X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FDesktop.java;h=61bef5e74728cb86a6408c81ee469de3a50f309c;hb=bea1d9b563d2fea018de3dbde9112dd59149126e;hp=0fa74d64e572da421c62718fb51a065da8d36fe9;hpb=4fc20cbfb109c5333892bf39a36c50b370cfef5d;p=jalview.git

diff --git a/src/jalview/gui/Desktop.java b/src/jalview/gui/Desktop.java
index 0fa74d6..61bef5e 100644
--- a/src/jalview/gui/Desktop.java
+++ b/src/jalview/gui/Desktop.java
@@ -20,11 +20,13 @@
  */
 package jalview.gui;
 
+import java.util.Locale;
 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;
@@ -47,13 +49,16 @@ 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.File;
 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;
@@ -114,6 +119,7 @@ import jalview.io.FormatAdapter;
 import jalview.io.IdentifyFile;
 import jalview.io.JalviewFileChooser;
 import jalview.io.JalviewFileView;
+import jalview.jbgui.APQHandlers;
 import jalview.jbgui.GDesktop;
 import jalview.jbgui.GSplitFrame;
 import jalview.jbgui.GStructureViewer;
@@ -121,7 +127,9 @@ 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.LaunchUtils;
 import jalview.util.MessageManager;
 import jalview.util.Platform;
 import jalview.util.UrlConstants;
@@ -143,12 +151,29 @@ public class Desktop extends GDesktop
         StructureSelectionManagerProvider, ApplicationSingletonI
 
 {
-  private static final String CITATION = "<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";
+  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)";
 
@@ -162,13 +187,15 @@ public class Desktop extends GDesktop
 
   private static final String EXPERIMENTAL_FEATURES = "EXPERIMENTAL_FEATURES";
 
-  protected static final String CONFIRM_KEYBOARD_QUIT = "CONFIRM_KEYBOARD_QUIT";
+  public static final String CONFIRM_KEYBOARD_QUIT = "CONFIRM_KEYBOARD_QUIT";
 
   public static HashMap<String, FileWriter> savingFiles = new HashMap<String, FileWriter>();
 
   @SuppressWarnings("deprecation")
   private JalviewChangeSupport changeSupport = new JalviewChangeSupport();
 
+  public static boolean nosplash = false;
+
   /**
    * news reader - null if it was never started.
    */
@@ -385,7 +412,7 @@ public class Desktop extends GDesktop
    */
   private Desktop()
   {
-    Cache.initLogger();
+    super();
     try
     {
       /**
@@ -395,36 +422,77 @@ public class Desktop extends GDesktop
        */
 
       doConfigureStructurePrefs();
-      setTitle("Jalview " + Cache.getProperty("VERSION"));
-      /*
-      if (!Platform.isAMac())
-      {
-      // this.setDefaultCloseOperation(WindowConstants.EXIT_ON_CLOSE);
-      }
-      else
+    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())
+    {
+      if (LaunchUtils.getJavaVersion() >= 11)
       {
-       this.setDefaultCloseOperation(WindowConstants.DO_NOTHING_ON_CLOSE);
+        jalview.bin.Console.info(
+                "Linux platform only! You may have the following warning next: \"WARNING: An illegal reflective access operation has occurred\"\nThis is expected and cannot be avoided, sorry about that.");
       }
-      */
-
       try
       {
-        APQHandlers.setAPQHandlers(this);
-      } catch (Throwable t)
-      {
-        System.out.println("Error setting APQHandlers: " + t.toString());
-        // t.printStackTrace();
-      }
+        Toolkit xToolkit = Toolkit.getDefaultToolkit();
+        Field[] declaredFields = xToolkit.getClass().getDeclaredFields();
+        Field awtAppClassNameField = null;
 
-      addWindowListener(new WindowAdapter()
-      {
+        if (Arrays.stream(declaredFields).anyMatch(f -> f.getName().equals("awtAppClassName"))) {
+          awtAppClassNameField = xToolkit.getClass().getDeclaredField("awtAppClassName");
+        }
 
-        @Override
-        public void windowClosing(WindowEvent ev)
+        String title = ChannelProperties.getProperty("app_name");
+        if (awtAppClassNameField != null) {
+          awtAppClassNameField.setAccessible(true);
+          awtAppClassNameField.set(xToolkit, title);
+        }
+        else
         {
-          quit();
+          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));
+      }
+    }
+
+    /**
+     * APQHandlers sets handlers for About, Preferences and Quit actions peculiar to
+     * macOS's application menu. APQHandlers will check to see if a handler is
+     * supported before setting it.
+     */
+    try {
+      APQHandlers.setAPQHandlers(this);
+    } catch (Exception e) {
+      System.out.println("Cannot set APQHandlers");
+      // e.printStackTrace();
+    } catch (Throwable t) {
+      jalview.bin.Console.warn("Error setting APQHandlers: " + t.toString());
+      jalview.bin.Console.trace(Cache.getStackTraceString(t));
+    }
+
+    setIconImages(ChannelProperties.getIconList());
+
+    addWindowListener(new WindowAdapter() {
+
+      @Override
+      public void windowClosing(WindowEvent ev) {
+        quit();
+      }
+    });
 
       boolean selmemusage = Cache.getDefault("SHOW_MEMUSAGE", false);
 
@@ -449,6 +517,7 @@ public class Desktop extends GDesktop
       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
@@ -472,8 +541,6 @@ public class Desktop extends GDesktop
         setBounds(xPos, yPos, 900, 650);
       }
 
-      getIdentifiersOrgData();
-
       if (!Platform.isJS())
       /**
        * Java only
@@ -485,25 +552,28 @@ public class Desktop extends GDesktop
         jconsole.setHeader(Cache.getVersionDetailsForConsole());
         showConsole(showjconsole);
 
-        showNews.setVisible(false);
+        showNews.setVisible(false); // not sure if we should only do this for interactive session?
 
         experimentalFeatures.setSelected(showExperimental());
 
+        getIdentifiersOrgData();
+
         if (Jalview.isInteractive())
         {
           // disabled for SeqCanvasTest
           checkURLLinks();
 
           // Spawn a thread that shows the splashscreen
-
+          if (!nosplash) {
           SwingUtilities.invokeLater(new Runnable()
-          {
-            @Override
-            public void run()
-            {
-              new SplashScreen(true);
-            }
-          });
+           {
+             @Override
+             public void run()
+             {
+               new SplashScreen(true);
+             }
+           });
+          }
 
           // Thread off a new instance of the file chooser - this reduces the
           // time
@@ -514,11 +584,11 @@ public class Desktop extends GDesktop
             @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
@@ -529,13 +599,14 @@ public class Desktop extends GDesktop
                     @Override
                     public void propertyChange(PropertyChangeEvent evt)
                     {
-                      Cache.log.debug("Firing service changed event for "
+                      jalview.bin.Console.debug("Firing service changed event for "
                               + evt.getNewValue());
                       JalviewServicesChanged(evt);
                     }
                   });
         }
       }
+
       this.setDropTarget(new java.awt.dnd.DropTarget(desktopPane, this));
 
       this.addWindowListener(new WindowAdapter()
@@ -558,7 +629,6 @@ public class Desktop extends GDesktop
             showPasteMenu(evt.getX(), evt.getY());
           }
         }
-
         @Override
         public void mouseReleased(MouseEvent evt)
         {
@@ -573,7 +643,6 @@ public class Desktop extends GDesktop
     {
       t.printStackTrace();
     }
-
   }
 
   /**
@@ -592,74 +661,64 @@ public class Desktop extends GDesktop
   public void doConfigureStructurePrefs()
   {
     // configure services
-    StructureSelectionManager ssm = StructureSelectionManager
-            .getStructureSelectionManager(this);
-    if (Cache.getDefault(Preferences.ADD_SS_ANN, true))
-    {
-      ssm.setAddTempFacAnnot(
-              Cache.getDefault(Preferences.ADD_TEMPFACT_ANN, true));
-      ssm.setProcessSecondaryStructure(
-              Cache.getDefault(Preferences.STRUCT_FROM_PDB, true));
-      ssm.setSecStructServices(
-              Cache.getDefault(Preferences.USE_RNAVIEW, true));
-    }
-    else
-    {
+    StructureSelectionManager ssm = StructureSelectionManager.getStructureSelectionManager(this);
+    if (Cache.getDefault(Preferences.ADD_SS_ANN, 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(Cache.getDefault(Preferences.USE_RNAVIEW, false));
+    } else {
       ssm.setAddTempFacAnnot(false);
       ssm.setProcessSecondaryStructure(false);
       ssm.setSecStructServices(false);
     }
   }
 
-  public void checkForNews()
-  {
+  public void checkForNews() {
     final Desktop me = this;
     // Thread off the news reader, in case there are connection problems.
-    new Thread(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
-    new Thread(new Runnable()
-    {
-      @Override
-      public void run()
-      {
-        Cache.log.debug("Downloading data from identifiers.org");
-        try
-        {
-          UrlDownloadClient.download(IdOrgSettings.getUrl(),
-                  IdOrgSettings.getDownloadLocation());
-        } catch (IOException e)
+  public void getIdentifiersOrgData() {
+    if (Cache.getProperty("NOIDENTIFIERSSERVICE") == null) {
+      // Thread off the identifiers fetcher
+      new Thread(new Runnable() {
+        @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();
-
+      }).start();
+    }
   }
 
   @Override
-  protected void showNews_actionPerformed(ActionEvent e)
-  {
+  protected void showNews_actionPerformed(ActionEvent e) {
     showNews(showNews.isSelected());
   }
 
   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())
     {
@@ -695,19 +754,15 @@ public class Desktop extends GDesktop
     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 (Cache.getProperty("SCREENGEOMETRY_WIDTH") != null)
-      {
+    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 (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(Cache.getProperty("SCREENGEOMETRY_WIDTH"))));
-        double sh = ((1f * screenSize.height) / (1f * Integer
-                .parseInt(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);
@@ -715,17 +770,17 @@ public class Desktop extends GDesktop
         ih = (int) (ih * sh);
         while (ix >= screenSize.width)
         {
-          Cache.log.debug(
+          jalview.bin.Console.debug(
                   "Window geometry location recall error: shifting horizontal to within screenbounds.");
           ix -= screenSize.width;
         }
         while (iy >= screenSize.height)
         {
-          Cache.log.debug(
+          jalview.bin.Console.debug(
                   "Window geometry location recall error: shifting vertical to within screenbounds.");
           iy -= screenSize.height;
         }
-        Cache.log.debug(
+        jalview.bin.Console.debug(
                 "Got last known dimensions for " + windowName + ": x:" + ix
                         + " y:" + iy + " width:" + iw + " height:" + ih);
       }
@@ -778,56 +833,7 @@ public class Desktop extends GDesktop
     }
   }
 
-//  /**
-//   * Add an internal frame to the Jalview desktop that is allowed to be resized,
-//   * has a minimum size of 300px and might or might not be visible
-//   * 
-//   * @param frame
-//   *          Frame to show
-//   * @param title
-//   *          Visible Title
-//   * @param makeVisible
-//   *          When true, display frame immediately, otherwise, caller must call
-//   *          setVisible themselves.
-//   * @param w
-//   *          width
-//   * @param h
-//   *          height
-//   */
-//  @Deprecated
-//  public static synchronized void addInternalFrame(
-//          final JInternalFrame frame, String title, boolean makeVisible,
-//          int w, int h)
-//  {
-//    // textbox, web services, sequenceFetcher, featureSettings
-//    getInstance().addFrame(frame, title, makeVisible, w, h,
-//            FRAME_ALLOW_RESIZE, FRAME_SET_MIN_SIZE_300);
-//  }
-//
-//  /**
-//   * Add an internal frame to the Jalview desktop that is visible, has a minimum
-//   * size of 300px, and may or may not be resizable
-//   * 
-//   * @param frame
-//   *          Frame to show
-//   * @param title
-//   *          Visible Title
-//   * @param w
-//   *          width
-//   * @param h
-//   *          height
-//   * @param resizable
-//   *          Allow resize
-//   */
-//  @Deprecated
-//  public static synchronized void addInternalFrame(
-//          final JInternalFrame frame, String title, int w, int h,
-//          boolean resizable)
-//  {
-//    // annotation, font, calculation, user-defined colors
-//    getInstance().addFrame(frame, title, FRAME_MAKE_VISIBLE, w, h,
-//            resizable, FRAME_SET_MIN_SIZE_300);
-//  }
+
 
   /**
    * Adds and opens the given frame to the desktop that is visible, allowed to
@@ -877,6 +883,7 @@ public class Desktop extends GDesktop
   {
     // 15 classes call this method directly.
     
+
     // 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
@@ -912,6 +919,7 @@ public class Desktop extends GDesktop
   {
 
     openFrameCount++;
+
     
     boolean isEmbedded = (Platform.getEmbeddedAttribute(frame, "id") != null);
     boolean hasEmbeddedSize = (Platform.getDimIfEmbedded(frame, -1, -1) != null);
@@ -920,6 +928,7 @@ public class Desktop extends GDesktop
     
     if (!ignoreMinSize)
     {
+
       // Set default dimension for Alignment Frame window.
       // The Alignment Frame window could be added from a number of places,
       // hence,
@@ -941,6 +950,7 @@ public class Desktop extends GDesktop
     frame.setMaximizable(resizable);
     frame.setIconifiable(resizable);
     frame.setOpaque(Platform.isJS());
+
     if (!isEmbedded && frame.getX() < 1 && frame.getY() < 1)
     {
       frame.setLocation(xOffset * openFrameCount,
@@ -1005,6 +1015,7 @@ public class Desktop extends GDesktop
         } catch (java.beans.PropertyVetoException ex)
         {
           // System.err.println(ex.toString());
+
         }
       }
     });
@@ -1024,8 +1035,8 @@ public class Desktop extends 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);
     }
   }
@@ -1038,6 +1049,7 @@ public class Desktop extends GDesktop
    */
   private static void setKeyBindings(JInternalFrame frame)
   {
+    @SuppressWarnings("serial")
     final Action closeAction = new AbstractAction()
     {
       @Override
@@ -1050,10 +1062,8 @@ public class Desktop extends GDesktop
     /*
      * 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,
-            Platform.SHORTCUT_KEY_MASK);
+    KeyStroke ctrlWKey = KeyStroke.getKeyStroke(KeyEvent.VK_W, InputEvent.CTRL_DOWN_MASK);
+    KeyStroke cmdWKey = KeyStroke.getKeyStroke(KeyEvent.VK_W, Platform.SHORTCUT_KEY_MASK);
 
     InputMap inputMap = frame
             .getInputMap(JComponent.WHEN_IN_FOCUSED_WINDOW);
@@ -1236,7 +1246,7 @@ public class Desktop extends GDesktop
      * JS: (pending JAL-3038) a plain text field
      */
     JComponent history;
-    String urlBase = "http://www.";
+    String urlBase = "https://www.";
     if (Platform.isJS())
     {
       history = new JTextField(urlBase, 35);
@@ -1272,26 +1282,16 @@ public class Desktop extends GDesktop
       public void run()
       {
         @SuppressWarnings("unchecked")
-        String url = (history instanceof JTextField
-                ? ((JTextField) history).getText()
-                : ((JComboBox<String>) history).getSelectedItem()
-                        .toString());
-
-        if (url.toLowerCase().endsWith(".jar"))
-        {
-          if (viewport != null)
-          {
-            new FileLoader().LoadFile(viewport, url, DataSourceType.URL,
-                    FileFormat.Jalview);
+        String url = (history instanceof JTextField ? ((JTextField) history).getText()
+            : ((JComboBox<String>) history).getEditor().getItem().toString().trim());
+
+        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
-          {
-            new FileLoader().LoadFile(url, DataSourceType.URL,
-                    FileFormat.Jalview);
-          }
-        }
-        else
-        {
+        } else {
           FileFormatI format = null;
           try
           {
@@ -1392,9 +1392,9 @@ public class Desktop extends GDesktop
 
   private void storeLastKnownDimensions(String string, Rectangle jc)
   {
-    Cache.log.debug("Storing last known dimensions for " + string + ": x:"
-            + jc.x + " y:" + jc.y + " width:" + jc.width + " height:"
-            + jc.height);
+    jalview.bin.Console.debug("Storing last known dimensions for " + string
+            + ": x:" + jc.x + " y:" + jc.y + " width:" + jc.width
+            + " height:" + jc.height);
 
     Cache.setProperty(string + "SCREEN_X", jc.x + "");
     Cache.setProperty(string + "SCREEN_Y", jc.y + "");
@@ -1431,39 +1431,28 @@ public class Desktop extends GDesktop
   public String getAboutMessage()
   {
     StringBuilder message = new StringBuilder(1024);
-    message.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("<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>");
 
     String latestVersion = Cache.getDefault("LATEST_VERSION", "Checking");
-    if (latestVersion.equals("Checking"))
-    {
+    if (latestVersion.equals("Checking")) {
       // JBP removed this message for 2.11: May be reinstated in future version
       // message.append("<br>...Checking latest version...</br>");
-    }
-    else if (!latestVersion.equals(Cache.getProperty("VERSION")))
-    {
+    } else if (!latestVersion.equals(Cache.getProperty("VERSION"))) {
       boolean red = false;
-      if (Cache.getProperty("VERSION").toLowerCase()
-              .indexOf("automated build") == -1)
-      {
+      if (Cache.getProperty("VERSION").toLowerCase(Locale.ROOT).indexOf("automated build") == -1) {
         red = true;
         // Displayed when code version and jnlp version do not match and code
         // version is not a development build
         message.append("<div style=\"color: #FF0000;font-style: bold;\">");
       }
 
-      message.append("<br>!! Version ")
-              .append(Cache.getDefault("LATEST_VERSION", "..Checking.."))
-              .append(" is available for download from ")
-              .append(Cache.getDefault("www.jalview.org",
-                      "http://www.jalview.org"))
-              .append(" !!");
-      if (red)
-      {
+      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>");
       }
     }
@@ -1471,6 +1460,8 @@ public class Desktop extends GDesktop
     message.append(Cache.getDefault("AUTHORFNAMES", DEFAULT_AUTHORS));
     message.append(CITATION);
 
+    message.append("</div>");
+
     return message.toString();
   }
 
@@ -1478,15 +1469,11 @@ public class Desktop extends GDesktop
    * Action on requesting Help documentation
    */
   @Override
-  public void documentationMenuItem_actionPerformed()
-  {
-    try
-    {
-      if (Platform.isJS())
-      {
-        BrowserLauncher.openURL("http://www.jalview.org/help.html");
-      }
-      else
+  public void documentationMenuItem_actionPerformed() {
+    try {
+      if (Platform.isJS()) {
+        BrowserLauncher.openURL("https://www.jalview.org/help.html");
+      } else
       /**
        * Java only
        * 
@@ -1495,8 +1482,7 @@ public class Desktop extends GDesktop
       {
         Help.showHelpWindow();
       }
-    } catch (Exception ex)
-    {
+    } catch (Exception ex) {
       System.err.println("Error opening help: " + ex.getMessage());
     }
   }
@@ -1557,9 +1543,9 @@ public class Desktop extends GDesktop
   protected void garbageCollect_actionPerformed(ActionEvent e)
   {
     // We simply collect the garbage
-    Cache.log.debug("Collecting garbage...");
+    jalview.bin.Console.debug("Collecting garbage...");
     System.gc();
-    Cache.log.debug("Finished garbage collection.");
+    jalview.bin.Console.debug("Finished garbage collection.");
   }
 
   /*
@@ -1692,9 +1678,8 @@ public class Desktop extends GDesktop
    *          DOCUMENT ME!
    */
   @Override
-  protected void preferences_actionPerformed(ActionEvent e)
-  {
-    new Preferences();
+  protected void preferences_actionPerformed(ActionEvent e) {
+    Preferences.openPreferences();
   }
 
   /**
@@ -1737,8 +1722,7 @@ public class Desktop extends GDesktop
       }
     }
 
-    if (approveSave || autoSave)
-    {
+    if (approveSave || autoSave) {
       final Desktop me = this;
       final java.io.File chosenFile = projectFile;
       new Thread(new Runnable()
@@ -1773,7 +1757,7 @@ public class Desktop extends GDesktop
                     + chosenFile.getName(), oom);
           } catch (Exception ex)
           {
-            Cache.log.error("Problems whilst trying to save to "
+            jalview.bin.Console.error("Problems whilst trying to save to "
                     + chosenFile.getName(), ex);
             JvOptionPane.showMessageDialog(me,
                     MessageManager.formatMessage(
@@ -1845,7 +1829,7 @@ public class Desktop extends GDesktop
               new OOMWarning("Whilst loading project from " + choice, oom);
             } catch (Exception ex)
             {
-              Cache.log.error(
+              jalview.bin.Console.error(
                       "Problems whilst loading project from " + choice, ex);
               JvOptionPane.showMessageDialog(getDesktopPane(),
                       MessageManager.formatMessage(
@@ -1857,7 +1841,7 @@ public class Desktop extends GDesktop
                       JvOptionPane.WARNING_MESSAGE);
             }
           }
-        }).start();
+        }, "Project Loader").start();
       }
     });
 
@@ -2159,6 +2143,7 @@ public class Desktop extends GDesktop
     {
       source.showFeatureSettingsUI();
     }
+
   }
 
   public JInternalFrame[] getAllFrames()
@@ -2352,6 +2337,9 @@ public class Desktop extends GDesktop
                   10, getHeight() - fm.getHeight());
         }
       }
+
+      // output debug scale message. Important for jalview.bin.HiDPISettingTest2
+      Desktop.debugScaleMessage(Desktop.getDesktopPane().getGraphics());
     }
   }
 
@@ -2447,7 +2435,7 @@ public class Desktop extends GDesktop
       openGroovyConsole();
     } catch (Exception ex)
     {
-      Cache.log.error("Groovy Shell Creation failed.", ex);
+      jalview.bin.Console.error("Groovy Shell Creation failed.", ex);
       JvOptionPane.showInternalMessageDialog(desktopPane,
 
               MessageManager.getString("label.couldnt_create_groovy_shell"),
@@ -2584,6 +2572,13 @@ public class Desktop extends GDesktop
   }
   
   @Override
+  public void addProgressBar(long id, String message)
+  {
+    // TODO
+    throw new UnsupportedOperationException("not implemented");
+  }
+
+  @Override
   public void removeProgressBar(long id)
   {
     //TODO
@@ -2701,14 +2696,23 @@ public class Desktop extends 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)
   {
-    System.out.println("Starting service discovery");
+    jalview.bin.Console.debug("Starting service discovery");
+
     var tasks = new ArrayList<Future<?>>();
     // JAL-940 - JALVIEW 1 services are now being EOLed as of JABA 2.1 release
 
@@ -2822,7 +2826,7 @@ public class Desktop extends GDesktop
         }
         else
         {
-          Cache.log.error(
+          jalview.bin.Console.error(
                   "Errors reported by JABA discovery service. Check web services preferences.\n"
                           + ermsg);
         }
@@ -2915,15 +2919,8 @@ public class Desktop extends 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.");
-          }
+          // TODO does error send to stderr if no log exists ?
+          jalview.bin.Console.error("Couldn't handle string " + url + " as a URL.");
         }
         // ignore any exceptions due to dud links.
       }
@@ -2978,7 +2975,7 @@ public class Desktop extends 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);
         }
       }
     });
@@ -3017,7 +3014,7 @@ public class Desktop extends 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());
       }
     };
@@ -3232,7 +3229,8 @@ public class Desktop extends 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))
@@ -3247,7 +3245,7 @@ public class Desktop extends 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;
         }
@@ -3261,13 +3259,13 @@ public class Desktop extends GDesktop
         }
       } 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 (File file : (List<File>) t
               .getTransferData(DataFlavor.javaFileListFlavor))
       {
@@ -3282,14 +3280,15 @@ public class Desktop extends 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");
@@ -3298,7 +3297,7 @@ public class Desktop extends 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));
 
       }
@@ -3306,7 +3305,7 @@ public class Desktop extends 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);
         }
@@ -3321,7 +3320,7 @@ public class Desktop extends 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());
@@ -3336,7 +3335,7 @@ public class Desktop extends GDesktop
         }
       }
 
-      if (Cache.log.isDebugEnabled())
+      if (jalview.bin.Console.isDebugEnabled())
       {
         if (data == null || !added)
         {
@@ -3344,39 +3343,39 @@ public class Desktop extends 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.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")))
@@ -3387,16 +3386,16 @@ public class Desktop extends 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);
           }
@@ -3452,4 +3451,32 @@ public class Desktop extends 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));
+    }
+  }
 }