X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fbin%2FJalview.java;h=0ec9ee0e685c5e38f347014808b105283af6f945;hb=b87512d6e28a2a93ea2f08dcfbee320856c5c8de;hp=cdd8cc16a50a003fbade1d25d184ae9f4dbf3bda;hpb=ab0e5f2223a993371761baf240d815abdfcbb950;p=jalview.git

diff --git a/src/jalview/bin/Jalview.java b/src/jalview/bin/Jalview.java
index cdd8cc1..0ec9ee0 100755
--- a/src/jalview/bin/Jalview.java
+++ b/src/jalview/bin/Jalview.java
@@ -20,27 +20,50 @@
  */
 package jalview.bin;
 
+import jalview.api.AlignCalcWorkerI;
+import jalview.api.AlignFrameI;
+import jalview.api.AlignViewportI;
+import jalview.api.JalviewApp;
+import jalview.api.StructureSelectionManagerProvider;
+import jalview.bin.ApplicationSingletonProvider.ApplicationSingletonI;
+import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.HiddenColumns;
+import jalview.datamodel.PDBEntry;
+import jalview.datamodel.SequenceGroup;
+import jalview.datamodel.SequenceI;
 import jalview.ext.so.SequenceOntology;
 import jalview.gui.AlignFrame;
+import jalview.gui.AlignViewport;
+import jalview.gui.AlignmentPanel;
+import jalview.gui.CalculationChooser;
 import jalview.gui.Desktop;
+import jalview.gui.Preferences;
 import jalview.gui.PromptUserConfig;
+import jalview.gui.StructureViewer;
 import jalview.io.AppletFormatAdapter;
 import jalview.io.BioJsHTMLOutput;
 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.HtmlSvgOutput;
 import jalview.io.IdentifyFile;
 import jalview.io.NewickFile;
 import jalview.io.gff.SequenceOntologyFactory;
+import jalview.javascript.JSFunctionExec;
+import jalview.javascript.MouseOverStructureListener;
+import jalview.renderer.seqfeatures.FeatureRenderer;
 import jalview.schemes.ColourSchemeI;
 import jalview.schemes.ColourSchemeProperty;
+import jalview.structure.SelectionSource;
+import jalview.structure.VamsasSource;
 import jalview.util.MessageManager;
 import jalview.util.Platform;
 import jalview.ws.jws2.Jws2Discoverer;
 
+import java.applet.AppletContext;
 import java.io.BufferedReader;
 import java.io.File;
 import java.io.FileOutputStream;
@@ -58,19 +81,17 @@ import java.security.PermissionCollection;
 import java.security.Permissions;
 import java.security.Policy;
 import java.util.HashMap;
+import java.util.Hashtable;
 import java.util.Map;
 import java.util.Vector;
-import java.util.logging.ConsoleHandler;
-import java.util.logging.Level;
-import java.util.logging.Logger;
 
 import javax.swing.LookAndFeel;
+import javax.swing.SwingUtilities;
 import javax.swing.UIManager;
 
-import com.threerings.getdown.util.LaunchUtil;
-
 import groovy.lang.Binding;
 import groovy.util.GroovyScriptEngine;
+import netscape.javascript.JSObject;
 
 /**
  * Main class for Jalview Application <br>
@@ -87,20 +108,78 @@ import groovy.util.GroovyScriptEngine;
  * @author $author$
  * @version $Revision$
  */
-public class Jalview
+public class Jalview implements ApplicationSingletonI, JalviewJSApi
 {
+
+  public static Jalview getInstance()
+  {
+    return (Jalview) ApplicationSingletonProvider
+            .getInstance(Jalview.class);
+  }
+
+  private Jalview()
+  {
+  }
+
   static
   {
     Platform.getURLCommandArguments();
   }
 
-  // singleton instance of this class
+  private boolean headless;
 
-  private static Jalview instance;
+  public static boolean isHeadlessMode()
+  {
+    return getInstance().headless;
+  }
 
   private Desktop desktop;
 
-  public static AlignFrame currentAlignFrame;
+  private AlignFrame currentAlignFrame;
+
+  public boolean isJavaAppletTag;
+
+  public String appletResourcePath;
+
+  JalviewAppLoader appLoader;
+
+  protected JSFunctionExec jsFunctionExec;
+
+  private boolean noCalculation, noMenuBar, noStatus;
+
+  private boolean noAnnotation;
+
+  public static final String TERMINATOR_LINE = "Jalview argument parsing complete.";
+
+  public boolean getStartCalculations()
+  {
+    return !noCalculation;
+  }
+
+  public boolean getAllowMenuBar()
+  {
+    return !noMenuBar;
+  }
+
+  public boolean getShowStatus()
+  {
+    return !noStatus;
+  }
+
+  public boolean getShowAnnotation()
+  {
+    return !noAnnotation;
+  }
+
+  public static AlignFrame getCurrentAlignFrame()
+  {
+    return getInstance().currentAlignFrame;
+  }
+
+  public static void setCurrentAlignFrame(AlignFrame currentAlignFrame)
+  {
+    getInstance().currentAlignFrame = currentAlignFrame;
+  }
 
   static
   {
@@ -112,21 +191,21 @@ public class Jalview
      */
     {
       // grab all the rights we can for the JVM
-	    Policy.setPolicy(new Policy()
-	    {
-	      @Override
-	      public PermissionCollection getPermissions(CodeSource codesource)
-	      {
-	        Permissions perms = new Permissions();
-	        perms.add(new AllPermission());
-	        return (perms);
-	      }
-	
-	      @Override
-	      public void refresh()
-	      {
-	      }
-	    });
+      Policy.setPolicy(new Policy()
+      {
+        @Override
+        public PermissionCollection getPermissions(CodeSource codesource)
+        {
+          Permissions perms = new Permissions();
+          perms.add(new AllPermission());
+          return (perms);
+        }
+
+        @Override
+        public void refresh()
+        {
+        }
+      });
     }
   }
 
@@ -139,8 +218,8 @@ public class Jalview
   class FeatureFetcher
   {
     /*
-     * TODO: generalise to track all jalview events to orchestrate batch processing
-     * events.
+     * TODO: generalise to track all jalview events to orchestrate batch
+     * processing events.
      */
 
     private int queued = 0;
@@ -189,138 +268,96 @@ public class Jalview
 
   }
 
-  public static Jalview getInstance()
-  {
-    return instance;
-  }
-
   /**
    * main class for Jalview application
    * 
    * @param args
-   *               open <em>filename</em>
+   *          open <em>filename</em>
    */
   public static void main(String[] args)
   {
-//	setLogging(); // BH - for event debugging in JavaScript
-    instance = new Jalview();
-    instance.doMain(args);
-}
-
-  private static void logClass(String name) 
-  {	
-	  // BH - for event debugging in JavaScript
-      ConsoleHandler consoleHandler = new ConsoleHandler();
-      consoleHandler.setLevel(Level.ALL);
-      Logger logger = Logger.getLogger(name);
-      logger.setLevel(Level.ALL);
-      logger.addHandler(consoleHandler);
-  }
-
-  @SuppressWarnings("unused")
-  private static void setLogging() 
-  {
-
-    /**
-     * @j2sIgnore
-     * 
-     */
-    {
-      System.out.println("not in js");
-    }
-
-	  // BH - for event debugging in JavaScript (Java mode only)
-    if (!Platform.isJS())
-    /**
-     * Java only
-     * 
-     * @j2sIgnore
-     */
-  	{
-  		Logger.getLogger("").setLevel(Level.ALL);
-        logClass("java.awt.EventDispatchThread");
-        logClass("java.awt.EventQueue");
-        logClass("java.awt.Component");
-        logClass("java.awt.focus.Component");
-        logClass("java.awt.focus.DefaultKeyboardFocusManager"); 
-  	}	
-
+    // Platform.startJavaLogging();
+    getInstance().doMain(args);
   }
-  
 
-  
 
+  @SuppressWarnings("unused")
   /**
    * @param args
    */
   void doMain(String[] args)
   {
 
-    if (!Platform.isJS())
+    boolean isJS = Platform.isJS();
+    if (isJS)
+    {
+      Platform.setAppClass(this);
+    }
+    else
     {
       System.setSecurityManager(null);
     }
 
     System.out
-            .println("Java version: "
-                    + System.getProperty("java.version"));
-    System.out.println("Java Home: " + System.getProperty("java.home"));
+            .println("Java version: " + System.getProperty("java.version"));
     System.out.println(System.getProperty("os.arch") + " "
             + System.getProperty("os.name") + " "
             + System.getProperty("os.version"));
-    String val = System.getProperty("sys.install4jVersion");
-    if (val != null) {
-    System.out.println("Install4j version: " + val);
-    }
-    val = System.getProperty("installer_template_version");
-    if (val != null) {
-      System.out.println("Install4j template version: " + val);
-    }
-    val = System.getProperty("launcher_version");
-    if (val != null) {
-      System.out.println("Launcher version: " + val);
-    }
-
-    // report Jalview version
-    Cache.loadBuildProperties(true);
 
     ArgsParser aparser = new ArgsParser(args);
-    boolean headless = false;
 
-    String usrPropsFile = aparser.getValue("props");
-    Cache.loadProperties(usrPropsFile); // must do this before
-    if (usrPropsFile != null)
+    String usrPropsFile = aparser.getValue(ArgsParser.PROPS);
+    Cache.loadProperties(usrPropsFile);
+
+    if (aparser.contains(ArgsParser.NODISPLAY)
+            || aparser.contains(ArgsParser.NOGUI)
+            || aparser.contains(ArgsParser.HEADLESS)
+            || "true".equals(System.getProperty("java.awt.headless")))
     {
-      System.out.println(
-              "CMD [-props " + usrPropsFile + "] executed successfully!");
+      headless = true;
+      setSynchronous(true);
     }
 
-    if (!Platform.isJS())
+    if (isJS)
+    {
+      isJavaAppletTag = aparser.isApplet();
+      if (isJavaAppletTag)
+      {
+        Preferences.setAppletDefaults();
+        Cache.loadProperties(usrPropsFile); // again, because we
+        // might be changing defaults here?
+      }
+      System.out.println(
+              "<Applet> found: " + aparser.getValue("Info.j2sAppletID"));
+      appletResourcePath = aparser.getValue("Info.resourcePath");
+    }
+    else
     /**
      * Java only
      * 
      * @j2sIgnore
      */
     {
+      if (usrPropsFile != null)
+      {
+        System.out.println(
+                "CMD [-props " + usrPropsFile + "] executed successfully!");
+      }
+
       if (aparser.contains("help") || aparser.contains("h"))
       {
         showUsage();
         System.exit(0);
       }
-      if (aparser.contains("nodisplay") || aparser.contains("nogui")
-              || aparser.contains("headless"))
-      {
-        System.setProperty("java.awt.headless", "true");
-        headless = true;
-      }
+
       // anything else!
 
-      final String jabawsUrl = aparser.getValue("jabaws");
+      final String jabawsUrl = aparser.getValue(ArgsParser.JABAWS);
       if (jabawsUrl != null)
       {
         try
         {
-          Jws2Discoverer.getDiscoverer().setPreferredUrl(jabawsUrl);
+          Jws2Discoverer.getInstance().setPreferredUrl(jabawsUrl);
           System.out.println(
                   "CMD [-jabaws " + jabawsUrl + "] executed successfully!");
         } catch (MalformedURLException e)
@@ -331,7 +368,8 @@ public class Jalview
       }
 
     }
-    String defs = aparser.getValue("setprop");
+    // check for property setting
+    String defs = aparser.getValue(ArgsParser.SETPROP);
     while (defs != null)
     {
       int p = defs.indexOf('=');
@@ -342,17 +380,12 @@ public class Jalview
       else
       {
         System.out.println("Executing setprop argument: " + defs);
-        if (Platform.isJS())
+        if (isJS)
         {
-          Cache.setProperty(defs.substring(0,p), defs.substring(p+1));
+          Cache.setProperty(defs.substring(0, p), defs.substring(p + 1));
         }
       }
-      defs = aparser.getValue("setprop");
-    }
-    if (System.getProperty("java.awt.headless") != null
-            && System.getProperty("java.awt.headless").equals("true"))
-    {
-      headless = true;
+      defs = aparser.getValue(ArgsParser.SETPROP);
     }
     System.setProperty("http.agent",
             "Jalview Desktop/" + Cache.getDefault("VERSION", "Unknown"));
@@ -371,7 +404,13 @@ public class Jalview
 
     try
     {
-      UIManager.setLookAndFeel(UIManager.getSystemLookAndFeelClassName());
+      if (!isJS && Platform.isWin())
+      {
+        UIManager.setLookAndFeel(
+                headless ? "javax.swing.plaf.metal.MetalLookAndFeel"
+                        : UIManager.getSystemLookAndFeelClassName());
+        // UIManager.setLookAndFeel(UIManager.getSystemLookAndFeelClassName());
+      }
     } catch (Exception ex)
     {
       System.err.println("Unexpected Look and Feel Exception");
@@ -416,31 +455,35 @@ public class Jalview
     }
 
     /*
-     * configure 'full' SO model if preferences say to, else use the default (full SO)
-     * - as JS currently doesn't have OBO parsing, it must use 'Lite' version
+     * configure 'full' SO model if preferences say to, 
+     * else use the default (SO Lite)
      */
-    boolean soDefault = !Platform.isJS();
-    if (Cache.getDefault("USE_FULL_SO", soDefault))
+    if (Cache.getDefault(Preferences.USE_FULL_SO, false))
     {
-      SequenceOntologyFactory.setInstance(new SequenceOntology());
+      SequenceOntologyFactory.setSequenceOntology(new SequenceOntology());
     }
 
-    if (!headless)
+    if (headless)
     {
-      desktop = new Desktop();
-      desktop.setInBatchMode(true); // indicate we are starting up
+      // If this is not tested, then
 
-      try
+      if (aparser.contains(ArgsParser.NOUSAGESTATS))
       {
-        JalviewTaskbar.setTaskbar(this);
-      } catch (Throwable t)
+        System.err.println("CMD [-nousagestats] executed successfully!");
+      }
+      if (aparser.contains(ArgsParser.NOQUESTIONNAIRE))
       {
-        System.out.println("Error setting Taskbar: " + t.getMessage());
+        System.err.println("CMD [-noquestionnaire] executed successfully!");
       }
 
+    }
+    else
+    {
+      desktop = Desktop.getInstance();
+      desktop.setInBatchMode(true); // indicate we are starting up
       desktop.setVisible(true);
 
-      if (!Platform.isJS())
+      if (!isJS)
       /**
        * Java only
        * 
@@ -448,7 +491,7 @@ public class Jalview
        */
       {
         desktop.startServiceDiscovery();
-        if (!aparser.contains("nousagestats"))
+        if (!aparser.contains(ArgsParser.NOUSAGESTATS))
         {
           startUsageStats(desktop);
         }
@@ -457,9 +500,9 @@ public class Jalview
           System.err.println("CMD [-nousagestats] executed successfully!");
         }
 
-        if (!aparser.contains("noquestionnaire"))
+        if (!aparser.contains(ArgsParser.NOQUESTIONNAIRE))
         {
-          String url = aparser.getValue("questionnaire");
+          String url = aparser.getValue(ArgsParser.QUESTIONNAIRE);
           if (url != null)
           {
             // Start the desktop questionnaire prompter with the specified
@@ -471,7 +514,7 @@ public class Jalview
           }
           else
           {
-            if (Cache.getProperty("NOQUESTIONNAIRES") == null)
+            if (Cache.getProperty(Preferences.NOQUESTIONNAIRES) == null)
             {
               // Start the desktop questionnaire prompter with the specified
               // questionnaire
@@ -491,7 +534,7 @@ public class Jalview
                   .println("CMD [-noquestionnaire] executed successfully!");
         }
 
-        if (!aparser.contains("nonews"))
+        if (!aparser.contains(ArgsParser.NONEWS))
         {
           desktop.checkForNews();
         }
@@ -500,45 +543,85 @@ public class Jalview
       }
     }
 
-    // Move any new getdown-launcher-new.jar into place over old
-    // getdown-launcher.jar
-    String appdirString = System.getProperty("getdownappdir");
-    if (appdirString != null && appdirString.length() > 0)
+    parseArguments(aparser, true);
+    System.err.println(TERMINATOR_LINE);
+  }
+
+  /**
+   * Allow an outside entity to initiate the second half of argument parsing
+   * (only).
+   * 
+   * @param args
+   * @return null is good
+   */
+  @Override
+  public Object parseArguments(String[] args)
+  {
+
+    try
     {
-      final File appdir = new File(appdirString);
-      new Thread()
-      {
-        @Override
-        public void run()
-        {
-          LaunchUtil.upgradeGetdown(
-                  new File(appdir, "getdown-launcher-old.jar"),
-                  new File(appdir, "getdown-launcher.jar"),
-                  new File(appdir, "getdown-launcher-new.jar"));
-        }
-      }.start();
+      ArgsParser aparser = new ArgsParser(args);
+      return parseArguments(aparser, false);
+    } catch (Throwable t)
+    {
+      return t;
     }
+  }
 
-    String file = null, data = null;
-    FileFormatI format = null;
-    DataSourceType protocol = null;
-    FileLoader fileLoader = new FileLoader(!headless);
+  /**
+   * 
+   * @param aparser
+   * @param isStartup
+   * @return
+   */
+  private Object parseArguments(ArgsParser aparser, boolean isStartup)
+  {
+    boolean isJS = Platform.isJS();
 
-    String groovyscript = null; // script to execute after all loading is
+    Desktop desktop = (headless ? null : Desktop.getInstance());
+    // script to execute after all loading is
     // completed one way or another
     // extract groovy argument and execute if necessary
-    groovyscript = aparser.getValue("groovy", true);
-    file = aparser.getValue("open", true);
+    String groovyscript = (isJS ? null
+            : aparser.getValue(ArgsParser.GROOVY, true));
+    String file = aparser.getValue(ArgsParser.OPEN, true);
+    // BH this here to allow split frame; not working as of 5/17/2019
+    String file2 = aparser.getValue(ArgsParser.OPEN2, true);
+    String fileFormat = (isJavaAppletTag
+            ? aparser.getAppletValue("format", null)
+            : null);
+    FileFormatI format = null;
+    DataSourceType protocol = null;
 
     if (file == null && desktop == null)
     {
       System.out.println("No files to open!");
       System.exit(1);
     }
-    long progress = -1;
+    boolean haveImport = false;// checkStartVamas(aparser);
     // Finally, deal with the remaining input data.
+    long progress = -1;
+    if (file == null && isJavaAppletTag)
+    {
+      // Maybe the sequences are added as parameters
+      StringBuffer data = new StringBuffer("PASTE");
+      int i = 1;
+      while ((file = aparser.getAppletValue("sequence" + i, null)) != null)
+      {
+        data.append(file.toString() + "\n");
+        i++;
+      }
+      if (data.length() > 5)
+      {
+        file = data.toString();
+      }
+    }
+
+    String data;
+
     if (file != null)
     {
+
       if (!headless)
       {
         desktop.setProgressBar(
@@ -546,14 +629,14 @@ public class Jalview
                         .getString("status.processing_commandline_args"),
                 progress = System.currentTimeMillis());
       }
-      System.out.println("CMD [-open " + file + "] executed successfully!");
 
-      if (!Platform.isJS())
-        /**
-         * ignore in JavaScript -- can't just file existence - could load it?
-         * 
-         * @j2sIgnore
-         */
+      if (!isJS)
+      /**
+       * ignore in JavaScript -- can't just check file existence - could load
+       * it?
+       * 
+       * @j2sIgnore
+       */
       {
         if (!file.startsWith("http://") && !file.startsWith("https://"))
         // BH 2019 added https check for Java
@@ -569,26 +652,88 @@ public class Jalview
         }
       }
 
-        protocol = AppletFormatAdapter.checkProtocol(file);
+      protocol = AppletFormatAdapter.checkProtocol(file);
 
       try
       {
-        format = new IdentifyFile().identify(file, protocol);
+        format = (isJavaAppletTag && fileFormat != null
+                ? FileFormats.getInstance().forName(fileFormat)
+                : null);
+        if (format == null)
+        {
+          format = new IdentifyFile().identify(file, protocol);
+        }
       } catch (FileFormatException e1)
       {
         // TODO ?
       }
 
-      AlignFrame af = fileLoader.LoadFileWaitTillLoaded(file, protocol,
-              format);
+      if (aparser.contains(ArgsParser.NOMENUBAR))
+      {
+        noMenuBar = true;
+        System.out.println("CMD [nomenu] executed successfully!");
+      }
+
+      if (aparser.contains(ArgsParser.NOSTATUS))
+      {
+        noStatus = true;
+        System.out.println("CMD [nostatus] executed successfully!");
+      }
+
+      if (aparser.contains(ArgsParser.NOANNOTATION)
+              || aparser.contains(ArgsParser.NOANNOTATION2))
+      {
+        noAnnotation = true;
+        System.out.println("CMD no-annotation executed successfully!");
+      }
+      if (aparser.contains(ArgsParser.NOCALCULATION))
+      {
+        noCalculation = true;
+        System.out.println("CMD [nocalculation] executed successfully!");
+      }
+
+      AlignFrame af = new FileLoader(!headless).LoadFileWaitTillLoaded(file,
+              protocol, format);
       if (af == null)
       {
         System.out.println("error");
       }
       else
       {
+        System.out
+                .println("CMD [-open " + file + "] executed successfully!");
+        if (file2 != null)
+        {
+          protocol = AppletFormatAdapter.checkProtocol(file2);
+          try
+          {
+            format = new IdentifyFile().identify(file2, protocol);
+          } catch (FileFormatException e1)
+          {
+            // TODO ?
+          }
+          AlignFrame af2 = new FileLoader(!headless)
+                  .LoadFileWaitTillLoaded(file2, protocol, format);
+          if (af2 == null)
+          {
+            System.out.println("error");
+          }
+          else
+          {
+            AlignViewport.openLinkedAlignmentAs(af,
+                    af.getViewport().getAlignment(),
+                    af2.getViewport().getAlignment(), "",
+                    AlignViewport.SPLIT_FRAME);
+            System.out.println(
+                    "CMD [-open2 " + file2 + "] executed successfully!");
+          }
+        }
+
         setCurrentAlignFrame(af);
-        data = aparser.getValue("colour", true);
+
+        // TODO: file2 How to implement file2 for the applet spit screen?
+
+        data = aparser.getValue(ArgsParser.COLOUR, true);
         if (data != null)
         {
           data.replaceAll("%20", " ");
@@ -605,7 +750,7 @@ public class Jalview
         }
 
         // Must maintain ability to use the groups flag
-        data = aparser.getValue("groups", true);
+        data = aparser.getValue(ArgsParser.GROUPS, true);
         if (data != null)
         {
           af.parseFeaturesFile(data,
@@ -614,7 +759,7 @@ public class Jalview
           System.out.println(
                   "CMD groups[-" + data + "]  executed successfully!");
         }
-        data = aparser.getValue("features", true);
+        data = aparser.getValue(ArgsParser.FEATURES, true);
         if (data != null)
         {
           af.parseFeaturesFile(data,
@@ -624,7 +769,7 @@ public class Jalview
                   "CMD [-features " + data + "]  executed successfully!");
         }
 
-        data = aparser.getValue("annotations", true);
+        data = aparser.getValue(ArgsParser.ANNOTATIONS, true);
         if (data != null)
         {
           af.loadJalviewDataFile(data, null, null, null);
@@ -632,8 +777,15 @@ public class Jalview
           System.out.println(
                   "CMD [-annotations " + data + "] executed successfully!");
         }
+
+        if (aparser.contains(ArgsParser.SHOWOVERVIEW))
+        {
+          af.overviewMenuItem_actionPerformed(null);
+          System.out.println("CMD [showoverview] executed successfully!");
+        }
+
         // set or clear the sortbytree flag.
-        if (aparser.contains("sortbytree"))
+        if (aparser.contains(ArgsParser.SORTBYTREE))
         {
           af.getViewport().setSortByTree(true);
           if (af.getViewport().getSortByTree())
@@ -641,24 +793,48 @@ public class Jalview
             System.out.println("CMD [-sortbytree] executed successfully!");
           }
         }
-        if (aparser.contains("no-annotation"))
+
+        boolean doUpdateAnnotation = false;
+
+        /**
+         * we do this earlier in JalviewJS because of a complication with
+         * SHOWOVERVIEW
+         * 
+         * For now, just fixing this in JalviewJS.
+         *
+         * 
+         * @j2sIgnore
+         * 
+         */
         {
-          af.getViewport().setShowAnnotation(false);
-          if (!af.getViewport().isShowAnnotation())
+          if (aparser.contains(ArgsParser.NOANNOTATION)
+                  || aparser.contains(ArgsParser.NOANNOTATION2))
           {
-            System.out.println("CMD no-annotation executed successfully!");
+            af.getViewport().setShowAnnotation(false);
+            if (!af.getViewport().isShowAnnotation())
+            {
+              doUpdateAnnotation = true;
+              System.out
+                      .println("CMD no-annotation executed successfully!");
+            }
           }
         }
-        if (aparser.contains("nosortbytree"))
+        if (aparser.contains(ArgsParser.NOSORTBYTREE))
         {
           af.getViewport().setSortByTree(false);
           if (!af.getViewport().getSortByTree())
           {
+            doUpdateAnnotation = true;
             System.out
                     .println("CMD [-nosortbytree] executed successfully!");
           }
         }
-        data = aparser.getValue("tree", true);
+        if (doUpdateAnnotation)
+        { // BH 2019.07.24
+          af.setMenusForViewport();
+          af.alignPanel.updateLayout();
+        }
+        data = aparser.getValue(ArgsParser.TREE, true);
         if (data != null)
         {
           try
@@ -678,97 +854,30 @@ public class Jalview
         // TODO - load PDB structure(s) to alignment JAL-629
         // (associate with identical sequence in alignment, or a specified
         // sequence)
-        if (groovyscript != null)
+        if (isJavaAppletTag)
         {
-          // Execute the groovy script after we've done all the rendering stuff
-          // and before any images or figures are generated.
-          System.out.println("Executing script " + groovyscript);
-          executeGroovyScript(groovyscript, af);
-          System.out.println("CMD groovy[" + groovyscript
-                  + "] executed successfully!");
-          groovyscript = null;
+          loadAppletParams(aparser, af);
         }
-        String imageName = "unnamed.png";
-        while (aparser.getSize() > 1)
+        else if (!isJS)
+        /**
+         * Java only
+         * 
+         * @j2sIgnore
+         */
         {
-          String outputFormat = aparser.nextValue();
-          file = aparser.nextValue();
-
-          if (outputFormat.equalsIgnoreCase("png"))
-          {
-            af.createPNG(new File(file));
-            imageName = (new File(file)).getName();
-            System.out.println("Creating PNG image: " + file);
-            continue;
-          }
-          else if (outputFormat.equalsIgnoreCase("svg"))
-          {
-            File imageFile = new File(file);
-            imageName = imageFile.getName();
-            af.createSVG(imageFile);
-            System.out.println("Creating SVG image: " + file);
-            continue;
-          }
-          else if (outputFormat.equalsIgnoreCase("html"))
-          {
-            File imageFile = new File(file);
-            imageName = imageFile.getName();
-            HtmlSvgOutput htmlSVG = new HtmlSvgOutput(af.alignPanel);
-            htmlSVG.exportHTML(file);
-
-            System.out.println("Creating HTML image: " + file);
-            continue;
-          }
-          else if (outputFormat.equalsIgnoreCase("biojsmsa"))
-          {
-            if (file == null)
-            {
-              System.err.println("The output html file must not be null");
-              return;
-            }
-            try
-            {
-              BioJsHTMLOutput.refreshVersionInfo(
-                      BioJsHTMLOutput.BJS_TEMPLATES_LOCAL_DIRECTORY);
-            } catch (URISyntaxException e)
-            {
-              e.printStackTrace();
-            }
-            BioJsHTMLOutput bjs = new BioJsHTMLOutput(af.alignPanel);
-            bjs.exportHTML(file);
-            System.out
-                    .println("Creating BioJS MSA Viwer HTML file: " + file);
-            continue;
-          }
-          else if (outputFormat.equalsIgnoreCase("imgMap"))
-          {
-            af.createImageMap(new File(file), imageName);
-            System.out.println("Creating image map: " + file);
-            continue;
-          }
-          else if (outputFormat.equalsIgnoreCase("eps"))
-          {
-            File outputFile = new File(file);
-            System.out.println(
-                    "Creating EPS file: " + outputFile.getAbsolutePath());
-            af.createEPS(outputFile);
-            continue;
-          }
-
-          af.saveAlignment(file, format);
-          if (af.isSaveAlignmentSuccessful())
-          {
-            System.out.println("Written alignment in " + format
-                    + " format to " + file);
-          }
-          else
+          if (groovyscript != null)
           {
-            System.out.println("Error writing file " + file + " in "
-                    + format + " format!!");
+            // Execute the groovy script after we've done all the rendering
+            // stuff
+            // and before any images or figures are generated.
+            System.out.println("Executing script " + groovyscript);
+            executeGroovyScript(groovyscript, af);
+            System.out.println("CMD groovy[" + groovyscript
+                    + "] executed successfully!");
+            groovyscript = null;
           }
-
         }
-
+        createOutputFiles(aparser, af, format);
         while (aparser.getSize() > 0)
         {
           System.out.println("Unknown arg: " + aparser.nextValue());
@@ -780,16 +889,16 @@ public class Jalview
     // And the user
     // ////////////////////
 
-    if (!Platform.isJS() && !headless && file == null
-            && Cache.getDefault("SHOW_STARTUP_FILE", true))
+    if (!isJS && !headless && file == null && !haveImport
+            && jalview.bin.Cache.getDefault("SHOW_STARTUP_FILE", true))
     /**
      * Java only
      * 
      * @j2sIgnore
      */
     {
-      file = Cache.getDefault("STARTUP_FILE",
-              Cache.getDefault("www.jalview.org",
+      file = jalview.bin.Cache.getDefault("STARTUP_FILE",
+              jalview.bin.Cache.getDefault("www.jalview.org",
                       "http://www.jalview.org")
                       + "/examples/exampleFile_2_7.jar");
       if (file.equals(
@@ -798,7 +907,7 @@ public class Jalview
         // hardwire upgrade of the startup file
         file.replace("_2_3.jar", "_2_7.jar");
         // and remove the stale setting
-        Cache.removeProperty("STARTUP_FILE");
+        jalview.bin.Cache.removeProperty("STARTUP_FILE");
       }
 
       protocol = DataSourceType.FILE;
@@ -823,8 +932,8 @@ public class Jalview
         }
       }
 
-      startUpAlframe = fileLoader.LoadFileWaitTillLoaded(file, protocol,
-              format);
+      startUpAlframe = new FileLoader(!headless)
+              .LoadFileWaitTillLoaded(file, protocol, format);
       // extract groovy arguments before anything else.
     }
 
@@ -852,34 +961,140 @@ public class Jalview
       }
       desktop.setInBatchMode(false);
     }
+
+    return null;
   }
 
-  private static void showUsage()
+  /**
+   * Writes an output file for each format (if any) specified in the
+   * command-line arguments. Supported formats are currently
+   * <ul>
+   * <li>png</li>
+   * <li>svg</li>
+   * <li>html</li>
+   * <li>biojsmsa</li>
+   * <li>imgMap</li>
+   * <li>eps</li>
+   * </ul>
+   * A format parameter should be followed by a parameter specifying the output
+   * file name. {@code imgMap} parameters should follow those for the
+   * corresponding alignment image output.
+   * 
+   * @param aparser
+   * @param af
+   * @param format
+   */
+  private void createOutputFiles(ArgsParser aparser, AlignFrame af,
+          FileFormatI format)
   {
-    System.out.println(
-            "Usage: jalview -open [FILE] [OUTPUT_FORMAT] [OUTPUT_FILE]\n\n"
-                    + "-nodisplay\tRun Jalview without User Interface.\n"
-                    + "-props FILE\tUse the given Jalview properties file instead of users default.\n"
-                    + "-colour COLOURSCHEME\tThe colourscheme to be applied to the alignment\n"
-                    + "-annotations FILE\tAdd precalculated annotations to the alignment.\n"
-                    + "-tree FILE\tLoad the given newick format tree file onto the alignment\n"
-                    + "-features FILE\tUse the given file to mark features on the alignment.\n"
-                    + "-fasta FILE\tCreate alignment file FILE in Fasta format.\n"
-                    + "-clustal FILE\tCreate alignment file FILE in Clustal format.\n"
-                    + "-pfam FILE\tCreate alignment file FILE in PFAM format.\n"
-                    + "-msf FILE\tCreate alignment file FILE in MSF format.\n"
-                    + "-pileup FILE\tCreate alignment file FILE in Pileup format\n"
-                    + "-pir FILE\tCreate alignment file FILE in PIR format.\n"
-                    + "-blc FILE\tCreate alignment file FILE in BLC format.\n"
-                    + "-json FILE\tCreate alignment file FILE in JSON format.\n"
-                    + "-jalview FILE\tCreate alignment file FILE in Jalview format.\n"
-                    + "-png FILE\tCreate PNG image FILE from alignment.\n"
-                    + "-svg FILE\tCreate SVG image FILE from alignment.\n"
-                    + "-html FILE\tCreate HTML file from alignment.\n"
-                    + "-biojsMSA FILE\tCreate BioJS MSA Viewer HTML file from alignment.\n"
-                    + "-imgMap FILE\tCreate HTML file FILE with image map of PNG image.\n"
-                    + "-eps FILE\tCreate EPS file FILE from alignment.\n"
-                    + "-questionnaire URL\tQueries the given URL for information about any Jalview user questionnaires.\n"
+    String imageName = "unnamed.png";
+    while (aparser.getSize() > 1)
+    {
+      String outputFormat = aparser.nextValue();
+      String file = aparser.nextValue();
+      // System.out.println("format " + outputFormat);
+
+      if (outputFormat.equalsIgnoreCase("png"))
+      {
+        af.createPNG(new File(file));
+        imageName = (new File(file)).getName();
+        System.out.println("Creating PNG image: " + file);
+        continue;
+      }
+      else if (outputFormat.equalsIgnoreCase("svg"))
+      {
+        File imageFile = new File(file);
+        imageName = imageFile.getName();
+        af.createSVG(imageFile);
+        System.out.println("Creating SVG image: " + file);
+        continue;
+      }
+      else if (outputFormat.equalsIgnoreCase("html"))
+      {
+        File imageFile = new File(file);
+        imageName = imageFile.getName();
+        HtmlSvgOutput htmlSVG = new HtmlSvgOutput(af.alignPanel);
+        htmlSVG.exportHTML(file);
+
+        System.out.println("Creating HTML image: " + file);
+        continue;
+      }
+      else if (outputFormat.equalsIgnoreCase("biojsmsa"))
+      {
+        if (file == null)
+        {
+          System.err.println("The output html file must not be null");
+          return;
+        }
+        try
+        {
+          BioJsHTMLOutput.refreshVersionInfo(
+                  BioJsHTMLOutput.BJS_TEMPLATES_LOCAL_DIRECTORY);
+        } catch (URISyntaxException e)
+        {
+          e.printStackTrace();
+        }
+        BioJsHTMLOutput bjs = new BioJsHTMLOutput(af.alignPanel);
+        bjs.exportHTML(file);
+        System.out.println("Creating BioJS MSA Viwer HTML file: " + file);
+        continue;
+      }
+      else if (outputFormat.equalsIgnoreCase("imgMap"))
+      {
+        af.createImageMap(new File(file), imageName);
+        System.out.println("Creating image map: " + file);
+        continue;
+      }
+      else if (outputFormat.equalsIgnoreCase("eps"))
+      {
+        File outputFile = new File(file);
+        System.out.println(
+                "Creating EPS file: " + outputFile.getAbsolutePath());
+        af.createEPS(outputFile);
+        continue;
+      }
+
+      af.saveAlignment(file, format);
+      if (af.isSaveAlignmentSuccessful())
+      {
+        System.out.println(
+                "Written alignment in " + format + " format to " + file);
+      }
+      else
+      {
+        System.out.println("Error writing file " + file + " in " + format
+                + " format!!");
+      }
+
+    }
+  }
+
+  private static void showUsage()
+  {
+    System.out.println(
+            "Usage: jalview -open [FILE] [OUTPUT_FORMAT] [OUTPUT_FILE]\n\n"
+                    + "-nodisplay\tRun Jalview without User Interface.\n"
+                    + "-props FILE\tUse the given Jalview properties file instead of users default.\n"
+                    + "-colour COLOURSCHEME\tThe colourscheme to be applied to the alignment\n"
+                    + "-annotations FILE\tAdd precalculated annotations to the alignment.\n"
+                    + "-tree FILE\tLoad the given newick format tree file onto the alignment\n"
+                    + "-features FILE\tUse the given file to mark features on the alignment.\n"
+                    + "-fasta FILE\tCreate alignment file FILE in Fasta format.\n"
+                    + "-clustal FILE\tCreate alignment file FILE in Clustal format.\n"
+                    + "-pfam FILE\tCreate alignment file FILE in PFAM format.\n"
+                    + "-msf FILE\tCreate alignment file FILE in MSF format.\n"
+                    + "-pileup FILE\tCreate alignment file FILE in Pileup format\n"
+                    + "-pir FILE\tCreate alignment file FILE in PIR format.\n"
+                    + "-blc FILE\tCreate alignment file FILE in BLC format.\n"
+                    + "-json FILE\tCreate alignment file FILE in JSON format.\n"
+                    + "-jalview FILE\tCreate alignment file FILE in Jalview format.\n"
+                    + "-png FILE\tCreate PNG image FILE from alignment.\n"
+                    + "-svg FILE\tCreate SVG image FILE from alignment.\n"
+                    + "-html FILE\tCreate HTML file from alignment.\n"
+                    + "-biojsMSA FILE\tCreate BioJS MSA Viewer HTML file from alignment.\n"
+                    + "-imgMap FILE\tCreate HTML file FILE with image map of PNG image.\n"
+                    + "-eps FILE\tCreate EPS file FILE from alignment.\n"
+                    + "-questionnaire URL\tQueries the given URL for information about any Jalview user questionnaires.\n"
                     + "-noquestionnaire\tTurn off questionnaire check.\n"
                     + "-nonews\tTurn off check for Jalview news.\n"
                     + "-nousagestats\tTurn off google analytics tracking for this session.\n"
@@ -891,6 +1106,10 @@ public class Jalview
                     // passed in correctly)"
                     + "-jabaws URL\tSpecify URL for Jabaws services (e.g. for a local installation).\n"
                     + "-fetchfrom nickname\tQuery nickname for features for the alignments and display them.\n"
+                    // +
+                    // "-vdoc vamsas-document\tImport vamsas document into new
+                    // session or join existing session with same URN\n"
+                    // + "-vses vamsas-session\tJoin session with given URN\n"
                     + "-groovy FILE\tExecute groovy script in FILE, after all other arguments have been processed (if FILE is the text 'STDIN' then the file will be read from STDIN)\n"
                     + "\n~Read documentation in Application or visit http://www.jalview.org for description of Features and Annotations file~\n\n");
   }
@@ -900,8 +1119,9 @@ public class Jalview
     /**
      * start a User Config prompt asking if we can log usage statistics.
      */
-    PromptUserConfig prompter = new PromptUserConfig(Desktop.desktop,
-            "USAGESTATS", "Jalview Usage Statistics",
+    PromptUserConfig prompter = new PromptUserConfig(
+            Desktop.getDesktopPane(), "USAGESTATS",
+            "Jalview Usage Statistics",
             "Do you want to help make Jalview better by enabling "
                     + "the collection of usage statistics with Google Analytics ?"
                     + "\n\n(you can enable or disable usage tracking in the preferences)",
@@ -930,10 +1150,10 @@ public class Jalview
    * Locate the given string as a file and pass it to the groovy interpreter.
    * 
    * @param groovyscript
-   *                         the script to execute
+   *          the script to execute
    * @param jalviewContext
-   *                         the Jalview Desktop object passed in to the groovy
-   *                         binding as the 'Jalview' object.
+   *          the Jalview Desktop object passed in to the groovy binding as the
+   *          'Jalview' object.
    */
   private void executeGroovyScript(String groovyscript, AlignFrame af)
   {
@@ -1020,7 +1240,7 @@ public class Jalview
     }
     try
     {
-      Map<String, java.lang.Object> vbinding = new HashMap<>();
+      Map<String, Object> vbinding = new HashMap<>();
       vbinding.put("Jalview", this);
       if (af != null)
       {
@@ -1044,16 +1264,6 @@ public class Jalview
     }
   }
 
-  public static boolean isHeadlessMode()
-  {
-    String isheadless = System.getProperty("java.awt.headless");
-    if (isheadless != null && isheadless.equalsIgnoreCase("true"))
-    {
-      return true;
-    }
-    return false;
-  }
-
   public AlignFrame[] getAlignFrames()
   {
     return desktop == null ? new AlignFrame[] { getCurrentAlignFrame() }
@@ -1062,11 +1272,17 @@ public class Jalview
   }
 
   /**
-   * Quit method delegates to Desktop.quit - unless running in headless mode when
-   * it just ends the JVM
+   * Quit method delegates to Desktop.quit - unless running in headless mode
+   * when it just ends the JVM
    */
   public void quit()
   {
+    if (jsFunctionExec != null)
+    {
+      jsFunctionExec.tidyUp();
+      jsFunctionExec = null;
+    }
+
     if (desktop != null)
     {
       desktop.quit();
@@ -1077,13 +1293,884 @@ public class Jalview
     }
   }
 
-  public static AlignFrame getCurrentAlignFrame()
+  /**
+   * Handle all JalviewLite applet parameters
+   * 
+   * @param aparser
+   * @param af
+   */
+  private void loadAppletParams(ArgsParser aparser, AlignFrame af)
+  {
+    JalviewApp app = new JalviewApp()
+    {
+
+      // TODO BH 2019
+      //
+      // These are methods that are in JalviewLite that various classes call
+      // but are not in JalviewLiteJsApi. Or, even if they are, other classes
+      // call
+      // them to JalviewLite directly. Some may not be necessary, but they have
+      // to
+      // be at least mentioned here, or the classes calling them should
+      // reference
+      // JalviewLite itself.
+
+      private boolean alignPDBStructures; // From JalviewLite; not implemented
+
+      private Hashtable<String, Hashtable<String, String[]>> jsmessages;
+
+      private Hashtable<String, int[]> jshashes;
+
+      @Override
+      public String getParameter(String name)
+      {
+        return aparser.getAppletValue(name, null);
+      }
+
+      @Override
+      public boolean getDefaultParameter(String name, boolean def)
+      {
+        String stn;
+        return ((stn = getParameter(name)) == null ? def
+                : "true".equalsIgnoreCase(stn));
+      }
+
+      /**
+       * Get the applet-like document base even though this is an application.
+       */
+      @Override
+      public URL getDocumentBase()
+      {
+        return Platform.getDocumentBase();
+      }
+
+      /**
+       * Get the applet-like code base even though this is an application.
+       */
+      @Override
+      public URL getCodeBase()
+      {
+        return Platform.getCodeBase();
+      }
+
+      @Override
+      public AlignViewportI getViewport()
+      {
+        return af.getViewport();
+      }
+
+      /**
+       * features
+       * 
+       */
+      @Override
+      public boolean parseFeaturesFile(String filename,
+              DataSourceType protocol)
+      {
+        return af.parseFeaturesFile(filename, protocol);
+      }
+
+      /**
+       * scorefile
+       * 
+       */
+      @Override
+      public boolean loadScoreFile(String sScoreFile) throws IOException
+      {
+        af.loadJalviewDataFile(sScoreFile, null, null, null);
+        return true;
+      }
+
+      /**
+       * annotations, jpredfile, jnetfile
+       * 
+       */
+      @Override
+      public void updateForAnnotations()
+      {
+        af.updateForAnnotations();
+      }
+
+      @Override
+      public void loadTree(NewickFile fin, String treeFile)
+              throws IOException
+      {
+        // n/a -- already done by standard Jalview command line processing
+      }
+
+      @Override
+      public void setAlignPdbStructures(boolean defaultParameter)
+      {
+        alignPDBStructures = true;
+      }
+
+      @Override
+      public void newStructureView(PDBEntry pdb, SequenceI[] seqs,
+              String[] chains, DataSourceType protocol)
+      {
+        StructureViewer.launchStructureViewer(af.alignPanel, pdb, seqs);
+      }
+
+      @Override
+      public void setFeatureGroupState(String[] groups, boolean state)
+      {
+        af.setFeatureGroupState(groups, state);
+      }
+
+      @Override
+      public void alignedStructureView(PDBEntry[] pdb, SequenceI[][] seqs,
+              String[][] chains, String[] protocols)
+      {
+        System.err.println(
+                "Jalview applet interface alignedStructureView not implemented");
+      }
+
+      @Override
+      public void newFeatureSettings()
+      {
+        System.err.println(
+                "Jalview applet interface newFeatureSettings not implemented");
+      }
+
+      private Vector<Runnable> jsExecQueue;
+
+      @Override
+      public Vector<Runnable> getJsExecQueue(JSFunctionExec exec)
+      {
+        jsFunctionExec = exec;
+        return (jsExecQueue == null ? (jsExecQueue = new Vector<>())
+                : jsExecQueue);
+      }
+
+      @Override
+      public AppletContext getAppletContext()
+      {
+        // TODO Auto-generated method stub
+        return null;
+      }
+
+      @Override
+      public boolean isJsfallbackEnabled()
+      {
+        // TODO Auto-generated method stub
+        return false;
+      }
+
+      @Override
+      public JSObject getJSObject()
+      {
+        // TODO Auto-generated method stub
+        return null;
+      }
+
+      @Override
+      public StructureSelectionManagerProvider getStructureSelectionManagerProvider()
+      {
+        // TODO Q: what exactly is this? BH
+        return null;
+      }
+
+      @Override
+      public void updateColoursFromMouseOver(Object source,
+              MouseOverStructureListener mouseOverStructureListener)
+      {
+        // TODO Auto-generated method stub
+
+      }
+
+      @Override
+      public Object[] getSelectionForListener(SequenceGroup seqsel,
+              ColumnSelection colsel, HiddenColumns hidden,
+              SelectionSource source, Object alignFrame)
+      {
+        return appLoader.getSelectionForListener(getCurrentAlignFrame(),
+                seqsel, colsel, hidden, source, alignFrame);
+      }
+
+      @Override
+      public String arrayToSeparatorList(String[] array)
+      {
+        return appLoader.arrayToSeparatorList(array);
+      }
+
+      @Override
+      public Hashtable<String, int[]> getJSHashes()
+      {
+        return (jshashes == null ? (jshashes = new Hashtable<>())
+                : jshashes);
+      }
+
+      @Override
+      public Hashtable<String, Hashtable<String, String[]>> getJSMessages()
+      {
+        return (jsmessages == null ? (jsmessages = new Hashtable<>())
+                : jsmessages);
+      }
+
+      @Override
+      public Object getFrameForSource(VamsasSource source)
+      {
+        if (source != null)
+        {
+          AlignFrame af;
+          if (source instanceof jalview.gui.AlignViewport
+                  && source == (af = getCurrentAlignFrame()).getViewport())
+          {
+            // should be valid if it just generated an event!
+            return af;
+          }
+          // TODO: ensure that if '_af' is specified along with a handler
+          // function, then only events from that alignFrame are sent to that
+          // function
+        }
+        return null;
+      }
+
+      @Override
+      public FeatureRenderer getNewFeatureRenderer(AlignViewportI vp)
+      {
+        return new jalview.gui.FeatureRenderer((AlignmentPanel) vp);
+      }
+
+    };
+
+    appLoader = new JalviewAppLoader(true);
+    appLoader.load(app);
+  }
+
+  /**
+   * 
+   * @see jalview.bin.JalviewLiteJsApi#getSelectedSequences()
+   */
+  @Override
+  public String getSelectedSequences()
   {
-    return Jalview.currentAlignFrame;
+    return getSelectedSequencesFrom(getCurrentAlignFrame());
   }
 
-  public static void setCurrentAlignFrame(AlignFrame currentAlignFrame)
+  /**
+   * 
+   * @see jalview.bin.JalviewLiteJsApi#getSelectedSequences(java.lang.String)
+   */
+  @Override
+  public String getSelectedSequences(String sep)
+  {
+    return getSelectedSequencesFrom(getCurrentAlignFrame(), sep);
+  }
+
+  /**
+   * 
+   * @see jalview.bin.JalviewLiteJsApi#getSelectedSequencesFrom(jalview.appletgui
+   *      .AlignFrame)
+   */
+  @Override
+  public String getSelectedSequencesFrom(AlignFrameI alf)
+  {
+    if (alf == null)
+    {
+      alf = getCurrentAlignFrame();
+    }
+    return getSelectedSequencesFrom(alf, null);
+  }
+
+  /**
+   * 
+   * @see jalview.bin.JalviewLiteJsApi#getSelectedSequencesFrom(jalview.appletgui
+   *      .AlignFrame, java.lang.String)
+   */
+  @Override
+  public String getSelectedSequencesFrom(AlignFrameI alf, String sep)
+  {
+    if (alf == null)
+    {
+      alf = getCurrentAlignFrame();
+    }
+    return appLoader.getSelectedSequencesFrom(alf, sep);
+  }
+
+  /**
+   * 
+   * @see jalview.bin.JalviewLiteJsApi#getSelectedSequencesFrom(jalview.appletgui
+   *      .AlignFrame, java.lang.String)
+   */
+  @Override
+  public void highlight(String sequenceId, String position,
+          String alignedPosition)
+  {
+    highlightIn(null, sequenceId, position,
+            alignedPosition);
+  }
+
+  @Override
+  public void highlightIn(AlignFrameI alf, String sequenceId,
+          String position, String alignedPosition)
+  {
+    if (alf == null)
+    {
+      alf = getCurrentAlignFrame();
+    }
+    appLoader.highlightIn(alf, sequenceId, position, alignedPosition);
+  }
+
+  @Override
+  public void select(String sequenceIds, String columns)
+  {
+    selectIn(getCurrentAlignFrame(), sequenceIds, columns, null);
+  }
+
+  @Override
+  public void select(String sequenceIds, String columns, String sep)
+  {
+    selectIn(null, sequenceIds, columns, sep);
+  }
+
+  @Override
+  public void selectIn(AlignFrameI alf, String sequenceIds, String columns)
+  {
+    selectIn(alf, sequenceIds, columns, null);
+  }
+
+  @Override
+  public void selectIn(AlignFrameI alf, String sequenceIds, String columns,
+          String sep)
+  {
+    if (alf == null)
+    {
+      alf = getCurrentAlignFrame();
+    }
+    appLoader.selectIn(alf, sequenceIds, columns, sep);
+  }
+
+  @Override
+  public String getSelectedSequencesAsAlignment(String format,
+          String suffix)
+  {
+    return getSelectedSequencesAsAlignmentFrom(null,
+            format, suffix);
+  }
+
+  @Override
+  public String getSelectedSequencesAsAlignmentFrom(AlignFrameI alf,
+          String format, String sep)
+  {
+    if (alf == null)
+    {
+      alf = getCurrentAlignFrame();
+    }
+    return appLoader.getSelectedSequencesAsAlignmentFrom(alf, format, sep);
+  }
+
+  @Override
+  public String getAlignmentOrder()
+  {
+    return getAlignmentFrom(getCurrentAlignFrame(), null);
+  }
+
+  @Override
+  public String getAlignmentOrderFrom(AlignFrameI alf)
+  {
+    return getAlignmentFrom(alf, null);
+  }
+
+  @Override
+  public String getAlignmentOrderFrom(AlignFrameI alf, String sep)
+  {
+    if (alf == null)
+    {
+      alf = getCurrentAlignFrame();
+    }
+    return appLoader.getAlignmentOrderFrom(alf, sep);
+  }
+
+  @Override
+  public String orderBy(String order, String undoName)
+  {
+    return orderBy(order, undoName, null);
+  }
+
+  @Override
+  public String orderBy(String order, String undoName, String sep)
+  {
+    return orderAlignmentBy(getCurrentAlignFrame(), order, undoName, sep);
+  }
+
+  @Override
+  public String orderAlignmentBy(AlignFrameI alf, String order,
+          String undoName, String sep)
+  {
+    if (alf == null)
+    {
+      alf = getCurrentAlignFrame();
+    }
+    return appLoader.orderAlignmentBy(alf, order, undoName, sep);
+  }
+
+  @Override
+  public String getAlignment(String format)
+  {
+    return getAlignmentFrom(null, format, null);
+  }
+
+  @Override
+  public String getAlignmentFrom(AlignFrameI alf, String format)
+  {
+    return getAlignmentFrom(alf, format, null);
+  }
+
+  @Override
+  public String getAlignment(String format, String suffix)
+  {
+    return getAlignmentFrom(getCurrentAlignFrame(), format, suffix);
+  }
+
+  @Override
+  public String getAlignmentFrom(AlignFrameI alf, String format,
+          String suffix)
+  {
+    return appLoader.getAlignmentFrom(alf, format, suffix);
+  }
+
+  @Override
+  public void loadAnnotation(String annotation)
+  {
+    loadAnnotationFrom(getCurrentAlignFrame(), annotation);
+  }
+
+  @Override
+  public void loadAnnotationFrom(AlignFrameI alf, String annotation)
+  {
+    if (alf == null)
+    {
+      alf = getCurrentAlignFrame();
+    }
+    appLoader.loadAnnotationFrom(alf, annotation);
+  }
+
+  @Override
+  public void loadFeatures(String features, boolean autoenabledisplay)
+  {
+    loadFeaturesFrom(currentAlignFrame, features, autoenabledisplay);
+  }
+
+  @Override
+  public boolean loadFeaturesFrom(AlignFrameI alf, String features,
+          boolean autoenabledisplay)
+  {
+    if (alf == null)
+    {
+      alf = getCurrentAlignFrame();
+    }
+    return appLoader.loadFeaturesFrom(alf, features, autoenabledisplay);
+  }
+
+  @Override
+  public String getFeatures(String format)
+  {
+    return getFeaturesFrom(null, format);
+  }
+
+  @Override
+  public String getFeaturesFrom(AlignFrameI alf, String format)
+  {
+    if (alf == null)
+    {
+      alf = getCurrentAlignFrame();
+    }
+    return appLoader.getFeaturesFrom(alf, format, true, false);
+  }
+
+  @Override
+  public String getAnnotation()
+  {
+    return getAnnotationFrom(null);
+  }
+
+  @Override
+  public String getAnnotationFrom(AlignFrameI alf)
+  {
+    if (alf == null)
+    {
+      alf = getCurrentAlignFrame();
+    }
+    return appLoader.getAnnotationFrom(alf);
+  }
+
+  @Override
+  public AlignFrameI newView()
+  {
+    return newViewFrom(null, null);
+  }
+
+  @Override
+  public AlignFrameI newView(String name)
+  {
+    return newViewFrom(null, name);
+  }
+
+  @Override
+  public AlignFrameI newViewFrom(AlignFrameI alf)
+  {
+    return newViewFrom(alf, null);
+  }
+
+  @Override
+  public AlignFrameI newViewFrom(AlignFrameI alf, String name)
+  {
+    if (alf == null)
+    {
+      alf = getCurrentAlignFrame();
+    }
+    return appLoader.newViewFrom(alf, name);
+  }
+
+  @Override
+  public AlignFrameI loadAlignment(String text, String title)
+  {
+    return appLoader.loadAlignment(text, AlignFrame.DEFAULT_WIDTH,
+            AlignFrame.DEFAULT_HEIGHT, title);
+  }
+
+  @Override
+  public boolean addPdbFile(AlignFrameI alFrame, String sequenceId,
+          String pdbEntryString, String pdbFile)
+  {
+    if (alFrame == null)
+    {
+      alFrame = getCurrentAlignFrame();
+    }
+    return appLoader.addPdbFile(alFrame, sequenceId, pdbEntryString,
+            pdbFile);
+  }
+
+  @Override
+  public void scrollViewToIn(AlignFrameI alf, String topRow,
+          String leftHandColumn)
+  {
+    if (alf == null)
+    {
+      alf = getCurrentAlignFrame();
+    }
+    appLoader.scrollViewToIn(alf, topRow, leftHandColumn);
+  }
+
+  @Override
+  public void scrollViewToRowIn(AlignFrameI alf, String topRow)
+  {
+    if (alf == null)
+    {
+      alf = getCurrentAlignFrame();
+    }
+    appLoader.scrollViewToRowIn(alf, topRow);
+  }
+
+  @Override
+  public void scrollViewToColumnIn(AlignFrameI alf, String leftHandColumn)
+  {
+    if (alf == null)
+    {
+      alf = getCurrentAlignFrame();
+    }
+    appLoader.scrollViewToColumnIn(alf, leftHandColumn);
+  }
+
+  @Override
+  public String getFeatureGroups()
+  {
+    return getFeatureGroupsOn(null);
+  }
+
+  @Override
+  public String getFeatureGroupsOn(AlignFrameI alf)
+  {
+    if (alf == null)
+    {
+      alf = getCurrentAlignFrame();
+    }
+    return appLoader.getFeatureGroupsOn(alf);
+  }
+
+  @Override
+  public String getFeatureGroupsOfState(boolean visible)
+  {
+    return getFeatureGroupsOfStateOn(null, visible);
+  }
+
+  @Override
+  public String getFeatureGroupsOfStateOn(AlignFrameI alf, boolean visible)
+  {
+    if (alf == null)
+    {
+      alf = getCurrentAlignFrame();
+    }
+    return appLoader.getFeatureGroupsOfStateOn(alf, visible);
+  }
+
+  @Override
+  public void setFeatureGroupState(String groups, boolean state)
+  { // JalviewLite API
+    setFeatureGroupStateOn(null, groups, state);
+  }
+
+  @Override
+  public void setFeatureGroupStateOn(AlignFrameI alf, String groups,
+          boolean state)
+  {
+    if (alf == null)
+    {
+      alf = getCurrentAlignFrame();
+    }
+    appLoader.setFeatureGroupStateOn(alf, groups, state);
+  }
+
+  @Override
+  public String getSeparator()
   {
-    Jalview.currentAlignFrame = currentAlignFrame;
+    return appLoader.getSeparator();
   }
-}
+
+  @Override
+  public void setSeparator(String separator)
+  {
+    appLoader.setSeparator(separator);
+  }
+
+  @Override
+  public String getJsMessage(String messageclass, String viewId)
+  {
+    // see http://www.jalview.org/examples/jalviewLiteJs.html
+    return null;
+  }
+
+  /**
+   * Open a new Tree panel on the desktop statically. Params are standard (not
+   * set by Groovy). No dialog is opened.
+   * 
+   * @param af
+   * @param treeType
+   * @param modelName
+   * @return null, or the string "label.you_need_at_least_n_sequences" if number
+   *         of sequences selected is inappropriate
+   */
+  @Override
+  public Object openTreePanel(AlignFrame af, String treeType,
+          String modelName)
+  { // JalviewJS api
+    if (af == null)
+    {
+      af = getCurrentAlignFrame();
+    }
+    return CalculationChooser.openTreePanel(af, treeType, modelName, null);
+  }
+
+  /**
+   * public static method for JalviewJS API to open a PCAPanel without
+   * necessarily using a dialog.
+   * 
+   * @param af
+   * @param modelName
+   * @return the PCAPanel, or the string "label.you_need_at_least_n_sequences"
+   *         if number of sequences selected is inappropriate
+   */
+  @Override
+  public Object openPcaPanel(AlignFrame af, String modelName)
+  {
+    if (af == null)
+    {
+      af = getCurrentAlignFrame();
+    }
+    return CalculationChooser.openPcaPanel(af, modelName, null);
+  }
+
+  @Override
+  public String getSelectedSequencesAsAlignment(String format,
+          boolean suffix)
+  {
+    return getSelectedSequencesAsAlignmentFrom(null,
+            format, suffix);
+  }
+
+  @Override
+  public String getSelectedSequencesAsAlignmentFrom(AlignFrameI alf,
+          String format, boolean suffix)
+  {
+    if (alf == null)
+    {
+      alf = getCurrentAlignFrame();
+    }
+    return appLoader.getSelectedSequencesAsAlignmentFrom(alf, format,
+            "" + suffix);
+  }
+
+  @Override
+  public String arrayToSeparatorList(String[] array)
+  {
+    return appLoader.arrayToSeparatorList(array);
+  }
+
+  @Override
+  public String[] separatorListToArray(String list)
+  {
+    return appLoader.separatorListToArray(list);
+  }
+
+  //// probably not needed in JalviewJS -- From when Jmol and Jalview did not
+  //// have a direct connection?
+
+  @Override
+  public void setMouseoverListener(String listener)
+  {
+    // TODO Auto-generated method stub
+
+  }
+
+  @Override
+  public void setMouseoverListener(AlignFrameI af, String listener)
+  {
+    // TODO Auto-generated method stub
+
+  }
+
+  @Override
+  public void setSelectionListener(String listener)
+  {
+    // TODO Auto-generated method stub
+
+  }
+
+  @Override
+  public void setSelectionListener(AlignFrameI af, String listener)
+  {
+    // TODO Auto-generated method stub
+
+  }
+
+  @Override
+  public void setStructureListener(String listener, String modelSet)
+  {
+    // TODO Auto-generated method stub
+
+  }
+
+  @Override
+  public void removeJavascriptListener(AlignFrameI af, String listener)
+  {
+    // TODO Auto-generated method stub
+
+  }
+
+  @Override
+  public void mouseOverStructure(String pdbResNum, String chain,
+          String pdbfile)
+  {
+    // TODO Auto-generated method stub
+
+  }
+
+  @Override
+  public void showOverview()
+  {
+    currentAlignFrame.overviewMenuItem_actionPerformed(null);
+  }
+
+  public void notifyWorker(AlignCalcWorkerI worker, String status)
+  {
+    // System.out.println("Jalview worker " + worker.getClass().getSimpleName()
+    // + " " + status);
+  }
+
+  /**
+   * flag to allow selected Runnable and Thread processes to run synchronously
+   * 
+   * JAL-3563
+   * 
+   */
+  private static boolean isSynchronous = false;
+
+  /**
+   * Set Jalview to run selected processes synchronously in test and headless
+   * environments.
+   * 
+   * JAL-3563
+   * 
+   * @param b
+   * @author Bob Hanson
+   */
+  public static void setSynchronous(boolean b)
+  {
+    isSynchronous = b;
+  }
+
+  /**
+   * Allows optional synchronous running of a Runnable that would otherwise use
+   * SwingUtilities.invokeLater.
+   * 
+   * JAL-3563
+   * 
+   * @param t
+   * @author Bob Hanson
+   */
+  public static boolean isSynchronous()
+  {
+    return isSynchronous;
+  }
+
+  /**
+   * Allows optional synchronous running of a Runnable that would otherwise use
+   * SwingUtilities.invokeLater.
+   * 
+   * JAL-3563
+   * 
+   * @param t
+   * @author Bob Hanson
+   */
+  public static void execRunnable(Runnable r)
+  {
+    if (isSynchronous())
+    {
+      r.run();
+    }
+    else
+    {
+      SwingUtilities.invokeLater(r);
+    }
+  }
+
+  /**
+   * Allows optional synchronous running of a thread that would otherwise be run
+   * using start().
+   * 
+   * JAL-3563
+   * 
+   * @param t
+   * @author Bob Hanson
+   */
+  public static void execThread(Thread t)
+  {
+    if (isSynchronous())
+    {
+      t.run();
+    }
+    else
+    {
+      t.start();
+    }
+  }
+
+  /**
+   * Get the SwingJS applet ID and combine that with the frameType
+   * 
+   * @param frameType
+   *          "alignment", "desktop", etc., or null
+   * @return
+   */
+  public static String getAppID(String frameType)
+  {
+    String id = Cache.getProperty("Info.j2sAppletID");
+    if (id == null)
+    {
+      id = "jalview";
+    }
+    return id + (frameType == null ? "" : "-" + frameType);
+  }
+
+}
\ No newline at end of file