X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FDesktop.java;h=16603df6309dbb4d184836d4710afcd47865729e;hb=53fe06e7ae7a8c00ec902413391cea15362bdbf2;hp=4f12de4d5480d9a155263ac095aa95f8ea9c356f;hpb=a6152ff382c65a2cbd95163478cce7a65b1c641a;p=jalview.git

diff --git a/src/jalview/gui/Desktop.java b/src/jalview/gui/Desktop.java
index 4f12de4..16603df 100644
--- a/src/jalview/gui/Desktop.java
+++ b/src/jalview/gui/Desktop.java
@@ -20,8 +20,6 @@
  */
 package jalview.gui;
 
-import java.util.Locale;
-
 import java.awt.BorderLayout;
 import java.awt.Color;
 import java.awt.Dimension;
@@ -64,6 +62,7 @@ import java.util.HashMap;
 import java.util.Hashtable;
 import java.util.List;
 import java.util.ListIterator;
+import java.util.Locale;
 import java.util.Vector;
 import java.util.concurrent.ExecutorService;
 import java.util.concurrent.Executors;
@@ -122,6 +121,7 @@ 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.ShortcutKeyMaskExWrapper;
@@ -138,7 +138,9 @@ import jalview.ws.utils.UrlDownloadClient;
  * @version $Revision: 1.155 $
  */
 public class Desktop extends jalview.jbgui.GDesktop
-    implements DropTargetListener, ClipboardOwner, IProgressIndicator, jalview.api.StructureSelectionManagerProvider {
+        implements DropTargetListener, ClipboardOwner, IProgressIndicator,
+        jalview.api.StructureSelectionManagerProvider
+{
   private static final String CITATION;
   static
   {
@@ -181,7 +183,7 @@ public class Desktop extends jalview.jbgui.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>();
 
@@ -200,7 +202,9 @@ public class Desktop extends jalview.jbgui.GDesktop
    * @param listener
    * @see jalview.gui.JalviewChangeSupport#addJalviewPropertyChangeListener(java.beans.PropertyChangeListener)
    */
-  public void addJalviewPropertyChangeListener(PropertyChangeListener listener) {
+  public void addJalviewPropertyChangeListener(
+          PropertyChangeListener listener)
+  {
     changeSupport.addJalviewPropertyChangeListener(listener);
   }
 
@@ -210,7 +214,9 @@ public class Desktop extends jalview.jbgui.GDesktop
    * @see jalview.gui.JalviewChangeSupport#addJalviewPropertyChangeListener(java.lang.String,
    *      java.beans.PropertyChangeListener)
    */
-  public void addJalviewPropertyChangeListener(String propertyName, PropertyChangeListener listener) {
+  public void addJalviewPropertyChangeListener(String propertyName,
+          PropertyChangeListener listener)
+  {
     changeSupport.addJalviewPropertyChangeListener(propertyName, listener);
   }
 
@@ -220,8 +226,11 @@ public class Desktop extends jalview.jbgui.GDesktop
    * @see jalview.gui.JalviewChangeSupport#removeJalviewPropertyChangeListener(java.lang.String,
    *      java.beans.PropertyChangeListener)
    */
-  public void removeJalviewPropertyChangeListener(String propertyName, PropertyChangeListener listener) {
-    changeSupport.removeJalviewPropertyChangeListener(propertyName, listener);
+  public void removeJalviewPropertyChangeListener(String propertyName,
+          PropertyChangeListener listener)
+  {
+    changeSupport.removeJalviewPropertyChangeListener(propertyName,
+            listener);
   }
 
   /** Singleton Desktop instance */
@@ -229,7 +238,8 @@ public class Desktop extends jalview.jbgui.GDesktop
 
   public static MyDesktopPane desktop;
 
-  public static MyDesktopPane getDesktop() {
+  public static MyDesktopPane getDesktop()
+  {
     // BH 2018 could use currentThread() here as a reference to a
     // Hashtable<Thread, MyDesktopPane> in JavaScript
     return desktop;
@@ -249,99 +259,122 @@ public class Desktop extends jalview.jbgui.GDesktop
 
   static int fileLoadingCount = 0;
 
-  class MyDesktopManager implements DesktopManager {
+  class MyDesktopManager implements DesktopManager
+  {
 
     private DesktopManager delegate;
 
-    public MyDesktopManager(DesktopManager delegate) {
+    public MyDesktopManager(DesktopManager delegate)
+    {
       this.delegate = delegate;
     }
 
     @Override
-    public void activateFrame(JInternalFrame f) {
-      try {
+    public void activateFrame(JInternalFrame f)
+    {
+      try
+      {
         delegate.activateFrame(f);
-      } catch (NullPointerException npe) {
+      } catch (NullPointerException npe)
+      {
         Point p = getMousePosition();
         instance.showPasteMenu(p.x, p.y);
       }
     }
 
     @Override
-    public void beginDraggingFrame(JComponent f) {
+    public void beginDraggingFrame(JComponent f)
+    {
       delegate.beginDraggingFrame(f);
     }
 
     @Override
-    public void beginResizingFrame(JComponent f, int direction) {
+    public void beginResizingFrame(JComponent f, int direction)
+    {
       delegate.beginResizingFrame(f, direction);
     }
 
     @Override
-    public void closeFrame(JInternalFrame f) {
+    public void closeFrame(JInternalFrame f)
+    {
       delegate.closeFrame(f);
     }
 
     @Override
-    public void deactivateFrame(JInternalFrame f) {
+    public void deactivateFrame(JInternalFrame f)
+    {
       delegate.deactivateFrame(f);
     }
 
     @Override
-    public void deiconifyFrame(JInternalFrame f) {
+    public void deiconifyFrame(JInternalFrame f)
+    {
       delegate.deiconifyFrame(f);
     }
 
     @Override
-    public void dragFrame(JComponent f, int newX, int newY) {
-      if (newY < 0) {
+    public void dragFrame(JComponent f, int newX, int newY)
+    {
+      if (newY < 0)
+      {
         newY = 0;
       }
       delegate.dragFrame(f, newX, newY);
     }
 
     @Override
-    public void endDraggingFrame(JComponent f) {
+    public void endDraggingFrame(JComponent f)
+    {
       delegate.endDraggingFrame(f);
       desktop.repaint();
     }
 
     @Override
-    public void endResizingFrame(JComponent f) {
+    public void endResizingFrame(JComponent f)
+    {
       delegate.endResizingFrame(f);
       desktop.repaint();
     }
 
     @Override
-    public void iconifyFrame(JInternalFrame f) {
+    public void iconifyFrame(JInternalFrame f)
+    {
       delegate.iconifyFrame(f);
     }
 
     @Override
-    public void maximizeFrame(JInternalFrame f) {
+    public void maximizeFrame(JInternalFrame f)
+    {
       delegate.maximizeFrame(f);
     }
 
     @Override
-    public void minimizeFrame(JInternalFrame f) {
+    public void minimizeFrame(JInternalFrame f)
+    {
       delegate.minimizeFrame(f);
     }
 
     @Override
-    public void openFrame(JInternalFrame f) {
+    public void openFrame(JInternalFrame f)
+    {
       delegate.openFrame(f);
     }
 
     @Override
-    public void resizeFrame(JComponent f, int newX, int newY, int newWidth, int newHeight) {
-      if (newY < 0) {
+    public void resizeFrame(JComponent f, int newX, int newY, int newWidth,
+            int newHeight)
+    {
+      if (newY < 0)
+      {
         newY = 0;
       }
       delegate.resizeFrame(f, newX, newY, newWidth, newHeight);
     }
 
     @Override
-    public void setBoundsForFrame(JComponent f, int newX, int newY, int newWidth, int newHeight) {
+    public void setBoundsForFrame(JComponent f, int newX, int newY,
+            int newWidth, int newHeight)
+    {
       delegate.setBoundsForFrame(f, newX, newY, newWidth, newHeight);
     }
 
@@ -352,72 +385,78 @@ public class Desktop extends jalview.jbgui.GDesktop
   /**
    * Creates a new Desktop object.
    */
-  public Desktop() {
+  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;
 
     doConfigureStructurePrefs();
-    setTitle(ChannelProperties.getProperty("app_name") + " " + Cache.getProperty("VERSION"));
+    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
+     * 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()) {
-      try {
+    if (Platform.isLinux())
+    {
+      if (LaunchUtils.getJavaVersion() >= 11)
+      {
+        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
+      {
         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");
+        if (Arrays.stream(declaredFields)
+                .anyMatch(f -> f.getName().equals("awtAppClassName")))
+        {
+          awtAppClassNameField = xToolkit.getClass()
+                  .getDeclaredField("awtAppClassName");
         }
 
         String title = ChannelProperties.getProperty("app_name");
-        if (awtAppClassNameField != null) {
+        if (awtAppClassNameField != null)
+        {
           awtAppClassNameField.setAccessible(true);
           awtAppClassNameField.set(xToolkit, title);
-        } else {
+        }
+        else
+        {
           jalview.bin.Console.debug("XToolkit: awtAppClassName not found");
         }
-      } catch (Exception e) {
+      } 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() {
+    addWindowListener(new WindowAdapter()
+    {
 
       @Override
-      public void windowClosing(WindowEvent ev) {
+      public void windowClosing(WindowEvent ev)
+      {
         quit();
       }
     });
@@ -437,7 +476,8 @@ public class Desktop extends jalview.jbgui.GDesktop
     // getContentPane().add(sp, BorderLayout.CENTER);
 
     // BH 2018 - just an experiment to try unclipped JInternalFrames.
-    if (Platform.isJS()) {
+    if (Platform.isJS())
+    {
       getRootPane().putClientProperty("swingjs.overflow.hidden", "false");
     }
 
@@ -446,14 +486,20 @@ public class Desktop extends jalview.jbgui.GDesktop
 
     // This line prevents Windows Look&Feel resizing all new windows to maximum
     // if previous window was maximised
-    desktop.setDesktopManager(new MyDesktopManager((Platform.isWindowsAndNotJS() ? new DefaultDesktopManager()
-        : Platform.isAMacAndNotJS() ? new AquaInternalFrameManager(desktop.getDesktopManager())
-            : desktop.getDesktopManager())));
+    desktop.setDesktopManager(new MyDesktopManager(
+            (Platform.isWindowsAndNotJS() ? new DefaultDesktopManager()
+                    : Platform.isAMacAndNotJS()
+                            ? new AquaInternalFrameManager(
+                                    desktop.getDesktopManager())
+                            : desktop.getDesktopManager())));
 
     Rectangle dims = getLastKnownDimensions("");
-    if (dims != null) {
+    if (dims != null)
+    {
       setBounds(dims);
-    } else {
+    }
+    else
+    {
       Dimension screenSize = Toolkit.getDefaultToolkit().getScreenSize();
       int xPos = Math.max(5, (screenSize.width - 900) / 2);
       int yPos = Math.max(5, (screenSize.height - 650) / 2);
@@ -480,10 +526,13 @@ public class Desktop extends jalview.jbgui.GDesktop
       checkURLLinks();
 
       // Spawn a thread that shows the splashscreen
-      if (!nosplash) {
-        SwingUtilities.invokeLater(new Runnable() {
+      if (!nosplash)
+      {
+        SwingUtilities.invokeLater(new Runnable()
+        {
           @Override
-          public void run() {
+          public void run()
+          {
             new SplashScreen(true);
           }
         });
@@ -492,39 +541,51 @@ public class Desktop extends jalview.jbgui.GDesktop
       // Thread off a new instance of the file chooser - this reduces the time
       // it
       // takes to open it later on.
-      new Thread(new Runnable() {
+      new Thread(new Runnable()
+      {
         @Override
-        public void run() {
+        public void run()
+        {
           jalview.bin.Console.debug("Filechooser init thread started.");
           String fileFormat = Cache.getProperty("DEFAULT_FILE_FORMAT");
-          JalviewFileChooser.forRead(Cache.getProperty("LAST_DIRECTORY"), fileFormat);
+          JalviewFileChooser.forRead(Cache.getProperty("LAST_DIRECTORY"),
+                  fileFormat);
           jalview.bin.Console.debug("Filechooser init thread finished.");
         }
       }).start();
       // Add the service change listener
-      changeSupport.addJalviewPropertyChangeListener("services", new PropertyChangeListener() {
+      changeSupport.addJalviewPropertyChangeListener("services",
+              new PropertyChangeListener()
+              {
 
-        @Override
-        public void propertyChange(PropertyChangeEvent evt) {
-          jalview.bin.Console.debug("Firing service changed event for " + evt.getNewValue());
-          JalviewServicesChanged(evt);
-        }
-      });
+                @Override
+                public void propertyChange(PropertyChangeEvent evt)
+                {
+                  jalview.bin.Console
+                          .debug("Firing service changed event for "
+                                  + evt.getNewValue());
+                  JalviewServicesChanged(evt);
+                }
+              });
     }
 
     this.setDropTarget(new java.awt.dnd.DropTarget(desktop, this));
 
-    this.addWindowListener(new WindowAdapter() {
+    this.addWindowListener(new WindowAdapter()
+    {
       @Override
-      public void windowClosing(WindowEvent evt) {
+      public void windowClosing(WindowEvent evt)
+      {
         quit();
       }
     });
 
     MouseAdapter ma;
-    this.addMouseListener(ma = new MouseAdapter() {
+    this.addMouseListener(ma = new MouseAdapter()
+    {
       @Override
-      public void mousePressed(MouseEvent evt) {
+      public void mousePressed(MouseEvent evt)
+      {
         if (evt.isPopupTrigger()) // Mac
         {
           showPasteMenu(evt.getX(), evt.getY());
@@ -532,7 +593,8 @@ public class Desktop extends jalview.jbgui.GDesktop
       }
 
       @Override
-      public void mouseReleased(MouseEvent evt) {
+      public void mouseReleased(MouseEvent evt)
+      {
         if (evt.isPopupTrigger()) // Windows
         {
           showPasteMenu(evt.getX(), evt.getY());
@@ -548,32 +610,45 @@ public class Desktop extends jalview.jbgui.GDesktop
    * 
    * @return
    */
-  public boolean showExperimental() {
-    String experimental = Cache.getDefault(EXPERIMENTAL_FEATURES, Boolean.FALSE.toString());
+  public boolean showExperimental()
+  {
+    String experimental = Cache.getDefault(EXPERIMENTAL_FEATURES,
+            Boolean.FALSE.toString());
     return Boolean.valueOf(experimental).booleanValue();
   }
 
-  public void doConfigureStructurePrefs() {
+  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));
+    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.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() {
+      public void run()
+      {
         jalview.bin.Console.debug("Starting news thread.");
         jvnews = new BlogReader(me);
         showNews.setVisible(true);
@@ -591,15 +666,17 @@ public class Desktop extends jalview.jbgui.GDesktop
         @Override
         public void run()
         {
-          jalview.bin.Console.debug("Downloading data from identifiers.org");
+          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());
+            jalview.bin.Console
+                    .debug("Exception downloading identifiers.org data"
+                            + e.getMessage());
           }
         }
       }).start();
@@ -608,19 +685,25 @@ public class Desktop extends jalview.jbgui.GDesktop
   }
 
   @Override
-  protected void showNews_actionPerformed(ActionEvent e) {
+  protected void showNews_actionPerformed(ActionEvent e)
+  {
     showNews(showNews.isSelected());
   }
 
-  void showNews(boolean visible) {
+  void showNews(boolean visible)
+  {
     jalview.bin.Console.debug((visible ? "Showing" : "Hiding") + " news.");
     showNews.setSelected(visible);
-    if (visible && !jvnews.isVisible()) {
-      new Thread(new Runnable() {
+    if (visible && !jvnews.isVisible())
+    {
+      new Thread(new Runnable()
+      {
         @Override
-        public void run() {
+        public void run()
+        {
           long now = System.currentTimeMillis();
-          Desktop.instance.setProgressBar(MessageManager.getString("status.refreshing_news"), now);
+          Desktop.instance.setProgressBar(
+                  MessageManager.getString("status.refreshing_news"), now);
           jvnews.refreshNews();
           Desktop.instance.setProgressBar(null, now);
           jvnews.showNews();
@@ -632,42 +715,52 @@ public class Desktop extends jalview.jbgui.GDesktop
   /**
    * recover the last known dimensions for a jalview window
    * 
-   * @param windowName - empty string is desktop, all other windows have unique
-   *                   prefix
+   * @param windowName
+   *          - empty string is desktop, all other windows have unique prefix
    * @return null or last known dimensions scaled to current geometry (if last
    *         window geom was known)
    */
-  Rectangle getLastKnownDimensions(String windowName) {
+  Rectangle getLastKnownDimensions(String windowName)
+  {
     // TODO: lock aspect ratio for scaling desktop Bug #0058199
     Dimension screenSize = Toolkit.getDefaultToolkit().getScreenSize();
     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 (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);
         iy = (int) (iy * sh);
         ih = (int) (ih * sh);
-        while (ix >= screenSize.width) {
-          jalview.bin.Console.debug("Window geometry location recall error: shifting horizontal to within screenbounds.");
+        while (ix >= screenSize.width)
+        {
+          jalview.bin.Console.debug(
+                  "Window geometry location recall error: shifting horizontal to within screenbounds.");
           ix -= screenSize.width;
         }
-        while (iy >= screenSize.height) {
-          jalview.bin.Console.debug("Window geometry location recall error: shifting vertical to within screenbounds.");
+        while (iy >= screenSize.height)
+        {
+          jalview.bin.Console.debug(
+                  "Window geometry location recall error: shifting vertical to within screenbounds.");
           iy -= screenSize.height;
         }
-        jalview.bin.Console.debug("Got last known dimensions for " + windowName + ": x:" + ix + " y:" + iy + " width:" + iw
-            + " height:" + ih);
+        jalview.bin.Console.debug(
+                "Got last known dimensions for " + windowName + ": x:" + ix
+                        + " y:" + iy + " width:" + iw + " height:" + ih);
       }
       // return dimensions for new instance
       return new Rectangle(ix, iy, iw, ih);
@@ -675,12 +768,16 @@ public class Desktop extends jalview.jbgui.GDesktop
     return null;
   }
 
-  void showPasteMenu(int x, int y) {
+  void showPasteMenu(int x, int y)
+  {
     JPopupMenu popup = new JPopupMenu();
-    JMenuItem item = new JMenuItem(MessageManager.getString("label.paste_new_window"));
-    item.addActionListener(new ActionListener() {
+    JMenuItem item = new JMenuItem(
+            MessageManager.getString("label.paste_new_window"));
+    item.addActionListener(new ActionListener()
+    {
       @Override
-      public void actionPerformed(ActionEvent evt) {
+      public void actionPerformed(ActionEvent evt)
+      {
         paste();
       }
     });
@@ -689,79 +786,115 @@ public class Desktop extends jalview.jbgui.GDesktop
     popup.show(this, x, y);
   }
 
-  public void paste() {
-    try {
+  public void paste()
+  {
+    try
+    {
       Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
       Transferable contents = c.getContents(this);
 
-      if (contents != null) {
-        String file = (String) contents.getTransferData(DataFlavor.stringFlavor);
+      if (contents != null)
+      {
+        String file = (String) contents
+                .getTransferData(DataFlavor.stringFlavor);
 
-        FileFormatI format = new IdentifyFile().identify(file, DataSourceType.PASTE);
+        FileFormatI format = new IdentifyFile().identify(file,
+                DataSourceType.PASTE);
 
         new FileLoader().LoadFile(file, DataSourceType.PASTE, format);
 
       }
-    } catch (Exception ex) {
-      System.out.println("Unable to paste alignment from system clipboard:\n" + ex);
+    } catch (Exception ex)
+    {
+      System.out.println(
+              "Unable to paste alignment from system clipboard:\n" + ex);
     }
   }
 
   /**
    * Adds and opens the given frame to the desktop
    * 
-   * @param frame Frame to show
-   * @param title Visible Title
-   * @param w     width
-   * @param h     height
-   */
-  public static synchronized void addInternalFrame(final JInternalFrame frame, String title, int w, int h) {
+   * @param frame
+   *          Frame to show
+   * @param title
+   *          Visible Title
+   * @param w
+   *          width
+   * @param h
+   *          height
+   */
+  public static synchronized void addInternalFrame(
+          final JInternalFrame frame, String title, int w, int h)
+  {
     addInternalFrame(frame, title, true, w, h, true, false);
   }
 
   /**
    * Add an internal frame to the Jalview desktop
    * 
-   * @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
-   */
-  public static synchronized void addInternalFrame(final JInternalFrame frame, String title, boolean makeVisible, int w,
-      int h) {
+   * @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
+   */
+  public static synchronized void addInternalFrame(
+          final JInternalFrame frame, String title, boolean makeVisible,
+          int w, int h)
+  {
     addInternalFrame(frame, title, makeVisible, w, h, true, false);
   }
 
   /**
    * Add an internal frame to the Jalview desktop and make it visible
    * 
-   * @param frame     Frame to show
-   * @param title     Visible Title
-   * @param w         width
-   * @param h         height
-   * @param resizable Allow resize
-   */
-  public static synchronized void addInternalFrame(final JInternalFrame frame, String title, int w, int h,
-      boolean resizable) {
+   * @param frame
+   *          Frame to show
+   * @param title
+   *          Visible Title
+   * @param w
+   *          width
+   * @param h
+   *          height
+   * @param resizable
+   *          Allow resize
+   */
+  public static synchronized void addInternalFrame(
+          final JInternalFrame frame, String title, int w, int h,
+          boolean resizable)
+  {
     addInternalFrame(frame, title, true, w, h, resizable, false);
   }
 
   /**
    * Add an internal frame to the Jalview desktop
    * 
-   * @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
-   * @param resizable     Allow resize
-   * @param ignoreMinSize Do not set the default minimum size for frame
-   */
-  public static synchronized void addInternalFrame(final JInternalFrame frame, String title, boolean makeVisible, int w,
-      int h, boolean resizable, boolean ignoreMinSize) {
+   * @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
+   * @param resizable
+   *          Allow resize
+   * @param ignoreMinSize
+   *          Do not set the default minimum size for frame
+   */
+  public static synchronized void addInternalFrame(
+          final JInternalFrame frame, String title, boolean makeVisible,
+          int w, int h, boolean resizable, boolean ignoreMinSize)
+  {
 
     // TODO: allow callers to determine X and Y position of frame (eg. via
     // bounds object).
@@ -769,7 +902,8 @@ public class Desktop extends jalview.jbgui.GDesktop
     // the current window title
 
     frame.setTitle(title);
-    if (frame.getWidth() < 1 || frame.getHeight() < 1) {
+    if (frame.getWidth() < 1 || frame.getHeight() < 1)
+    {
       frame.setSize(w, h);
     }
     // THIS IS A PUBLIC STATIC METHOD, SO IT MAY BE CALLED EVEN IN
@@ -777,21 +911,26 @@ public class Desktop extends jalview.jbgui.GDesktop
     // IF JALVIEW IS RUNNING HEADLESS
     // ///////////////////////////////////////////////
     if (instance == null || (System.getProperty("java.awt.headless") != null
-        && System.getProperty("java.awt.headless").equals("true"))) {
+            && System.getProperty("java.awt.headless").equals("true")))
+    {
       return;
     }
 
     openFrameCount++;
 
-    if (!ignoreMinSize) {
-      frame.setMinimumSize(new Dimension(DEFAULT_MIN_WIDTH, DEFAULT_MIN_HEIGHT));
+    if (!ignoreMinSize)
+    {
+      frame.setMinimumSize(
+              new Dimension(DEFAULT_MIN_WIDTH, DEFAULT_MIN_HEIGHT));
 
       // Set default dimension for Alignment Frame window.
       // The Alignment Frame window could be added from a number of places,
       // hence,
       // I did this here in order not to miss out on any Alignment frame.
-      if (frame instanceof AlignFrame) {
-        frame.setMinimumSize(new Dimension(ALIGN_FRAME_DEFAULT_MIN_WIDTH, ALIGN_FRAME_DEFAULT_MIN_HEIGHT));
+      if (frame instanceof AlignFrame)
+      {
+        frame.setMinimumSize(new Dimension(ALIGN_FRAME_DEFAULT_MIN_WIDTH,
+                ALIGN_FRAME_DEFAULT_MIN_HEIGHT));
       }
     }
 
@@ -802,8 +941,10 @@ public class Desktop extends jalview.jbgui.GDesktop
     frame.setIconifiable(resizable);
     frame.setOpaque(Platform.isJS());
 
-    if (frame.getX() < 1 && frame.getY() < 1) {
-      frame.setLocation(xOffset * openFrameCount, yOffset * ((openFrameCount - 1) % 10) + yOffset);
+    if (frame.getX() < 1 && frame.getY() < 1)
+    {
+      frame.setLocation(xOffset * openFrameCount,
+              yOffset * ((openFrameCount - 1) % 10) + yOffset);
     }
 
     /*
@@ -811,12 +952,16 @@ public class Desktop extends jalview.jbgui.GDesktop
      * frame is closed)
      */
     final JMenuItem menuItem = new JMenuItem(title);
-    frame.addInternalFrameListener(new InternalFrameAdapter() {
+    frame.addInternalFrameListener(new InternalFrameAdapter()
+    {
       @Override
-      public void internalFrameActivated(InternalFrameEvent evt) {
+      public void internalFrameActivated(InternalFrameEvent evt)
+      {
         JInternalFrame itf = desktop.getSelectedFrame();
-        if (itf != null) {
-          if (itf instanceof AlignFrame) {
+        if (itf != null)
+        {
+          if (itf instanceof AlignFrame)
+          {
             Jalview.setCurrentAlignFrame((AlignFrame) itf);
           }
           itf.requestFocus();
@@ -824,33 +969,40 @@ public class Desktop extends jalview.jbgui.GDesktop
       }
 
       @Override
-      public void internalFrameClosed(InternalFrameEvent evt) {
+      public void internalFrameClosed(InternalFrameEvent evt)
+      {
         PaintRefresher.RemoveComponent(frame);
 
         /*
          * defensive check to prevent frames being added half off the window
          */
-        if (openFrameCount > 0) {
+        if (openFrameCount > 0)
+        {
           openFrameCount--;
         }
 
         /*
          * ensure no reference to alignFrame retained by menu item listener
          */
-        if (menuItem.getActionListeners().length > 0) {
+        if (menuItem.getActionListeners().length > 0)
+        {
           menuItem.removeActionListener(menuItem.getActionListeners()[0]);
         }
         windowMenu.remove(menuItem);
       }
     });
 
-    menuItem.addActionListener(new ActionListener() {
+    menuItem.addActionListener(new ActionListener()
+    {
       @Override
-      public void actionPerformed(ActionEvent e) {
-        try {
+      public void actionPerformed(ActionEvent e)
+      {
+        try
+        {
           frame.setSelected(true);
           frame.setIcon(false);
-        } catch (java.beans.PropertyVetoException ex) {
+        } catch (java.beans.PropertyVetoException ex)
+        {
 
         }
       }
@@ -863,28 +1015,34 @@ public class Desktop extends jalview.jbgui.GDesktop
     windowMenu.add(menuItem);
 
     frame.toFront();
-    try {
+    try
+    {
       frame.setSelected(true);
       frame.requestFocus();
-    } catch (java.beans.PropertyVetoException ve) {
-    } catch (java.lang.ClassCastException cex) {
+    } catch (java.beans.PropertyVetoException ve)
+    {
+    } catch (java.lang.ClassCastException cex)
+    {
       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);
+              "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
    */
-  private static void setKeyBindings(JInternalFrame frame) {
+  private static void setKeyBindings(JInternalFrame frame)
+  {
     @SuppressWarnings("serial")
-    final Action closeAction = new AbstractAction() {
+    final Action closeAction = new AbstractAction()
+    {
       @Override
-      public void actionPerformed(ActionEvent e) {
+      public void actionPerformed(ActionEvent e)
+      {
         frame.dispose();
       }
     };
@@ -892,10 +1050,13 @@ public class Desktop extends jalview.jbgui.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, ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx());
+    KeyStroke ctrlWKey = KeyStroke.getKeyStroke(KeyEvent.VK_W,
+            InputEvent.CTRL_DOWN_MASK);
+    KeyStroke cmdWKey = KeyStroke.getKeyStroke(KeyEvent.VK_W,
+            ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx());
 
-    InputMap inputMap = frame.getInputMap(JComponent.WHEN_IN_FOCUSED_WINDOW);
+    InputMap inputMap = frame
+            .getInputMap(JComponent.WHEN_IN_FOCUSED_WINDOW);
     String ctrlW = ctrlWKey.toString();
     inputMap.put(ctrlWKey, ctrlW);
     inputMap.put(cmdWKey, ctrlW);
@@ -905,8 +1066,10 @@ public class Desktop extends jalview.jbgui.GDesktop
   }
 
   @Override
-  public void lostOwnership(Clipboard clipboard, Transferable contents) {
-    if (!internalCopy) {
+  public void lostOwnership(Clipboard clipboard, Transferable contents)
+  {
+    if (!internalCopy)
+    {
       Desktop.jalviewClipboard = null;
     }
 
@@ -914,28 +1077,34 @@ public class Desktop extends jalview.jbgui.GDesktop
   }
 
   @Override
-  public void dragEnter(DropTargetDragEvent evt) {
+  public void dragEnter(DropTargetDragEvent evt)
+  {
   }
 
   @Override
-  public void dragExit(DropTargetEvent evt) {
+  public void dragExit(DropTargetEvent evt)
+  {
   }
 
   @Override
-  public void dragOver(DropTargetDragEvent evt) {
+  public void dragOver(DropTargetDragEvent evt)
+  {
   }
 
   @Override
-  public void dropActionChanged(DropTargetDragEvent evt) {
+  public void dropActionChanged(DropTargetDragEvent evt)
+  {
   }
 
   /**
    * DOCUMENT ME!
    * 
-   * @param evt DOCUMENT ME!
+   * @param evt
+   *          DOCUMENT ME!
    */
   @Override
-  public void drop(DropTargetDropEvent evt) {
+  public void drop(DropTargetDropEvent evt)
+  {
     boolean success = true;
     // JAL-1552 - acceptDrop required before getTransferable call for
     // Java's Transferable for native dnd
@@ -944,35 +1113,47 @@ public class Desktop extends jalview.jbgui.GDesktop
     List<Object> files = new ArrayList<>();
     List<DataSourceType> protocols = new ArrayList<>();
 
-    try {
+    try
+    {
       Desktop.transferFromDropTarget(files, protocols, evt, t);
-    } catch (Exception e) {
+    } catch (Exception e)
+    {
       e.printStackTrace();
       success = false;
     }
 
-    if (files != null) {
-      try {
-        for (int i = 0; i < files.size(); i++) {
+    if (files != null)
+    {
+      try
+      {
+        for (int i = 0; i < files.size(); i++)
+        {
           // BH 2018 File or String
           Object file = files.get(i);
           String fileName = file.toString();
-          DataSourceType protocol = (protocols == null) ? DataSourceType.FILE : protocols.get(i);
+          DataSourceType protocol = (protocols == null)
+                  ? DataSourceType.FILE
+                  : protocols.get(i);
           FileFormatI format = null;
 
-          if (fileName.endsWith(".jar")) {
+          if (fileName.endsWith(".jar"))
+          {
             format = FileFormat.Jalview;
 
-          } else {
+          }
+          else
+          {
             format = new IdentifyFile().identify(file, protocol);
           }
-          if (file instanceof File) {
+          if (file instanceof File)
+          {
             Platform.cacheFileData((File) file);
           }
           new FileLoader().LoadFile(null, file, protocol, format);
 
         }
-      } catch (Exception ex) {
+      } catch (Exception ex)
+      {
         success = false;
       }
     }
@@ -983,21 +1164,27 @@ public class Desktop extends jalview.jbgui.GDesktop
   /**
    * DOCUMENT ME!
    * 
-   * @param e DOCUMENT ME!
+   * @param e
+   *          DOCUMENT ME!
    */
   @Override
-  public void inputLocalFileMenuItem_actionPerformed(AlignViewport viewport) {
+  public void inputLocalFileMenuItem_actionPerformed(AlignViewport viewport)
+  {
     String fileFormat = Cache.getProperty("DEFAULT_FILE_FORMAT");
-    JalviewFileChooser chooser = JalviewFileChooser.forRead(Cache.getProperty("LAST_DIRECTORY"), fileFormat,
-        BackupFiles.getEnabled());
+    JalviewFileChooser chooser = JalviewFileChooser.forRead(
+            Cache.getProperty("LAST_DIRECTORY"), fileFormat,
+            BackupFiles.getEnabled());
 
     chooser.setFileView(new JalviewFileView());
-    chooser.setDialogTitle(MessageManager.getString("label.open_local_file"));
+    chooser.setDialogTitle(
+            MessageManager.getString("label.open_local_file"));
     chooser.setToolTipText(MessageManager.getString("action.open"));
 
-    chooser.setResponseHandler(0, new Runnable() {
+    chooser.setResponseHandler(0, new Runnable()
+    {
       @Override
-      public void run() {
+      public void run()
+      {
         File selectedFile = chooser.getSelectedFile();
         Cache.setProperty("LAST_DIRECTORY", selectedFile.getParent());
 
@@ -1008,15 +1195,20 @@ public class Desktop extends jalview.jbgui.GDesktop
          * Skip this step for dynamically added file formats, because IdentifyFile does
          * not know how to recognise them.
          */
-        if (FileFormats.getInstance().isIdentifiable(format)) {
-          try {
-            format = new IdentifyFile().identify(selectedFile, DataSourceType.FILE);
-          } catch (FileFormatException e) {
+        if (FileFormats.getInstance().isIdentifiable(format))
+        {
+          try
+          {
+            format = new IdentifyFile().identify(selectedFile,
+                    DataSourceType.FILE);
+          } catch (FileFormatException e)
+          {
             // format = null; //??
           }
         }
 
-        new FileLoader().LoadFile(viewport, selectedFile, DataSourceType.FILE, format);
+        new FileLoader().LoadFile(viewport, selectedFile,
+                DataSourceType.FILE, format);
       }
     });
     chooser.showOpenDialog(this);
@@ -1028,10 +1220,12 @@ public class Desktop extends jalview.jbgui.GDesktop
    * @param viewport
    */
   @Override
-  public void inputURLMenuItem_actionPerformed(AlignViewport viewport) {
+  public void inputURLMenuItem_actionPerformed(AlignViewport viewport)
+  {
     // This construct allows us to have a wider textfield
     // for viewing
-    JLabel label = new JLabel(MessageManager.getString("label.input_file_url"));
+    JLabel label = new JLabel(
+            MessageManager.getString("label.input_file_url"));
 
     JPanel panel = new JPanel(new GridLayout(2, 1));
     panel.add(label);
@@ -1042,9 +1236,11 @@ public class Desktop extends jalview.jbgui.GDesktop
      */
     JComponent history;
     String urlBase = "https://www.";
-    if (Platform.isJS()) {
+    if (Platform.isJS())
+    {
       history = new JTextField(urlBase, 35);
-    } else
+    }
+    else
     /**
      * Java only
      * 
@@ -1056,8 +1252,10 @@ public class Desktop extends jalview.jbgui.GDesktop
       asCombo.setEditable(true);
       asCombo.addItem(urlBase);
       String historyItems = Cache.getProperty("RECENT_URL");
-      if (historyItems != null) {
-        for (String token : historyItems.split("\\t")) {
+      if (historyItems != null)
+      {
+        for (String token : historyItems.split("\\t"))
+        {
           asCombo.addItem(token);
         }
       }
@@ -1067,87 +1265,122 @@ public class Desktop extends jalview.jbgui.GDesktop
 
     Object[] options = new Object[] { MessageManager.getString("action.ok"),
         MessageManager.getString("action.cancel") };
-    Runnable action = new Runnable() {
+    Runnable action = new Runnable()
+    {
       @Override
-      public void run() {
+      public void run()
+      {
         @SuppressWarnings("unchecked")
-        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);
+        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 {
+          else
+          {
+            new FileLoader().LoadFile(url, DataSourceType.URL,
+                    FileFormat.Jalview);
+          }
+        }
+        else
+        {
           FileFormatI format = null;
-          try {
+          try
+          {
             format = new IdentifyFile().identify(url, DataSourceType.URL);
-          } catch (FileFormatException e) {
+          } catch (FileFormatException e)
+          {
             // TODO revise error handling, distinguish between
             // URL not found and response not valid
           }
 
-          if (format == null) {
-            String msg = MessageManager.formatMessage("label.couldnt_locate", url);
+          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);
+                    MessageManager.getString("label.url_not_found"),
+                    JvOptionPane.WARNING_MESSAGE);
 
             return;
           }
 
-          if (viewport != null) {
-            new FileLoader().LoadFile(viewport, url, DataSourceType.URL, format);
-          } else {
+          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"));
+    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"));
   }
 
   /**
    * Opens the CutAndPaste window for the user to paste an alignment in to
    * 
-   * @param viewPanel - if not null, the pasted alignment is added to the current
-   *                  alignment; if null, to a new alignment window
+   * @param viewPanel
+   *          - if not null, the pasted alignment is added to the current
+   *          alignment; if null, to a new alignment window
    */
   @Override
-  public void inputTextboxMenuItem_actionPerformed(AlignmentViewPanel viewPanel) {
+  public void inputTextboxMenuItem_actionPerformed(
+          AlignmentViewPanel viewPanel)
+  {
     CutAndPasteTransfer cap = new CutAndPasteTransfer();
     cap.setForInput(viewPanel);
-    Desktop.addInternalFrame(cap, MessageManager.getString("label.cut_paste_alignmen_file"), true, 600, 500);
+    Desktop.addInternalFrame(cap,
+            MessageManager.getString("label.cut_paste_alignmen_file"), true,
+            600, 500);
   }
 
   /*
    * Exit the program
    */
   @Override
-  public void quit() {
+  public void quit()
+  {
     Dimension screen = Toolkit.getDefaultToolkit().getScreenSize();
     Cache.setProperty("SCREENGEOMETRY_WIDTH", screen.width + "");
     Cache.setProperty("SCREENGEOMETRY_HEIGHT", screen.height + "");
-    storeLastKnownDimensions("", new Rectangle(getBounds().x, getBounds().y, getWidth(), getHeight()));
+    storeLastKnownDimensions("", new Rectangle(getBounds().x, getBounds().y,
+            getWidth(), getHeight()));
 
-    if (jconsole != null) {
+    if (jconsole != null)
+    {
       storeLastKnownDimensions("JAVA_CONSOLE_", jconsole.getBounds());
       jconsole.stopConsole();
     }
-    if (jvnews != null) {
+    if (jvnews != null)
+    {
       storeLastKnownDimensions("JALVIEW_RSS_WINDOW_", jvnews.getBounds());
 
     }
-    if (dialogExecutor != null) {
+    if (dialogExecutor != null)
+    {
       dialogExecutor.shutdownNow();
     }
     closeAll_actionPerformed(null);
 
-    if (groovyConsole != null) {
+    if (groovyConsole != null)
+    {
       // suppress a possible repeat prompt to save script
       groovyConsole.setDirty(false);
       groovyConsole.exit();
@@ -1155,9 +1388,11 @@ public class Desktop extends jalview.jbgui.GDesktop
     System.exit(0);
   }
 
-  private void storeLastKnownDimensions(String string, Rectangle jc) {
-    jalview.bin.Console.debug("Storing last known dimensions for " + string + ": x:" + jc.x + " y:" + jc.y + " width:" + jc.width
-        + " height:" + jc.height);
+  private void storeLastKnownDimensions(String string, Rectangle jc)
+  {
+    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 + "");
@@ -1168,13 +1403,17 @@ public class Desktop extends jalview.jbgui.GDesktop
   /**
    * DOCUMENT ME!
    * 
-   * @param e DOCUMENT ME!
+   * @param e
+   *          DOCUMENT ME!
    */
   @Override
-  public void aboutMenuItem_actionPerformed(ActionEvent e) {
-    new Thread(new Runnable() {
+  public void aboutMenuItem_actionPerformed(ActionEvent e)
+  {
+    new Thread(new Runnable()
+    {
       @Override
-      public void run() {
+      public void run()
+      {
         new SplashScreen(false);
       }
     }).start();
@@ -1182,35 +1421,48 @@ public class Desktop extends jalview.jbgui.GDesktop
 
   /**
    * 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
+   * number, build details, author details and citation reference, but without
+   * the enclosing {@code html} tags
    * 
    * @return
    */
-  public String getAboutMessage() {
+  public String getAboutMessage()
+  {
     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("<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(Locale.ROOT).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", "https://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>");
       }
     }
@@ -1227,11 +1479,15 @@ public class Desktop extends jalview.jbgui.GDesktop
    * Action on requesting Help documentation
    */
   @Override
-  public void documentationMenuItem_actionPerformed() {
-    try {
-      if (Platform.isJS()) {
+  public void documentationMenuItem_actionPerformed()
+  {
+    try
+    {
+      if (Platform.isJS())
+      {
         BrowserLauncher.openURL("https://www.jalview.org/help.html");
-      } else
+      }
+      else
       /**
        * Java only
        * 
@@ -1240,19 +1496,24 @@ public class Desktop extends jalview.jbgui.GDesktop
       {
         Help.showHelpWindow();
       }
-    } catch (Exception ex) {
+    } catch (Exception ex)
+    {
       System.err.println("Error opening help: " + ex.getMessage());
     }
   }
 
   @Override
-  public void closeAll_actionPerformed(ActionEvent e) {
+  public void closeAll_actionPerformed(ActionEvent e)
+  {
     // TODO show a progress bar while closing?
     JInternalFrame[] frames = desktop.getAllFrames();
-    for (int i = 0; i < frames.length; i++) {
-      try {
+    for (int i = 0; i < frames.length; i++)
+    {
+      try
+      {
         frames[i].setClosed(true);
-      } catch (java.beans.PropertyVetoException ex) {
+      } catch (java.beans.PropertyVetoException ex)
+      {
       }
     }
     Jalview.setCurrentAlignFrame(null);
@@ -1262,23 +1523,28 @@ public class Desktop extends jalview.jbgui.GDesktop
      * reset state of singleton objects as appropriate (clear down session state
      * when all windows are closed)
      */
-    StructureSelectionManager ssm = StructureSelectionManager.getStructureSelectionManager(this);
-    if (ssm != null) {
+    StructureSelectionManager ssm = StructureSelectionManager
+            .getStructureSelectionManager(this);
+    if (ssm != null)
+    {
       ssm.resetAll();
     }
   }
 
   @Override
-  public void raiseRelated_actionPerformed(ActionEvent e) {
+  public void raiseRelated_actionPerformed(ActionEvent e)
+  {
     reorderAssociatedWindows(false, false);
   }
 
   @Override
-  public void minimizeAssociated_actionPerformed(ActionEvent e) {
+  public void minimizeAssociated_actionPerformed(ActionEvent e)
+  {
     reorderAssociatedWindows(true, false);
   }
 
-  void closeAssociatedWindows() {
+  void closeAssociatedWindows()
+  {
     reorderAssociatedWindows(false, true);
   }
 
@@ -1289,7 +1555,8 @@ public class Desktop extends jalview.jbgui.GDesktop
    * ActionEvent)
    */
   @Override
-  protected void garbageCollect_actionPerformed(ActionEvent e) {
+  protected void garbageCollect_actionPerformed(ActionEvent e)
+  {
     // We simply collect the garbage
     jalview.bin.Console.debug("Collecting garbage...");
     System.gc();
@@ -1303,7 +1570,8 @@ public class Desktop extends jalview.jbgui.GDesktop
    * ActionEvent )
    */
   @Override
-  protected void showMemusage_actionPerformed(ActionEvent e) {
+  protected void showMemusage_actionPerformed(ActionEvent e)
+  {
     desktop.showMemoryUsage(showMemusage.isSelected());
   }
 
@@ -1315,7 +1583,8 @@ public class Desktop extends jalview.jbgui.GDesktop
    * )
    */
   @Override
-  protected void showConsole_actionPerformed(ActionEvent e) {
+  protected void showConsole_actionPerformed(ActionEvent e)
+  {
     showConsole(showConsole.isSelected());
   }
 
@@ -1326,61 +1595,89 @@ public class Desktop extends jalview.jbgui.GDesktop
    * 
    * @param selected
    */
-  void showConsole(boolean selected) {
+  void showConsole(boolean selected)
+  {
     // TODO: decide if we should update properties file
     if (jconsole != null) // BH 2018
     {
       showConsole.setSelected(selected);
-      Cache.setProperty("SHOW_JAVA_CONSOLE", Boolean.valueOf(selected).toString());
+      Cache.setProperty("SHOW_JAVA_CONSOLE",
+              Boolean.valueOf(selected).toString());
       jconsole.setVisible(selected);
     }
   }
 
-  void reorderAssociatedWindows(boolean minimize, boolean close) {
+  void reorderAssociatedWindows(boolean minimize, boolean close)
+  {
     JInternalFrame[] frames = desktop.getAllFrames();
-    if (frames == null || frames.length < 1) {
+    if (frames == null || frames.length < 1)
+    {
       return;
     }
 
     AlignmentViewport source = null, target = null;
-    if (frames[0] instanceof AlignFrame) {
+    if (frames[0] instanceof AlignFrame)
+    {
       source = ((AlignFrame) frames[0]).getCurrentView();
-    } else if (frames[0] instanceof TreePanel) {
+    }
+    else if (frames[0] instanceof TreePanel)
+    {
       source = ((TreePanel) frames[0]).getViewPort();
-    } else if (frames[0] instanceof PCAPanel) {
+    }
+    else if (frames[0] instanceof PCAPanel)
+    {
       source = ((PCAPanel) frames[0]).av;
-    } else if (frames[0].getContentPane() instanceof PairwiseAlignPanel) {
+    }
+    else if (frames[0].getContentPane() instanceof PairwiseAlignPanel)
+    {
       source = ((PairwiseAlignPanel) frames[0].getContentPane()).av;
     }
 
-    if (source != null) {
-      for (int i = 0; i < frames.length; i++) {
+    if (source != null)
+    {
+      for (int i = 0; i < frames.length; i++)
+      {
         target = null;
-        if (frames[i] == null) {
+        if (frames[i] == null)
+        {
           continue;
         }
-        if (frames[i] instanceof AlignFrame) {
+        if (frames[i] instanceof AlignFrame)
+        {
           target = ((AlignFrame) frames[i]).getCurrentView();
-        } else if (frames[i] instanceof TreePanel) {
+        }
+        else if (frames[i] instanceof TreePanel)
+        {
           target = ((TreePanel) frames[i]).getViewPort();
-        } else if (frames[i] instanceof PCAPanel) {
+        }
+        else if (frames[i] instanceof PCAPanel)
+        {
           target = ((PCAPanel) frames[i]).av;
-        } else if (frames[i].getContentPane() instanceof PairwiseAlignPanel) {
+        }
+        else if (frames[i].getContentPane() instanceof PairwiseAlignPanel)
+        {
           target = ((PairwiseAlignPanel) frames[i].getContentPane()).av;
         }
 
-        if (source == target) {
-          try {
-            if (close) {
+        if (source == target)
+        {
+          try
+          {
+            if (close)
+            {
               frames[i].setClosed(true);
-            } else {
+            }
+            else
+            {
               frames[i].setIcon(minimize);
-              if (!minimize) {
+              if (!minimize)
+              {
                 frames[i].toFront();
               }
             }
 
-          } catch (java.beans.PropertyVetoException ex) {
+          } catch (java.beans.PropertyVetoException ex)
+          {
           }
         }
       }
@@ -1390,10 +1687,12 @@ public class Desktop extends jalview.jbgui.GDesktop
   /**
    * DOCUMENT ME!
    * 
-   * @param e DOCUMENT ME!
+   * @param e
+   *          DOCUMENT ME!
    */
   @Override
-  protected void preferences_actionPerformed(ActionEvent e) {
+  protected void preferences_actionPerformed(ActionEvent e)
+  {
     Preferences.openPreferences();
   }
 
@@ -1402,66 +1701,86 @@ public class Desktop extends jalview.jbgui.GDesktop
    * Jalview project file
    */
   @Override
-  public void saveState_actionPerformed() {
+  public void saveState_actionPerformed()
+  {
     saveState_actionPerformed(false);
   }
 
-  public void saveState_actionPerformed(boolean saveAs) {
+  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();
+    boolean autoSave = projectFile != null && !saveAs
+            && BackupFiles.getEnabled();
 
     // System.out.println("autoSave="+autoSave+", projectFile='"+projectFile+"',
     // saveAs="+saveAs+", Backups
     // "+(BackupFiles.getEnabled()?"enabled":"disabled"));
 
     boolean approveSave = false;
-    if (!autoSave) {
-      JalviewFileChooser chooser = new JalviewFileChooser("jvp", "Jalview Project");
+    if (!autoSave)
+    {
+      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) {
+      if (value == JalviewFileChooser.APPROVE_OPTION)
+      {
         projectFile = chooser.getSelectedFile();
         setProjectFile(projectFile);
         approveSave = true;
       }
     }
 
-    if (approveSave || autoSave) {
+    if (approveSave || autoSave)
+    {
       final Desktop me = this;
       final java.io.File chosenFile = projectFile;
-      new Thread(new Runnable() {
+      new Thread(new Runnable()
+      {
         @Override
-        public void run() {
+        public void run()
+        {
           // TODO: refactor to Jalview desktop session controller action.
-          setProgressBar(
-              MessageManager.formatMessage("label.saving_jalview_project", new Object[] { chosenFile.getName() }),
-              chosenFile.hashCode());
+          setProgressBar(MessageManager.formatMessage(
+                  "label.saving_jalview_project", new Object[]
+                  { 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 {
+          try
+          {
             boolean doBackup = BackupFiles.getEnabled();
-            BackupFiles backupfiles = doBackup ? new BackupFiles(chosenFile) : null;
+            BackupFiles backupfiles = doBackup ? new BackupFiles(chosenFile)
+                    : null;
 
-            new Jalview2XML().saveState(doBackup ? backupfiles.getTempFile() : chosenFile);
+            new Jalview2XML().saveState(
+                    doBackup ? backupfiles.getTempFile() : chosenFile);
 
-            if (doBackup) {
+            if (doBackup)
+            {
               backupfiles.setWriteSuccess(true);
               backupfiles.rollBackupsAndRenameTempFile();
             }
-          } catch (OutOfMemoryError oom) {
-            new OOMWarning("Whilst saving current state to " + chosenFile.getName(), oom);
-          } catch (Exception ex) {
-            jalview.bin.Console.error("Problems whilst trying to save to " + chosenFile.getName(), ex);
+          } catch (OutOfMemoryError oom)
+          {
+            new OOMWarning("Whilst saving current state to "
+                    + chosenFile.getName(), oom);
+          } catch (Exception 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[] { chosenFile.getName() }),
-                MessageManager.getString("label.couldnt_save_project"), JvOptionPane.WARNING_MESSAGE);
+                    MessageManager.formatMessage(
+                            "label.error_whilst_saving_current_state_to",
+                            new Object[]
+                            { chosenFile.getName() }),
+                    MessageManager.getString("label.couldnt_save_project"),
+                    JvOptionPane.WARNING_MESSAGE);
           }
           setProgressBar(null, chosenFile.hashCode());
         }
@@ -1470,15 +1789,18 @@ public class Desktop extends jalview.jbgui.GDesktop
   }
 
   @Override
-  public void saveAsState_actionPerformed(ActionEvent e) {
+  public void saveAsState_actionPerformed(ActionEvent e)
+  {
     saveState_actionPerformed(true);
   }
 
-  private void setProjectFile(File choice) {
+  private void setProjectFile(File choice)
+  {
     this.projectFile = choice;
   }
 
-  public File getProjectFile() {
+  public File getProjectFile()
+  {
     return this.projectFile;
   }
 
@@ -1487,35 +1809,51 @@ public class Desktop extends jalview.jbgui.GDesktop
    * Jalview project
    */
   @Override
-  public void loadState_actionPerformed() {
+  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"), suffix, desc,
-        "Jalview Project", true, BackupFiles.getEnabled()); // last two
-                                                            // booleans:
-                                                            // allFiles,
+    final String[] desc = new String[] { "Jalview Project",
+        "Jalview Project (old)" };
+    JalviewFileChooser chooser = new JalviewFileChooser(
+            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"));
-    chooser.setResponseHandler(0, new Runnable() {
+    chooser.setResponseHandler(0, new Runnable()
+    {
       @Override
-      public void run() {
+      public void run()
+      {
         File selectedFile = chooser.getSelectedFile();
         setProjectFile(selectedFile);
         String choice = selectedFile.getAbsolutePath();
         Cache.setProperty("LAST_DIRECTORY", selectedFile.getParent());
-        new Thread(new Runnable() {
+        new Thread(new Runnable()
+        {
           @Override
-          public void run() {
-            try {
+          public void run()
+          {
+            try
+            {
               new Jalview2XML().loadJalviewAlign(selectedFile);
-            } catch (OutOfMemoryError oom) {
+            } 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);
+            } 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);
+                      MessageManager.formatMessage(
+                              "label.error_whilst_loading_project_from",
+                              new Object[]
+                              { choice }),
+                      MessageManager
+                              .getString("label.couldnt_load_project"),
+                      JvOptionPane.WARNING_MESSAGE);
             }
           }
         }, "Project Loader").start();
@@ -1526,7 +1864,8 @@ public class Desktop extends jalview.jbgui.GDesktop
   }
 
   @Override
-  public void inputSequence_actionPerformed(ActionEvent e) {
+  public void inputSequence_actionPerformed(ActionEvent e)
+  {
     new SequenceFetcher(this);
   }
 
@@ -1534,16 +1873,21 @@ public class Desktop extends jalview.jbgui.GDesktop
 
   ArrayList<JPanel> fileLoadingPanels = new ArrayList<>();
 
-  public void startLoading(final Object fileName) {
-    if (fileLoadingCount == 0) {
-      fileLoadingPanels
-          .add(addProgressPanel(MessageManager.formatMessage("label.loading_file", new Object[] { fileName })));
+  public void startLoading(final Object fileName)
+  {
+    if (fileLoadingCount == 0)
+    {
+      fileLoadingPanels.add(addProgressPanel(MessageManager
+              .formatMessage("label.loading_file", new Object[]
+              { fileName })));
     }
     fileLoadingCount++;
   }
 
-  private JPanel addProgressPanel(String string) {
-    if (progressPanel == null) {
+  private JPanel addProgressPanel(String string)
+  {
+    if (progressPanel == null)
+    {
       progressPanel = new JPanel(new GridLayout(1, 1));
       totalProgressCount = 0;
       instance.getContentPane().add(progressPanel, BorderLayout.SOUTH);
@@ -1556,7 +1900,8 @@ public class Desktop extends jalview.jbgui.GDesktop
 
     thisprogress.add(progressBar, BorderLayout.CENTER);
     progressPanel.add(thisprogress);
-    ((GridLayout) progressPanel.getLayout()).setRows(((GridLayout) progressPanel.getLayout()).getRows() + 1);
+    ((GridLayout) progressPanel.getLayout()).setRows(
+            ((GridLayout) progressPanel.getLayout()).getRows() + 1);
     ++totalProgressCount;
     instance.validate();
     return thisprogress;
@@ -1564,13 +1909,17 @@ public class Desktop extends jalview.jbgui.GDesktop
 
   int totalProgressCount = 0;
 
-  private void removeProgressPanel(JPanel progbar) {
-    if (progressPanel != null) {
-      synchronized (progressPanel) {
+  private void removeProgressPanel(JPanel progbar)
+  {
+    if (progressPanel != null)
+    {
+      synchronized (progressPanel)
+      {
         progressPanel.remove(progbar);
         GridLayout gl = (GridLayout) progressPanel.getLayout();
         gl.setRows(gl.getRows() - 1);
-        if (--totalProgressCount < 1) {
+        if (--totalProgressCount < 1)
+        {
           this.getContentPane().remove(progressPanel);
           progressPanel = null;
         }
@@ -1579,10 +1928,13 @@ public class Desktop extends jalview.jbgui.GDesktop
     validate();
   }
 
-  public void stopLoading() {
+  public void stopLoading()
+  {
     fileLoadingCount--;
-    if (fileLoadingCount < 1) {
-      while (fileLoadingPanels.size() > 0) {
+    if (fileLoadingCount < 1)
+    {
+      while (fileLoadingPanels.size() > 0)
+      {
         removeProgressPanel(fileLoadingPanels.remove(0));
       }
       fileLoadingPanels.clear();
@@ -1591,35 +1943,45 @@ public class Desktop extends jalview.jbgui.GDesktop
     validate();
   }
 
-  public static int getViewCount(String alignmentId) {
+  public static int getViewCount(String alignmentId)
+  {
     AlignmentViewport[] aps = getViewports(alignmentId);
     return (aps == null) ? 0 : aps.length;
   }
 
   /**
    * 
-   * @param alignmentId - if null, all sets are returned
+   * @param alignmentId
+   *          - if null, all sets are returned
    * @return all AlignmentPanels concerning the alignmentId sequence set
    */
-  public static AlignmentPanel[] getAlignmentPanels(String alignmentId) {
-    if (Desktop.desktop == null) {
+  public static AlignmentPanel[] getAlignmentPanels(String alignmentId)
+  {
+    if (Desktop.desktop == null)
+    {
       // no frames created and in headless mode
       // TODO: verify that frames are recoverable when in headless mode
       return null;
     }
     List<AlignmentPanel> aps = new ArrayList<>();
     AlignFrame[] frames = getAlignFrames();
-    if (frames == null) {
+    if (frames == null)
+    {
       return null;
     }
-    for (AlignFrame af : frames) {
-      for (AlignmentPanel ap : af.alignPanels) {
-        if (alignmentId == null || alignmentId.equals(ap.av.getSequenceSetId())) {
+    for (AlignFrame af : frames)
+    {
+      for (AlignmentPanel ap : af.alignPanels)
+      {
+        if (alignmentId == null
+                || alignmentId.equals(ap.av.getSequenceSetId()))
+        {
           aps.add(ap);
         }
       }
     }
-    if (aps.size() == 0) {
+    if (aps.size() == 0)
+    {
       return null;
     }
     AlignmentPanel[] vap = aps.toArray(new AlignmentPanel[aps.size()]);
@@ -1629,29 +1991,42 @@ public class Desktop extends jalview.jbgui.GDesktop
   /**
    * get all the viewports on an alignment.
    * 
-   * @param sequenceSetId unique alignment id (may be null - all viewports
-   *                      returned in that case)
+   * @param sequenceSetId
+   *          unique alignment id (may be null - all viewports returned in that
+   *          case)
    * @return all viewports on the alignment bound to sequenceSetId
    */
-  public static AlignmentViewport[] getViewports(String sequenceSetId) {
+  public static AlignmentViewport[] getViewports(String sequenceSetId)
+  {
     List<AlignmentViewport> viewp = new ArrayList<>();
-    if (desktop != null) {
+    if (desktop != null)
+    {
       AlignFrame[] frames = Desktop.getAlignFrames();
 
-      for (AlignFrame afr : frames) {
-        if (sequenceSetId == null || afr.getViewport().getSequenceSetId().equals(sequenceSetId)) {
-          if (afr.alignPanels != null) {
-            for (AlignmentPanel ap : afr.alignPanels) {
-              if (sequenceSetId == null || sequenceSetId.equals(ap.av.getSequenceSetId())) {
+      for (AlignFrame afr : frames)
+      {
+        if (sequenceSetId == null || afr.getViewport().getSequenceSetId()
+                .equals(sequenceSetId))
+        {
+          if (afr.alignPanels != null)
+          {
+            for (AlignmentPanel ap : afr.alignPanels)
+            {
+              if (sequenceSetId == null
+                      || sequenceSetId.equals(ap.av.getSequenceSetId()))
+              {
                 viewp.add(ap.av);
               }
             }
-          } else {
+          }
+          else
+          {
             viewp.add(afr.getViewport());
           }
         }
       }
-      if (viewp.size() > 0) {
+      if (viewp.size() > 0)
+      {
         return viewp.toArray(new AlignmentViewport[viewp.size()]);
       }
     }
@@ -1663,25 +2038,29 @@ public class Desktop extends jalview.jbgui.GDesktop
    * 
    * @param af
    */
-  public static void explodeViews(AlignFrame af) {
+  public static void explodeViews(AlignFrame af)
+  {
     int size = af.alignPanels.size();
-    if (size < 2) {
+    if (size < 2)
+    {
       return;
     }
 
     // FIXME: ideally should use UI interface API
-    FeatureSettings viewFeatureSettings = (af.featureSettings != null && af.featureSettings.isOpen())
-        ? af.featureSettings
-        : null;
+    FeatureSettings viewFeatureSettings = (af.featureSettings != null
+            && af.featureSettings.isOpen()) ? af.featureSettings : null;
     Rectangle fsBounds = af.getFeatureSettingsGeometry();
-    for (int i = 0; i < size; i++) {
+    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) {
+      if (ap == af.alignPanel)
+      {
+        if (viewFeatureSettings != null && viewFeatureSettings.fr.ap == ap)
+        {
           newaf.featureSettings = viewFeatureSettings;
         }
         newaf.setFeatureSettingsGeometry(fsBounds);
@@ -1692,18 +2071,22 @@ public class Desktop extends jalview.jbgui.GDesktop
        * one exploded frame share and restore the same (frame) position and size.
        */
       Rectangle geometry = ap.av.getExplodedGeometry();
-      if (geometry != null) {
+      if (geometry != null)
+      {
         newaf.setBounds(geometry);
       }
 
       ap.av.setGatherViewsHere(false);
 
-      addInternalFrame(newaf, af.getTitle(), AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
+      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()) {
+      if (ap == af.alignPanel && newaf.featureSettings != null
+              && newaf.featureSettings.isOpen()
+              && af.alignPanel.getAlignViewport().isShowSequenceFeatures())
+      {
         newaf.showFeatureSettingsUI();
       }
     }
@@ -1716,24 +2099,29 @@ 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
    */
-  public void gatherViews(AlignFrame source) {
+  public void gatherViews(AlignFrame source)
+  {
     source.viewport.setGatherViewsHere(true);
     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) {
+    for (int t = 0; t < frames.length; t++)
+    {
+      if (frames[t] instanceof AlignFrame && frames[t] != source)
+      {
         AlignFrame af = (AlignFrame) frames[t];
         boolean gatherThis = false;
-        for (int a = 0; a < af.alignPanels.size(); a++) {
+        for (int a = 0; a < af.alignPanels.size(); a++)
+        {
           AlignmentPanel ap = af.alignPanels.get(a);
-          if (viewId.equals(ap.av.getSequenceSetId())) {
+          if (viewId.equals(ap.av.getSequenceSetId()))
+          {
             gatherThis = true;
             ap.av.setGatherViewsHere(false);
             ap.av.setExplodedGeometry(af.getBounds());
@@ -1741,13 +2129,19 @@ public class Desktop extends jalview.jbgui.GDesktop
           }
         }
 
-        if (gatherThis) {
-          if (af.featureSettings != null && af.featureSettings.isOpen()) {
-            if (source.featureSettings == null) {
+        if (gatherThis)
+        {
+          if (af.featureSettings != null && af.featureSettings.isOpen())
+          {
+            if (source.featureSettings == null)
+            {
               // preserve the feature settings geometry for this frame
               source.featureSettings = af.featureSettings;
-              source.setFeatureSettingsGeometry(af.getFeatureSettingsGeometry());
-            } else {
+              source.setFeatureSettingsGeometry(
+                      af.getFeatureSettingsGeometry());
+            }
+            else
+            {
               // close it and forget
               af.featureSettings.close();
             }
@@ -1759,13 +2153,15 @@ public class Desktop extends jalview.jbgui.GDesktop
     }
 
     // refresh the feature setting UI for the source frame if it exists
-    if (source.featureSettings != null && source.featureSettings.isOpen()) {
+    if (source.featureSettings != null && source.featureSettings.isOpen())
+    {
       source.showFeatureSettingsUI();
     }
 
   }
 
-  public JInternalFrame[] getAllFrames() {
+  public JInternalFrame[] getAllFrames()
+  {
     return desktop.getAllFrames();
   }
 
@@ -1775,37 +2171,49 @@ public class Desktop extends jalview.jbgui.GDesktop
    * 
    * @param url
    */
-  public void checkForQuestionnaire(String url) {
+  public void checkForQuestionnaire(String url)
+  {
     UserQuestionnaireCheck jvq = new UserQuestionnaireCheck(url);
     // javax.swing.SwingUtilities.invokeLater(jvq);
     new Thread(jvq).start();
   }
 
-  public void checkURLLinks() {
+  public void checkURLLinks()
+  {
     // Thread off the URL link checker
-    addDialogThread(new Runnable() {
+    addDialogThread(new Runnable()
+    {
       @Override
-      public void run() {
-        if (Cache.getDefault("CHECKURLLINKS", true)) {
+      public void run()
+      {
+        if (Cache.getDefault("CHECKURLLINKS", true))
+        {
           // check what the actual links are - if it's just the default don't
           // bother with the warning
-          List<String> links = Preferences.sequenceUrlLinks.getLinksForMenu();
+          List<String> links = Preferences.sequenceUrlLinks
+                  .getLinksForMenu();
 
           // only need to check links if there is one with a
           // SEQUENCE_ID which is not the default EMBL_EBI link
           ListIterator<String> li = links.listIterator();
           boolean check = false;
           List<JLabel> urls = new ArrayList<>();
-          while (li.hasNext()) {
+          while (li.hasNext())
+          {
             String link = li.next();
-            if (link.contains(jalview.util.UrlConstants.SEQUENCE_ID) && !UrlConstants.isDefaultString(link)) {
+            if (link.contains(jalview.util.UrlConstants.SEQUENCE_ID)
+                    && !UrlConstants.isDefaultString(link))
+            {
               check = true;
               int barPos = link.indexOf("|");
-              String urlMsg = barPos == -1 ? link : link.substring(0, barPos) + ": " + link.substring(barPos + 1);
+              String urlMsg = barPos == -1 ? link
+                      : link.substring(0, barPos) + ": "
+                              + link.substring(barPos + 1);
               urls.add(new JLabel(urlMsg));
             }
           }
-          if (!check) {
+          if (!check)
+          {
             return;
           }
 
@@ -1814,27 +2222,36 @@ public class Desktop extends jalview.jbgui.GDesktop
           JPanel msgPanel = new JPanel();
           msgPanel.setLayout(new BoxLayout(msgPanel, BoxLayout.PAGE_AXIS));
           msgPanel.add(Box.createVerticalGlue());
-          JLabel msg = new JLabel(MessageManager.getString("label.SEQUENCE_ID_for_DB_ACCESSION1"));
-          JLabel msg2 = new JLabel(MessageManager.getString("label.SEQUENCE_ID_for_DB_ACCESSION2"));
+          JLabel msg = new JLabel(MessageManager
+                  .getString("label.SEQUENCE_ID_for_DB_ACCESSION1"));
+          JLabel msg2 = new JLabel(MessageManager
+                  .getString("label.SEQUENCE_ID_for_DB_ACCESSION2"));
           msgPanel.add(msg);
-          for (JLabel url : urls) {
+          for (JLabel url : urls)
+          {
             msgPanel.add(url);
           }
           msgPanel.add(msg2);
 
-          final JCheckBox jcb = new JCheckBox(MessageManager.getString("label.do_not_display_again"));
-          jcb.addActionListener(new ActionListener() {
+          final JCheckBox jcb = new JCheckBox(
+                  MessageManager.getString("label.do_not_display_again"));
+          jcb.addActionListener(new ActionListener()
+          {
             @Override
-            public void actionPerformed(ActionEvent e) {
+            public void actionPerformed(ActionEvent e)
+            {
               // update Cache settings for "don't show this again"
               boolean showWarningAgain = !jcb.isSelected();
-              Cache.setProperty("CHECKURLLINKS", Boolean.valueOf(showWarningAgain).toString());
+              Cache.setProperty("CHECKURLLINKS",
+                      Boolean.valueOf(showWarningAgain).toString());
             }
           });
           msgPanel.add(jcb);
 
           JvOptionPane.showMessageDialog(Desktop.desktop, msgPanel,
-              MessageManager.getString("label.SEQUENCE_ID_no_longer_used"), JvOptionPane.WARNING_MESSAGE);
+                  MessageManager
+                          .getString("label.SEQUENCE_ID_no_longer_used"),
+                  JvOptionPane.WARNING_MESSAGE);
         }
       }
     });
@@ -1842,11 +2259,13 @@ 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 {
+  public class MyDesktopPane extends JDesktopPane implements Runnable
+  {
     private static final float ONE_MB = 1048576f;
 
     boolean showMemoryUsage = false;
@@ -1855,33 +2274,41 @@ public class Desktop extends jalview.jbgui.GDesktop
 
     java.text.NumberFormat df;
 
-    float maxMemory, allocatedMemory, freeMemory, totalFreeMemory, percentUsage;
+    float maxMemory, allocatedMemory, freeMemory, totalFreeMemory,
+            percentUsage;
 
-    public MyDesktopPane(boolean showMemoryUsage) {
+    public MyDesktopPane(boolean showMemoryUsage)
+    {
       showMemoryUsage(showMemoryUsage);
     }
 
-    public void showMemoryUsage(boolean showMemory) {
+    public void showMemoryUsage(boolean showMemory)
+    {
       this.showMemoryUsage = showMemory;
-      if (showMemory) {
+      if (showMemory)
+      {
         Thread worker = new Thread(this);
         worker.start();
       }
       repaint();
     }
 
-    public boolean isShowMemoryUsage() {
+    public boolean isShowMemoryUsage()
+    {
       return showMemoryUsage;
     }
 
     @Override
-    public void run() {
+    public void run()
+    {
       df = java.text.NumberFormat.getNumberInstance();
       df.setMaximumFractionDigits(2);
       runtime = Runtime.getRuntime();
 
-      while (showMemoryUsage) {
-        try {
+      while (showMemoryUsage)
+      {
+        try
+        {
           maxMemory = runtime.maxMemory() / ONE_MB;
           allocatedMemory = runtime.totalMemory() / ONE_MB;
           freeMemory = runtime.freeMemory() / ONE_MB;
@@ -1898,24 +2325,30 @@ public class Desktop extends jalview.jbgui.GDesktop
           repaint();
           // sleep after showing usage
           Thread.sleep(3000);
-        } catch (Exception ex) {
+        } catch (Exception ex)
+        {
           ex.printStackTrace();
         }
       }
     }
 
     @Override
-    public void paintComponent(Graphics g) {
-      if (showMemoryUsage && g != null && df != null) {
-        if (percentUsage < 20) {
+    public void paintComponent(Graphics g)
+    {
+      if (showMemoryUsage && g != null && df != null)
+      {
+        if (percentUsage < 20)
+        {
           g.setColor(Color.red);
         }
         FontMetrics fm = g.getFontMetrics();
-        if (fm != null) {
-          g.drawString(
-              MessageManager.formatMessage("label.memory_stats",
-                  new Object[] { df.format(totalFreeMemory), df.format(maxMemory), df.format(percentUsage) }),
-              10, getHeight() - fm.getHeight());
+        if (fm != null)
+        {
+          g.drawString(MessageManager.formatMessage("label.memory_stats",
+                  new Object[]
+                  { df.format(totalFreeMemory), df.format(maxMemory),
+                      df.format(percentUsage) }),
+                  10, getHeight() - fm.getHeight());
         }
       }
 
@@ -1929,36 +2362,46 @@ public class Desktop extends jalview.jbgui.GDesktop
    * 
    * @return an array of AlignFrame, or null if none found
    */
-  public static AlignFrame[] getAlignFrames() {
-    if (Jalview.isHeadlessMode()) {
+  public static AlignFrame[] getAlignFrames()
+  {
+    if (Jalview.isHeadlessMode())
+    {
       // Desktop.desktop is null in headless mode
       return new AlignFrame[] { Jalview.currentAlignFrame };
     }
 
     JInternalFrame[] frames = Desktop.desktop.getAllFrames();
 
-    if (frames == null) {
+    if (frames == null)
+    {
       return null;
     }
     List<AlignFrame> avp = new ArrayList<>();
     // REVERSE ORDER
-    for (int i = frames.length - 1; i > -1; i--) {
-      if (frames[i] instanceof AlignFrame) {
+    for (int i = frames.length - 1; i > -1; i--)
+    {
+      if (frames[i] instanceof AlignFrame)
+      {
         avp.add((AlignFrame) frames[i]);
-      } else if (frames[i] instanceof SplitFrame) {
+      }
+      else if (frames[i] instanceof SplitFrame)
+      {
         /*
          * Also check for a split frame containing an AlignFrame
          */
         GSplitFrame sf = (GSplitFrame) frames[i];
-        if (sf.getTopFrame() instanceof AlignFrame) {
+        if (sf.getTopFrame() instanceof AlignFrame)
+        {
           avp.add((AlignFrame) sf.getTopFrame());
         }
-        if (sf.getBottomFrame() instanceof AlignFrame) {
+        if (sf.getBottomFrame() instanceof AlignFrame)
+        {
           avp.add((AlignFrame) sf.getBottomFrame());
         }
       }
     }
-    if (avp.size() == 0) {
+    if (avp.size() == 0)
+    {
       return null;
     }
     AlignFrame afs[] = avp.toArray(new AlignFrame[avp.size()]);
@@ -1970,21 +2413,26 @@ public class Desktop extends jalview.jbgui.GDesktop
    * 
    * @return
    */
-  public GStructureViewer[] getJmols() {
+  public GStructureViewer[] getJmols()
+  {
     JInternalFrame[] frames = Desktop.desktop.getAllFrames();
 
-    if (frames == null) {
+    if (frames == null)
+    {
       return null;
     }
     List<GStructureViewer> avp = new ArrayList<>();
     // REVERSE ORDER
-    for (int i = frames.length - 1; i > -1; i--) {
-      if (frames[i] instanceof AppJmol) {
+    for (int i = frames.length - 1; i > -1; i--)
+    {
+      if (frames[i] instanceof AppJmol)
+      {
         GStructureViewer af = (GStructureViewer) frames[i];
         avp.add(af);
       }
     }
-    if (avp.size() == 0) {
+    if (avp.size() == 0)
+    {
       return null;
     }
     GStructureViewer afs[] = avp.toArray(new GStructureViewer[avp.size()]);
@@ -1995,23 +2443,29 @@ public class Desktop extends jalview.jbgui.GDesktop
    * Add Groovy Support to Jalview
    */
   @Override
-  public void groovyShell_actionPerformed() {
-    try {
+  public void groovyShell_actionPerformed()
+  {
+    try
+    {
       openGroovyConsole();
-    } catch (Exception ex) {
+    } catch (Exception ex)
+    {
       jalview.bin.Console.error("Groovy Shell Creation failed.", ex);
       JvOptionPane.showInternalMessageDialog(Desktop.desktop,
 
-          MessageManager.getString("label.couldnt_create_groovy_shell"),
-          MessageManager.getString("label.groovy_support_failed"), JvOptionPane.ERROR_MESSAGE);
+              MessageManager.getString("label.couldnt_create_groovy_shell"),
+              MessageManager.getString("label.groovy_support_failed"),
+              JvOptionPane.ERROR_MESSAGE);
     }
   }
 
   /**
    * Open the Groovy console
    */
-  void openGroovyConsole() {
-    if (groovyConsole == null) {
+  void openGroovyConsole()
+  {
+    if (groovyConsole == null)
+    {
       groovyConsole = new groovy.ui.Console();
       groovyConsole.setVariable("Jalview", this);
       groovyConsole.run();
@@ -2023,9 +2477,11 @@ public class Desktop extends jalview.jbgui.GDesktop
        * closed
        */
       Window window = (Window) groovyConsole.getFrame();
-      window.addWindowListener(new WindowAdapter() {
+      window.addWindowListener(new WindowAdapter()
+      {
         @Override
-        public void windowClosed(WindowEvent e) {
+        public void windowClosed(WindowEvent e)
+        {
           /*
            * rebind CMD-Q from Groovy Console to Jalview Quit
            */
@@ -2048,16 +2504,23 @@ public class Desktop extends jalview.jbgui.GDesktop
   }
 
   /**
-   * 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, jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx()),
-        "Quit");
-    getRootPane().getActionMap().put("Quit", new AbstractAction() {
+   * 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,
+                                    jalview.util.ShortcutKeyMaskExWrapper
+                                            .getMenuShortcutKeyMaskEx()),
+                    "Quit");
+    getRootPane().getActionMap().put("Quit", new AbstractAction()
+    {
       @Override
-      public void actionPerformed(ActionEvent e) {
+      public void actionPerformed(ActionEvent e)
+      {
         quit();
       }
     });
@@ -2066,9 +2529,11 @@ public class Desktop extends jalview.jbgui.GDesktop
   /**
    * Enable or disable 'Run Groovy script' in AlignFrame calculate menus
    * 
-   * @param enabled true if Groovy console is open
+   * @param enabled
+   *          true if Groovy console is open
    */
-  public void enableExecuteGroovy(boolean enabled) {
+  public void enableExecuteGroovy(boolean enabled)
+  {
     /*
      * disable opening a second Groovy console (or re-enable when the console is
      * closed)
@@ -2076,8 +2541,10 @@ public class Desktop extends jalview.jbgui.GDesktop
     groovyShell.setEnabled(!enabled);
 
     AlignFrame[] alignFrames = getAlignFrames();
-    if (alignFrames != null) {
-      for (AlignFrame af : alignFrames) {
+    if (alignFrames != null)
+    {
+      for (AlignFrame af : alignFrames)
+      {
         af.setGroovyEnabled(enabled);
       }
     }
@@ -2096,19 +2563,25 @@ public class Desktop extends jalview.jbgui.GDesktop
    * @see jalview.gui.IProgressIndicator#setProgressBar(java.lang.String, long)
    */
   @Override
-  public void setProgressBar(String message, long id) {
-    if (progressBars == null) {
+  public void setProgressBar(String message, long id)
+  {
+    if (progressBars == null)
+    {
       progressBars = new Hashtable<>();
       progressBarHandlers = new Hashtable<>();
     }
 
-    if (progressBars.get(Long.valueOf(id)) != null) {
+    if (progressBars.get(Long.valueOf(id)) != null)
+    {
       JPanel panel = progressBars.remove(Long.valueOf(id));
-      if (progressBarHandlers.contains(Long.valueOf(id))) {
+      if (progressBarHandlers.contains(Long.valueOf(id)))
+      {
         progressBarHandlers.remove(Long.valueOf(id));
       }
       removeProgressPanel(panel);
-    } else {
+    }
+    else
+    {
       progressBars.put(Long.valueOf(id), addProgressPanel(message));
     }
   }
@@ -2120,22 +2593,33 @@ public class Desktop extends jalview.jbgui.GDesktop
    * jalview.gui.IProgressIndicatorHandler)
    */
   @Override
-  public void registerHandler(final long id, final IProgressIndicatorHandler handler) {
-    if (progressBarHandlers == null || !progressBars.containsKey(Long.valueOf(id))) {
-      throw new Error(MessageManager.getString("error.call_setprogressbar_before_registering_handler"));
+  public void registerHandler(final long id,
+          final IProgressIndicatorHandler handler)
+  {
+    if (progressBarHandlers == null
+            || !progressBars.containsKey(Long.valueOf(id)))
+    {
+      throw new Error(MessageManager.getString(
+              "error.call_setprogressbar_before_registering_handler"));
     }
     progressBarHandlers.put(Long.valueOf(id), handler);
     final JPanel progressPanel = progressBars.get(Long.valueOf(id));
-    if (handler.canCancel()) {
-      JButton cancel = new JButton(MessageManager.getString("action.cancel"));
+    if (handler.canCancel())
+    {
+      JButton cancel = new JButton(
+              MessageManager.getString("action.cancel"));
       final IProgressIndicator us = this;
-      cancel.addActionListener(new ActionListener() {
+      cancel.addActionListener(new ActionListener()
+      {
 
         @Override
-        public void actionPerformed(ActionEvent e) {
+        public void actionPerformed(ActionEvent e)
+        {
           handler.cancelActivity(id);
-          us.setProgressBar(MessageManager.formatMessage("label.cancelled_params",
-              new Object[] { ((JLabel) progressPanel.getComponent(0)).getText() }), id);
+          us.setProgressBar(MessageManager
+                  .formatMessage("label.cancelled_params", new Object[]
+                  { ((JLabel) progressPanel.getComponent(0)).getText() }),
+                  id);
         }
       });
       progressPanel.add(cancel, BorderLayout.EAST);
@@ -2147,25 +2631,33 @@ public class Desktop extends jalview.jbgui.GDesktop
    * @return true if any progress bars are still active
    */
   @Override
-  public boolean operationInProgress() {
-    if (progressBars != null && progressBars.size() > 0) {
+  public boolean operationInProgress()
+  {
+    if (progressBars != null && progressBars.size() > 0)
+    {
       return true;
     }
     return false;
   }
 
   /**
-   * This will return the first AlignFrame holding the given viewport instance. It
-   * will break if there are more than one AlignFrames viewing a particular av.
+   * This will return the first AlignFrame holding the given viewport instance.
+   * It will break if there are more than one AlignFrames viewing a particular
+   * av.
    * 
    * @param viewport
    * @return alignFrame for viewport
    */
-  public static AlignFrame getAlignFrameFor(AlignViewportI viewport) {
-    if (desktop != null) {
-      AlignmentPanel[] aps = getAlignmentPanels(viewport.getSequenceSetId());
-      for (int panel = 0; aps != null && panel < aps.length; panel++) {
-        if (aps[panel] != null && aps[panel].av == viewport) {
+  public static AlignFrame getAlignFrameFor(AlignViewportI viewport)
+  {
+    if (desktop != null)
+    {
+      AlignmentPanel[] aps = getAlignmentPanels(
+              viewport.getSequenceSetId());
+      for (int panel = 0; aps != null && panel < aps.length; panel++)
+      {
+        if (aps[panel] != null && aps[panel].av == viewport)
+        {
           return aps[panel].alignFrame;
         }
       }
@@ -2173,7 +2665,8 @@ public class Desktop extends jalview.jbgui.GDesktop
     return null;
   }
 
-  public VamsasApplication getVamsasApplication() {
+  public VamsasApplication getVamsasApplication()
+  {
     // TODO: JAL-3311 remove remaining code from Jalview relating to VAMSAS
     return null;
 
@@ -2189,7 +2682,8 @@ public class Desktop extends jalview.jbgui.GDesktop
    * 
    * @return inBatchMode
    */
-  public boolean isInBatchMode() {
+  public boolean isInBatchMode()
+  {
     return inBatchMode;
   }
 
@@ -2198,7 +2692,8 @@ public class Desktop extends jalview.jbgui.GDesktop
    * 
    * @param inBatchMode
    */
-  public void setInBatchMode(boolean inBatchMode) {
+  public void setInBatchMode(boolean inBatchMode)
+  {
     this.inBatchMode = inBatchMode;
   }
 
@@ -2217,25 +2712,29 @@ public class Desktop extends jalview.jbgui.GDesktop
    */
   public void startServiceDiscovery(boolean blocking)
   {
-    startServiceDiscovery(blocking,false);
+    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
+   * @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) {
+  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
-    if (true) {
+    if (true)
+    {
       // todo: changesupport handlers need to be transferred
-      if (discoverer == null) {
+      if (discoverer == null)
+      {
         discoverer = new jalview.ws.jws1.Discoverer();
         // register PCS handler for desktop.
         discoverer.addPropertyChangeListener(changeSupport);
@@ -2245,21 +2744,29 @@ public class Desktop extends jalview.jbgui.GDesktop
       (t0 = new Thread(discoverer)).start();
     }
 
-    if (ignore_SHOW_JWS2_SERVICES_preference || Cache.getDefault("SHOW_JWS2_SERVICES", true)) {
-      t2 = jalview.ws.jws2.Jws2Discoverer.getDiscoverer().startDiscoverer(changeSupport);
+    if (ignore_SHOW_JWS2_SERVICES_preference
+            || Cache.getDefault("SHOW_JWS2_SERVICES", true))
+    {
+      t2 = jalview.ws.jws2.Jws2Discoverer.getDiscoverer()
+              .startDiscoverer(changeSupport);
     }
     Thread t3 = null;
     {
       // TODO: do rest service discovery
     }
-    if (blocking) {
-      while (alive) {
-        try {
+    if (blocking)
+    {
+      while (alive)
+      {
+        try
+        {
           Thread.sleep(15);
-        } catch (Exception e) {
+        } catch (Exception e)
+        {
         }
-        alive = (t1 != null && t1.isAlive()) || (t2 != null && t2.isAlive()) || (t3 != null && t3.isAlive())
-            || (t0 != null && t0.isAlive());
+        alive = (t1 != null && t1.isAlive()) || (t2 != null && t2.isAlive())
+                || (t3 != null && t3.isAlive())
+                || (t0 != null && t0.isAlive());
       }
     }
   }
@@ -2269,16 +2776,24 @@ public class Desktop extends jalview.jbgui.GDesktop
    * 
    * @param evt
    */
-  protected void JalviewServicesChanged(PropertyChangeEvent evt) {
-    if (evt.getNewValue() == null || evt.getNewValue() instanceof Vector) {
-      final String ermsg = jalview.ws.jws2.Jws2Discoverer.getDiscoverer().getErrorMessages();
-      if (ermsg != null) {
-        if (Cache.getDefault("SHOW_WSDISCOVERY_ERRORS", true)) {
-          if (serviceChangedDialog == null) {
+  protected void JalviewServicesChanged(PropertyChangeEvent evt)
+  {
+    if (evt.getNewValue() == null || evt.getNewValue() instanceof Vector)
+    {
+      final String ermsg = jalview.ws.jws2.Jws2Discoverer.getDiscoverer()
+              .getErrorMessages();
+      if (ermsg != null)
+      {
+        if (Cache.getDefault("SHOW_WSDISCOVERY_ERRORS", true))
+        {
+          if (serviceChangedDialog == null)
+          {
             // only run if we aren't already displaying one of these.
-            addDialogThread(serviceChangedDialog = new Runnable() {
+            addDialogThread(serviceChangedDialog = new Runnable()
+            {
               @Override
-              public void run() {
+              public void run()
+              {
 
                 /*
                  * JalviewDialog jd =new JalviewDialog() {
@@ -2300,19 +2815,26 @@ public class Desktop extends jalview.jbgui.GDesktop
                  * jd.waitForInput();
                  */
                 JvOptionPane.showConfirmDialog(Desktop.desktop,
-                    new JLabel("<html><table width=\"450\"><tr><td>" + ermsg + "</td></tr></table>"
-                        + "<p>It may be that you have invalid JABA URLs<br/>in your web service preferences,"
-                        + "<br>or as a command-line argument, or mis-configured HTTP proxy settings.</p>"
-                        + "<p>Check the <em>Connections</em> and <em>Web services</em> tab<br/>of the"
-                        + " Tools->Preferences dialog box to change them.</p></html>"),
-                    "Web Service Configuration Problem", JvOptionPane.DEFAULT_OPTION, JvOptionPane.ERROR_MESSAGE);
+                        new JLabel("<html><table width=\"450\"><tr><td>"
+                                + ermsg + "</td></tr></table>"
+                                + "<p>It may be that you have invalid JABA URLs<br/>in your web service preferences,"
+                                + "<br>or as a command-line argument, or mis-configured HTTP proxy settings.</p>"
+                                + "<p>Check the <em>Connections</em> and <em>Web services</em> tab<br/>of the"
+                                + " Tools->Preferences dialog box to change them.</p></html>"),
+                        "Web Service Configuration Problem",
+                        JvOptionPane.DEFAULT_OPTION,
+                        JvOptionPane.ERROR_MESSAGE);
                 serviceChangedDialog = null;
 
               }
             });
           }
-        } else {
-          jalview.bin.Console.error("Errors reported by JABA discovery service. Check web services preferences.\n" + ermsg);
+        }
+        else
+        {
+          jalview.bin.Console.error(
+                  "Errors reported by JABA discovery service. Check web services preferences.\n"
+                          + ermsg);
         }
       }
     }
@@ -2327,7 +2849,8 @@ public class Desktop extends jalview.jbgui.GDesktop
    * 
    * @param url
    */
-  public static void showUrl(final String url) {
+  public static void showUrl(final String url)
+  {
     showUrl(url, Desktop.instance);
   }
 
@@ -2335,26 +2858,38 @@ public class Desktop extends jalview.jbgui.GDesktop
    * Like showUrl but allows progress handler to be specified
    * 
    * @param url
-   * @param progress (null) or object implementing IProgressIndicator
+   * @param progress
+   *          (null) or object implementing IProgressIndicator
    */
-  public static void showUrl(final String url, final IProgressIndicator progress) {
-    new Thread(new Runnable() {
+  public static void showUrl(final String url,
+          final IProgressIndicator progress)
+  {
+    new Thread(new Runnable()
+    {
       @Override
-      public void run() {
-        try {
-          if (progress != null) {
-            progress.setProgressBar(MessageManager.formatMessage("status.opening_params", new Object[] { url }),
-                this.hashCode());
+      public void run()
+      {
+        try
+        {
+          if (progress != null)
+          {
+            progress.setProgressBar(MessageManager
+                    .formatMessage("status.opening_params", new Object[]
+                    { url }), this.hashCode());
           }
           jalview.util.BrowserLauncher.openURL(url);
-        } catch (Exception ex) {
+        } catch (Exception ex)
+        {
           JvOptionPane.showInternalMessageDialog(Desktop.desktop,
-              MessageManager.getString("label.web_browser_not_found_unix"),
-              MessageManager.getString("label.web_browser_not_found"), JvOptionPane.WARNING_MESSAGE);
+                  MessageManager
+                          .getString("label.web_browser_not_found_unix"),
+                  MessageManager.getString("label.web_browser_not_found"),
+                  JvOptionPane.WARNING_MESSAGE);
 
           ex.printStackTrace();
         }
-        if (progress != null) {
+        if (progress != null)
+        {
           progress.setProgressBar(null, this.hashCode());
         }
       }
@@ -2363,8 +2898,10 @@ public class Desktop extends jalview.jbgui.GDesktop
 
   public static WsParamSetManager wsparamManager = null;
 
-  public static ParamManager getUserParameterStore() {
-    if (wsparamManager == null) {
+  public static ParamManager getUserParameterStore()
+  {
+    if (wsparamManager == null)
+    {
       wsparamManager = new WsParamSetManager();
     }
     return wsparamManager;
@@ -2375,15 +2912,21 @@ public class Desktop extends jalview.jbgui.GDesktop
    * 
    * @param e
    */
-  public static void hyperlinkUpdate(HyperlinkEvent e) {
-    if (e.getEventType() == EventType.ACTIVATED) {
+  public static void hyperlinkUpdate(HyperlinkEvent e)
+  {
+    if (e.getEventType() == EventType.ACTIVATED)
+    {
       String url = null;
-      try {
+      try
+      {
         url = e.getURL().toString();
         Desktop.showUrl(url);
-      } catch (Exception x) {
-        if (url != null) {
-          jalview.bin.Console.error("Couldn't handle string " + url + " as a URL.");
+      } catch (Exception x)
+      {
+        if (url != null)
+        {
+          jalview.bin.Console
+                  .error("Couldn't handle string " + url + " as a URL.");
         }
         // ignore any exceptions due to dud links.
       }
@@ -2413,29 +2956,40 @@ public class Desktop extends jalview.jbgui.GDesktop
    * 
    * @param prompter
    */
-  public void addDialogThread(final Runnable prompter) {
-    dialogExecutor.submit(new Runnable() {
+  public void addDialogThread(final Runnable prompter)
+  {
+    dialogExecutor.submit(new Runnable()
+    {
       @Override
-      public void run() {
-        if (dialogPause) {
-          try {
+      public void run()
+      {
+        if (dialogPause)
+        {
+          try
+          {
             block.acquire();
-          } catch (InterruptedException x) {
+          } catch (InterruptedException x)
+          {
           }
         }
-        if (instance == null) {
+        if (instance == null)
+        {
           return;
         }
-        try {
+        try
+        {
           SwingUtilities.invokeAndWait(prompter);
-        } catch (Exception q) {
-          jalview.bin.Console.warn("Unexpected Exception in dialog thread.", q);
+        } catch (Exception q)
+        {
+          jalview.bin.Console.warn("Unexpected Exception in dialog thread.",
+                  q);
         }
       }
     });
   }
 
-  public void startDialogQueue() {
+  public void startDialogQueue()
+  {
     // set the flag so we don't pause waiting for another permit and semaphore
     // the current task to begin
     dialogPause = false;
@@ -2452,41 +3006,51 @@ public class Desktop extends jalview.jbgui.GDesktop
    * </pre>
    */
   @Override
-  protected void snapShotWindow_actionPerformed(ActionEvent e) {
+  protected void snapShotWindow_actionPerformed(ActionEvent e)
+  {
     // currently the menu option to do this is not shown
     invalidate();
 
     int width = getWidth();
     int height = getHeight();
-    File of = new File("Jalview_snapshot_" + System.currentTimeMillis() + ".eps");
-    ImageWriterI writer = new ImageWriterI() {
+    File of = new File(
+            "Jalview_snapshot_" + System.currentTimeMillis() + ".eps");
+    ImageWriterI writer = new ImageWriterI()
+    {
       @Override
-      public void exportImage(Graphics g) throws Exception {
+      public void exportImage(Graphics g) throws Exception
+      {
         paintAll(g);
-        jalview.bin.Console.info("Successfully written snapshot to file " + of.getAbsolutePath());
+        jalview.bin.Console.info("Successfully written snapshot to file "
+                + of.getAbsolutePath());
       }
     };
     String title = "View of desktop";
-    ImageExporter exporter = new ImageExporter(writer, null, TYPE.EPS, title);
+    ImageExporter exporter = new ImageExporter(writer, null, TYPE.EPS,
+            title);
     exporter.doExport(of, this, width, height, title);
   }
 
   /**
    * Explode the views in the given SplitFrame into separate SplitFrame windows.
-   * This respects (remembers) any previous 'exploded geometry' i.e. the size and
-   * location last time the view was expanded (if any). However it does not
+   * This respects (remembers) any previous 'exploded geometry' i.e. the size
+   * and location last time the view was expanded (if any). However it does not
    * remember the split pane divider location - this is set to match the
    * 'exploding' frame.
    * 
    * @param sf
    */
-  public void explodeViews(SplitFrame sf) {
+  public void explodeViews(SplitFrame sf)
+  {
     AlignFrame oldTopFrame = (AlignFrame) sf.getTopFrame();
     AlignFrame oldBottomFrame = (AlignFrame) sf.getBottomFrame();
-    List<? extends AlignmentViewPanel> topPanels = oldTopFrame.getAlignPanels();
-    List<? extends AlignmentViewPanel> bottomPanels = oldBottomFrame.getAlignPanels();
+    List<? extends AlignmentViewPanel> topPanels = oldTopFrame
+            .getAlignPanels();
+    List<? extends AlignmentViewPanel> bottomPanels = oldBottomFrame
+            .getAlignPanels();
     int viewCount = topPanels.size();
-    if (viewCount < 2) {
+    if (viewCount < 2)
+    {
       return;
     }
 
@@ -2494,7 +3058,8 @@ 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!
      */
-    for (int i = viewCount - 1; i >= 0; i--) {
+    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
@@ -2507,8 +3072,10 @@ public class Desktop extends jalview.jbgui.GDesktop
       AlignFrame newTopFrame = new AlignFrame(topPanel);
       newTopFrame.setSize(oldTopFrame.getSize());
       newTopFrame.setVisible(true);
-      Rectangle geometry = ((AlignViewport) topPanel.getAlignViewport()).getExplodedGeometry();
-      if (geometry != null) {
+      Rectangle geometry = ((AlignViewport) topPanel.getAlignViewport())
+              .getExplodedGeometry();
+      if (geometry != null)
+      {
         newTopFrame.setSize(geometry.getSize());
       }
 
@@ -2516,15 +3083,19 @@ public class Desktop extends jalview.jbgui.GDesktop
       AlignFrame newBottomFrame = new AlignFrame(bottomPanel);
       newBottomFrame.setSize(oldBottomFrame.getSize());
       newBottomFrame.setVisible(true);
-      geometry = ((AlignViewport) bottomPanel.getAlignViewport()).getExplodedGeometry();
-      if (geometry != null) {
+      geometry = ((AlignViewport) bottomPanel.getAlignViewport())
+              .getExplodedGeometry();
+      if (geometry != null)
+      {
         newBottomFrame.setSize(geometry.getSize());
       }
 
       topPanel.av.setGatherViewsHere(false);
       bottomPanel.av.setGatherViewsHere(false);
-      JInternalFrame splitFrame = new SplitFrame(newTopFrame, newBottomFrame);
-      if (geometry != null) {
+      JInternalFrame splitFrame = new SplitFrame(newTopFrame,
+              newBottomFrame);
+      if (geometry != null)
+      {
         splitFrame.setLocation(geometry.getLocation());
       }
       Desktop.addInternalFrame(splitFrame, sf.getTitle(), -1, -1);
@@ -2546,7 +3117,8 @@ public class Desktop extends jalview.jbgui.GDesktop
    * 
    * @param source
    */
-  public void gatherViews(GSplitFrame source) {
+  public void gatherViews(GSplitFrame source)
+  {
     /*
      * special handling of explodedGeometry for a view within a SplitFrame: - it
      * holds the (x, y) position of the enclosing SplitFrame, and the (width,
@@ -2554,38 +3126,46 @@ public class Desktop extends jalview.jbgui.GDesktop
      */
     AlignFrame myTopFrame = (AlignFrame) source.getTopFrame();
     AlignFrame myBottomFrame = (AlignFrame) source.getBottomFrame();
-    myTopFrame.viewport.setExplodedGeometry(
-        new Rectangle(source.getX(), source.getY(), myTopFrame.getWidth(), myTopFrame.getHeight()));
-    myBottomFrame.viewport.setExplodedGeometry(
-        new Rectangle(source.getX(), source.getY(), myBottomFrame.getWidth(), myBottomFrame.getHeight()));
+    myTopFrame.viewport.setExplodedGeometry(new Rectangle(source.getX(),
+            source.getY(), myTopFrame.getWidth(), myTopFrame.getHeight()));
+    myBottomFrame.viewport
+            .setExplodedGeometry(new Rectangle(source.getX(), source.getY(),
+                    myBottomFrame.getWidth(), myBottomFrame.getHeight()));
     myTopFrame.viewport.setGatherViewsHere(true);
     myBottomFrame.viewport.setGatherViewsHere(true);
     String topViewId = myTopFrame.viewport.getSequenceSetId();
     String bottomViewId = myBottomFrame.viewport.getSequenceSetId();
 
     JInternalFrame[] frames = desktop.getAllFrames();
-    for (JInternalFrame frame : frames) {
-      if (frame instanceof SplitFrame && frame != source) {
+    for (JInternalFrame frame : frames)
+    {
+      if (frame instanceof SplitFrame && frame != source)
+      {
         SplitFrame sf = (SplitFrame) frame;
         AlignFrame topFrame = (AlignFrame) sf.getTopFrame();
         AlignFrame bottomFrame = (AlignFrame) sf.getBottomFrame();
         boolean gatherThis = false;
-        for (int a = 0; a < topFrame.alignPanels.size(); a++) {
+        for (int a = 0; a < topFrame.alignPanels.size(); a++)
+        {
           AlignmentPanel topPanel = topFrame.alignPanels.get(a);
           AlignmentPanel bottomPanel = bottomFrame.alignPanels.get(a);
           if (topViewId.equals(topPanel.av.getSequenceSetId())
-              && bottomViewId.equals(bottomPanel.av.getSequenceSetId())) {
+                  && bottomViewId.equals(bottomPanel.av.getSequenceSetId()))
+          {
             gatherThis = true;
             topPanel.av.setGatherViewsHere(false);
             bottomPanel.av.setGatherViewsHere(false);
-            topPanel.av.setExplodedGeometry(new Rectangle(sf.getLocation(), topFrame.getSize()));
-            bottomPanel.av.setExplodedGeometry(new Rectangle(sf.getLocation(), bottomFrame.getSize()));
+            topPanel.av.setExplodedGeometry(
+                    new Rectangle(sf.getLocation(), topFrame.getSize()));
+            bottomPanel.av.setExplodedGeometry(
+                    new Rectangle(sf.getLocation(), bottomFrame.getSize()));
             myTopFrame.addAlignmentPanel(topPanel, false);
             myBottomFrame.addAlignmentPanel(bottomPanel, false);
           }
         }
 
-        if (gatherThis) {
+        if (gatherThis)
+        {
           topFrame.getAlignPanels().clear();
           bottomFrame.getAlignPanels().clear();
           sf.close();
@@ -2599,7 +3179,8 @@ public class Desktop extends jalview.jbgui.GDesktop
     myTopFrame.setDisplayedView(myTopFrame.alignPanel);
   }
 
-  public static groovy.ui.Console getGroovyConsole() {
+  public static groovy.ui.Console getGroovyConsole()
+  {
     return groovyConsole;
   }
 
@@ -2608,88 +3189,127 @@ public class Desktop extends jalview.jbgui.GDesktop
    * 
    * TODO refactor to desktop utilities class
    * 
-   * @param files     - Data source strings extracted from the drop event
-   * @param protocols - protocol for each data source extracted from the drop
-   *                  event
-   * @param evt       - the drop event
-   * @param t         - the payload from the drop event
+   * @param files
+   *          - Data source strings extracted from the drop event
+   * @param protocols
+   *          - protocol for each data source extracted from the drop event
+   * @param evt
+   *          - the drop event
+   * @param t
+   *          - the payload from the drop event
    * @throws Exception
    */
-  public static void transferFromDropTarget(List<Object> files, List<DataSourceType> protocols, DropTargetDropEvent evt,
-      Transferable t) throws Exception {
+  public static void transferFromDropTarget(List<Object> files,
+          List<DataSourceType> protocols, DropTargetDropEvent evt,
+          Transferable t) throws Exception
+  {
 
-    DataFlavor uriListFlavor = new DataFlavor("text/uri-list;class=java.lang.String"), urlFlavour = null;
-    try {
-      urlFlavour = new DataFlavor("application/x-java-url; class=java.net.URL");
-    } catch (ClassNotFoundException cfe) {
-      jalview.bin.Console.debug("Couldn't instantiate the URL dataflavor.", cfe);
+    DataFlavor uriListFlavor = new DataFlavor(
+            "text/uri-list;class=java.lang.String"), urlFlavour = null;
+    try
+    {
+      urlFlavour = new DataFlavor(
+              "application/x-java-url; class=java.net.URL");
+    } catch (ClassNotFoundException cfe)
+    {
+      jalview.bin.Console.debug("Couldn't instantiate the URL dataflavor.",
+              cfe);
     }
 
-    if (urlFlavour != null && t.isDataFlavorSupported(urlFlavour)) {
+    if (urlFlavour != null && t.isDataFlavorSupported(urlFlavour))
+    {
 
-      try {
+      try
+      {
         java.net.URL url = (URL) t.getTransferData(urlFlavour);
         // nb: java 8 osx bug https://bugs.openjdk.java.net/browse/JDK-8156099
         // means url may be null.
-        if (url != null) {
+        if (url != null)
+        {
           protocols.add(DataSourceType.URL);
           files.add(url.toString());
-          jalview.bin.Console.debug("Drop handled as URL dataflavor " + files.get(files.size() - 1));
+          jalview.bin.Console.debug("Drop handled as URL dataflavor "
+                  + files.get(files.size() - 1));
           return;
-        } else {
-          if (Platform.isAMacAndNotJS()) {
-            System.err.println("Please ignore plist error - occurs due to problem with java 8 on OSX");
+        }
+        else
+        {
+          if (Platform.isAMacAndNotJS())
+          {
+            System.err.println(
+                    "Please ignore plist error - occurs due to problem with java 8 on OSX");
           }
         }
-      } catch (Throwable ex) {
+      } catch (Throwable ex)
+      {
         jalview.bin.Console.debug("URL drop handler failed.", ex);
       }
     }
-    if (t.isDataFlavorSupported(DataFlavor.javaFileListFlavor)) {
+    if (t.isDataFlavorSupported(DataFlavor.javaFileListFlavor))
+    {
       // Works on Windows and MacOSX
       jalview.bin.Console.debug("Drop handled as javaFileListFlavor");
-      for (Object file : (List) t.getTransferData(DataFlavor.javaFileListFlavor)) {
+      for (Object file : (List) t
+              .getTransferData(DataFlavor.javaFileListFlavor))
+      {
         files.add(file);
         protocols.add(DataSourceType.FILE);
       }
-    } else {
+    }
+    else
+    {
       // Unix like behaviour
       boolean added = false;
       String data = null;
-      if (t.isDataFlavorSupported(uriListFlavor)) {
+      if (t.isDataFlavorSupported(uriListFlavor))
+      {
         jalview.bin.Console.debug("Drop handled as uriListFlavor");
         // This is used by Unix drag system
         data = (String) t.getTransferData(uriListFlavor);
       }
-      if (data == null) {
+      if (data == null)
+      {
         // fallback to text: workaround - on OSX where there's a JVM bug
-        jalview.bin.Console.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");
-        if (t.isDataFlavorSupported(textDf)) {
+        DataFlavor textDf = new DataFlavor(
+                "text/plain;class=java.lang.String");
+        if (t.isDataFlavorSupported(textDf))
+        {
           data = (String) t.getTransferData(textDf);
         }
 
-        jalview.bin.Console.debug("Plain text drop content returned " + (data == null ? "Null - failed" : data));
+        jalview.bin.Console.debug("Plain text drop content returned "
+                + (data == null ? "Null - failed" : data));
 
       }
-      if (data != null) {
-        while (protocols.size() < files.size()) {
-          jalview.bin.Console.debug("Adding missing FILE protocol for " + files.get(protocols.size()));
+      if (data != null)
+      {
+        while (protocols.size() < files.size())
+        {
+          jalview.bin.Console.debug("Adding missing FILE protocol for "
+                  + files.get(protocols.size()));
           protocols.add(DataSourceType.FILE);
         }
-        for (java.util.StringTokenizer st = new java.util.StringTokenizer(data, "\r\n"); st.hasMoreTokens();) {
+        for (java.util.StringTokenizer st = new java.util.StringTokenizer(
+                data, "\r\n"); st.hasMoreTokens();)
+        {
           added = true;
           String s = st.nextToken();
-          if (s.startsWith("#")) {
+          if (s.startsWith("#"))
+          {
             // the line is a comment (as per the RFC 2483)
             continue;
           }
           java.net.URI uri = new java.net.URI(s);
-          if (uri.getScheme().toLowerCase(Locale.ROOT).startsWith("http")) {
+          if (uri.getScheme().toLowerCase(Locale.ROOT).startsWith("http"))
+          {
             protocols.add(DataSourceType.URL);
             files.add(uri.toString());
-          } else {
+          }
+          else
+          {
             // otherwise preserve old behaviour: catch all for file objects
             java.io.File file = new java.io.File(uri);
             protocols.add(DataSourceType.FILE);
@@ -2698,46 +3318,71 @@ public class Desktop extends jalview.jbgui.GDesktop
         }
       }
 
-      if (jalview.bin.Console.isDebugEnabled()) {
-        if (data == null || !added) {
+      if (jalview.bin.Console.isDebugEnabled())
+      {
+        if (data == null || !added)
+        {
 
-          if (t.getTransferDataFlavors() != null && t.getTransferDataFlavors().length > 0) {
-            jalview.bin.Console.debug("Couldn't resolve drop data. Here are the supported flavors:");
-            for (DataFlavor fl : t.getTransferDataFlavors()) {
-              jalview.bin.Console.debug("Supported transfer dataflavor: " + fl.toString());
+          if (t.getTransferDataFlavors() != null
+                  && t.getTransferDataFlavors().length > 0)
+          {
+            jalview.bin.Console.debug(
+                    "Couldn't resolve drop data. Here are the supported flavors:");
+            for (DataFlavor fl : t.getTransferDataFlavors())
+            {
+              jalview.bin.Console.debug(
+                      "Supported transfer dataflavor: " + fl.toString());
               Object df = t.getTransferData(fl);
-              if (df != null) {
+              if (df != null)
+              {
                 jalview.bin.Console.debug("Retrieves: " + df);
-              } else {
+              }
+              else
+              {
                 jalview.bin.Console.debug("Retrieved nothing");
               }
             }
-          } else {
-            jalview.bin.Console.debug("Couldn't resolve dataflavor for drop: " + t.toString());
+          }
+          else
+          {
+            jalview.bin.Console
+                    .debug("Couldn't resolve dataflavor for drop: "
+                            + t.toString());
           }
         }
       }
     }
-    if (Platform.isWindowsAndNotJS()) {
-      jalview.bin.Console.debug("Scanning dropped content for Windows Link Files");
+    if (Platform.isWindowsAndNotJS())
+    {
+      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++) {
+      for (int f = 0; f < files.size(); f++)
+      {
         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"))) {
-          try {
+                && (source.endsWith(".lnk") || source.endsWith(".url")
+                        || source.endsWith(".site")))
+        {
+          try
+          {
             Object obj = files.get(f);
-            File lf = (obj instanceof File ? (File) obj : new File((String) obj));
+            File lf = (obj instanceof File ? (File) obj
+                    : new File((String) obj));
             // process link file to get a URL
             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);
-            jalview.bin.Console.debug("Parsed real filename " + fullname + " to extract protocol: " + protocols.get(f));
-          } catch (Exception ex) {
-            jalview.bin.Console.error("Couldn't parse " + files.get(f) + " as a link file.", ex);
+            jalview.bin.Console.debug("Parsed real filename " + fullname
+                    + " to extract protocol: " + protocols.get(f));
+          } catch (Exception ex)
+          {
+            jalview.bin.Console.error(
+                    "Couldn't parse " + files.get(f) + " as a link file.",
+                    ex);
           }
         }
       }
@@ -2749,30 +3394,40 @@ public class Desktop extends jalview.jbgui.GDesktop
    * depending on the state of the controlling menu item
    */
   @Override
-  protected void showExperimental_actionPerformed(boolean selected) {
+  protected void showExperimental_actionPerformed(boolean selected)
+  {
     Cache.setProperty(EXPERIMENTAL_FEATURES, Boolean.toString(selected));
   }
 
   /**
-   * Answers a (possibly empty) list of any structure viewer frames (currently for
-   * either Jmol or Chimera) which are currently open. This may optionally be
-   * restricted to viewers of a specified class, or viewers linked to a specified
-   * alignment panel.
+   * Answers a (possibly empty) list of any structure viewer frames (currently
+   * for either Jmol or Chimera) which are currently open. This may optionally
+   * be restricted to viewers of a specified class, or viewers linked to a
+   * specified alignment panel.
    * 
-   * @param apanel               if not null, only return viewers linked to this
-   *                             panel
-   * @param structureViewerClass if not null, only return viewers of this class
+   * @param apanel
+   *          if not null, only return viewers linked to this panel
+   * @param structureViewerClass
+   *          if not null, only return viewers of this class
    * @return
    */
-  public List<StructureViewerBase> getStructureViewers(AlignmentPanel apanel,
-      Class<? extends StructureViewerBase> structureViewerClass) {
+  public List<StructureViewerBase> getStructureViewers(
+          AlignmentPanel apanel,
+          Class<? extends StructureViewerBase> structureViewerClass)
+  {
     List<StructureViewerBase> result = new ArrayList<>();
     JInternalFrame[] frames = Desktop.instance.getAllFrames();
 
-    for (JInternalFrame frame : frames) {
-      if (frame instanceof StructureViewerBase) {
-        if (structureViewerClass == null || structureViewerClass.isInstance(frame)) {
-          if (apanel == null || ((StructureViewerBase) frame).isLinkedWith(apanel)) {
+    for (JInternalFrame frame : frames)
+    {
+      if (frame instanceof StructureViewerBase)
+      {
+        if (structureViewerClass == null
+                || structureViewerClass.isInstance(frame))
+        {
+          if (apanel == null
+                  || ((StructureViewerBase) frame).isLinkedWith(apanel))
+          {
             result.add((StructureViewerBase) frame);
           }
         }
@@ -2785,24 +3440,31 @@ public class Desktop extends jalview.jbgui.GDesktop
 
   private static boolean debugScaleMessageDone = false;
 
-  public static void debugScaleMessage(Graphics g) {
-    if (debugScaleMessageDone) {
+  public static void debugScaleMessage(Graphics g)
+  {
+    if (debugScaleMessageDone)
+    {
       return;
     }
     // output used by tests to check HiDPI scaling settings in action
-    try {
+    try
+    {
       Graphics2D gg = (Graphics2D) g;
-      if (gg != null) {
+      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 {
+      }
+      else
+      {
         jalview.bin.Console.debug("Desktop graphics null");
       }
-    } catch (Exception e) {
+    } catch (Exception e)
+    {
       jalview.bin.Console.debug(Cache.getStackTraceString(e));
     }
   }