X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fbin%2FJalview.java;h=84fec4569df2aad30c78c0ea9171e28f16861235;hb=4ba1c57b4ce0b3708b245633a109442dc88f586c;hp=9e3382af429652ca477c0fc1d298380fc3faff8a;hpb=208f2c3de82e3327c4f930ab7d04f5b812ccd277;p=jalview.git

diff --git a/src/jalview/bin/Jalview.java b/src/jalview/bin/Jalview.java
index 9e3382a..84fec45 100755
--- a/src/jalview/bin/Jalview.java
+++ b/src/jalview/bin/Jalview.java
@@ -20,45 +20,49 @@
  */
 package jalview.bin;
 
-import jalview.analysis.AlignmentSorter;
-import jalview.analysis.scoremodels.ScoreModels;
+import jalview.api.AlignFrameI;
+import jalview.api.AlignViewportI;
+import jalview.api.JalviewApp;
 import jalview.api.StructureSelectionManagerProvider;
-import jalview.ext.ensembl.EnsemblInfo;
+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.fts.service.pdb.PDBFTSRestClient;
-import jalview.fts.service.uniprot.UniProtFTSRestClient;
 import jalview.gui.AlignFrame;
+import jalview.gui.AlignViewport;
+import jalview.gui.AlignmentPanel;
 import jalview.gui.Desktop;
+import jalview.gui.Preferences;
 import jalview.gui.PromptUserConfig;
-import jalview.httpserver.HttpServer;
+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.io.gff.SequenceOntologyI;
-import jalview.rest.RestHandler;
+import jalview.javascript.JSFunctionExec;
+import jalview.javascript.JalviewLiteJsApi;
+import jalview.javascript.MouseOverStructureListener;
+import jalview.renderer.seqfeatures.FeatureRenderer;
 import jalview.schemes.ColourSchemeI;
 import jalview.schemes.ColourSchemeProperty;
-import jalview.structure.StructureImportSettings;
-import jalview.structure.StructureSelectionManager;
-import jalview.urls.IdOrgSettings;
+import jalview.structure.SelectionSource;
+import jalview.structure.VamsasSource;
 import jalview.util.MessageManager;
 import jalview.util.Platform;
-import jalview.ws.SequenceFetcher;
-import jalview.ws.jws1.Discoverer;
 import jalview.ws.jws2.Jws2Discoverer;
-import jalview.ws.jws2.jabaws2.Jws2InstanceFactory;
-import jalview.ws.rest.RestClient;
-import jalview.ws.sifts.SiftsSettings;
 
-import java.awt.Color;
+import java.applet.AppletContext;
 import java.io.BufferedReader;
 import java.io.File;
 import java.io.FileOutputStream;
@@ -76,7 +80,7 @@ import java.security.PermissionCollection;
 import java.security.Permissions;
 import java.security.Policy;
 import java.util.HashMap;
-import java.util.IdentityHashMap;
+import java.util.Hashtable;
 import java.util.Map;
 import java.util.Vector;
 import java.util.logging.ConsoleHandler;
@@ -88,6 +92,7 @@ import javax.swing.UIManager;
 
 import groovy.lang.Binding;
 import groovy.util.GroovyScriptEngine;
+import netscape.javascript.JSObject;
 
 /**
  * Main class for Jalview Application <br>
@@ -104,8 +109,19 @@ import groovy.util.GroovyScriptEngine;
  * @author $author$
  * @version $Revision$
  */
-public class Jalview
+public class Jalview implements ApplicationSingletonI, JalviewLiteJsApi
 {
+
+  public static Jalview getInstance()
+  {
+    return (Jalview) ApplicationSingletonProvider
+            .getInstance(Jalview.class);
+  }
+
+  private Jalview()
+  {
+  }
+
   static
   {
     Platform.getURLCommandArguments();
@@ -118,41 +134,17 @@ public class Jalview
     return getInstance().headless;
   }
 
-  /**
-   * singleton instance of this class in Java only
-   */
+  private Desktop desktop;
 
-  private static Jalview instance;
+  private AlignFrame currentAlignFrame;
 
-  public static Jalview getInstance()
-  {
-    Jalview j;
-    @SuppressWarnings("unused")
-    ThreadGroup g = Thread.currentThread().getThreadGroup();
-    /**
-     * @j2sNative j = g._jalviewInstance;
-     */
-    {
-      j = instance;
-    }
-    return j;
-  }
+  public boolean isJavaAppletTag;
 
-  private static void setInstance(Jalview j)
-  {
-    @SuppressWarnings("unused")
-    ThreadGroup g = Thread.currentThread().getThreadGroup();
-    /**
-     * @j2sNative g._jalviewInstance = j;
-     */
-    {
-      instance = j;
-    }
-  }
+  public String appletResourcePath;
 
-  private Desktop desktop;
+  private JalviewAppLoader appLoader;
 
-  private AlignFrame currentAlignFrame;
+  protected JSFunctionExec jsFunctionExec;
 
   public static AlignFrame getCurrentAlignFrame()
   {
@@ -260,7 +252,6 @@ public class Jalview
   public static void main(String[] args)
   {
     // setLogging(); // BH - for event debugging in JavaScript
-    setInstance(new Jalview());
     getInstance().doMain(args);
   }
 
@@ -310,7 +301,8 @@ public class Jalview
   void doMain(String[] args)
   {
 
-    if (!Platform.isJS())
+    boolean isJS = Platform.isJS();
+    if (!isJS)
     {
       System.setSecurityManager(null);
     }
@@ -325,19 +317,32 @@ public class Jalview
 
     String usrPropsFile = aparser.getValue(ArgsParser.PROPS);
     Cache.loadProperties(usrPropsFile);
-    if (usrPropsFile != null)
+    if (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");
     }
-
-    if (!Platform.isJS())
+    else
     /**
      * Java only
      * 
      * @j2sIgnore
      */
     {
+      if (usrPropsFile != null)
+      {
+        System.out.println(
+                "CMD [-props " + usrPropsFile + "] executed successfully!");
+      }
+
       if (aparser.contains("help") || aparser.contains("h"))
       {
         showUsage();
@@ -358,7 +363,7 @@ public class Jalview
       {
         try
         {
-          Jws2Discoverer.getDiscoverer().setPreferredUrl(jabawsUrl);
+          Jws2Discoverer.getInstance().setPreferredUrl(jabawsUrl);
           System.out.println(
                   "CMD [-jabaws " + jabawsUrl + "] executed successfully!");
         } catch (MalformedURLException e)
@@ -381,7 +386,7 @@ 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));
         }
@@ -453,18 +458,18 @@ public class Jalview
      * configure 'full' SO model if preferences say to, 
      * else use the default (SO Lite)
      */
-    if (Cache.getDefault("USE_FULL_SO", false))
+    if (Cache.getDefault(Preferences.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);
 
-      if (!Platform.isJS())
+      if (!isJS)
       /**
        * Java only
        * 
@@ -495,7 +500,7 @@ public class Jalview
           }
           else
           {
-            if (Cache.getProperty("NOQUESTIONNAIRES") == null)
+            if (Cache.getProperty(Preferences.NOQUESTIONNAIRES) == null)
             {
               // Start the desktop questionnaire prompter with the specified
               // questionnaire
@@ -524,109 +529,45 @@ public class Jalview
       }
     }
 
-    String data = null;
-    FileFormatI format = null;
-    DataSourceType protocol = null;
-    FileLoader fileLoader = new FileLoader(!headless);
-
     // script to execute after all loading is
     // completed one way or another
     // extract groovy argument and execute if necessary
-    String groovyscript = aparser.getValue(ArgsParser.GROOVY, 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);
     }
-    String vamsasImport = aparser.getValue(ArgsParser.VDOC);
-    String vamsasSession = aparser.getValue(ArgsParser.VSESS);
-    if (vamsasImport != null || vamsasSession != null)
+    boolean haveImport = checkStartVamas(aparser);
+    // Finally, deal with the remaining input data.
+    long progress = -1;
+    if (file == null && isJavaAppletTag)
     {
-      if (desktop == null || headless)
+      // Maybe the sequences are added as parameters
+      StringBuffer data = new StringBuffer("PASTE");
+      int i = 1;
+      while ((file = aparser.getAppletValue("sequence" + i, null)) != null)
       {
-        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.
-      boolean inSession = false;
-      if (vamsasImport != null)
-      {
-        try
-        {
-          DataSourceType viprotocol = AppletFormatAdapter
-                  .checkProtocol(vamsasImport);
-          if (viprotocol == DataSourceType.FILE)
-          {
-            inSession = desktop.vamsasImport(new File(vamsasImport));
-          }
-          else if (viprotocol == DataSourceType.URL)
-          {
-            inSession = desktop.vamsasImport(new URL(vamsasImport));
-          }
-
-        } catch (Exception e)
-        {
-          System.err.println("Exeption when importing " + vamsasImport
-                  + " as a vamsas document.");
-          e.printStackTrace();
-        }
-        if (!inSession)
-        {
-          System.err.println("Failed to import " + vamsasImport
-                  + " as a vamsas document.");
-        }
-        else
-        {
-          System.out.println("Imported Successfully into new session "
-                  + desktop.getVamsasApplication().getCurrentSession());
-        }
+        data.append(file.toString() + "\n");
+        i++;
       }
-      if (vamsasSession != null)
+      if (data.length() > 5)
       {
-        if (vamsasImport != null)
-        {
-          // close the newly imported session and import the Jalview specific
-          // remnants into the new session later on.
-          desktop.vamsasStop_actionPerformed(null);
-        }
-        // now join the new session
-        try
-        {
-          if (desktop.joinVamsasSession(vamsasSession))
-          {
-            System.out.println(
-                    "Successfully joined vamsas session " + vamsasSession);
-          }
-          else
-          {
-            System.err.println("WARNING: Failed to join vamsas session "
-                    + vamsasSession);
-          }
-        } catch (Exception e)
-        {
-          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:
-          // enable
-          // this
-          // when
-          // debugged
-          // desktop.getVamsasApplication().push_update();
-        }
+        file = data.toString();
       }
     }
-    long progress = -1;
-    // Finally, deal with the remaining input data.
+
     if (file != null)
     {
       if (!headless)
@@ -636,9 +577,8 @@ public class Jalview
                         .getString("status.processing_commandline_args"),
                 progress = System.currentTimeMillis());
       }
-      System.out.println("CMD [-open " + file + "] executed successfully!");
 
-      if (!Platform.isJS())
+      if (!isJS)
       /**
        * ignore in JavaScript -- can't just check file existence - could load
        * it?
@@ -664,22 +604,60 @@ public class Jalview
 
       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);
+      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(ArgsParser.COLOUR, true);
+
+        // TODO: file2 How to implement file2 for the applet spit screen?
+
+        String data = aparser.getValue(ArgsParser.COLOUR, true);
         if (data != null)
         {
           data.replaceAll("%20", " ");
@@ -770,104 +748,33 @@ 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
+         */
         {
-          // 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())
+          if (groovyscript != null)
           {
-            System.out.println("Written alignment in " + format
-                    + " format to " + file);
+            // 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;
           }
-          else
+          checkOutputFile(aparser, af, format);
+          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());
         }
       }
     }
@@ -876,8 +783,7 @@ public class Jalview
     // And the user
     // ////////////////////
 
-    if (!Platform.isJS() && !headless && file == null
-            && vamsasImport == null
+    if (!isJS && !headless && file == null && !haveImport
             && jalview.bin.Cache.getDefault("SHOW_STARTUP_FILE", true))
     /**
      * Java only
@@ -920,8 +826,8 @@ public class Jalview
         }
       }
 
-      startUpAlframe = fileLoader.LoadFileWaitTillLoaded(file, protocol,
-              format);
+      startUpAlframe = new FileLoader(!headless)
+              .loadFileWaitTillLoaded(file, protocol, format);
       // extract groovy arguments before anything else.
     }
 
@@ -951,6 +857,185 @@ public class Jalview
     }
   }
 
+  private boolean checkStartVamas(ArgsParser aparser)
+  {
+    String vamsasImport = aparser.getValue(ArgsParser.VDOC);
+    String vamsasSession = aparser.getValue(ArgsParser.VSESS);
+    if (vamsasImport == null && vamsasSession == null)
+    {
+      return false;
+    }
+    if (desktop == null || headless)
+    {
+      System.out.println(
+              "Headless vamsas sessions not yet supported. Sorry.");
+      System.exit(1);
+    }
+    boolean haveImport = (vamsasImport != null);
+    if (haveImport)
+    {
+      // if we have a file, start a new session and import it.
+      boolean inSession = false;
+      try
+      {
+        DataSourceType viprotocol = AppletFormatAdapter
+                .checkProtocol(vamsasImport);
+        if (viprotocol == DataSourceType.FILE)
+        {
+          inSession = desktop.vamsasImport(new File(vamsasImport));
+        }
+        else if (viprotocol == DataSourceType.URL)
+        {
+          inSession = desktop.vamsasImport(new URL(vamsasImport));
+        }
+
+      } catch (Exception e)
+      {
+        System.err.println("Exeption when importing " + vamsasImport
+                + " as a vamsas document.");
+        e.printStackTrace();
+      }
+      if (!inSession)
+      {
+        System.err.println("Failed to import " + vamsasImport
+                + " as a vamsas document.");
+      }
+      else
+      {
+        System.out.println("Imported Successfully into new session "
+                + desktop.getVamsasApplication().getCurrentSession());
+      }
+    }
+    if (vamsasSession != null)
+    {
+      if (vamsasImport != null)
+      {
+        // close the newly imported session and import the Jalview specific
+        // remnants into the new session later on.
+        desktop.vamsasStop_actionPerformed(null);
+      }
+      // now join the new session
+      try
+      {
+        if (desktop.joinVamsasSession(vamsasSession))
+        {
+          System.out.println(
+                  "Successfully joined vamsas session " + vamsasSession);
+        }
+        else
+        {
+          System.err.println("WARNING: Failed to join vamsas session "
+                  + vamsasSession);
+        }
+      } catch (Exception e)
+      {
+        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:
+        // enable
+        // this
+        // when
+        // debugged
+        // desktop.getVamsasApplication().push_update();
+      }
+    }
+    return haveImport;
+  }
+
+  private void checkOutputFile(ArgsParser aparser, AlignFrame af,
+          FileFormatI format)
+  {
+    String imageName = "unnamed.png";
+    while (aparser.getSize() > 1)
+    {
+      // PNG filename
+      // SVG filename
+      // HTML filename
+      // biojsmsa filename
+      String outputFormat = aparser.nextValue();
+      String 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!!");
+      }
+
+    }
+  }
+
   private static void showUsage()
   {
     System.out.println(
@@ -1159,6 +1244,12 @@ public class Jalview
    */
   public void quit()
   {
+    if (jsFunctionExec != null)
+    {
+      jsFunctionExec.tidyUp();
+      jsFunctionExec = null;
+    }
+
     if (desktop != null)
     {
       desktop.quit();
@@ -1169,46 +1260,667 @@ public class Jalview
     }
   }
 
-  // singleton instances
+  /**
+   * 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);
+  }
 
-  public Cache cache;
+  /**
+   * Handle all JalviewLite applet parameters
+   * 
+   * @param aparser
+   * @param af
+   */
+  private void loadAppletParams(ArgsParser aparser, AlignFrame af)
+  {
+    JalviewApp app = new JalviewApp()
+    {
 
-  public AlignmentSorter alignmentSorter;
+      private boolean alignPDBStructures; // From JalviewLite; not implemented
 
-  public EnsemblInfo ensemblInfo;
+      private Hashtable<String, Hashtable<String, String[]>> jsmessages;
 
-  public HttpServer httpServer;
+      private Hashtable<String, int[]> jshashes;
 
-  public IdentityHashMap<StructureSelectionManagerProvider, StructureSelectionManager> structureSelections;
+      @Override
+      public String getParameter(String name)
+      {
+        return aparser.getAppletValue(name, null);
+      }
 
-  public PDBFTSRestClient pdbFTSRestClient;
+      @Override
+      public boolean getDefaultParameter(String name, boolean def)
+      {
+        String stn;
+        return ((stn = getParameter(name)) == null ? def
+                : "true".equalsIgnoreCase(stn));
+      }
 
-  public RestHandler restHandler;
+      /**
+       * Get the applet-like document base even though this is an application.
+       */
+      @Override
+      public URL getDocumentBase()
+      {
+        return Platform.getDocumentBase();
+      }
 
-  public ScoreModels scoreModels;
+      /**
+       * Get the applet-like code base even though this is an application.
+       */
+      @Override
+      public URL getCodeBase()
+      {
+        return Platform.getCodeBase();
+      }
 
-  public SequenceFetcher sequenceFetcher;
+      @Override
+      public AlignViewportI getViewport()
+      {
+        return af.getViewport();
+      }
 
-  public SequenceOntologyI sequenceOntology;
+      /**
+       * features
+       * 
+       */
+      @Override
+      public boolean parseFeaturesFile(String filename,
+              DataSourceType protocol)
+      {
+        return af.parseFeaturesFile(filename, protocol);
+      }
 
-  public UniProtFTSRestClient uniprotFTSRestClient;
+      /**
+       * 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 Auto-generated method stub
+        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)
+      {
+        // TODO Auto-generated method stub
+        return null;
+      }
+
+      @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);
+  }
+
+  @Override
+  public String getSelectedSequences()
+  {
+    // TODO Auto-generated method stub
+    return null;
+  }
+
+  @Override
+  public String getSelectedSequences(String sep)
+  {
+    // TODO Auto-generated method stub
+    return null;
+  }
 
-  public StructureSelectionManager nullProvider;
+  @Override
+  public String getSelectedSequencesFrom(AlignFrameI alf)
+  {
+    // TODO Auto-generated method stub
+    return null;
+  }
+
+  @Override
+  public String getSelectedSequencesFrom(AlignFrameI alf,
+          String sep)
+  {
+    // TODO Auto-generated method stub
+    return null;
+  }
+
+  @Override
+  public void highlight(String sequenceId, String position,
+          String alignedPosition)
+  {
+    // TODO Auto-generated method stub
+
+  }
 
-  public Color[] rnaHelices = null;
+  @Override
+  public void highlightIn(AlignFrameI alf,
+          String sequenceId, String position, String alignedPosition)
+  {
+    // TODO Auto-generated method stub
 
-  public StructureImportSettings structureImportSettings;
+  }
 
-  public IdOrgSettings idOrgSettings;
+  @Override
+  public void select(String sequenceIds, String columns)
+  {
+    // TODO Auto-generated method stub
 
-  public SiftsSettings siftsSettings;
+  }
 
-  public RestClient restClient;
+  @Override
+  public void select(String sequenceIds, String columns, String sep)
+  {
+    // TODO Auto-generated method stub
 
-  public Jws2Discoverer j2s2discoverer;
+  }
 
-  public Jws2InstanceFactory jws2InstanceFactory;
+  @Override
+  public void selectIn(AlignFrameI alf, String sequenceIds,
+          String columns)
+  {
+    // TODO Auto-generated method stub
 
-  public Discoverer discoverer;
+  }
+
+  @Override
+  public void selectIn(AlignFrameI alf, String sequenceIds,
+          String columns, String sep)
+  {
+    // TODO Auto-generated method stub
+
+  }
+
+  @Override
+  public String getSelectedSequencesAsAlignment(String format,
+          String suffix)
+  {
+    // TODO Auto-generated method stub
+    return null;
+  }
+
+  @Override
+  public String getSelectedSequencesAsAlignmentFrom(
+          AlignFrameI alf, String format, String suffix)
+  {
+    // TODO Auto-generated method stub
+    return null;
+  }
+
+  @Override
+  public String getAlignmentOrder()
+  {
+    // TODO Auto-generated method stub
+    return null;
+  }
+
+  @Override
+  public String getAlignmentOrderFrom(AlignFrameI alf)
+  {
+    // TODO Auto-generated method stub
+    return null;
+  }
+
+  @Override
+  public String getAlignmentOrderFrom(AlignFrameI alf,
+          String sep)
+  {
+    // TODO Auto-generated method stub
+    return null;
+  }
+
+  @Override
+  public String orderBy(String order, String undoName)
+  {
+    // TODO Auto-generated method stub
+    return null;
+  }
+
+  @Override
+  public String orderBy(String order, String undoName, String sep)
+  {
+    // TODO Auto-generated method stub
+    return null;
+  }
+
+  @Override
+  public String orderAlignmentBy(AlignFrameI alf,
+          String order, String undoName, String sep)
+  {
+    // TODO Auto-generated method stub
+    return null;
+  }
+
+  @Override
+  public String getAlignment(String format)
+  {
+    // TODO Auto-generated method stub
+    return null;
+  }
+
+  @Override
+  public String getAlignmentFrom(AlignFrameI alf,
+          String format)
+  {
+    // TODO Auto-generated method stub
+    return null;
+  }
+
+  @Override
+  public String getAlignment(String format, String suffix)
+  {
+    // TODO Auto-generated method stub
+    return null;
+  }
+
+  @Override
+  public String getAlignmentFrom(AlignFrameI alf,
+          String format, String suffix)
+  {
+    // TODO Auto-generated method stub
+    return null;
+  }
+
+  @Override
+  public void loadAnnotation(String annotation)
+  {
+    // TODO Auto-generated method stub
+
+  }
+
+  @Override
+  public void loadAnnotationFrom(AlignFrameI alf,
+          String annotation)
+  {
+    // TODO Auto-generated method stub
+
+  }
+
+  @Override
+  public void loadFeatures(String features, boolean autoenabledisplay)
+  {
+    // TODO Auto-generated method stub
+
+  }
+
+  @Override
+  public boolean loadFeaturesFrom(AlignFrameI alf,
+          String features, boolean autoenabledisplay)
+  {
+    // TODO Auto-generated method stub
+    return false;
+  }
+
+  @Override
+  public String getFeatures(String format)
+  {
+    // TODO Auto-generated method stub
+    return null;
+  }
+
+  @Override
+  public String getFeaturesFrom(AlignFrameI alf,
+          String format)
+  {
+    // TODO Auto-generated method stub
+    return null;
+  }
+
+  @Override
+  public String getAnnotation()
+  {
+    // TODO Auto-generated method stub
+    return null;
+  }
+
+  @Override
+  public String getAnnotationFrom(AlignFrameI alf)
+  {
+    // TODO Auto-generated method stub
+    return null;
+  }
+
+  @Override
+  public AlignFrameI newView()
+  {
+    // TODO Auto-generated method stub
+    return null;
+  }
+
+  @Override
+  public AlignFrameI newView(String name)
+  {
+    // TODO Auto-generated method stub
+    return null;
+  }
+
+  @Override
+  public AlignFrameI newViewFrom(AlignFrameI alf)
+  {
+    // TODO Auto-generated method stub
+    return null;
+  }
+
+  @Override
+  public AlignFrameI newViewFrom(AlignFrameI alf, String name)
+  {
+    // TODO Auto-generated method stub
+    return null;
+  }
+
+  @Override
+  public AlignFrameI loadAlignment(String text,
+          String title)
+  {
+    // TODO Auto-generated method stub
+    return null;
+  }
+
+  @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 boolean addPdbFile(AlignFrameI alFrame,
+          String sequenceId, String pdbEntryString, String pdbFile)
+  {
+    // TODO Auto-generated method stub
+    return false;
+  }
+
+  @Override
+  public void scrollViewToIn(AlignFrameI alf,
+          String topRow, String leftHandColumn)
+  {
+    // TODO Auto-generated method stub
+
+  }
+
+  @Override
+  public void scrollViewToRowIn(AlignFrameI alf,
+          String topRow)
+  {
+    // TODO Auto-generated method stub
+
+  }
+
+  @Override
+  public void scrollViewToColumnIn(AlignFrameI alf,
+          String leftHandColumn)
+  {
+    // TODO Auto-generated method stub
+
+  }
+
+  @Override
+  public String getFeatureGroups()
+  {
+    // TODO Auto-generated method stub
+    return null;
+  }
+
+  @Override
+  public String getFeatureGroupsOn(AlignFrameI alf)
+  {
+    // TODO Auto-generated method stub
+    return null;
+  }
+
+  @Override
+  public String getFeatureGroupsOfState(boolean visible)
+  {
+    // TODO Auto-generated method stub
+    return null;
+  }
+
+  @Override
+  public String getFeatureGroupsOfStateOn(AlignFrameI alf,
+          boolean visible)
+  {
+    // TODO Auto-generated method stub
+    return null;
+  }
+
+  @Override
+  public void setFeatureGroupStateOn(AlignFrameI alf,
+          String groups, boolean state)
+  {
+    // TODO Auto-generated method stub
+
+  }
+
+  @Override
+  public void setFeatureGroupState(String groups, boolean state)
+  {
+    // TODO Auto-generated method stub
+
+  }
+
+  @Override
+  public String getSeparator()
+  {
+    // TODO Auto-generated method stub
+    return null;
+  }
+
+  @Override
+  public void setSeparator(String separator)
+  {
+    // TODO Auto-generated method stub
+
+  }
+
+  @Override
+  public String getJsMessage(String messageclass, String viewId)
+  {
+    // TODO Auto-generated method stub
+    return null;
+  }
 
 }