message.toString();
   }
 
   /**
@@ -1367,11 +1477,16 @@ public class Desktop extends jalview.jbgui.GDesktop
   {
     try
     {
-      if (Jalview.isJS())
+      if (Platform.isJS())
       {
-        BrowserLauncher.openURL("http://www.jalview.org/help.html");
+        BrowserLauncher.openURL("https://www.jalview.org/help.html");
       }
       else
+      /**
+       * Java only
+       * 
+       * @j2sIgnore
+       */
       {
         Help.showHelpWindow();
       }
@@ -1397,10 +1512,6 @@ public class Desktop extends jalview.jbgui.GDesktop
     }
     Jalview.setCurrentAlignFrame(null);
     System.out.println("ALL CLOSED");
-    if (v_client != null)
-    {
-      // TODO clear binding to vamsas document objects on close_all
-    }
 
     /*
      * reset state of singleton objects as appropriate (clear down session state
@@ -1441,17 +1552,16 @@ public class Desktop extends jalview.jbgui.GDesktop
   protected void garbageCollect_actionPerformed(ActionEvent e)
   {
     // We simply collect the garbage
-    jalview.bin.Cache.log.debug("Collecting garbage...");
+    jalview.bin.Console.debug("Collecting garbage...");
     System.gc();
-    jalview.bin.Cache.log.debug("Finished garbage collection.");
+    jalview.bin.Console.debug("Finished garbage collection.");
   }
 
   /*
    * (non-Javadoc)
    * 
-   * @see
-   * jalview.jbgui.GDesktop#showMemusage_actionPerformed(java.awt.event.ActionEvent
-   * )
+   * @see jalview.jbgui.GDesktop#showMemusage_actionPerformed(java.awt.event.
+   * ActionEvent )
    */
   @Override
   protected void showMemusage_actionPerformed(ActionEvent e)
@@ -1577,7 +1687,7 @@ public class Desktop extends jalview.jbgui.GDesktop
   @Override
   protected void preferences_actionPerformed(ActionEvent e)
   {
-    new Preferences();
+    Preferences.openPreferences();
   }
 
   /**
@@ -1587,20 +1697,43 @@ public class Desktop extends jalview.jbgui.GDesktop
   @Override
   public void saveState_actionPerformed()
   {
-    JalviewFileChooser chooser = new JalviewFileChooser("jvp",
-            "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
@@ -1609,38 +1742,52 @@ public class Desktop extends jalview.jbgui.GDesktop
           // TODO: refactor to Jalview desktop session controller action.
           setProgressBar(MessageManager.formatMessage(
                   "label.saving_jalview_project", new Object[]
-                  { choice.getName() }), choice.hashCode());
-          jalview.bin.Cache.setProperty("LAST_DIRECTORY",
-                  choice.getParent());
+                  { chosenFile.getName() }), chosenFile.hashCode());
+          Cache.setProperty("LAST_DIRECTORY", 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);
+            new OOMWarning("Whilst saving current state to "
+                    + chosenFile.getName(), oom);
           } catch (Exception ex)
           {
-            Cache.log.error(
-                    "Problems whilst trying to save to " + choice.getName(),
-                    ex);
+            jalview.bin.Console.error("Problems whilst trying to save to "
+                    + chosenFile.getName(), ex);
             JvOptionPane.showMessageDialog(me,
                     MessageManager.formatMessage(
                             "label.error_whilst_saving_current_state_to",
                             new Object[]
-                            { choice.getName() }),
+                            { 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)
   {
     this.projectFile = choice;
@@ -1652,58 +1799,62 @@ public class Desktop extends jalview.jbgui.GDesktop
   }
 
   /**
-   * Prompts the user to choose a file and loads in as a Jalview project file
+   * Shows a file chooser dialog and tries to read in the selected file as a
+   * Jalview project
    */
   @Override
   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(
-            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, BackupFiles.getEnabled()); // 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();
-      Cache.setProperty("LAST_DIRECTORY", selectedFile.getParent());
-      new Thread(new Runnable()
+      @Override
+      public void run()
       {
-        @Override
-        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
+          @Override
+          public void run()
           {
-            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.desktop,
-                    MessageManager.formatMessage(
-                            "label.error_whilst_loading_project_from",
-                            new Object[]
-                            { choice }),
-                    MessageManager.getString("label.couldnt_load_project"),
-                    JvOptionPane.WARNING_MESSAGE);
+            try
+            {
+              new Jalview2XML().loadJalviewAlign(selectedFile);
+            } catch (OutOfMemoryError oom)
+            {
+              new OOMWarning("Whilst loading project from " + choice, oom);
+            } catch (Exception ex)
+            {
+              jalview.bin.Console.error(
+                      "Problems whilst loading project from " + choice, ex);
+              JvOptionPane.showMessageDialog(Desktop.desktop,
+                      MessageManager.formatMessage(
+                              "label.error_whilst_loading_project_from",
+                              new Object[]
+                              { choice }),
+                      MessageManager
+                              .getString("label.couldnt_load_project"),
+                      JvOptionPane.WARNING_MESSAGE);
+            }
           }
-          setProgressBar(null, choice.hashCode());
-        }
-      }).start();
-    }
+        }, "Project Loader").start();
+      }
+    });
+
+    chooser.showOpenDialog(this);
   }
 
   @Override
@@ -1889,15 +2040,29 @@ public class Desktop extends jalview.jbgui.GDesktop
       return;
     }
 
+    // FIXME: ideally should use UI interface API
+    FeatureSettings viewFeatureSettings = (af.featureSettings != null
+            && af.featureSettings.isOpen()) ? af.featureSettings : null;
+    Rectangle fsBounds = af.getFeatureSettingsGeometry();
     for (int i = 0; i < size; i++)
     {
       AlignmentPanel ap = af.alignPanels.get(i);
+
       AlignFrame newaf = new AlignFrame(ap);
 
+      // transfer reference for existing feature settings to new alignFrame
+      if (ap == af.alignPanel)
+      {
+        if (viewFeatureSettings != null && viewFeatureSettings.fr.ap == ap)
+        {
+          newaf.featureSettings = viewFeatureSettings;
+        }
+        newaf.setFeatureSettingsGeometry(fsBounds);
+      }
+
       /*
-       * Restore the view's last exploded frame geometry if known. Multiple
-       * views from one exploded frame share and restore the same (frame)
-       * position and size.
+       * Restore the view's last exploded frame geometry if known. Multiple views from
+       * one exploded frame share and restore the same (frame) position and size.
        */
       Rectangle geometry = ap.av.getExplodedGeometry();
       if (geometry != null)
@@ -1909,8 +2074,18 @@ public class Desktop extends jalview.jbgui.GDesktop
 
       addInternalFrame(newaf, af.getTitle(), AlignFrame.DEFAULT_WIDTH,
               AlignFrame.DEFAULT_HEIGHT);
+      // and materialise a new feature settings dialog instance for the new
+      // alignframe
+      // (closes the old as if 'OK' was pressed)
+      if (ap == af.alignPanel && newaf.featureSettings != null
+              && newaf.featureSettings.isOpen()
+              && af.alignPanel.getAlignViewport().isShowSequenceFeatures())
+      {
+        newaf.showFeatureSettingsUI();
+      }
     }
 
+    af.featureSettings = null;
     af.alignPanels.clear();
     af.closeMenuItem_actionPerformed(true);
 
@@ -1918,9 +2093,9 @@ public class Desktop extends jalview.jbgui.GDesktop
 
   /**
    * 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
    */
@@ -1930,7 +2105,6 @@ public class Desktop extends jalview.jbgui.GDesktop
     source.viewport.setExplodedGeometry(source.getBounds());
     JInternalFrame[] frames = desktop.getAllFrames();
     String viewId = source.viewport.getSequenceSetId();
-
     for (int t = 0; t < frames.length; t++)
     {
       if (frames[t] instanceof AlignFrame && frames[t] != source)
@@ -1951,374 +2125,33 @@ public class Desktop extends jalview.jbgui.GDesktop
 
         if (gatherThis)
         {
-          af.alignPanels.clear();
-          af.closeMenuItem_actionPerformed(true);
-        }
-      }
-    }
-
-  }
-
-  jalview.gui.VamsasApplication v_client = null;
-
-  @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.
-      JalviewFileChooser chooser = new JalviewFileChooser(
-              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"));
-
-      int value = chooser.showOpenDialog(this);
-
-      if (value == JalviewFileChooser.APPROVE_OPTION)
-      {
-        String fle = chooser.getSelectedFile().toString();
-        if (!vamsasImport(chooser.getSelectedFile()))
-        {
-          JvOptionPane.showInternalMessageDialog(Desktop.desktop,
-                  MessageManager.formatMessage(
-                          "label.couldnt_import_as_vamsas_session",
-                          new Object[]
-                          { fle }),
-                  MessageManager
-                          .getString("label.vamsas_document_import_failed"),
-                  JvOptionPane.ERROR_MESSAGE);
-        }
-      }
-    }
-    else
-    {
-      jalview.bin.Cache.log.error(
-              "Implementation error - load session from a running session is not supported.");
-    }
-  }
-
-  /**
-   * import file into a new vamsas session (uses jalview.gui.VamsasApplication)
-   * 
-   * @param file
-   * @return true if import was a success and a session was started.
-   */
-  public boolean vamsasImport(URL url)
-  {
-    // TODO: create progress bar
-    if (v_client != null)
-    {
-
-      jalview.bin.Cache.log.error(
-              "Implementation error - load session from a running session is not supported.");
-      return false;
-    }
-
-    try
-    {
-      // copy the URL content to a temporary local file
-      // TODO: be a bit cleverer here with nio (?!)
-      File file = File.createTempFile("vdocfromurl", ".vdj");
-      FileOutputStream fos = new FileOutputStream(file);
-      BufferedInputStream bis = new BufferedInputStream(url.openStream());
-      byte[] buffer = new byte[2048];
-      int ln;
-      while ((ln = bis.read(buffer)) > -1)
-      {
-        fos.write(buffer, 0, ln);
-      }
-      bis.close();
-      fos.close();
-      v_client = new jalview.gui.VamsasApplication(this, file,
-              url.toExternalForm());
-    } catch (Exception ex)
-    {
-      jalview.bin.Cache.log.error(
-              "Failed to create new vamsas session from contents of URL "
-                      + url,
-              ex);
-      return false;
-    }
-    setupVamsasConnectedGui();
-    v_client.initial_update(); // TODO: thread ?
-    return v_client.inSession();
-  }
-
-  /**
-   * import file into a new vamsas session (uses jalview.gui.VamsasApplication)
-   * 
-   * @param file
-   * @return true if import was a success and a session was started.
-   */
-  public boolean vamsasImport(File file)
-  {
-    if (v_client != null)
-    {
-
-      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());
-    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());
-      jalview.bin.Cache.log.error(
-              "New vamsas session from existing session file failed:", ex);
-      return false;
-    }
-    setupVamsasConnectedGui();
-    v_client.initial_update(); // TODO: thread ?
-    setProgressBar(MessageManager.formatMessage(
-            "status.importing_vamsas_session_from", new Object[]
-            { file.getName() }), file.hashCode());
-    return v_client.inSession();
-  }
-
-  public boolean joinVamsasSession(String mysesid)
-  {
-    if (v_client != null)
-    {
-      throw new Error(MessageManager
-              .getString("error.try_join_vamsas_session_another"));
-    }
-    if (mysesid == null)
-    {
-      throw new Error(
-              MessageManager.getString("error.invalid_vamsas_session_id"));
-    }
-    v_client = new VamsasApplication(this, mysesid);
-    setupVamsasConnectedGui();
-    v_client.initial_update();
-    return (v_client.inSession());
-  }
-
-  @Override
-  public void vamsasStart_actionPerformed(ActionEvent e)
-  {
-    if (v_client == null)
-    {
-      // Start a session.
-      // we just start a default session for moment.
-      /*
-       * JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.
-       * getProperty("LAST_DIRECTORY"));
-       * 
-       * chooser.setFileView(new JalviewFileView());
-       * chooser.setDialogTitle("Load Vamsas file");
-       * chooser.setToolTipText("Import");
-       * 
-       * int value = chooser.showOpenDialog(this);
-       * 
-       * if (value == JalviewFileChooser.APPROVE_OPTION) { v_client = new
-       * jalview.gui.VamsasApplication(this, chooser.getSelectedFile());
-       */
-      v_client = new VamsasApplication(this);
-      setupVamsasConnectedGui();
-      v_client.initial_update(); // TODO: thread ?
-    }
-    else
-    {
-      // store current data in session.
-      v_client.push_update(); // TODO: thread
-    }
-  }
-
-  protected void setupVamsasConnectedGui()
-  {
-    vamsasStart.setText(MessageManager.getString("label.session_update"));
-    vamsasSave.setVisible(true);
-    vamsasStop.setVisible(true);
-    vamsasImport.setVisible(false); // Document import to existing session is
-    // not possible for vamsas-client-1.0.
-  }
-
-  protected void setupVamsasDisconnectedGui()
-  {
-    vamsasSave.setVisible(false);
-    vamsasStop.setVisible(false);
-    vamsasImport.setVisible(true);
-    vamsasStart
-            .setText(MessageManager.getString("label.new_vamsas_session"));
-  }
-
-  @Override
-  public void vamsasStop_actionPerformed(ActionEvent e)
-  {
-    if (v_client != null)
-    {
-      v_client.end_session();
-      v_client = null;
-      setupVamsasDisconnectedGui();
-    }
-  }
-
-  protected void buildVamsasStMenu()
-  {
-    if (v_client == null)
-    {
-      String[] sess = null;
-      try
-      {
-        sess = VamsasApplication.getSessionList();
-      } catch (Exception 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.");
-        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] }));
-          final Desktop dsktp = this;
-          final String mysesid = sess[i];
-          sessit.addActionListener(new ActionListener()
+          if (af.featureSettings != null && af.featureSettings.isOpen())
           {
-
-            @Override
-            public void actionPerformed(ActionEvent e)
+            if (source.featureSettings == null)
             {
-              if (dsktp.v_client == null)
-              {
-                Thread rthr = new Thread(new Runnable()
-                {
-
-                  @Override
-                  public void run()
-                  {
-                    dsktp.v_client = new VamsasApplication(dsktp, mysesid);
-                    dsktp.setupVamsasConnectedGui();
-                    dsktp.v_client.initial_update();
-                  }
-
-                });
-                rthr.start();
-              }
-            };
-          });
-          VamsasStMenu.add(sessit);
+              // preserve the feature settings geometry for this frame
+              source.featureSettings = af.featureSettings;
+              source.setFeatureSettingsGeometry(
+                      af.getFeatureSettingsGeometry());
+            }
+            else
+            {
+              // close it and forget
+              af.featureSettings.close();
+            }
+          }
+          af.alignPanels.clear();
+          af.closeMenuItem_actionPerformed(true);
         }
-        // don't show an empty menu.
-        VamsasStMenu.setVisible(sess.length > 0);
-
       }
-      else
-      {
-        jalview.bin.Cache.log.debug("No current vamsas sessions.");
-        VamsasStMenu.removeAll();
-        VamsasStMenu.setVisible(false);
-      }
-    }
-    else
-    {
-      // Not interested in the content. Just hide ourselves.
-      VamsasStMenu.setVisible(false);
     }
-  }
 
-  @Override
-  public void vamsasSave_actionPerformed(ActionEvent e)
-  {
-    // TODO: JAL-3048 not needed for Jalview-JS
-
-    if (v_client != null)
+    // refresh the feature setting UI for the source frame if it exists
+    if (source.featureSettings != null && source.featureSettings.isOpen())
     {
-      // TODO: VAMSAS DOCUMENT EXTENSION is VDJ
-      JalviewFileChooser chooser = new JalviewFileChooser("vdj",
-              "Vamsas Document");
-
-      chooser.setFileView(new JalviewFileView());
-      chooser.setDialogTitle(MessageManager
-              .getString("label.save_vamsas_document_archive"));
-
-      int value = chooser.showSaveDialog(this);
-
-      if (value == JalviewFileChooser.APPROVE_OPTION)
-      {
-        java.io.File choice = chooser.getSelectedFile();
-        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
-        {
-          v_client.vclient.storeDocument(choice);
-        } catch (Error ex)
-        {
-          warnttl = "Serious Problem saving Vamsas Document";
-          warnmsg = ex.toString();
-          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);
-
-        }
-        removeProgressPanel(progpanel);
-        if (warnmsg != null)
-        {
-          JvOptionPane.showInternalMessageDialog(Desktop.desktop,
-
-                  warnmsg, warnttl, JvOptionPane.ERROR_MESSAGE);
-        }
-      }
+      source.showFeatureSettingsUI();
     }
-  }
-
-  JPanel vamUpdate = null;
-
-  /**
-   * hide vamsas user gui bits when a vamsas document event is being handled.
-   * 
-   * @param b
-   *          true to hide gui, false to reveal gui
-   */
-  public void setVamsasUpdate(boolean b)
-  {
-    Cache.log.debug("Setting gui for Vamsas update "
-            + (b ? "in progress" : "finished"));
 
-    if (vamUpdate != null)
-    {
-      this.removeProgressPanel(vamUpdate);
-    }
-    if (b)
-    {
-      vamUpdate = this.addProgressPanel(
-              MessageManager.getString("label.updating_vamsas_session"));
-    }
-    vamsasStart.setVisible(!b);
-    vamsasStop.setVisible(!b);
-    vamsasSave.setVisible(!b);
   }
 
   public JInternalFrame[] getAllFrames()
@@ -2362,7 +2195,7 @@ public class Desktop extends jalview.jbgui.GDesktop
           while (li.hasNext())
           {
             String link = li.next();
-            if (link.contains(SEQUENCE_ID)
+            if (link.contains(jalview.util.UrlConstants.SEQUENCE_ID)
                     && !UrlConstants.isDefaultString(link))
             {
               check = true;
@@ -2420,154 +2253,13 @@ public class Desktop extends jalview.jbgui.GDesktop
 
   /**
    * 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, PropertyChangeListener
+  public class MyDesktopPane extends JDesktopPane implements Runnable
   {
-
-    public Object[] dialogData;
-
-    // @Override
-    @Override
-    public void propertyChange(PropertyChangeEvent event)
-    {
-      // TODO this is obsolete with JAL-3048 - delete?
-      Object val = event.getNewValue();
-      String name = event.getPropertyName();
-      System.out.println(name);
-      switch (event.getSource().getClass().getName())
-      {
-      case "javax.swing.JOptionPane":
-        switch (name)
-        {
-        case "inputValue":
-          onDialogReturn(val);
-          return;
-        case "value":
-          if (val instanceof Integer)
-          {
-            onDialogReturn(((Integer) val).intValue());
-          }
-          else
-          {
-            onDialogReturn(val);
-          }
-          return;
-        }
-        break;
-      case "javax.swing.JFileChooser":
-        switch (name)
-        {
-        case "SelectedFile":
-          // in JavaScript, this File object will have a _bytes property,
-          // because the file data has already been loaded
-          onDialogReturn(new Object[] { (File) val });
-          return;
-        }
-        break;
-      }
-      System.out.println(event.getSource().getClass().getName() + " "
-              + event.getPropertyName() + ": " + event.getNewValue());
-    }
-
-    // JSCOmponent.DialogCaller interface
-    void onDialogReturn(Object value)
-    {
-      switch ((String) dialogData[0])
-      {
-      case "SelectedFile":
-      case "runnable":
-        dialogData[0] = value;
-        ((Runnable) dialogData[1]).run();
-        break;
-      default:
-      }
-    }
-
-    // JSCOmponent.DialogCaller interface
-    void onDialogReturn(int value)
-    {
-      if (value != Math.floor(value))
-      {
-        // in JavaScript, this will be NaN, oddly enough
-        return;
-      }
-
-      switch ((String) dialogData[0])
-      {
-      case "runnable":
-        dialogData[0] = Integer.valueOf(value);
-        ((Runnable) dialogData[1]).run();
-        break;
-      case "label.input_alignment_from_url":
-        // reconstruct the parameter data
-        int reply = value;
-        AlignViewport viewport = (AlignViewport) dialogData[1];
-        JComboBox history = (JComboBox) dialogData[2];
-        // the rest of this is unchangaed
-        if (reply != JvOptionPane.OK_OPTION)
-        {
-          return;
-        }
-
-        String url = history.getSelectedItem().toString();
-
-        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 (format == null)
-          {
-            JvOptionPane.showInternalMessageDialog(Desktop.desktop,
-                    MessageManager.formatMessage("label.couldnt_locate",
-                            new Object[]
-                            { url }),
-                    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);
-          }
-        }
-
-        break;
-      }
-
-    }
-
     private static final float ONE_MB = 1048576f;
 
     boolean showMemoryUsage = false;
@@ -2653,6 +2345,9 @@ public class Desktop extends jalview.jbgui.GDesktop
                   10, getHeight() - fm.getHeight());
         }
       }
+
+      // output debug scale message. Important for jalview.bin.HiDPISettingTest2
+      Desktop.debugScaleMessage(Desktop.getDesktop().getGraphics());
     }
   }
 
@@ -2749,7 +2444,7 @@ public class Desktop extends jalview.jbgui.GDesktop
       openGroovyConsole();
     } catch (Exception ex)
     {
-      jalview.bin.Cache.log.error("Groovy Shell Creation failed.", ex);
+      jalview.bin.Console.error("Groovy Shell Creation failed.", ex);
       JvOptionPane.showInternalMessageDialog(Desktop.desktop,
 
               MessageManager.getString("label.couldnt_create_groovy_shell"),
@@ -2771,9 +2466,9 @@ public class Desktop extends jalview.jbgui.GDesktop
 
       /*
        * 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
+       * '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()
@@ -2796,21 +2491,24 @@ public class Desktop extends jalview.jbgui.GDesktop
     ((Window) groovyConsole.getFrame()).setVisible(true);
 
     /*
-     * if we got this far, enable 'Run Groovy' in AlignFrame menus
-     * and disable opening a second console
+     * 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
+   * 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()),
+    getRootPane()
+            .getInputMap(JComponent.WHEN_IN_FOCUSED_WINDOW).put(
+                    KeyStroke
+                            .getKeyStroke(KeyEvent.VK_Q,
+                                    jalview.util.ShortcutKeyMaskExWrapper
+                                            .getMenuShortcutKeyMaskEx()),
                     "Quit");
     getRootPane().getActionMap().put("Quit", new AbstractAction()
     {
@@ -2831,8 +2529,8 @@ public class Desktop extends jalview.jbgui.GDesktop
   public void enableExecuteGroovy(boolean enabled)
   {
     /*
-     * disable opening a second Groovy console
-     * (or re-enable when the console is closed)
+     * disable opening a second Groovy console (or re-enable when the console is
+     * closed)
      */
     groovyShell.setEnabled(!enabled);
 
@@ -2867,18 +2565,18 @@ public class Desktop extends jalview.jbgui.GDesktop
       progressBarHandlers = new Hashtable<>();
     }
 
-    if (progressBars.get(new Long(id)) != null)
+    if (progressBars.get(Long.valueOf(id)) != null)
     {
-      JPanel panel = progressBars.remove(new Long(id));
-      if (progressBarHandlers.contains(new Long(id)))
+      JPanel panel = progressBars.remove(Long.valueOf(id));
+      if (progressBarHandlers.contains(Long.valueOf(id)))
       {
-        progressBarHandlers.remove(new Long(id));
+        progressBarHandlers.remove(Long.valueOf(id));
       }
       removeProgressPanel(panel);
     }
     else
     {
-      progressBars.put(new Long(id), addProgressPanel(message));
+      progressBars.put(Long.valueOf(id), addProgressPanel(message));
     }
   }
 
@@ -2893,13 +2591,13 @@ public class Desktop extends jalview.jbgui.GDesktop
           final IProgressIndicatorHandler handler)
   {
     if (progressBarHandlers == null
-            || !progressBars.containsKey(new Long(id)))
+            || !progressBars.containsKey(Long.valueOf(id)))
     {
       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));
+    progressBarHandlers.put(Long.valueOf(id), handler);
+    final JPanel progressPanel = progressBars.get(Long.valueOf(id));
     if (handler.canCancel())
     {
       JButton cancel = new JButton(
@@ -2937,8 +2635,9 @@ public class Desktop extends jalview.jbgui.GDesktop
   }
 
   /**
-   * 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
@@ -2962,7 +2661,8 @@ public class Desktop extends jalview.jbgui.GDesktop
 
   public VamsasApplication getVamsasApplication()
   {
-    return v_client;
+    // TODO: JAL-3311 remove remaining code from Jalview relating to VAMSAS
+    return null;
 
   }
 
@@ -2991,13 +2691,36 @@ public class Desktop extends jalview.jbgui.GDesktop
     this.inBatchMode = inBatchMode;
   }
 
+  /**
+   * start service discovery and wait till it is done
+   */
   public void startServiceDiscovery()
   {
     startServiceDiscovery(false);
   }
 
+  /**
+   * start service discovery threads - blocking or non-blocking
+   * 
+   * @param blocking
+   */
   public void startServiceDiscovery(boolean blocking)
   {
+    startServiceDiscovery(blocking, false);
+  }
+
+  /**
+   * start service discovery threads
+   * 
+   * @param blocking
+   *          - false means call returns immediately
+   * @param ignore_SHOW_JWS2_SERVICES_preference
+   *          - when true JABA services are discovered regardless of user's JWS2
+   *          discovery preference setting
+   */
+  public void startServiceDiscovery(boolean blocking,
+          boolean ignore_SHOW_JWS2_SERVICES_preference)
+  {
     boolean alive = true;
     Thread t0 = null, t1 = null, t2 = null;
     // JAL-940 - JALVIEW 1 services are now being EOLed as of JABA 2.1 release
@@ -3015,7 +2738,8 @@ public class Desktop extends jalview.jbgui.GDesktop
       (t0 = new Thread(discoverer)).start();
     }
 
-    if (Cache.getDefault("SHOW_JWS2_SERVICES", true))
+    if (ignore_SHOW_JWS2_SERVICES_preference
+            || Cache.getDefault("SHOW_JWS2_SERVICES", true))
     {
       t2 = jalview.ws.jws2.Jws2Discoverer.getDiscoverer()
               .startDiscoverer(changeSupport);
@@ -3068,24 +2792,19 @@ public class Desktop extends jalview.jbgui.GDesktop
                 /*
                  * JalviewDialog jd =new JalviewDialog() {
                  * 
-                 * @Override protected void cancelPressed() { // TODO
-                 * Auto-generated method stub
+                 * @Override protected void cancelPressed() { // TODO Auto-generated method stub
                  * 
-                 * }@Override protected void okPressed() { // TODO
-                 * Auto-generated method stub
+                 * }@Override protected void okPressed() { // TODO Auto-generated method stub
                  * 
-                 * }@Override protected void raiseClosed() { // TODO
-                 * Auto-generated method stub
+                 * }@Override protected void raiseClosed() { // TODO Auto-generated method stub
                  * 
-                 * } }; jd.initDialogFrame(new
-                 * JLabel("<html><table width=\"450\"><tr><td>" + ermsg +
+                 * } }; jd.initDialogFrame(new JLabel("<html><table width=\"450\"><tr><td>" +
+                 * ermsg +
                  * "<br/>It may be that you have invalid JABA URLs in your web service preferences,"
                  * + " or mis-configured HTTP proxy settings.<br/>" +
-                 * "Check the <em>Connections</em> and <em>Web services</em> tab of the"
-                 * +
-                 * " Tools->Preferences dialog box to change them.</td></tr></table></html>"
-                 * ), true, true, "Web Service Configuration Problem", 450,
-                 * 400);
+                 * "Check the <em>Connections</em> and <em>Web services</em> tab of the" +
+                 * " Tools->Preferences dialog box to change them.</td></tr></table></html>" ),
+                 * true, true, "Web Service Configuration Problem", 450, 400);
                  * 
                  * jd.waitForInput();
                  */
@@ -3107,7 +2826,7 @@ public class Desktop extends jalview.jbgui.GDesktop
         }
         else
         {
-          Cache.log.error(
+          jalview.bin.Console.error(
                   "Errors reported by JABA discovery service. Check web services preferences.\n"
                           + ermsg);
         }
@@ -3200,15 +2919,8 @@ public class Desktop extends jalview.jbgui.GDesktop
       {
         if (url != null)
         {
-          if (Cache.log != null)
-          {
-            Cache.log.error("Couldn't handle string " + url + " as a URL.");
-          }
-          else
-          {
-            System.err.println(
-                    "Couldn't handle string " + url + " as a URL.");
-          }
+          jalview.bin.Console
+                  .error("Couldn't handle string " + url + " as a URL.");
         }
         // ignore any exceptions due to dud links.
       }
@@ -3253,7 +2965,6 @@ public class Desktop extends jalview.jbgui.GDesktop
           } catch (InterruptedException x)
           {
           }
-          ;
         }
         if (instance == null)
         {
@@ -3264,7 +2975,8 @@ public class Desktop extends jalview.jbgui.GDesktop
           SwingUtilities.invokeAndWait(prompter);
         } catch (Exception q)
         {
-          Cache.log.warn("Unexpected Exception in dialog thread.", q);
+          jalview.bin.Console.warn("Unexpected Exception in dialog thread.",
+                  q);
         }
       }
     });
@@ -3303,7 +3015,7 @@ public class Desktop extends jalview.jbgui.GDesktop
       public void exportImage(Graphics g) throws Exception
       {
         paintAll(g);
-        Cache.log.info("Successfully written snapshot to file "
+        jalview.bin.Console.info("Successfully written snapshot to file "
                 + of.getAbsolutePath());
       }
     };
@@ -3315,8 +3027,8 @@ public class Desktop extends jalview.jbgui.GDesktop
 
   /**
    * 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.
    * 
@@ -3337,16 +3049,15 @@ public class Desktop extends jalview.jbgui.GDesktop
     }
 
     /*
-     * Processing in reverse order works, forwards order leaves the first panels
-     * not visible. I don't know why!
+     * Processing in reverse order works, forwards order leaves the first panels not
+     * visible. I don't know why!
      */
     for (int i = viewCount - 1; i >= 0; i--)
     {
       /*
-       * Make new top and bottom frames. These take over the respective
-       * AlignmentPanel objects, including their AlignmentViewports, so the
-       * cdna/protein relationships between the viewports is carried over to the
-       * new split frames.
+       * Make new top and bottom frames. These take over the respective AlignmentPanel
+       * objects, including their AlignmentViewports, so the cdna/protein
+       * relationships between the viewports is carried over to the new split frames.
        * 
        * explodedGeometry holds the (x, y) position of the previously exploded
        * SplitFrame, and the (width, height) of the AlignFrame component
@@ -3385,8 +3096,8 @@ public class Desktop extends jalview.jbgui.GDesktop
     }
 
     /*
-     * Clear references to the panels (now relocated in the new SplitFrames)
-     * before closing the old SplitFrame.
+     * Clear references to the panels (now relocated in the new SplitFrames) before
+     * closing the old SplitFrame.
      */
     topPanels.clear();
     bottomPanels.clear();
@@ -3487,26 +3198,6 @@ public class Desktop extends jalview.jbgui.GDesktop
           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
@@ -3515,7 +3206,8 @@ public class Desktop extends jalview.jbgui.GDesktop
               "application/x-java-url; class=java.net.URL");
     } catch (ClassNotFoundException cfe)
     {
-      Cache.log.debug("Couldn't instantiate the URL dataflavor.", cfe);
+      jalview.bin.Console.debug("Couldn't instantiate the URL dataflavor.",
+              cfe);
     }
 
     if (urlFlavour != null && t.isDataFlavorSupported(urlFlavour))
@@ -3530,28 +3222,27 @@ public class Desktop extends jalview.jbgui.GDesktop
         {
           protocols.add(DataSourceType.URL);
           files.add(url.toString());
-          Cache.log.debug("Drop handled as URL dataflavor "
+          jalview.bin.Console.debug("Drop handled as URL dataflavor "
                   + files.get(files.size() - 1));
           return;
         }
         else
         {
-          if (Platform.isAMac())
+          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);
+        jalview.bin.Console.debug("URL drop handler failed.", ex);
       }
     }
     if (t.isDataFlavorSupported(DataFlavor.javaFileListFlavor))
     {
       // Works on Windows and MacOSX
-      Cache.log.debug("Drop handled as javaFileListFlavor");
+      jalview.bin.Console.debug("Drop handled as javaFileListFlavor");
       for (Object file : (List) t
               .getTransferData(DataFlavor.javaFileListFlavor))
       {
@@ -3566,14 +3257,15 @@ public class Desktop extends jalview.jbgui.GDesktop
       String data = null;
       if (t.isDataFlavorSupported(uriListFlavor))
       {
-        Cache.log.debug("Drop handled as uriListFlavor");
+        jalview.bin.Console.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");
+        jalview.bin.Console
+                .debug("standard URIListFlavor failed. Trying text");
         // try text fallback
         DataFlavor textDf = new DataFlavor(
                 "text/plain;class=java.lang.String");
@@ -3582,7 +3274,7 @@ public class Desktop extends jalview.jbgui.GDesktop
           data = (String) t.getTransferData(textDf);
         }
 
-        Cache.log.debug("Plain text drop content returned "
+        jalview.bin.Console.debug("Plain text drop content returned "
                 + (data == null ? "Null - failed" : data));
 
       }
@@ -3590,7 +3282,7 @@ public class Desktop extends jalview.jbgui.GDesktop
       {
         while (protocols.size() < files.size())
         {
-          Cache.log.debug("Adding missing FILE protocol for "
+          jalview.bin.Console.debug("Adding missing FILE protocol for "
                   + files.get(protocols.size()));
           protocols.add(DataSourceType.FILE);
         }
@@ -3605,7 +3297,7 @@ public class Desktop extends jalview.jbgui.GDesktop
             continue;
           }
           java.net.URI uri = new java.net.URI(s);
-          if (uri.getScheme().toLowerCase().startsWith("http"))
+          if (uri.getScheme().toLowerCase(Locale.ROOT).startsWith("http"))
           {
             protocols.add(DataSourceType.URL);
             files.add(uri.toString());
@@ -3620,7 +3312,7 @@ public class Desktop extends jalview.jbgui.GDesktop
         }
       }
 
-      if (Cache.log.isDebugEnabled())
+      if (jalview.bin.Console.isDebugEnabled())
       {
         if (data == null || !added)
         {
@@ -3628,40 +3320,41 @@ public class Desktop extends jalview.jbgui.GDesktop
           if (t.getTransferDataFlavors() != null
                   && t.getTransferDataFlavors().length > 0)
           {
-            Cache.log.debug(
+            jalview.bin.Console.debug(
                     "Couldn't resolve drop data. Here are the supported flavors:");
             for (DataFlavor fl : t.getTransferDataFlavors())
             {
-              Cache.log.debug(
+              jalview.bin.Console.debug(
                       "Supported transfer dataflavor: " + fl.toString());
               Object df = t.getTransferData(fl);
               if (df != null)
               {
-                Cache.log.debug("Retrieves: " + df);
+                jalview.bin.Console.debug("Retrieves: " + df);
               }
               else
               {
-                Cache.log.debug("Retrieved nothing");
+                jalview.bin.Console.debug("Retrieved nothing");
               }
             }
           }
           else
           {
-            Cache.log.debug("Couldn't resolve dataflavor for drop: "
-                    + t.toString());
+            jalview.bin.Console
+                    .debug("Couldn't resolve dataflavor for drop: "
+                            + t.toString());
           }
         }
       }
     }
-    if (Platform.isWindows())
-
+    if (Platform.isWindowsAndNotJS())
     {
-      Cache.log.debug("Scanning dropped content for Windows Link Files");
+      jalview.bin.Console
+              .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();
+        String source = files.get(f).toString().toLowerCase(Locale.ROOT);
         if (protocols.get(f).equals(DataSourceType.FILE)
                 && (source.endsWith(".lnk") || source.endsWith(".url")
                         || source.endsWith(".site")))
@@ -3672,16 +3365,16 @@ public class Desktop extends jalview.jbgui.GDesktop
             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);
+            jalview.bin.Console.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
+            jalview.bin.Console.debug("Parsed real filename " + fullname
                     + " to extract protocol: " + protocols.get(f));
           } catch (Exception ex)
           {
-            Cache.log.error(
+            jalview.bin.Console.error(
                     "Couldn't parse " + files.get(f) + " as a link file.",
                     ex);
           }
@@ -3701,10 +3394,10 @@ public class Desktop extends jalview.jbgui.GDesktop
   }
 
   /**
-   * 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.
+   * 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
@@ -3736,4 +3429,37 @@ public class Desktop extends jalview.jbgui.GDesktop
     }
     return result;
   }
+
+  public static final String debugScaleMessage = "Desktop graphics transform scale=";
+
+  private static boolean debugScaleMessageDone = false;
+
+  public static void debugScaleMessage(Graphics g)
+  {
+    if (debugScaleMessageDone)
+    {
+      return;
+    }
+    // output used by tests to check HiDPI scaling settings in action
+    try
+    {
+      Graphics2D gg = (Graphics2D) g;
+      if (gg != null)
+      {
+        AffineTransform t = gg.getTransform();
+        double scaleX = t.getScaleX();
+        double scaleY = t.getScaleY();
+        jalview.bin.Console.debug(debugScaleMessage + scaleX + " (X)");
+        jalview.bin.Console.debug(debugScaleMessage + scaleY + " (Y)");
+        debugScaleMessageDone = true;
+      }
+      else
+      {
+        jalview.bin.Console.debug("Desktop graphics null");
+      }
+    } catch (Exception e)
+    {
+      jalview.bin.Console.debug(Cache.getStackTraceString(e));
+    }
+  }
 }