X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fbin%2FJalview.java;h=402f9bfcdba5ccc23927f06504d9cc9283c402d8;hb=ad16d6cce49a40ea1943431b980b85a6212bb9bf;hp=cc41c534d9899d85b3e4f8b5a6fe0d7723e0ee85;hpb=16d109024847af92482237e43f99b82fd997451a;p=jalview.git

diff --git a/src/jalview/bin/Jalview.java b/src/jalview/bin/Jalview.java
index cc41c53..402f9bf 100755
--- a/src/jalview/bin/Jalview.java
+++ b/src/jalview/bin/Jalview.java
@@ -20,9 +20,15 @@
  */
 package jalview.bin;
 
+import jalview.api.AlignViewportI;
+import jalview.api.JalviewApp;
+import jalview.bin.ApplicationSingletonProvider.ApplicationSingletonI;
+import jalview.datamodel.PDBEntry;
+import jalview.datamodel.SequenceI;
 import jalview.ext.so.SequenceOntology;
 import jalview.gui.AlignFrame;
 import jalview.gui.Desktop;
+import jalview.gui.Preferences;
 import jalview.gui.PromptUserConfig;
 import jalview.io.AppletFormatAdapter;
 import jalview.io.BioJsHTMLOutput;
@@ -60,6 +66,9 @@ import java.security.Policy;
 import java.util.HashMap;
 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.UIManager;
@@ -82,35 +91,75 @@ import groovy.util.GroovyScriptEngine;
  * @author $author$
  * @version $Revision$
  */
-public class Jalview
+public class Jalview implements ApplicationSingletonI
 {
-  /*
-   * singleton instance of this class
-   */
-  private static Jalview instance;
+
+  public static Jalview getInstance()
+  {
+    return (Jalview) ApplicationSingletonProvider
+            .getInstance(Jalview.class);
+  }
+
+  private Jalview()
+  {
+  }
+
+  static
+  {
+    Platform.getURLCommandArguments();
+  }
+
+  private boolean headless;
+
+  public static boolean isHeadlessMode()
+  {
+    return getInstance().headless;
+  }
 
   private Desktop desktop;
 
-  public static AlignFrame currentAlignFrame;
+  private AlignFrame currentAlignFrame;
+
+  public boolean isJavaAppletTag;
+
+  public String appletResourcePath;
+
+  public static AlignFrame getCurrentAlignFrame()
+  {
+    return getInstance().currentAlignFrame;
+  }
+
+  public static void setCurrentAlignFrame(AlignFrame currentAlignFrame)
+  {
+    getInstance().currentAlignFrame = currentAlignFrame;
+  }
 
   static
   {
-    // grab all the rights we can the JVM
-    Policy.setPolicy(new Policy()
+    if (!Platform.isJS())
+    /**
+     * Java only
+     * 
+     * @j2sIgnore
+     */
     {
-      @Override
-      public PermissionCollection getPermissions(CodeSource codesource)
+      // grab all the rights we can for the JVM
+      Policy.setPolicy(new Policy()
       {
-        Permissions perms = new Permissions();
-        perms.add(new AllPermission());
-        return (perms);
-      }
+        @Override
+        public PermissionCollection getPermissions(CodeSource codesource)
+        {
+          Permissions perms = new Permissions();
+          perms.add(new AllPermission());
+          return (perms);
+        }
 
-      @Override
-      public void refresh()
-      {
-      }
-    });
+        @Override
+        public void refresh()
+        {
+        }
+      });
+    }
   }
 
   /**
@@ -172,11 +221,6 @@ public class Jalview
 
   }
 
-  public static Jalview getInstance()
-  {
-    return instance;
-  }
-
   /**
    * main class for Jalview application
    * 
@@ -185,8 +229,48 @@ public class Jalview
    */
   public static void main(String[] args)
   {
-    instance = new Jalview();
-    instance.doMain(args);
+    // setLogging(); // BH - for event debugging in JavaScript
+    getInstance().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");
+    }
+
   }
 
   /**
@@ -194,7 +278,12 @@ public class Jalview
    */
   void doMain(String[] args)
   {
-    System.setSecurityManager(null);
+
+    if (!Platform.isJS())
+    {
+      System.setSecurityManager(null);
+    }
+
     System.out
             .println("Java version: " + System.getProperty("java.version"));
     System.out.println(System.getProperty("os.arch") + " "
@@ -202,45 +291,68 @@ public class Jalview
             + System.getProperty("os.version"));
 
     ArgsParser aparser = new ArgsParser(args);
-    boolean headless = false;
 
-    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;
-    }
-    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 (Platform.isJS())
     {
+      isJavaAppletTag = aparser.isApplet();
+      if (isJavaAppletTag)
+      {
+        Preferences.setAppletDefaults();
+        Cache.loadProperties(usrPropsFile); // again, because we
+        // might be changing defaults here?
+      }
       System.out.println(
-              "CMD [-props " + usrPropsFile + "] executed successfully!");
+              "<Applet> found: " + aparser.getValue("Info.j2sAppletID"));
+      appletResourcePath = aparser.getValue("Info.resourcePath");
     }
-
-    // anything else!
-
-    final String jabawsUrl = aparser.getValue("jabaws");
-    if (jabawsUrl != null)
+    else
+    /**
+     * Java only
+     * 
+     * @j2sIgnore
+     */
     {
-      try
+      if (usrPropsFile != null)
       {
-        Jws2Discoverer.getDiscoverer().setPreferredUrl(jabawsUrl);
         System.out.println(
-                "CMD [-jabaws " + jabawsUrl + "] executed successfully!");
-      } catch (MalformedURLException e)
+                "CMD [-props " + usrPropsFile + "] executed successfully!");
+      }
+
+      if (aparser.contains("help") || aparser.contains("h"))
       {
-        System.err.println(
-                "Invalid jabaws parameter: " + jabawsUrl + " ignored");
+        showUsage();
+        System.exit(0);
+      }
+      if (aparser.contains(ArgsParser.NODISPLAY)
+              || aparser.contains(ArgsParser.NOGUI)
+              || aparser.contains(ArgsParser.HEADLESS)
+              || "true".equals(System.getProperty("java.awt.headless")))
+      {
+        headless = true;
+      }
+
+      // anything else!
+
+      final String jabawsUrl = aparser.getValue(ArgsParser.JABAWS);
+      if (jabawsUrl != null)
+      {
+        try
+        {
+          Jws2Discoverer.getInstance().setPreferredUrl(jabawsUrl);
+          System.out.println(
+                  "CMD [-jabaws " + jabawsUrl + "] executed successfully!");
+        } catch (MalformedURLException e)
+        {
+          System.err.println(
+                  "Invalid jabaws parameter: " + jabawsUrl + " ignored");
+        }
       }
-    }
 
-    String defs = aparser.getValue("setprop");
+    }
+    // check for property setting
+    String defs = aparser.getValue(ArgsParser.SETPROP);
     while (defs != null)
     {
       int p = defs.indexOf('=');
@@ -251,16 +363,12 @@ public class Jalview
       else
       {
         System.out.println("Executing setprop argument: " + defs);
-        // DISABLED FOR SECURITY REASONS
-        // TODO: add a property to allow properties to be overriden by cli args
-        // Cache.setProperty(defs.substring(0,p), defs.substring(p+1));
+        if (Platform.isJS())
+        {
+          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"));
@@ -285,7 +393,7 @@ public class Jalview
       System.err.println("Unexpected Look and Feel Exception");
       ex.printStackTrace();
     }
-    if (Platform.isAMac())
+    if (Platform.isAMacAndNotJS())
     {
 
       LookAndFeel lookAndFeel = ch.randelshofer.quaqua.QuaquaManager
@@ -304,8 +412,9 @@ public class Jalview
                   "Failed to set QuaQua look and feel: " + e.toString());
         }
       }
-      if (lookAndFeel == null || !(lookAndFeel.getClass()
-              .isAssignableFrom(UIManager.getLookAndFeel().getClass()))
+      if (lookAndFeel == null
+              || !(lookAndFeel.getClass().isAssignableFrom(
+                      UIManager.getLookAndFeel().getClass()))
               || !UIManager.getLookAndFeel().getClass().toString()
                       .toLowerCase().contains("quaqua"))
       {
@@ -328,83 +437,93 @@ public class Jalview
      */
     if (Cache.getDefault("USE_FULL_SO", false))
     {
-      SequenceOntologyFactory.setInstance(new SequenceOntology());
+      SequenceOntologyFactory.setSequenceOntology(new SequenceOntology());
     }
 
     if (!headless)
     {
-      desktop = new Desktop();
+      desktop = Desktop.getInstance();
       desktop.setInBatchMode(true); // indicate we are starting up
       desktop.setVisible(true);
-      desktop.startServiceDiscovery();
-      if (!aparser.contains("nousagestats"))
-      {
-        startUsageStats(desktop);
-      }
-      else
-      {
-        System.err.println("CMD [-nousagestats] executed successfully!");
-      }
 
-      if (!aparser.contains("noquestionnaire"))
+      if (!Platform.isJS())
+      /**
+       * Java only
+       * 
+       * @j2sIgnore
+       */
       {
-        String url = aparser.getValue("questionnaire");
-        if (url != null)
+        desktop.startServiceDiscovery();
+        if (!aparser.contains(ArgsParser.NOUSAGESTATS))
         {
-          // Start the desktop questionnaire prompter with the specified
-          // questionnaire
-          Cache.log.debug("Starting questionnaire url at " + url);
-          desktop.checkForQuestionnaire(url);
-          System.out.println(
-                  "CMD questionnaire[-" + url + "] executed successfully!");
+          startUsageStats(desktop);
         }
         else
         {
-          if (Cache.getProperty("NOQUESTIONNAIRES") == null)
+          System.err.println("CMD [-nousagestats] executed successfully!");
+        }
+
+        if (!aparser.contains(ArgsParser.NOQUESTIONNAIRE))
+        {
+          String url = aparser.getValue(ArgsParser.QUESTIONNAIRE);
+          if (url != null)
           {
             // Start the desktop questionnaire prompter with the specified
             // questionnaire
-            // String defurl =
-            // "http://anaplog.compbio.dundee.ac.uk/cgi-bin/questionnaire.pl";
-            // //
-            String defurl = "http://www.jalview.org/cgi-bin/questionnaire.pl";
-            Cache.log.debug(
-                    "Starting questionnaire with default url: " + defurl);
-            desktop.checkForQuestionnaire(defurl);
+            Cache.log.debug("Starting questionnaire url at " + url);
+            desktop.checkForQuestionnaire(url);
+            System.out.println("CMD questionnaire[-" + url
+                    + "] executed successfully!");
+          }
+          else
+          {
+            if (Cache.getProperty("NOQUESTIONNAIRES") == null)
+            {
+              // Start the desktop questionnaire prompter with the specified
+              // questionnaire
+              // String defurl =
+              // "http://anaplog.compbio.dundee.ac.uk/cgi-bin/questionnaire.pl";
+              // //
+              String defurl = "http://www.jalview.org/cgi-bin/questionnaire.pl";
+              Cache.log.debug(
+                      "Starting questionnaire with default url: " + defurl);
+              desktop.checkForQuestionnaire(defurl);
+            }
           }
         }
-      }
-      else
-      {
-        System.err.println("CMD [-noquestionnaire] executed successfully!");
-      }
+        else
+        {
+          System.err
+                  .println("CMD [-noquestionnaire] executed successfully!");
+        }
 
-      if (!aparser.contains("nonews"))
-      {
-        desktop.checkForNews();
-      }
+        if (!aparser.contains(ArgsParser.NONEWS))
+        {
+          desktop.checkForNews();
+        }
 
-      BioJsHTMLOutput.updateBioJS();
+        BioJsHTMLOutput.updateBioJS();
+      }
     }
 
-    String file = null, data = null;
+    String data = null;
     FileFormatI format = null;
     DataSourceType protocol = null;
     FileLoader fileLoader = new FileLoader(!headless);
 
-    String groovyscript = null; // script to execute after all loading is
+    // 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 = aparser.getValue(ArgsParser.GROOVY, true);
+    String file = aparser.getValue(ArgsParser.OPEN, true);
 
     if (file == null && desktop == null)
     {
       System.out.println("No files to open!");
       System.exit(1);
     }
-    String vamsasImport = aparser.getValue("vdoc");
-    String vamsasSession = aparser.getValue("vsess");
+    String vamsasImport = aparser.getValue(ArgsParser.VDOC);
+    String vamsasSession = aparser.getValue(ArgsParser.VSESS);
     if (vamsasImport != null || vamsasSession != null)
     {
       if (desktop == null || headless)
@@ -501,14 +620,24 @@ public class Jalview
       }
       System.out.println("CMD [-open " + file + "] executed successfully!");
 
-      if (!file.startsWith("http://"))
+      if (!Platform.isJS())
+      /**
+       * ignore in JavaScript -- can't just check file existence - could load
+       * it?
+       * 
+       * @j2sIgnore
+       */
       {
-        if (!(new File(file)).exists())
+        if (!file.startsWith("http://") && !file.startsWith("https://"))
+        // BH 2019 added https check for Java
         {
-          System.out.println("Can't find " + file);
-          if (headless)
+          if (!(new File(file)).exists())
           {
-            System.exit(1);
+            System.out.println("Can't find " + file);
+            if (headless)
+            {
+              System.exit(1);
+            }
           }
         }
       }
@@ -532,14 +661,13 @@ public class Jalview
       else
       {
         setCurrentAlignFrame(af);
-        data = aparser.getValue("colour", true);
+        data = aparser.getValue(ArgsParser.COLOUR, true);
         if (data != null)
         {
           data.replaceAll("%20", " ");
 
-          ColourSchemeI cs = ColourSchemeProperty
-                  .getColourScheme(af.getViewport(),
-                          af.getViewport().getAlignment(), data);
+          ColourSchemeI cs = ColourSchemeProperty.getColourScheme(
+                  af.getViewport(), af.getViewport().getAlignment(), data);
 
           if (cs != null)
           {
@@ -550,7 +678,7 @@ 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,
@@ -559,7 +687,7 @@ 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,
@@ -569,7 +697,7 @@ 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);
@@ -578,7 +706,7 @@ public class Jalview
                   "CMD [-annotations " + data + "] 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())
@@ -586,7 +714,8 @@ public class Jalview
             System.out.println("CMD [-sortbytree] executed successfully!");
           }
         }
-        if (aparser.contains("no-annotation"))
+        if (aparser.contains(ArgsParser.NOANNOTATION)
+                || aparser.contains(ArgsParser.NOANNOTATION2))
         {
           af.getViewport().setShowAnnotation(false);
           if (!af.getViewport().isShowAnnotation())
@@ -594,7 +723,7 @@ public class Jalview
             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())
@@ -603,7 +732,7 @@ public class Jalview
                     .println("CMD [-nosortbytree] executed successfully!");
           }
         }
-        data = aparser.getValue("tree", true);
+        data = aparser.getValue(ArgsParser.TREE, true);
         if (data != null)
         {
           try
@@ -633,89 +762,103 @@ public class Jalview
                   + "] executed successfully!");
           groovyscript = null;
         }
-        String imageName = "unnamed.png";
-        while (aparser.getSize() > 1)
+
+        if (isJavaAppletTag)
+        {
+          loadAppletParams(aparser, af);
+        }
+        else
         {
-          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"))
+          String imageName = "unnamed.png";
+          while (aparser.getSize() > 1)
           {
-            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);
+            // PNG filename
+            // SVG filename
+            // HTML filename
+            // biojsmsa filename
+            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.out.println("Creating HTML image: " + file);
+              continue;
+            }
+            else if (outputFormat.equalsIgnoreCase("biojsmsa"))
             {
-              System.err.println("The output html file must not be null");
-              return;
+              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;
             }
-            try
+            else if (outputFormat.equalsIgnoreCase("imgMap"))
             {
-              BioJsHTMLOutput.refreshVersionInfo(
-                      BioJsHTMLOutput.BJS_TEMPLATES_LOCAL_DIRECTORY);
-            } catch (URISyntaxException e)
+              af.createImageMap(new File(file), imageName);
+              System.out.println("Creating image map: " + file);
+              continue;
+            }
+            else if (outputFormat.equalsIgnoreCase("eps"))
             {
-              e.printStackTrace();
+              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!!");
             }
-            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;
-          }
 
-          if (af.saveAlignment(file, format))
-          {
-            System.out.println("Written alignment in " + format
-                    + " format to " + file);
           }
-          else
+
+          while (aparser.getSize() > 0)
           {
-            System.out.println("Error writing file " + file + " in "
-                    + format + " format!!");
+            System.out.println("Unknown arg: " + aparser.nextValue());
           }
-
-        }
-
-        while (aparser.getSize() > 0)
-        {
-          System.out.println("Unknown arg: " + aparser.nextValue());
         }
       }
     }
@@ -724,8 +867,14 @@ public class Jalview
     // And the user
     // ////////////////////
 
-    if (!headless && file == null && vamsasImport == null
+    if (!Platform.isJS() && !headless && file == null
+            && vamsasImport == null
             && jalview.bin.Cache.getDefault("SHOW_STARTUP_FILE", true))
+    /**
+     * Java only
+     * 
+     * @j2sIgnore
+     */
     {
       file = jalview.bin.Cache.getDefault("STARTUP_FILE",
               jalview.bin.Cache.getDefault("www.jalview.org",
@@ -843,8 +992,9 @@ 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)",
@@ -987,16 +1137,6 @@ 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() }
@@ -1020,13 +1160,132 @@ public class Jalview
     }
   }
 
-  public static AlignFrame getCurrentAlignFrame()
+  /**
+   * 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)
   {
-    return Jalview.currentAlignFrame;
+    String id = Cache.getProperty("Info.j2sAppletID");
+    if (id == null)
+    {
+      id = "jalview";
+    }
+    return id + (frameType == null ? "" : "-" + frameType);
   }
 
-  public static void setCurrentAlignFrame(AlignFrame currentAlignFrame)
+  private void loadAppletParams(ArgsParser aparser, AlignFrame af)
   {
-    Jalview.currentAlignFrame = currentAlignFrame;
+    Jalview me = this;
+    JalviewApp app = new JalviewApp()
+    {
+
+
+      @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));
+      }
+
+      @Override
+      public URL getDocumentBase()
+      {
+        return Platform.getDocumentBase();
+      }
+
+      @Override
+      public URL getCodeBase()
+      {
+        return Platform.getCodeBase();
+      }
+
+      @Override
+      public AlignViewportI getViewport()
+      {
+        return Jalview.getCurrentAlignFrame().getViewport();
+      }
+
+      @Override
+      public boolean loadScoreFile(String sScoreFile) throws IOException
+      {
+        Jalview.getCurrentAlignFrame().loadJalviewDataFile(sScoreFile, null,
+                null, null);
+        return true;
+      }
+
+      @Override
+      public boolean parseFeaturesFile(String filename,
+              DataSourceType protocol)
+      {
+        return af.parseFeaturesFile(filename, protocol);
+      }
+
+      @Override
+      public void loadTree(NewickFile fin, String treeFile)
+              throws IOException
+      {
+        // n/a -- already done
+      }
+
+      @Override
+      public void setAlignPdbStructures(boolean defaultParameter)
+      {
+        // TODO Auto-generated method stub
+
+      }
+
+      @Override
+      public void newStructureView(PDBEntry pdb, SequenceI[] seqs,
+              String[] chains, DataSourceType protocol)
+      {
+        // TODO Auto-generated method stub
+
+      }
+
+      @Override
+      public void alignedStructureView(PDBEntry[] pdb, SequenceI[][] seqs,
+              String[][] chains, String[] protocols)
+      {
+        // TODO Auto-generated method stub
+
+      }
+
+      @Override
+      public void updateForLoader()
+      {
+        // TODO Auto-generated method stub
+
+      }
+
+      @Override
+      public void setFeatureGroupState(String[] groups, boolean state)
+      {
+        // TODO Auto-generated method stub
+
+      }
+
+      @Override
+      public void newFeatureSettings()
+      {
+        // TODO Auto-generated method stub
+
+      }
+
+    };
+
+    new JalviewAppLoader(true).load(app);
+
   }
+
 }