X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fbin%2FJalview.java;h=402f9bfcdba5ccc23927f06504d9cc9283c402d8;hb=ad16d6cce49a40ea1943431b980b85a6212bb9bf;hp=76ae3ff68853611646efd564066bf2ed30476103;hpb=8c7fd90d480e2671e0fa251ada3c89fa1d18862a;p=jalview.git

diff --git a/src/jalview/bin/Jalview.java b/src/jalview/bin/Jalview.java
index 76ae3ff..402f9bf 100755
--- a/src/jalview/bin/Jalview.java
+++ b/src/jalview/bin/Jalview.java
@@ -20,22 +20,29 @@
  */
 package jalview.bin;
 
-import groovy.lang.Binding;
-import groovy.util.GroovyScriptEngine;
-
+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;
+import jalview.io.DataSourceType;
+import jalview.io.FileFormat;
+import jalview.io.FileFormatException;
+import jalview.io.FileFormatI;
 import jalview.io.FileLoader;
-import jalview.io.FormatAdapter;
 import jalview.io.HtmlSvgOutput;
 import jalview.io.IdentifyFile;
 import jalview.io.NewickFile;
+import jalview.io.gff.SequenceOntologyFactory;
 import jalview.schemes.ColourSchemeI;
 import jalview.schemes.ColourSchemeProperty;
-import jalview.schemes.UserColourScheme;
 import jalview.util.MessageManager;
 import jalview.util.Platform;
 import jalview.ws.jws2.Jws2Discoverer;
@@ -49,6 +56,7 @@ import java.io.OutputStreamWriter;
 import java.io.PrintWriter;
 import java.net.MalformedURLException;
 import java.net.URI;
+import java.net.URISyntaxException;
 import java.net.URL;
 import java.security.AllPermission;
 import java.security.CodeSource;
@@ -58,46 +66,100 @@ 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;
 
+import groovy.lang.Binding;
+import groovy.util.GroovyScriptEngine;
+
 /**
  * Main class for Jalview Application <br>
  * <br>
- * start with java -Djava.ext.dirs=$PATH_TO_LIB$ jalview.bin.Jalview
+ * start with: java -classpath "$PATH_TO_LIB$/*:$PATH_TO_CLASSES$" \
+ * jalview.bin.Jalview
+ * 
+ * or on Windows: java -classpath "$PATH_TO_LIB$/*;$PATH_TO_CLASSES$" \
+ * jalview.bin.Jalview jalview.bin.Jalview
+ * 
+ * (ensure -classpath arg is quoted to avoid shell expansion of '*' and do not
+ * embellish '*' to e.g. '*.jar')
  * 
  * @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()
+        {
+        }
+      });
+    }
   }
 
   /**
@@ -143,7 +205,6 @@ public class Jalview
           af.setProgressBar(MessageManager
                   .getString("status.das_features_being_retrived"), id);
           af.featureSettings_actionPerformed(null);
-          af.featureSettings.fetchDasFeatures(dasSources, true);
           af.setProgressBar(null, id);
           synchronized (us)
           {
@@ -160,11 +221,6 @@ public class Jalview
 
   }
 
-  public static Jalview getInstance()
-  {
-    return instance;
-  }
-
   /**
    * main class for Jalview application
    * 
@@ -173,8 +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");
+    }
+
   }
 
   /**
@@ -182,53 +278,81 @@ public class Jalview
    */
   void doMain(String[] args)
   {
-    System.setSecurityManager(null);
-    System.out.println("Java version: "
-            + System.getProperty("java.version"));
+
+    if (!Platform.isJS())
+    {
+      System.setSecurityManager(null);
+    }
+
+    System.out
+            .println("Java version: " + System.getProperty("java.version"));
     System.out.println(System.getProperty("os.arch") + " "
             + System.getProperty("os.name") + " "
             + 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"))
+    String usrPropsFile = aparser.getValue(ArgsParser.PROPS);
+    Cache.loadProperties(usrPropsFile);
+    if (Platform.isJS())
     {
-      System.setProperty("java.awt.headless", "true");
-      headless = true;
+      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");
     }
-    String usrPropsFile = aparser.getValue("props");
-    Cache.loadProperties(usrPropsFile); // must do this before
-    if (usrPropsFile != null)
+    else
+    /**
+     * Java only
+     * 
+     * @j2sIgnore
+     */
     {
-      System.out.println("CMD [-props " + usrPropsFile
-              + "] executed successfully!");
-    }
-
-    // anything else!
+      if (usrPropsFile != null)
+      {
+        System.out.println(
+                "CMD [-props " + usrPropsFile + "] executed successfully!");
+      }
 
-    final String jabawsUrl = aparser.getValue("jabaws");
-    if (jabawsUrl != null)
-    {
-      try
+      if (aparser.contains("help") || aparser.contains("h"))
       {
-        Jws2Discoverer.getDiscoverer().setPreferredUrl(jabawsUrl);
-        System.out.println("CMD [-jabaws " + jabawsUrl
-                + "] executed successfully!");
-      } catch (MalformedURLException e)
+        showUsage();
+        System.exit(0);
+      }
+      if (aparser.contains(ArgsParser.NODISPLAY)
+              || aparser.contains(ArgsParser.NOGUI)
+              || aparser.contains(ArgsParser.HEADLESS)
+              || "true".equals(System.getProperty("java.awt.headless")))
       {
-        System.err.println("Invalid jabaws parameter: " + jabawsUrl
-                + " ignored");
+        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('=');
@@ -239,16 +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"));
@@ -258,9 +378,8 @@ public class Jalview
     } catch (NoClassDefFoundError error)
     {
       error.printStackTrace();
-      System.out
-              .println("\nEssential logging libraries not found."
-                      + "\nUse: java -Djava.ext.dirs=$PATH_TO_LIB$ jalview.bin.Jalview");
+      System.out.println("\nEssential logging libraries not found."
+              + "\nUse: java -classpath \"$PATH_TO_LIB$/*:$PATH_TO_CLASSES$\" jalview.bin.Jalview");
       System.exit(0);
     }
 
@@ -271,104 +390,146 @@ public class Jalview
       UIManager.setLookAndFeel(UIManager.getSystemLookAndFeelClassName());
     } catch (Exception ex)
     {
+      System.err.println("Unexpected Look and Feel Exception");
+      ex.printStackTrace();
     }
-    if (Platform.isAMac())
+    if (Platform.isAMacAndNotJS())
     {
+
+      LookAndFeel lookAndFeel = ch.randelshofer.quaqua.QuaquaManager
+              .getLookAndFeel();
       System.setProperty("com.apple.mrj.application.apple.menu.about.name",
               "Jalview");
       System.setProperty("apple.laf.useScreenMenuBar", "true");
-      try
+      if (lookAndFeel != null)
       {
-        UIManager.setLookAndFeel(ch.randelshofer.quaqua.QuaquaManager
-                .getLookAndFeel());
-      } catch (Throwable e)
+        try
+        {
+          UIManager.setLookAndFeel(lookAndFeel);
+        } catch (Throwable e)
+        {
+          System.err.println(
+                  "Failed to set QuaQua look and feel: " + e.toString());
+        }
+      }
+      if (lookAndFeel == null
+              || !(lookAndFeel.getClass().isAssignableFrom(
+                      UIManager.getLookAndFeel().getClass()))
+              || !UIManager.getLookAndFeel().getClass().toString()
+                      .toLowerCase().contains("quaqua"))
       {
-        System.err.println("Failed to set QuaQua look and feel: "
-                + e.toString());
+        try
+        {
+          System.err.println(
+                  "Quaqua LaF not available on this plaform. Using VAqua(4).\nSee https://issues.jalview.org/browse/JAL-2976");
+          UIManager.setLookAndFeel("org.violetlib.aqua.AquaLookAndFeel");
+        } catch (Throwable e)
+        {
+          System.err.println(
+                  "Failed to reset look and feel: " + e.toString());
+        }
       }
     }
 
+    /*
+     * configure 'full' SO model if preferences say to, 
+     * else use the default (SO Lite)
+     */
+    if (Cache.getDefault("USE_FULL_SO", false))
+    {
+      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!");
-      }
-      desktop.checkForNews();
-    }
+        else
+        {
+          System.err
+                  .println("CMD [-noquestionnaire] executed successfully!");
+        }
 
-    if (!isHeadlessMode())
-    {
-      BioJsHTMLOutput.updateBioJS();
+        if (!aparser.contains(ArgsParser.NONEWS))
+        {
+          desktop.checkForNews();
+        }
+
+        BioJsHTMLOutput.updateBioJS();
+      }
     }
 
-    String file = null, protocol = null, format = null, data = null;
+    String data = null;
+    FileFormatI format = null;
+    DataSourceType protocol = null;
     FileLoader fileLoader = new FileLoader(!headless);
-    Vector<String> getFeatures = null; // vector of das source nicknames to
-                                       // fetch
-    // features from
-    // loading is done.
-    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)
       {
-        System.out
-                .println("Headless vamsas sessions not yet supported. Sorry.");
+        System.out.println(
+                "Headless vamsas sessions not yet supported. Sorry.");
         System.exit(1);
       }
       // if we have a file, start a new session and import it.
@@ -377,13 +538,13 @@ public class Jalview
       {
         try
         {
-          String viprotocol = AppletFormatAdapter
+          DataSourceType viprotocol = AppletFormatAdapter
                   .checkProtocol(vamsasImport);
-          if (viprotocol == jalview.io.FormatAdapter.FILE)
+          if (viprotocol == DataSourceType.FILE)
           {
             inSession = desktop.vamsasImport(new File(vamsasImport));
           }
-          else if (viprotocol == FormatAdapter.URL)
+          else if (viprotocol == DataSourceType.URL)
           {
             inSession = desktop.vamsasImport(new URL(vamsasImport));
           }
@@ -418,8 +579,8 @@ public class Jalview
         {
           if (desktop.joinVamsasSession(vamsasSession))
           {
-            System.out.println("Successfully joined vamsas session "
-                    + vamsasSession);
+            System.out.println(
+                    "Successfully joined vamsas session " + vamsasSession);
           }
           else
           {
@@ -428,16 +589,16 @@ public class Jalview
           }
         } catch (Exception e)
         {
-          System.err.println("ERROR: Failed to join vamsas session "
-                  + vamsasSession);
+          System.err.println(
+                  "ERROR: Failed to join vamsas session " + vamsasSession);
           e.printStackTrace();
         }
         if (vamsasImport != null)
         {
           // the Jalview specific remnants can now be imported into the new
           // session at the user's leisure.
-          Cache.log
-                  .info("Skipping Push for import of data into existing vamsas session."); // TODO:
+          Cache.log.info(
+                  "Skipping Push for import of data into existing vamsas session."); // TODO:
           // enable
           // this
           // when
@@ -452,27 +613,44 @@ public class Jalview
     {
       if (!headless)
       {
-        desktop.setProgressBar(MessageManager
-                .getString("status.processing_commandline_args"),
+        desktop.setProgressBar(
+                MessageManager
+                        .getString("status.processing_commandline_args"),
                 progress = System.currentTimeMillis());
       }
       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);
+            }
           }
         }
       }
 
       protocol = AppletFormatAdapter.checkProtocol(file);
 
-      format = new IdentifyFile().identify(file, protocol);
+      try
+      {
+        format = new IdentifyFile().identify(file, protocol);
+      } catch (FileFormatException e1)
+      {
+        // TODO ?
+      }
 
       AlignFrame af = fileLoader.LoadFileWaitTillLoaded(file, protocol,
               format);
@@ -483,58 +661,52 @@ 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.getColour(af
-                  .getViewport().getAlignment(), data);
+          ColourSchemeI cs = ColourSchemeProperty.getColourScheme(
+                  af.getViewport(), af.getViewport().getAlignment(), data);
 
-          if (cs == null)
+          if (cs != null)
           {
-            UserColourScheme ucs = new UserColourScheme("white");
-            ucs.parseAppletParameter(data);
-            cs = ucs;
-          }
-          else
-          {
-            System.out.println("CMD [-color " + data
-                    + "] executed successfully!");
+            System.out.println(
+                    "CMD [-color " + data + "] executed successfully!");
           }
           af.changeColour(cs);
         }
 
         // 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,
                   AppletFormatAdapter.checkProtocol(data));
           // System.out.println("Added " + data);
-          System.out.println("CMD groups[-" + data
-                  + "]  executed successfully!");
+          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,
                   AppletFormatAdapter.checkProtocol(data));
           // System.out.println("Added " + data);
-          System.out.println("CMD [-features " + data
-                  + "]  executed successfully!");
+          System.out.println(
+                  "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);
           // System.out.println("Added " + data);
-          System.out.println("CMD [-annotations " + data
-                  + "] executed successfully!");
+          System.out.println(
+                  "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())
@@ -542,7 +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())
@@ -550,7 +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())
@@ -559,21 +732,17 @@ public class Jalview
                     .println("CMD [-nosortbytree] executed successfully!");
           }
         }
-        data = aparser.getValue("tree", true);
+        data = aparser.getValue(ArgsParser.TREE, true);
         if (data != null)
         {
-          jalview.io.NewickFile fin = null;
           try
           {
-            System.out.println("CMD [-tree " + data
-                    + "] executed successfully!");
-            fin = new NewickFile(data,
+            System.out.println(
+                    "CMD [-tree " + data + "] executed successfully!");
+            NewickFile nf = new NewickFile(data,
                     AppletFormatAdapter.checkProtocol(data));
-            if (fin != null)
-            {
-              af.getViewport().setCurrentTree(
-                      af.ShowNewickTree(fin, data).getTree());
-            }
+            af.getViewport()
+                    .setCurrentTree(af.showNewickTree(nf, data).getTree());
           } catch (IOException ex)
           {
             System.err.println("Couldn't add tree " + data);
@@ -583,27 +752,6 @@ public class Jalview
         // TODO - load PDB structure(s) to alignment JAL-629
         // (associate with identical sequence in alignment, or a specified
         // sequence)
-
-        getFeatures = checkDasArguments(aparser);
-        if (af != null && getFeatures != null)
-        {
-          FeatureFetcher ff = startFeatureFetching(getFeatures);
-          if (ff != null)
-          {
-            while (!ff.allFinished() || af.operationInProgress())
-            {
-              // wait around until fetching is finished.
-              try
-              {
-                Thread.sleep(100);
-              } catch (Exception e)
-              {
-
-              }
-            }
-          }
-          getFeatures = null; // have retrieved features - forget them now.
-        }
         if (groovyscript != null)
         {
           // Execute the groovy script after we've done all the rendering stuff
@@ -614,66 +762,103 @@ public class Jalview
                   + "] executed successfully!");
           groovyscript = null;
         }
-        String imageName = "unnamed.png";
-        while (aparser.getSize() > 1)
+
+        if (isJavaAppletTag)
+        {
+          loadAppletParams(aparser, af);
+        }
+        else
         {
-          format = aparser.nextValue();
-          file = aparser.nextValue();
 
-          if (format.equalsIgnoreCase("png"))
-          {
-            af.createPNG(new File(file));
-            imageName = (new File(file)).getName();
-            System.out.println("Creating PNG image: " + file);
-            continue;
-          }
-          else if (format.equalsIgnoreCase("svg"))
-          {
-            File imageFile = new File(file);
-            imageName = imageFile.getName();
-            af.createSVG(imageFile);
-            System.out.println("Creating SVG image: " + file);
-            continue;
-          }
-          else if (format.equalsIgnoreCase("html"))
-          {
-            File imageFile = new File(file);
-            imageName = imageFile.getName();
-            new HtmlSvgOutput(new File(file), af.alignPanel);
-            System.out.println("Creating HTML image: " + file);
-            continue;
-          }
-          else if (format.equalsIgnoreCase("imgMap"))
-          {
-            af.createImageMap(new File(file), imageName);
-            System.out.println("Creating image map: " + file);
-            continue;
-          }
-          else if (format.equalsIgnoreCase("eps"))
+          String imageName = "unnamed.png";
+          while (aparser.getSize() > 1)
           {
-            File outputFile = new File(file);
-            System.out.println("Creating EPS file: "
-                    + outputFile.getAbsolutePath());
-            af.createEPS(outputFile);
-            continue;
-          }
+            // 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.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!!");
+            }
 
-          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());
         }
       }
     }
@@ -682,15 +867,21 @@ 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",
+      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("http://www.jalview.org/examples/exampleFile_2_3.jar"))
+      if (file.equals(
+              "http://www.jalview.org/examples/exampleFile_2_3.jar"))
       {
         // hardwire upgrade of the startup file
         file.replace("_2_3.jar", "_2_7.jar");
@@ -698,38 +889,33 @@ public class Jalview
         jalview.bin.Cache.removeProperty("STARTUP_FILE");
       }
 
-      protocol = "File";
+      protocol = DataSourceType.FILE;
 
       if (file.indexOf("http:") > -1)
       {
-        protocol = "URL";
+        protocol = DataSourceType.URL;
       }
 
       if (file.endsWith(".jar"))
       {
-        format = "Jalview";
+        format = FileFormat.Jalview;
       }
       else
       {
-        format = new IdentifyFile().identify(file, protocol);
+        try
+        {
+          format = new IdentifyFile().identify(file, protocol);
+        } catch (FileFormatException e)
+        {
+          // TODO what?
+        }
       }
 
       startUpAlframe = fileLoader.LoadFileWaitTillLoaded(file, protocol,
               format);
-      getFeatures = checkDasArguments(aparser);
       // extract groovy arguments before anything else.
     }
-    // If the user has specified features to be retrieved,
-    // or a groovy script to be executed, do them if they
-    // haven't been done already
-    // fetch features for the default alignment
-    if (getFeatures != null)
-    {
-      if (startUpAlframe != null)
-      {
-        startFeatureFetching(getFeatures);
-      }
-    }
+
     // Once all other stuff is done, execute any groovy scripts (in order)
     if (groovyscript != null)
     {
@@ -740,8 +926,8 @@ public class Jalview
       }
       else
       {
-        System.err
-                .println("Sorry. Groovy Support is not available, so ignoring the provided groovy script "
+        System.err.println(
+                "Sorry. Groovy Support is not available, so ignoring the provided groovy script "
                         + groovyscript);
       }
     }
@@ -758,8 +944,8 @@ public class Jalview
 
   private static void showUsage()
   {
-    System.out
-            .println("Usage: jalview -open [FILE] [OUTPUT_FORMAT] [OUTPUT_FILE]\n\n"
+    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"
@@ -778,21 +964,24 @@ public class Jalview
                     + "-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"
                     + "-sortbytree OR -nosortbytree\tEnable or disable sorting of the given alignment by the given tree\n"
                     // +
-                    // "-setprop PROPERTY=VALUE\tSet the given Jalview property, after all other properties files have been read\n\t (quote the 'PROPERTY=VALUE' pair to ensure spaces are passed in correctly)"
+                    // "-setprop PROPERTY=VALUE\tSet the given Jalview property,
+                    // after all other properties files have been read\n\t
+                    // (quote the 'PROPERTY=VALUE' pair to ensure spaces are
+                    // passed in correctly)"
                     + "-jabaws URL\tSpecify URL for Jabaws services (e.g. for a local installation).\n"
-                    + "-dasserver nickname=URL\tAdd and enable a das server with given nickname\n\t\t\t(alphanumeric or underscores only) for retrieval of features for all alignments.\n"
-                    + "\t\t\tSources that also support the sequence command may be specified by prepending the URL with sequence:\n"
-                    + "\t\t\t e.g. sequence:http://localdas.somewhere.org/das/source)\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"
+                    // "-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");
@@ -804,8 +993,7 @@ public class Jalview
      * start a User Config prompt asking if we can log usage statistics.
      */
     PromptUserConfig prompter = new PromptUserConfig(
-            Desktop.desktop,
-            "USAGESTATS",
+            Desktop.getDesktopPane(), "USAGESTATS",
             "Jalview Usage Statistics",
             "Do you want to help make Jalview better by enabling "
                     + "the collection of usage statistics with Google Analytics ?"
@@ -815,8 +1003,8 @@ public class Jalview
               @Override
               public void run()
               {
-                Cache.log
-                        .debug("Initialising googletracker for usage stats.");
+                Cache.log.debug(
+                        "Initialising googletracker for usage stats.");
                 Cache.initGoogleTracker();
                 Cache.log.debug("Tracking enabled.");
               }
@@ -856,10 +1044,10 @@ public class Jalview
       try
       {
         tfile = File.createTempFile("jalview", "groovy");
-        PrintWriter outfile = new PrintWriter(new OutputStreamWriter(
-                new FileOutputStream(tfile)));
-        BufferedReader br = new BufferedReader(new InputStreamReader(
-                System.in));
+        PrintWriter outfile = new PrintWriter(
+                new OutputStreamWriter(new FileOutputStream(tfile)));
+        BufferedReader br = new BufferedReader(
+                new InputStreamReader(System.in));
         String line = null;
         while ((line = br.readLine()) != null)
         {
@@ -872,8 +1060,8 @@ public class Jalview
       } catch (Exception ex)
       {
         System.err.println("Failed to read from STDIN into tempfile "
-                + ((tfile == null) ? "(tempfile wasn't created)" : tfile
-                        .toString()));
+                + ((tfile == null) ? "(tempfile wasn't created)"
+                        : tfile.toString()));
         ex.printStackTrace();
         return;
       }
@@ -882,8 +1070,8 @@ public class Jalview
         sfile = tfile.toURI().toURL();
       } catch (Exception x)
       {
-        System.err
-                .println("Unexpected Malformed URL Exception for temporary file created from STDIN: "
+        System.err.println(
+                "Unexpected Malformed URL Exception for temporary file created from STDIN: "
                         + tfile.toURI());
         x.printStackTrace();
         return;
@@ -925,7 +1113,7 @@ public class Jalview
     }
     try
     {
-      Map<String, Object> vbinding = new HashMap<String, Object>();
+      Map<String, Object> vbinding = new HashMap<>();
       vbinding.put("Jalview", this);
       if (af != null)
       {
@@ -949,105 +1137,6 @@ public class Jalview
     }
   }
 
-  /**
-   * Check commandline for any das server definitions or any fetchfrom switches
-   * 
-   * @return vector of DAS source nicknames to retrieve from
-   */
-  private static Vector<String> checkDasArguments(ArgsParser aparser)
-  {
-    Vector<String> source = null;
-    String data;
-    String locsources = Cache.getProperty(Cache.DAS_LOCAL_SOURCE);
-    while ((data = aparser.getValue("dasserver", true)) != null)
-    {
-      String nickname = null;
-      String url = null;
-      int pos = data.indexOf('=');
-      // determine capabilities
-      if (pos > 0)
-      {
-        nickname = data.substring(0, pos);
-      }
-      url = data.substring(pos + 1);
-      if (url != null
-              && (url.startsWith("http:") || url
-                      .startsWith("sequence:http:")))
-      {
-        if (nickname == null)
-        {
-          nickname = url;
-        }
-        if (locsources == null)
-        {
-          locsources = "";
-        }
-        else
-        {
-          locsources += "\t";
-        }
-        locsources = locsources + nickname + "|" + url;
-        System.err
-                .println("NOTE! dasserver parameter not yet really supported (got args of "
-                        + nickname + "|" + url);
-        if (source == null)
-        {
-          source = new Vector<String>();
-        }
-        source.addElement(nickname);
-      }
-      System.out.println("CMD [-dasserver " + data
-              + "] executed successfully!");
-    } // loop until no more server entries are found.
-    if (locsources != null && locsources.indexOf('|') > -1)
-    {
-      Cache.log.debug("Setting local source list in properties file to:\n"
-              + locsources);
-      Cache.setProperty(Cache.DAS_LOCAL_SOURCE, locsources);
-    }
-    while ((data = aparser.getValue("fetchfrom", true)) != null)
-    {
-      System.out.println("adding source '" + data + "'");
-      if (source == null)
-      {
-        source = new Vector<String>();
-      }
-      source.addElement(data);
-    }
-    return source;
-  }
-
-  /**
-   * start a feature fetcher for every alignment frame
-   * 
-   * @param dasSources
-   */
-  private FeatureFetcher startFeatureFetching(
-          final Vector<String> dasSources)
-  {
-    FeatureFetcher ff = new FeatureFetcher();
-    AlignFrame afs[] = Desktop.getAlignFrames();
-    if (afs == null || afs.length == 0)
-    {
-      return null;
-    }
-    for (int i = 0; i < afs.length; i++)
-    {
-      ff.addFetcher(afs[i], dasSources);
-    }
-    return ff;
-  }
-
-  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() }
@@ -1071,13 +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);
+
   }
+
 }