X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FDesktop.java;h=e9cc8e919442a449b14ab1119c9d07efc470ffce;hb=c679cc5e0b230c59517b89d50eb5b94dfe4a382a;hp=1a1fa459ff7e930a2f3d6163e3c9f3c7b450f596;hpb=fb7ba61b4b7e4bc0260a288cd07335321f61ad18;p=jalview.git

diff --git a/src/jalview/gui/Desktop.java b/src/jalview/gui/Desktop.java
index 1a1fa45..e9cc8e9 100644
--- a/src/jalview/gui/Desktop.java
+++ b/src/jalview/gui/Desktop.java
@@ -20,36 +20,6 @@
  */
 package jalview.gui;
 
-import static jalview.util.UrlConstants.SEQUENCE_ID;
-
-import jalview.api.AlignViewportI;
-import jalview.api.AlignmentViewPanel;
-import jalview.bin.Cache;
-import jalview.bin.Jalview;
-import jalview.io.BackupFiles;
-import jalview.io.DataSourceType;
-import jalview.io.FileFormat;
-import jalview.io.FileFormatException;
-import jalview.io.FileFormatI;
-import jalview.io.FileFormats;
-import jalview.io.FileLoader;
-import jalview.io.FormatAdapter;
-import jalview.io.IdentifyFile;
-import jalview.io.JalviewFileChooser;
-import jalview.io.JalviewFileView;
-import jalview.jbgui.GSplitFrame;
-import jalview.jbgui.GStructureViewer;
-import jalview.project.Jalview2XML;
-import jalview.structure.StructureSelectionManager;
-import jalview.urls.IdOrgSettings;
-import jalview.util.ImageMaker;
-import jalview.util.MessageManager;
-import jalview.util.Platform;
-import jalview.util.UrlConstants;
-import jalview.viewmodel.AlignmentViewport;
-import jalview.ws.params.ParamManager;
-import jalview.ws.utils.UrlDownloadClient;
-
 import java.awt.BorderLayout;
 import java.awt.Color;
 import java.awt.Dimension;
@@ -79,12 +49,13 @@ import java.awt.event.WindowAdapter;
 import java.awt.event.WindowEvent;
 import java.beans.PropertyChangeEvent;
 import java.beans.PropertyChangeListener;
-import java.io.BufferedInputStream;
 import java.io.File;
-import java.io.FileOutputStream;
+import java.io.FileWriter;
 import java.io.IOException;
+import java.lang.reflect.Field;
 import java.net.URL;
 import java.util.ArrayList;
+import java.util.HashMap;
 import java.util.Hashtable;
 import java.util.List;
 import java.util.ListIterator;
@@ -107,7 +78,6 @@ import javax.swing.JCheckBox;
 import javax.swing.JComboBox;
 import javax.swing.JComponent;
 import javax.swing.JDesktopPane;
-import javax.swing.JFrame;
 import javax.swing.JInternalFrame;
 import javax.swing.JLabel;
 import javax.swing.JMenuItem;
@@ -120,11 +90,37 @@ import javax.swing.event.HyperlinkEvent;
 import javax.swing.event.HyperlinkEvent.EventType;
 import javax.swing.event.InternalFrameAdapter;
 import javax.swing.event.InternalFrameEvent;
-import javax.swing.event.MenuEvent;
-import javax.swing.event.MenuListener;
 
 import org.stackoverflowusers.file.WindowsShortcut;
 
+import jalview.api.AlignViewportI;
+import jalview.api.AlignmentViewPanel;
+import jalview.bin.Cache;
+import jalview.bin.Jalview;
+import jalview.io.BackupFiles;
+import jalview.io.DataSourceType;
+import jalview.io.FileFormat;
+import jalview.io.FileFormatException;
+import jalview.io.FileFormatI;
+import jalview.io.FileFormats;
+import jalview.io.FileLoader;
+import jalview.io.FormatAdapter;
+import jalview.io.IdentifyFile;
+import jalview.io.JalviewFileChooser;
+import jalview.io.JalviewFileView;
+import jalview.jbgui.GSplitFrame;
+import jalview.jbgui.GStructureViewer;
+import jalview.project.Jalview2XML;
+import jalview.structure.StructureSelectionManager;
+import jalview.urls.IdOrgSettings;
+import jalview.util.ImageMaker;
+import jalview.util.MessageManager;
+import jalview.util.Platform;
+import jalview.util.UrlConstants;
+import jalview.viewmodel.AlignmentViewport;
+import jalview.ws.params.ParamManager;
+import jalview.ws.utils.UrlDownloadClient;
+
 /**
  * Jalview Desktop
  * 
@@ -146,6 +142,10 @@ 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 HashMap<String, FileWriter> savingFiles = new HashMap<String, FileWriter>();
+
   private JalviewChangeSupport changeSupport = new JalviewChangeSupport();
 
   /**
@@ -343,18 +343,68 @@ public class Desktop extends jalview.jbgui.GDesktop
      * constructor.
      */
     instance = this;
-    doVamsasClientCheck();
 
     doConfigureStructurePrefs();
-    setTitle("Jalview " + jalview.bin.Cache.getProperty("VERSION"));
-    setDefaultCloseOperation(JFrame.EXIT_ON_CLOSE);
+    String title = "Jalview " + Cache.getProperty("VERSION");
+    setTitle(title);
+    /*
+    if (!Platform.isAMac())
+    {
+      // this.setDefaultCloseOperation(WindowConstants.EXIT_ON_CLOSE);
+    }
+    else
+    {
+     this.setDefaultCloseOperation(WindowConstants.DO_NOTHING_ON_CLOSE);
+    }
+    */
+
+    try
+    {
+      APQHandlers.setAPQHandlers(this);
+    } catch (Exception e)
+    {
+      System.out.println("Cannot set APQHandlers");
+      // e.printStackTrace();
+    } catch (Throwable t)
+    {
+      System.out.println("Cannot set APQHandlers");
+      // t.printStackTrace();
+    }
+
+    if (Platform.isLinux())
+    {
+      try
+      {
+        Toolkit xToolkit = Toolkit.getDefaultToolkit();
+        Field awtAppClassNameField = xToolkit.getClass()
+                .getDeclaredField("awtAppClassName");
+        awtAppClassNameField.setAccessible(true);
+        awtAppClassNameField.set(xToolkit, "Jalview");
+      } catch (Exception e)
+      {
+        Cache.log.debug("Could not set awtAppClassName");
+      }
+    }
+
+    addWindowListener(new WindowAdapter()
+    {
+
+      @Override
+      public void windowClosing(WindowEvent ev)
+      {
+        quit();
+      }
+    });
+
     boolean selmemusage = jalview.bin.Cache.getDefault("SHOW_MEMUSAGE",
             false);
+
     boolean showjconsole = jalview.bin.Cache.getDefault("SHOW_JAVA_CONSOLE",
             false);
     desktop = new MyDesktopPane(selmemusage);
     showMemusage.setSelected(selmemusage);
     desktop.setBackground(Color.white);
+
     getContentPane().setLayout(new BorderLayout());
     // alternate config - have scrollbars - see notes in JAL-153
     // JScrollPane sp = new JScrollPane();
@@ -365,13 +415,12 @@ 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.isWindows() ? new DefaultDesktopManager()
-                            : Platform.isAMac()
-                                    ? new AquaInternalFrameManager(
-                                            desktop.getDesktopManager())
-                                    : desktop.getDesktopManager())));
+    desktop.setDesktopManager(new MyDesktopManager(
+            (Platform.isWindows() ? new DefaultDesktopManager()
+                    : Platform.isAMac()
+                            ? new AquaInternalFrameManager(
+                                    desktop.getDesktopManager())
+                            : desktop.getDesktopManager())));
 
     Rectangle dims = getLastKnownDimensions("");
     if (dims != null)
@@ -386,18 +435,7 @@ public class Desktop extends jalview.jbgui.GDesktop
     }
     jconsole = new Console(this, showjconsole);
     // add essential build information
-    jconsole.setHeader(
-            "Jalview Version: " + jalview.bin.Cache.getProperty("VERSION")
-                    + "\n" + "Jalview Installation: "
-                    + jalview.bin.Cache.getDefault("INSTALLATION",
-                            "unknown")
-                    + "\n" + "Build Date: "
-                    + jalview.bin.Cache.getDefault("BUILD_DATE", "unknown")
-                    + "\n" + "Java version: "
-                    + System.getProperty("java.version") + "\n"
-                    + System.getProperty("os.arch") + " "
-                    + System.getProperty("os.name") + " "
-                    + System.getProperty("os.version"));
+    jconsole.setHeader(jalview.bin.Cache.getVersionDetailsForConsole());
 
     showConsole(showjconsole);
 
@@ -537,26 +575,27 @@ public class Desktop extends jalview.jbgui.GDesktop
 
   public void getIdentifiersOrgData()
   {
-    // Thread off the identifiers fetcher
-    new Thread(new Runnable()
-    {
-      @Override
-      public void run()
+    if (Cache.getProperty("NOIDENTIFIERSSERVICE") == null)
+    {// Thread off the identifiers fetcher
+      new Thread(new Runnable()
       {
-        Cache.log.debug("Downloading data from identifiers.org");
-        UrlDownloadClient client = new UrlDownloadClient();
-        try
-        {
-          client.download(IdOrgSettings.getUrl(),
-                  IdOrgSettings.getDownloadLocation());
-        } catch (IOException e)
+        @Override
+        public void run()
         {
-          Cache.log.debug("Exception downloading identifiers.org data"
-                  + e.getMessage());
+          Cache.log.debug("Downloading data from identifiers.org");
+          try
+          {
+            UrlDownloadClient.download(IdOrgSettings.getUrl(),
+                    IdOrgSettings.getDownloadLocation());
+          } catch (IOException e)
+          {
+            Cache.log.debug("Exception downloading identifiers.org data"
+                    + e.getMessage());
+          }
         }
-      }
-    }).start();
-    ;
+      }).start();
+      ;
+    }
   }
 
   @Override
@@ -648,46 +687,6 @@ public class Desktop extends jalview.jbgui.GDesktop
     return null;
   }
 
-  private void doVamsasClientCheck()
-  {
-    if (jalview.bin.Cache.vamsasJarsPresent())
-    {
-      setupVamsasDisconnectedGui();
-      VamsasMenu.setVisible(true);
-      final Desktop us = this;
-      VamsasMenu.addMenuListener(new MenuListener()
-      {
-        // this listener remembers when the menu was first selected, and
-        // doesn't rebuild the session list until it has been cleared and
-        // reselected again.
-        boolean refresh = true;
-
-        @Override
-        public void menuCanceled(MenuEvent e)
-        {
-          refresh = true;
-        }
-
-        @Override
-        public void menuDeselected(MenuEvent e)
-        {
-          refresh = true;
-        }
-
-        @Override
-        public void menuSelected(MenuEvent e)
-        {
-          if (refresh)
-          {
-            us.buildVamsasStMenu();
-            refresh = false;
-          }
-        }
-      });
-      vamsasStart.setVisible(true);
-    }
-  }
-
   void showPasteMenu(int x, int y)
   {
     JPopupMenu popup = new JPopupMenu();
@@ -945,7 +944,7 @@ public class Desktop extends jalview.jbgui.GDesktop
     } catch (java.lang.ClassCastException cex)
     {
       Cache.log.warn(
-              "Squashed a possible GUI implementation error. If you can recreate this, please look at http://issues.jalview.org/browse/JAL-869",
+              "Squashed a possible GUI implementation error. If you can recreate this, please look at https://issues.jalview.org/browse/JAL-869",
               cex);
     }
   }
@@ -974,7 +973,8 @@ public class Desktop extends jalview.jbgui.GDesktop
     KeyStroke ctrlWKey = KeyStroke.getKeyStroke(KeyEvent.VK_W,
             InputEvent.CTRL_DOWN_MASK);
     KeyStroke cmdWKey = KeyStroke.getKeyStroke(KeyEvent.VK_W,
-            Toolkit.getDefaultToolkit().getMenuShortcutKeyMask());
+            jalview.util.ShortcutKeyMaskExWrapper
+                    .getMenuShortcutKeyMaskEx());
 
     InputMap inputMap = frame
             .getInputMap(JComponent.WHEN_IN_FOCUSED_WINDOW);
@@ -1087,8 +1087,9 @@ public class Desktop extends jalview.jbgui.GDesktop
   public void inputLocalFileMenuItem_actionPerformed(AlignViewport viewport)
   {
     String fileFormat = Cache.getProperty("DEFAULT_FILE_FORMAT");
-    JalviewFileChooser chooser = JalviewFileChooser
-            .forRead(Cache.getProperty("LAST_DIRECTORY"), fileFormat);
+    JalviewFileChooser chooser = JalviewFileChooser.forRead(
+            Cache.getProperty("LAST_DIRECTORY"), fileFormat,
+            BackupFiles.getEnabled());
 
     chooser.setFileView(new JalviewFileView());
     chooser.setDialogTitle(
@@ -1153,7 +1154,7 @@ public class Desktop extends jalview.jbgui.GDesktop
     panel.add(history);
     history.setPreferredSize(new Dimension(400, 20));
     history.setEditable(true);
-    history.addItem("http://www.");
+    history.addItem("https://www.");
 
     String historyItems = jalview.bin.Cache.getProperty("RECENT_URL");
 
@@ -1330,9 +1331,10 @@ public class Desktop extends jalview.jbgui.GDesktop
       message.append("<h1><strong>Version: "
               + jalview.bin.Cache.getProperty("VERSION")
               + "</strong></h1>");
-      message.append("<strong>Last Updated: <em>"
+      message.append("<strong>Built: <em>"
               + jalview.bin.Cache.getDefault("BUILD_DATE", "unknown")
-              + "</em></strong>");
+              + "</em> from " + jalview.bin.Cache.getBuildDetailsForSplash()
+              + "</strong>");
 
     }
     else
@@ -1347,7 +1349,8 @@ public class Desktop extends jalview.jbgui.GDesktop
     if (jalview.bin.Cache.getDefault("LATEST_VERSION", "Checking")
             .equals("Checking"))
     {
-      message.append("<br>...Checking latest version...</br>");
+      // JBP removed this message for 2.11: May be reinstated in future version
+      // message.append("<br>...Checking latest version...</br>");
     }
     else if (!jalview.bin.Cache.getDefault("LATEST_VERSION", "Checking")
             .equals(jalview.bin.Cache.getProperty("VERSION")))
@@ -1367,7 +1370,7 @@ public class Desktop extends jalview.jbgui.GDesktop
                       "..Checking..")
               + " is available for download from "
               + jalview.bin.Cache.getDefault("www.jalview.org",
-                      "http://www.jalview.org")
+                      "https://www.jalview.org")
               + " !!");
       if (red)
       {
@@ -1378,7 +1381,7 @@ public class Desktop extends jalview.jbgui.GDesktop
             "AUTHORFNAMES",
             "The Jalview Authors (See AUTHORS file for current list)")
             + "<br><br>Development managed by The Barton Group, University of Dundee, Scotland, UK.<br>"
-            + "<br><br>For help, see the FAQ at <a href=\"http://www.jalview.org/faq\">www.jalview.org/faq</a> and/or join the jalview-discuss@jalview.org mailing list"
+            + "<br><br>For help, see the FAQ at <a href=\"https://www.jalview.org/faq\">www.jalview.org/faq</a> and/or join the jalview-discuss@jalview.org mailing list"
             + "<br><br>If  you use Jalview, please cite:"
             + "<br>Waterhouse, A.M., Procter, J.B., Martin, D.M.A, Clamp, M. and Barton, G. J. (2009)"
             + "<br>Jalview Version 2 - a multiple sequence alignment editor and analysis workbench"
@@ -1420,10 +1423,6 @@ public class Desktop extends jalview.jbgui.GDesktop
     }
     Jalview.setCurrentAlignFrame(null);
     System.out.println("ALL CLOSED");
-    if (v_client != null)
-    {
-      // TODO clear binding to vamsas document objects on close_all
-    }
 
     /*
      * reset state of singleton objects as appropriate (clear down session state
@@ -1614,9 +1613,12 @@ public class Desktop extends jalview.jbgui.GDesktop
   {
     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"));
+    // System.out.println("autoSave="+autoSave+", projectFile='"+projectFile+"',
+    // saveAs="+saveAs+", Backups
+    // "+(BackupFiles.getEnabled()?"enabled":"disabled"));
 
     boolean approveSave = false;
     if (!autoSave)
@@ -1637,7 +1639,8 @@ public class Desktop extends jalview.jbgui.GDesktop
       }
     }
 
-    if (approveSave || autoSave) {
+    if (approveSave || autoSave)
+    {
       final Desktop me = this;
       final java.io.File chosenFile = projectFile;
       new Thread(new Runnable()
@@ -1663,14 +1666,12 @@ public class Desktop extends jalview.jbgui.GDesktop
             backupfiles.rollBackupsAndRenameTempFile();
           } catch (OutOfMemoryError oom)
           {
-            new OOMWarning(
-                    "Whilst saving current state to " + chosenFile.getName(),
-                    oom);
+            new OOMWarning("Whilst saving current state to "
+                    + chosenFile.getName(), oom);
           } catch (Exception ex)
           {
-            Cache.log.error(
-                    "Problems whilst trying to save to " + chosenFile.getName(),
-                    ex);
+            Cache.log.error("Problems whilst trying to save to "
+                    + chosenFile.getName(), ex);
             JvOptionPane.showMessageDialog(me,
                     MessageManager.formatMessage(
                             "label.error_whilst_saving_current_state_to",
@@ -1712,9 +1713,11 @@ public class Desktop extends jalview.jbgui.GDesktop
     final String[] desc = new String[] { "Jalview Project",
         "Jalview Project (old)" };
     JalviewFileChooser chooser = new JalviewFileChooser(
-            Cache.getProperty("LAST_DIRECTORY"), suffix,
-            desc,
-            "Jalview Project");
+            Cache.getProperty("LAST_DIRECTORY"), suffix, desc,
+            "Jalview Project", true, BackupFiles.getEnabled()); // last two
+                                                                // booleans:
+                                                                // allFiles,
+    // allowBackupFiles
     chooser.setFileView(new JalviewFileView());
     chooser.setDialogTitle(MessageManager.getString("label.restore_state"));
 
@@ -1941,11 +1944,26 @@ public class Desktop extends jalview.jbgui.GDesktop
       return;
     }
 
+    // FIXME: ideally should use UI interface API
+    FeatureSettings viewFeatureSettings = (af.featureSettings != null
+            && af.featureSettings.isOpen()) ? af.featureSettings : null;
+    Rectangle fsBounds = af.getFeatureSettingsGeometry();
     for (int i = 0; i < size; i++)
     {
       AlignmentPanel ap = af.alignPanels.get(i);
+
       AlignFrame newaf = new AlignFrame(ap);
 
+      // transfer reference for existing feature settings to new alignFrame
+      if (ap == af.alignPanel)
+      {
+        if (viewFeatureSettings != null && viewFeatureSettings.fr.ap == ap)
+        {
+          newaf.featureSettings = viewFeatureSettings;
+        }
+        newaf.setFeatureSettingsGeometry(fsBounds);
+      }
+
       /*
        * Restore the view's last exploded frame geometry if known. Multiple
        * views from one exploded frame share and restore the same (frame)
@@ -1961,8 +1979,18 @@ public class Desktop extends jalview.jbgui.GDesktop
 
       addInternalFrame(newaf, af.getTitle(), AlignFrame.DEFAULT_WIDTH,
               AlignFrame.DEFAULT_HEIGHT);
+      // and materialise a new feature settings dialog instance for the new
+      // alignframe
+      // (closes the old as if 'OK' was pressed)
+      if (ap == af.alignPanel && newaf.featureSettings != null
+              && newaf.featureSettings.isOpen()
+              && af.alignPanel.getAlignViewport().isShowSequenceFeatures())
+      {
+        newaf.showFeatureSettingsUI();
+      }
     }
 
+    af.featureSettings = null;
     af.alignPanels.clear();
     af.closeMenuItem_actionPerformed(true);
 
@@ -1982,7 +2010,6 @@ public class Desktop extends jalview.jbgui.GDesktop
     source.viewport.setExplodedGeometry(source.getBounds());
     JInternalFrame[] frames = desktop.getAllFrames();
     String viewId = source.viewport.getSequenceSetId();
-
     for (int t = 0; t < frames.length; t++)
     {
       if (frames[t] instanceof AlignFrame && frames[t] != source)
@@ -2003,370 +2030,32 @@ public class Desktop extends jalview.jbgui.GDesktop
 
         if (gatherThis)
         {
-          af.alignPanels.clear();
-          af.closeMenuItem_actionPerformed(true);
-        }
-      }
-    }
-
-  }
-
-  jalview.gui.VamsasApplication v_client = null;
-
-  @Override
-  public void vamsasImport_actionPerformed(ActionEvent e)
-  {
-    if (v_client == null)
-    {
-      // Load and try to start a session.
-      JalviewFileChooser chooser = new JalviewFileChooser(
-              jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
-
-      chooser.setFileView(new JalviewFileView());
-      chooser.setDialogTitle(
-              MessageManager.getString("label.open_saved_vamsas_session"));
-      chooser.setToolTipText(MessageManager.getString(
-              "label.select_vamsas_session_opened_as_new_vamsas_session"));
-
-      int value = chooser.showOpenDialog(this);
-
-      if (value == JalviewFileChooser.APPROVE_OPTION)
-      {
-        String fle = chooser.getSelectedFile().toString();
-        if (!vamsasImport(chooser.getSelectedFile()))
-        {
-          JvOptionPane.showInternalMessageDialog(Desktop.desktop,
-                  MessageManager.formatMessage(
-                          "label.couldnt_import_as_vamsas_session",
-                          new Object[]
-                          { fle }),
-                  MessageManager
-                          .getString("label.vamsas_document_import_failed"),
-                  JvOptionPane.ERROR_MESSAGE);
-        }
-      }
-    }
-    else
-    {
-      jalview.bin.Cache.log.error(
-              "Implementation error - load session from a running session is not supported.");
-    }
-  }
-
-  /**
-   * import file into a new vamsas session (uses jalview.gui.VamsasApplication)
-   * 
-   * @param file
-   * @return true if import was a success and a session was started.
-   */
-  public boolean vamsasImport(URL url)
-  {
-    // TODO: create progress bar
-    if (v_client != null)
-    {
-
-      jalview.bin.Cache.log.error(
-              "Implementation error - load session from a running session is not supported.");
-      return false;
-    }
-
-    try
-    {
-      // copy the URL content to a temporary local file
-      // TODO: be a bit cleverer here with nio (?!)
-      File file = File.createTempFile("vdocfromurl", ".vdj");
-      FileOutputStream fos = new FileOutputStream(file);
-      BufferedInputStream bis = new BufferedInputStream(url.openStream());
-      byte[] buffer = new byte[2048];
-      int ln;
-      while ((ln = bis.read(buffer)) > -1)
-      {
-        fos.write(buffer, 0, ln);
-      }
-      bis.close();
-      fos.close();
-      v_client = new jalview.gui.VamsasApplication(this, file,
-              url.toExternalForm());
-    } catch (Exception ex)
-    {
-      jalview.bin.Cache.log.error(
-              "Failed to create new vamsas session from contents of URL "
-                      + url,
-              ex);
-      return false;
-    }
-    setupVamsasConnectedGui();
-    v_client.initial_update(); // TODO: thread ?
-    return v_client.inSession();
-  }
-
-  /**
-   * import file into a new vamsas session (uses jalview.gui.VamsasApplication)
-   * 
-   * @param file
-   * @return true if import was a success and a session was started.
-   */
-  public boolean vamsasImport(File file)
-  {
-    if (v_client != null)
-    {
-
-      jalview.bin.Cache.log.error(
-              "Implementation error - load session from a running session is not supported.");
-      return false;
-    }
-
-    setProgressBar(MessageManager.formatMessage(
-            "status.importing_vamsas_session_from", new Object[]
-            { file.getName() }), file.hashCode());
-    try
-    {
-      v_client = new jalview.gui.VamsasApplication(this, file, null);
-    } catch (Exception ex)
-    {
-      setProgressBar(MessageManager.formatMessage(
-              "status.importing_vamsas_session_from", new Object[]
-              { file.getName() }), file.hashCode());
-      jalview.bin.Cache.log.error(
-              "New vamsas session from existing session file failed:", ex);
-      return false;
-    }
-    setupVamsasConnectedGui();
-    v_client.initial_update(); // TODO: thread ?
-    setProgressBar(MessageManager.formatMessage(
-            "status.importing_vamsas_session_from", new Object[]
-            { file.getName() }), file.hashCode());
-    return v_client.inSession();
-  }
-
-  public boolean joinVamsasSession(String mysesid)
-  {
-    if (v_client != null)
-    {
-      throw new Error(MessageManager
-              .getString("error.try_join_vamsas_session_another"));
-    }
-    if (mysesid == null)
-    {
-      throw new Error(
-              MessageManager.getString("error.invalid_vamsas_session_id"));
-    }
-    v_client = new VamsasApplication(this, mysesid);
-    setupVamsasConnectedGui();
-    v_client.initial_update();
-    return (v_client.inSession());
-  }
-
-  @Override
-  public void vamsasStart_actionPerformed(ActionEvent e)
-  {
-    if (v_client == null)
-    {
-      // Start a session.
-      // we just start a default session for moment.
-      /*
-       * JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.
-       * getProperty("LAST_DIRECTORY"));
-       * 
-       * chooser.setFileView(new JalviewFileView());
-       * chooser.setDialogTitle("Load Vamsas file");
-       * chooser.setToolTipText("Import");
-       * 
-       * int value = chooser.showOpenDialog(this);
-       * 
-       * if (value == JalviewFileChooser.APPROVE_OPTION) { v_client = new
-       * jalview.gui.VamsasApplication(this, chooser.getSelectedFile());
-       */
-      v_client = new VamsasApplication(this);
-      setupVamsasConnectedGui();
-      v_client.initial_update(); // TODO: thread ?
-    }
-    else
-    {
-      // store current data in session.
-      v_client.push_update(); // TODO: thread
-    }
-  }
-
-  protected void setupVamsasConnectedGui()
-  {
-    vamsasStart.setText(MessageManager.getString("label.session_update"));
-    vamsasSave.setVisible(true);
-    vamsasStop.setVisible(true);
-    vamsasImport.setVisible(false); // Document import to existing session is
-    // not possible for vamsas-client-1.0.
-  }
-
-  protected void setupVamsasDisconnectedGui()
-  {
-    vamsasSave.setVisible(false);
-    vamsasStop.setVisible(false);
-    vamsasImport.setVisible(true);
-    vamsasStart
-            .setText(MessageManager.getString("label.new_vamsas_session"));
-  }
-
-  @Override
-  public void vamsasStop_actionPerformed(ActionEvent e)
-  {
-    if (v_client != null)
-    {
-      v_client.end_session();
-      v_client = null;
-      setupVamsasDisconnectedGui();
-    }
-  }
-
-  protected void buildVamsasStMenu()
-  {
-    if (v_client == null)
-    {
-      String[] sess = null;
-      try
-      {
-        sess = VamsasApplication.getSessionList();
-      } catch (Exception e)
-      {
-        jalview.bin.Cache.log.warn("Problem getting current sessions list.",
-                e);
-        sess = null;
-      }
-      if (sess != null)
-      {
-        jalview.bin.Cache.log.debug(
-                "Got current sessions list: " + sess.length + " entries.");
-        VamsasStMenu.removeAll();
-        for (int i = 0; i < sess.length; i++)
-        {
-          JMenuItem sessit = new JMenuItem();
-          sessit.setText(sess[i]);
-          sessit.setToolTipText(MessageManager
-                  .formatMessage("label.connect_to_session", new Object[]
-                  { sess[i] }));
-          final Desktop dsktp = this;
-          final String mysesid = sess[i];
-          sessit.addActionListener(new ActionListener()
+          if (af.featureSettings != null && af.featureSettings.isOpen())
           {
-
-            @Override
-            public void actionPerformed(ActionEvent e)
+            if (source.featureSettings == null)
             {
-              if (dsktp.v_client == null)
-              {
-                Thread rthr = new Thread(new Runnable()
-                {
-
-                  @Override
-                  public void run()
-                  {
-                    dsktp.v_client = new VamsasApplication(dsktp, mysesid);
-                    dsktp.setupVamsasConnectedGui();
-                    dsktp.v_client.initial_update();
-                  }
-
-                });
-                rthr.start();
-              }
-            };
-          });
-          VamsasStMenu.add(sessit);
+              // preserve the feature settings geometry for this frame
+              source.featureSettings = af.featureSettings;
+              source.setFeatureSettingsGeometry(
+                      af.getFeatureSettingsGeometry());
+            }
+            else
+            {
+              // close it and forget
+              af.featureSettings.close();
+            }
+          }
+          af.alignPanels.clear();
+          af.closeMenuItem_actionPerformed(true);
         }
-        // don't show an empty menu.
-        VamsasStMenu.setVisible(sess.length > 0);
-
-      }
-      else
-      {
-        jalview.bin.Cache.log.debug("No current vamsas sessions.");
-        VamsasStMenu.removeAll();
-        VamsasStMenu.setVisible(false);
       }
     }
-    else
+    // refresh the feature setting UI for the source frame if it exists
+    if (source.featureSettings != null && source.featureSettings.isOpen())
     {
-      // Not interested in the content. Just hide ourselves.
-      VamsasStMenu.setVisible(false);
+      source.showFeatureSettingsUI();
     }
-  }
 
-  @Override
-  public void vamsasSave_actionPerformed(ActionEvent e)
-  {
-    if (v_client != null)
-    {
-      // TODO: VAMSAS DOCUMENT EXTENSION is VDJ
-      JalviewFileChooser chooser = new JalviewFileChooser("vdj",
-              "Vamsas Document");
-
-      chooser.setFileView(new JalviewFileView());
-      chooser.setDialogTitle(MessageManager
-              .getString("label.save_vamsas_document_archive"));
-
-      int value = chooser.showSaveDialog(this);
-
-      if (value == JalviewFileChooser.APPROVE_OPTION)
-      {
-        java.io.File choice = chooser.getSelectedFile();
-        JPanel progpanel = addProgressPanel(MessageManager
-                .formatMessage("label.saving_vamsas_doc", new Object[]
-                { choice.getName() }));
-        Cache.setProperty("LAST_DIRECTORY", choice.getParent());
-        String warnmsg = null;
-        String warnttl = null;
-        try
-        {
-          v_client.vclient.storeDocument(choice);
-        } catch (Error ex)
-        {
-          warnttl = "Serious Problem saving Vamsas Document";
-          warnmsg = ex.toString();
-          jalview.bin.Cache.log
-                  .error("Error Whilst saving document to " + choice, ex);
-
-        } catch (Exception ex)
-        {
-          warnttl = "Problem saving Vamsas Document.";
-          warnmsg = ex.toString();
-          jalview.bin.Cache.log.warn(
-                  "Exception Whilst saving document to " + choice, ex);
-
-        }
-        removeProgressPanel(progpanel);
-        if (warnmsg != null)
-        {
-          JvOptionPane.showInternalMessageDialog(Desktop.desktop,
-
-                  warnmsg, warnttl, JvOptionPane.ERROR_MESSAGE);
-        }
-      }
-    }
-  }
-
-  JPanel vamUpdate = null;
-
-  /**
-   * hide vamsas user gui bits when a vamsas document event is being handled.
-   * 
-   * @param b
-   *          true to hide gui, false to reveal gui
-   */
-  public void setVamsasUpdate(boolean b)
-  {
-    Cache.log.debug("Setting gui for Vamsas update "
-            + (b ? "in progress" : "finished"));
-
-    if (vamUpdate != null)
-    {
-      this.removeProgressPanel(vamUpdate);
-    }
-    if (b)
-    {
-      vamUpdate = this.addProgressPanel(
-              MessageManager.getString("label.updating_vamsas_session"));
-    }
-    vamsasStart.setVisible(!b);
-    vamsasStop.setVisible(!b);
-    vamsasSave.setVisible(!b);
   }
 
   public JInternalFrame[] getAllFrames()
@@ -2410,7 +2099,7 @@ public class Desktop extends jalview.jbgui.GDesktop
           while (li.hasNext())
           {
             String link = li.next();
-            if (link.contains(SEQUENCE_ID)
+            if (link.contains(jalview.util.UrlConstants.SEQUENCE_ID)
                     && !UrlConstants.isDefaultString(link))
             {
               check = true;
@@ -2564,7 +2253,6 @@ public class Desktop extends jalview.jbgui.GDesktop
     }
   }
 
-
   /**
    * Accessor method to quickly get all the AlignmentFrames loaded.
    * 
@@ -2717,9 +2405,12 @@ public class Desktop extends jalview.jbgui.GDesktop
    */
   protected void addQuitHandler()
   {
-    getRootPane().getInputMap(JComponent.WHEN_IN_FOCUSED_WINDOW)
-            .put(KeyStroke.getKeyStroke(KeyEvent.VK_Q,
-                    Toolkit.getDefaultToolkit().getMenuShortcutKeyMask()),
+    getRootPane()
+            .getInputMap(JComponent.WHEN_IN_FOCUSED_WINDOW).put(
+                    KeyStroke
+                            .getKeyStroke(KeyEvent.VK_Q,
+                                    jalview.util.ShortcutKeyMaskExWrapper
+                                            .getMenuShortcutKeyMaskEx()),
                     "Quit");
     getRootPane().getActionMap().put("Quit", new AbstractAction()
     {
@@ -2776,18 +2467,18 @@ public class Desktop extends jalview.jbgui.GDesktop
       progressBarHandlers = new Hashtable<>();
     }
 
-    if (progressBars.get(new Long(id)) != null)
+    if (progressBars.get(Long.valueOf(id)) != null)
     {
-      JPanel panel = progressBars.remove(new Long(id));
-      if (progressBarHandlers.contains(new Long(id)))
+      JPanel panel = progressBars.remove(Long.valueOf(id));
+      if (progressBarHandlers.contains(Long.valueOf(id)))
       {
-        progressBarHandlers.remove(new Long(id));
+        progressBarHandlers.remove(Long.valueOf(id));
       }
       removeProgressPanel(panel);
     }
     else
     {
-      progressBars.put(new Long(id), addProgressPanel(message));
+      progressBars.put(Long.valueOf(id), addProgressPanel(message));
     }
   }
 
@@ -2802,13 +2493,13 @@ public class Desktop extends jalview.jbgui.GDesktop
           final IProgressIndicatorHandler handler)
   {
     if (progressBarHandlers == null
-            || !progressBars.containsKey(new Long(id)))
+            || !progressBars.containsKey(Long.valueOf(id)))
     {
       throw new Error(MessageManager.getString(
               "error.call_setprogressbar_before_registering_handler"));
     }
-    progressBarHandlers.put(new Long(id), handler);
-    final JPanel progressPanel = progressBars.get(new Long(id));
+    progressBarHandlers.put(Long.valueOf(id), handler);
+    final JPanel progressPanel = progressBars.get(Long.valueOf(id));
     if (handler.canCancel())
     {
       JButton cancel = new JButton(
@@ -2872,7 +2563,8 @@ public class Desktop extends jalview.jbgui.GDesktop
 
   public VamsasApplication getVamsasApplication()
   {
-    return v_client;
+    // TODO: JAL-3311 remove remaining code from Jalview relating to VAMSAS
+    return null;
 
   }
 
@@ -2901,13 +2593,36 @@ public class Desktop extends jalview.jbgui.GDesktop
     this.inBatchMode = inBatchMode;
   }
 
+  /**
+   * start service discovery and wait till it is done
+   */
   public void startServiceDiscovery()
   {
     startServiceDiscovery(false);
   }
 
+  /**
+   * start service discovery threads - blocking or non-blocking
+   * 
+   * @param blocking
+   */
   public void startServiceDiscovery(boolean blocking)
   {
+    startServiceDiscovery(blocking, false);
+  }
+
+  /**
+   * start service discovery threads
+   * 
+   * @param blocking
+   *          - false means call returns immediately
+   * @param ignore_SHOW_JWS2_SERVICES_preference
+   *          - when true JABA services are discovered regardless of user's JWS2
+   *          discovery preference setting
+   */
+  public void startServiceDiscovery(boolean blocking,
+          boolean ignore_SHOW_JWS2_SERVICES_preference)
+  {
     boolean alive = true;
     Thread t0 = null, t1 = null, t2 = null;
     // JAL-940 - JALVIEW 1 services are now being EOLed as of JABA 2.1 release
@@ -2925,7 +2640,8 @@ public class Desktop extends jalview.jbgui.GDesktop
       (t0 = new Thread(discoverer)).start();
     }
 
-    if (Cache.getDefault("SHOW_JWS2_SERVICES", true))
+    if (ignore_SHOW_JWS2_SERVICES_preference
+            || Cache.getDefault("SHOW_JWS2_SERVICES", true))
     {
       t2 = jalview.ws.jws2.Jws2Discoverer.getDiscoverer()
               .startDiscoverer(changeSupport);
@@ -3402,15 +3118,15 @@ public class Desktop extends jalview.jbgui.GDesktop
 
       try
       {
-      java.net.URL url = (URL) t.getTransferData(urlFlavour);
+        java.net.URL url = (URL) t.getTransferData(urlFlavour);
         // nb: java 8 osx bug https://bugs.openjdk.java.net/browse/JDK-8156099
         // means url may be null.
-      if (url != null)
-      {
-        protocols.add(DataSourceType.URL);
-        files.add(url.toString());
-        Cache.log.debug("Drop handled as URL dataflavor "
-                + files.get(files.size() - 1));
+        if (url != null)
+        {
+          protocols.add(DataSourceType.URL);
+          files.add(url.toString());
+          Cache.log.debug("Drop handled as URL dataflavor "
+                  + files.get(files.size() - 1));
           return;
         }
         else
@@ -3421,7 +3137,7 @@ public class Desktop extends jalview.jbgui.GDesktop
                     "Please ignore plist error - occurs due to problem with java 8 on OSX");
           }
           ;
-      }
+        }
       } catch (Throwable ex)
       {
         Cache.log.debug("URL drop handler failed.", ex);
@@ -3545,7 +3261,8 @@ public class Desktop extends jalview.jbgui.GDesktop
                 && (source.endsWith(".lnk") || source.endsWith(".url")
                         || source.endsWith(".site")))
         {
-          try {
+          try
+          {
             File lf = new File(files.get(f));
             // process link file to get a URL
             Cache.log.debug("Found potential link file: " + lf);
@@ -3555,10 +3272,11 @@ public class Desktop extends jalview.jbgui.GDesktop
             files.set(f, fullname);
             Cache.log.debug("Parsed real filename " + fullname
                     + " to extract protocol: " + protocols.get(f));
-          }
-          catch (Exception ex)
+          } catch (Exception ex)
           {
-            Cache.log.error("Couldn't parse "+files.get(f)+" as a link file.",ex);
+            Cache.log.error(
+                    "Couldn't parse " + files.get(f) + " as a link file.",
+                    ex);
           }
         }
       }