X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fbin%2FJalview.java;h=fae2b7597ec10ca45093e7a9347c8cfe726dd022;hb=5014beeca83ef54a5740388c443d85f532a34db6;hp=ac6fcd666b8c8168915f461fea6dcbb8334d40b9;hpb=be94287924736b46264674a189fd1719d38273ad;p=jalview.git

diff --git a/src/jalview/bin/Jalview.java b/src/jalview/bin/Jalview.java
index ac6fcd6..fae2b75 100755
--- a/src/jalview/bin/Jalview.java
+++ b/src/jalview/bin/Jalview.java
@@ -20,14 +20,22 @@
  */
 package jalview.bin;
 
+import jalview.api.AlignCalcWorkerI;
+import jalview.api.AlignFrameI;
 import jalview.api.AlignViewportI;
 import jalview.api.JalviewApp;
+import jalview.api.StructureSelectionManagerProvider;
 import jalview.bin.ApplicationSingletonProvider.ApplicationSingletonI;
+import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.HiddenColumns;
 import jalview.datamodel.PDBEntry;
+import jalview.datamodel.SequenceGroup;
 import jalview.datamodel.SequenceI;
 import jalview.ext.so.SequenceOntology;
 import jalview.gui.AlignFrame;
 import jalview.gui.AlignViewport;
+import jalview.gui.AlignmentPanel;
+import jalview.gui.CalculationChooser;
 import jalview.gui.Desktop;
 import jalview.gui.Preferences;
 import jalview.gui.PromptUserConfig;
@@ -44,13 +52,18 @@ import jalview.io.HtmlSvgOutput;
 import jalview.io.IdentifyFile;
 import jalview.io.NewickFile;
 import jalview.io.gff.SequenceOntologyFactory;
-import jalview.javascript.JalviewLiteJsApi;
+import jalview.javascript.JSFunctionExec;
+import jalview.javascript.MouseOverStructureListener;
+import jalview.renderer.seqfeatures.FeatureRenderer;
 import jalview.schemes.ColourSchemeI;
 import jalview.schemes.ColourSchemeProperty;
+import jalview.structure.SelectionSource;
+import jalview.structure.VamsasSource;
 import jalview.util.MessageManager;
 import jalview.util.Platform;
 import jalview.ws.jws2.Jws2Discoverer;
 
+import java.applet.AppletContext;
 import java.io.BufferedReader;
 import java.io.File;
 import java.io.FileOutputStream;
@@ -68,17 +81,16 @@ import java.security.PermissionCollection;
 import java.security.Permissions;
 import java.security.Policy;
 import java.util.HashMap;
+import java.util.Hashtable;
 import java.util.Map;
 import java.util.Vector;
-import java.util.logging.ConsoleHandler;
-import java.util.logging.Level;
-import java.util.logging.Logger;
 
 import javax.swing.LookAndFeel;
 import javax.swing.UIManager;
 
 import groovy.lang.Binding;
 import groovy.util.GroovyScriptEngine;
+import netscape.javascript.JSObject;
 
 /**
  * Main class for Jalview Application <br>
@@ -95,7 +107,7 @@ import groovy.util.GroovyScriptEngine;
  * @author $author$
  * @version $Revision$
  */
-public class Jalview implements ApplicationSingletonI, JalviewLiteJsApi
+public class Jalview implements ApplicationSingletonI, JalviewJSApi
 {
 
   public static Jalview getInstance()
@@ -128,6 +140,34 @@ public class Jalview implements ApplicationSingletonI, JalviewLiteJsApi
 
   public String appletResourcePath;
 
+  JalviewAppLoader appLoader;
+
+  protected JSFunctionExec jsFunctionExec;
+
+  private boolean noCalculation, noMenuBar, noStatus;
+
+  private boolean noAnnotation;
+
+  public boolean getStartCalculations()
+  {
+    return !noCalculation;
+  }
+
+  public boolean getAllowMenuBar()
+  {
+    return !noMenuBar;
+  }
+
+  public boolean getShowStatus()
+  {
+    return !noStatus;
+  }
+
+  public boolean getShowAnnotation()
+  {
+    return !noAnnotation;
+  }
+
   public static AlignFrame getCurrentAlignFrame()
   {
     return getInstance().currentAlignFrame;
@@ -233,50 +273,12 @@ public class Jalview implements ApplicationSingletonI, JalviewLiteJsApi
    */
   public static void main(String[] args)
   {
-    // setLogging(); // BH - for event debugging in JavaScript
+    // Platform.startJavaLogging();
     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");
-    }
-
-  }
-
   /**
    * @param args
    */
@@ -284,7 +286,11 @@ public class Jalview implements ApplicationSingletonI, JalviewLiteJsApi
   {
 
     boolean isJS = Platform.isJS();
-    if (!isJS)
+    if (isJS)
+    {
+      Platform.setAppClass(this);
+    }
+    else
     {
       System.setSecurityManager(null);
     }
@@ -511,6 +517,41 @@ public class Jalview implements ApplicationSingletonI, JalviewLiteJsApi
       }
     }
 
+    parseArguments(aparser, true);
+  }
+
+  /**
+   * Allow an outside entity to initiate the second half of argument parsing
+   * (only).
+   * 
+   * @param args
+   * @return null is good
+   */
+  @Override
+  public Object parseArguments(String[] args)
+  {
+
+    try
+    {
+      ArgsParser aparser = new ArgsParser(args);
+      return parseArguments(aparser, false);
+    } catch (Throwable t)
+    {
+      return t;
+    }
+  }
+
+  /**
+   * 
+   * @param aparser
+   * @param isStartup
+   * @return
+   */
+  private Object parseArguments(ArgsParser aparser, boolean isStartup)
+  {
+    boolean isJS = Platform.isJS();
+
+    Desktop desktop = (headless ? null : Desktop.getInstance());
     // script to execute after all loading is
     // completed one way or another
     // extract groovy argument and execute if necessary
@@ -522,7 +563,6 @@ public class Jalview implements ApplicationSingletonI, JalviewLiteJsApi
     String fileFormat = (isJavaAppletTag
             ? aparser.getAppletValue("format", null)
             : null);
-
     FileFormatI format = null;
     DataSourceType protocol = null;
 
@@ -550,8 +590,11 @@ public class Jalview implements ApplicationSingletonI, JalviewLiteJsApi
       }
     }
 
+    String data;
+
     if (file != null)
     {
+
       if (!headless)
       {
         desktop.setProgressBar(
@@ -598,6 +641,30 @@ public class Jalview implements ApplicationSingletonI, JalviewLiteJsApi
         // TODO ?
       }
 
+      if (aparser.contains(ArgsParser.NOMENUBAR))
+      {
+        noMenuBar = true;
+        System.out.println("CMD [nomenu] executed successfully!");
+      }
+
+      if (aparser.contains(ArgsParser.NOSTATUS))
+      {
+        noStatus = true;
+        System.out.println("CMD [nostatus] executed successfully!");
+      }
+
+      if (aparser.contains(ArgsParser.NOANNOTATION)
+              || aparser.contains(ArgsParser.NOANNOTATION2))
+      {
+        noAnnotation = true;
+        System.out.println("CMD no-annotation executed successfully!");
+      }
+      if (aparser.contains(ArgsParser.NOCALCULATION))
+      {
+        noCalculation = true;
+        System.out.println("CMD [nocalculation] executed successfully!");
+      }
+
       AlignFrame af = new FileLoader(!headless).loadFileWaitTillLoaded(file,
               protocol, format);
       if (af == null)
@@ -639,7 +706,7 @@ public class Jalview implements ApplicationSingletonI, JalviewLiteJsApi
 
         // TODO: file2 How to implement file2 for the applet spit screen?
 
-        String data = aparser.getValue(ArgsParser.COLOUR, true);
+        data = aparser.getValue(ArgsParser.COLOUR, true);
         if (data != null)
         {
           data.replaceAll("%20", " ");
@@ -683,6 +750,13 @@ public class Jalview implements ApplicationSingletonI, JalviewLiteJsApi
           System.out.println(
                   "CMD [-annotations " + data + "] executed successfully!");
         }
+
+        if (aparser.contains(ArgsParser.SHOWOVERVIEW))
+        {
+          af.overviewMenuItem_actionPerformed(null);
+          System.out.println("CMD [showoverview] executed successfully!");
+        }
+
         // set or clear the sortbytree flag.
         if (aparser.contains(ArgsParser.SORTBYTREE))
         {
@@ -692,13 +766,30 @@ public class Jalview implements ApplicationSingletonI, JalviewLiteJsApi
             System.out.println("CMD [-sortbytree] executed successfully!");
           }
         }
-        if (aparser.contains(ArgsParser.NOANNOTATION)
-                || aparser.contains(ArgsParser.NOANNOTATION2))
+
+        boolean doUpdateAnnotation = false;
+
+        /**
+         * we do this earlier in JalviewJS because of a complication with
+         * SHOWOVERVIEW
+         * 
+         * For now, just fixing this in JalviewJS.
+         *
+         * 
+         * @j2sIgnore
+         * 
+         */
         {
-          af.getViewport().setShowAnnotation(false);
-          if (!af.getViewport().isShowAnnotation())
+          if (aparser.contains(ArgsParser.NOANNOTATION)
+                  || aparser.contains(ArgsParser.NOANNOTATION2))
           {
-            System.out.println("CMD no-annotation executed successfully!");
+            af.getViewport().setShowAnnotation(false);
+            if (!af.getViewport().isShowAnnotation())
+            {
+              doUpdateAnnotation = true;
+              System.out
+                      .println("CMD no-annotation executed successfully!");
+            }
           }
         }
         if (aparser.contains(ArgsParser.NOSORTBYTREE))
@@ -706,10 +797,16 @@ public class Jalview implements ApplicationSingletonI, JalviewLiteJsApi
           af.getViewport().setSortByTree(false);
           if (!af.getViewport().getSortByTree())
           {
+            doUpdateAnnotation = true;
             System.out
                     .println("CMD [-nosortbytree] executed successfully!");
           }
         }
+        if (doUpdateAnnotation)
+        { // BH 2019.07.24
+          af.setMenusForViewport();
+          af.alignPanel.updateLayout();
+        }
         data = aparser.getValue(ArgsParser.TREE, true);
         if (data != null)
         {
@@ -837,6 +934,8 @@ public class Jalview implements ApplicationSingletonI, JalviewLiteJsApi
       }
       desktop.setInBatchMode(false);
     }
+
+    return null;
   }
 
   private boolean checkStartVamas(ArgsParser aparser)
@@ -920,7 +1019,8 @@ public class Jalview implements ApplicationSingletonI, JalviewLiteJsApi
         // 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:
+                "Skipping Push for import of data into existing vamsas session.");
+        // TODO:
         // enable
         // this
         // when
@@ -1226,6 +1326,12 @@ public class Jalview implements ApplicationSingletonI, JalviewLiteJsApi
    */
   public void quit()
   {
+    if (jsFunctionExec != null)
+    {
+      jsFunctionExec.tidyUp();
+      jsFunctionExec = null;
+    }
+
     if (desktop != null)
     {
       desktop.quit();
@@ -1264,8 +1370,23 @@ public class Jalview implements ApplicationSingletonI, JalviewLiteJsApi
     JalviewApp app = new JalviewApp()
     {
 
+      // TODO BH 2019
+      //
+      // These are methods that are in JalviewLite that various classes call
+      // but are not in JalviewLiteJsApi. Or, even if they are, other classes
+      // call
+      // them to JalviewLite directly. Some may not be necessary, but they have
+      // to
+      // be at least mentioned here, or the classes calling them should
+      // reference
+      // JalviewLite itself.
+
       private boolean alignPDBStructures; // From JalviewLite; not implemented
 
+      private Hashtable<String, Hashtable<String, String[]>> jsmessages;
+
+      private Hashtable<String, int[]> jshashes;
+
       @Override
       public String getParameter(String name)
       {
@@ -1377,421 +1498,563 @@ public class Jalview implements ApplicationSingletonI, JalviewLiteJsApi
                 "Jalview applet interface newFeatureSettings not implemented");
       }
 
+      private Vector<Runnable> jsExecQueue;
+
+      @Override
+      public Vector<Runnable> getJsExecQueue(JSFunctionExec exec)
+      {
+        jsFunctionExec = exec;
+        return (jsExecQueue == null ? (jsExecQueue = new Vector<>())
+                : jsExecQueue);
+      }
+
+      @Override
+      public AppletContext getAppletContext()
+      {
+        // TODO Auto-generated method stub
+        return null;
+      }
+
+      @Override
+      public boolean isJsfallbackEnabled()
+      {
+        // TODO Auto-generated method stub
+        return false;
+      }
+
+      @Override
+      public JSObject getJSObject()
+      {
+        // TODO Auto-generated method stub
+        return null;
+      }
+
+      @Override
+      public StructureSelectionManagerProvider getStructureSelectionManagerProvider()
+      {
+        // TODO Q: what exactly is this? BH
+        return null;
+      }
+
+      @Override
+      public void updateColoursFromMouseOver(Object source,
+              MouseOverStructureListener mouseOverStructureListener)
+      {
+        // TODO Auto-generated method stub
+
+      }
+
+      @Override
+      public Object[] getSelectionForListener(SequenceGroup seqsel,
+              ColumnSelection colsel, HiddenColumns hidden,
+              SelectionSource source, Object alignFrame)
+      {
+        return appLoader.getSelectionForListener(getCurrentAlignFrame(),
+                seqsel, colsel, hidden, source, alignFrame);
+      }
+
+      @Override
+      public String arrayToSeparatorList(String[] array)
+      {
+        return appLoader.arrayToSeparatorList(array);
+      }
+
+      @Override
+      public Hashtable<String, int[]> getJSHashes()
+      {
+        return (jshashes == null ? (jshashes = new Hashtable<>())
+                : jshashes);
+      }
+
+      @Override
+      public Hashtable<String, Hashtable<String, String[]>> getJSMessages()
+      {
+        return (jsmessages == null ? (jsmessages = new Hashtable<>())
+                : jsmessages);
+      }
+
+      @Override
+      public Object getFrameForSource(VamsasSource source)
+      {
+        if (source != null)
+        {
+          AlignFrame af;
+          if (source instanceof jalview.gui.AlignViewport
+                  && source == (af = getCurrentAlignFrame()).getViewport())
+          {
+            // should be valid if it just generated an event!
+            return af;
+          }
+          // TODO: ensure that if '_af' is specified along with a handler
+          // function, then only events from that alignFrame are sent to that
+          // function
+        }
+        return null;
+      }
+
+      @Override
+      public FeatureRenderer getNewFeatureRenderer(AlignViewportI vp)
+      {
+        return new jalview.gui.FeatureRenderer((AlignmentPanel) vp);
+      }
+
     };
 
-    new JalviewAppLoader(true).load(app);
+    appLoader = new JalviewAppLoader(true);
+    appLoader.load(app);
   }
 
+  /**
+   * 
+   * @see jalview.bin.JalviewLiteJsApi#getSelectedSequences()
+   */
   @Override
   public String getSelectedSequences()
   {
-    // TODO Auto-generated method stub
-    return null;
+    return getSelectedSequencesFrom(getCurrentAlignFrame());
   }
 
+  /**
+   * 
+   * @see jalview.bin.JalviewLiteJsApi#getSelectedSequences(java.lang.String)
+   */
   @Override
   public String getSelectedSequences(String sep)
   {
-    // TODO Auto-generated method stub
-    return null;
+    return getSelectedSequencesFrom(getCurrentAlignFrame(), sep);
   }
 
+  /**
+   * 
+   * @see jalview.bin.JalviewLiteJsApi#getSelectedSequencesFrom(jalview.appletgui
+   *      .AlignFrame)
+   */
   @Override
-  public String getSelectedSequencesFrom(jalview.appletgui.AlignFrame alf)
+  public String getSelectedSequencesFrom(AlignFrameI alf)
   {
-    // TODO Auto-generated method stub
-    return null;
+    return getSelectedSequencesFrom(alf, null);
   }
 
+  /**
+   * 
+   * @see jalview.bin.JalviewLiteJsApi#getSelectedSequencesFrom(jalview.appletgui
+   *      .AlignFrame, java.lang.String)
+   */
   @Override
-  public String getSelectedSequencesFrom(jalview.appletgui.AlignFrame alf,
-          String sep)
+  public String getSelectedSequencesFrom(AlignFrameI alf, String sep)
   {
-    // TODO Auto-generated method stub
-    return null;
+    return appLoader.getSelectedSequencesFrom(alf, sep);
   }
 
+  /**
+   * 
+   * @see jalview.bin.JalviewLiteJsApi#getSelectedSequencesFrom(jalview.appletgui
+   *      .AlignFrame, java.lang.String)
+   */
   @Override
   public void highlight(String sequenceId, String position,
           String alignedPosition)
   {
-    // TODO Auto-generated method stub
-
+    highlightIn(getCurrentAlignFrame(), sequenceId, position,
+            alignedPosition);
   }
 
   @Override
-  public void highlightIn(jalview.appletgui.AlignFrame alf,
-          String sequenceId, String position, String alignedPosition)
+  public void highlightIn(AlignFrameI alf, String sequenceId,
+          String position, String alignedPosition)
   {
-    // TODO Auto-generated method stub
-
+    appLoader.highlightIn(alf, sequenceId, position, alignedPosition);
   }
 
   @Override
   public void select(String sequenceIds, String columns)
   {
-    // TODO Auto-generated method stub
-
+    selectIn(getCurrentAlignFrame(), sequenceIds, columns, null);
   }
 
   @Override
   public void select(String sequenceIds, String columns, String sep)
   {
-    // TODO Auto-generated method stub
-
+    selectIn(getCurrentAlignFrame(), sequenceIds, columns, sep);
   }
 
   @Override
-  public void selectIn(jalview.appletgui.AlignFrame alf, String sequenceIds,
-          String columns)
+  public void selectIn(AlignFrameI alf, String sequenceIds, String columns)
   {
-    // TODO Auto-generated method stub
-
+    selectIn(alf, sequenceIds, columns, null);
   }
 
   @Override
-  public void selectIn(jalview.appletgui.AlignFrame alf, String sequenceIds,
-          String columns, String sep)
+  public void selectIn(AlignFrameI alf, String sequenceIds, String columns,
+          String sep)
   {
-    // TODO Auto-generated method stub
-
+    appLoader.selectIn(alf, sequenceIds, columns, sep);
   }
 
   @Override
   public String getSelectedSequencesAsAlignment(String format,
           String suffix)
   {
-    // TODO Auto-generated method stub
-    return null;
+    return getSelectedSequencesAsAlignmentFrom(getCurrentAlignFrame(),
+            format, suffix);
   }
 
   @Override
-  public String getSelectedSequencesAsAlignmentFrom(
-          jalview.appletgui.AlignFrame alf, String format, String suffix)
+  public String getSelectedSequencesAsAlignmentFrom(AlignFrameI alf,
+          String format, String sep)
   {
-    // TODO Auto-generated method stub
-    return null;
+    return appLoader.getSelectedSequencesAsAlignmentFrom(alf, format, sep);
   }
 
   @Override
   public String getAlignmentOrder()
   {
-    // TODO Auto-generated method stub
-    return null;
+    return getAlignmentFrom(getCurrentAlignFrame(), null);
   }
 
   @Override
-  public String getAlignmentOrderFrom(jalview.appletgui.AlignFrame alf)
+  public String getAlignmentOrderFrom(AlignFrameI alf)
   {
-    // TODO Auto-generated method stub
-    return null;
+    return getAlignmentFrom(alf, null);
   }
 
   @Override
-  public String getAlignmentOrderFrom(jalview.appletgui.AlignFrame alf,
-          String sep)
+  public String getAlignmentOrderFrom(AlignFrameI alf, String sep)
   {
-    // TODO Auto-generated method stub
-    return null;
+    return appLoader.getAlignmentOrderFrom(alf, sep);
   }
 
   @Override
   public String orderBy(String order, String undoName)
   {
-    // TODO Auto-generated method stub
-    return null;
+    return orderBy(order, undoName, null);
   }
 
   @Override
   public String orderBy(String order, String undoName, String sep)
   {
-    // TODO Auto-generated method stub
-    return null;
+    return orderAlignmentBy(getCurrentAlignFrame(), order, undoName, sep);
   }
 
   @Override
-  public String orderAlignmentBy(jalview.appletgui.AlignFrame alf,
-          String order, String undoName, String sep)
+  public String orderAlignmentBy(AlignFrameI alf, String order,
+          String undoName, String sep)
   {
-    // TODO Auto-generated method stub
-    return null;
+    return appLoader.orderAlignmentBy(alf, order, undoName, sep);
   }
 
   @Override
   public String getAlignment(String format)
   {
-    // TODO Auto-generated method stub
-    return null;
+    return getAlignmentFrom(null, format, null);
   }
 
   @Override
-  public String getAlignmentFrom(jalview.appletgui.AlignFrame alf,
-          String format)
+  public String getAlignmentFrom(AlignFrameI alf, String format)
   {
-    // TODO Auto-generated method stub
-    return null;
+    return getAlignmentFrom(alf, format, null);
   }
 
   @Override
   public String getAlignment(String format, String suffix)
   {
-    // TODO Auto-generated method stub
-    return null;
+    return getAlignmentFrom(getCurrentAlignFrame(), format, suffix);
   }
 
   @Override
-  public String getAlignmentFrom(jalview.appletgui.AlignFrame alf,
-          String format, String suffix)
+  public String getAlignmentFrom(AlignFrameI alf, String format,
+          String suffix)
   {
-    // TODO Auto-generated method stub
-    return null;
+    return appLoader.getAlignmentFrom(alf, format, suffix);
   }
 
   @Override
   public void loadAnnotation(String annotation)
   {
-    // TODO Auto-generated method stub
-
+    loadAnnotationFrom(getCurrentAlignFrame(), annotation);
   }
 
   @Override
-  public void loadAnnotationFrom(jalview.appletgui.AlignFrame alf,
-          String annotation)
+  public void loadAnnotationFrom(AlignFrameI alf, String annotation)
   {
-    // TODO Auto-generated method stub
-
+    appLoader.loadAnnotationFrom(alf, annotation);
   }
 
   @Override
   public void loadFeatures(String features, boolean autoenabledisplay)
   {
-    // TODO Auto-generated method stub
-
+    loadFeaturesFrom(currentAlignFrame, features, autoenabledisplay);
   }
 
   @Override
-  public boolean loadFeaturesFrom(jalview.appletgui.AlignFrame alf,
-          String features, boolean autoenabledisplay)
+  public boolean loadFeaturesFrom(AlignFrameI alf, String features,
+          boolean autoenabledisplay)
   {
-    // TODO Auto-generated method stub
-    return false;
+    return appLoader.loadFeaturesFrom(alf, features, autoenabledisplay);
   }
 
   @Override
   public String getFeatures(String format)
   {
-    // TODO Auto-generated method stub
-    return null;
+    return getFeaturesFrom(getCurrentAlignFrame(), format);
   }
 
   @Override
-  public String getFeaturesFrom(jalview.appletgui.AlignFrame alf,
-          String format)
+  public String getFeaturesFrom(AlignFrameI alf, String format)
   {
-    // TODO Auto-generated method stub
-    return null;
+    return appLoader.getFeaturesFrom(alf, format);
   }
 
   @Override
   public String getAnnotation()
   {
-    // TODO Auto-generated method stub
-    return null;
+    return getAnnotationFrom(getCurrentAlignFrame());
   }
 
   @Override
-  public String getAnnotationFrom(jalview.appletgui.AlignFrame alf)
+  public String getAnnotationFrom(AlignFrameI alf)
   {
-    // TODO Auto-generated method stub
-    return null;
+    return appLoader.getAnnotationFrom(alf);
   }
 
   @Override
-  public jalview.appletgui.AlignFrame newView()
+  public AlignFrameI newView()
   {
-    // TODO Auto-generated method stub
-    return null;
+    return newViewFrom(getCurrentAlignFrame(), null);
   }
 
   @Override
-  public jalview.appletgui.AlignFrame newView(String name)
+  public AlignFrameI newView(String name)
   {
-    // TODO Auto-generated method stub
-    return null;
+    return newViewFrom(getCurrentAlignFrame(), name);
   }
 
   @Override
-  public jalview.appletgui.AlignFrame newViewFrom(
-          jalview.appletgui.AlignFrame alf)
+  public AlignFrameI newViewFrom(AlignFrameI alf)
   {
-    // TODO Auto-generated method stub
-    return null;
+    return newViewFrom(alf, null);
   }
 
   @Override
-  public jalview.appletgui.AlignFrame newViewFrom(
-          jalview.appletgui.AlignFrame alf, String name)
+  public AlignFrameI newViewFrom(AlignFrameI alf, String name)
   {
-    // TODO Auto-generated method stub
-    return null;
+    return appLoader.newViewFrom(alf, name);
   }
 
   @Override
-  public jalview.appletgui.AlignFrame loadAlignment(String text,
-          String title)
+  public AlignFrameI loadAlignment(String text, String title)
   {
-    // TODO Auto-generated method stub
-    return null;
+    return appLoader.loadAlignment(text, AlignFrame.DEFAULT_WIDTH,
+            AlignFrame.DEFAULT_HEIGHT, title);
   }
 
   @Override
-  public void setMouseoverListener(String listener)
+  public boolean addPdbFile(AlignFrameI alFrame, String sequenceId,
+          String pdbEntryString, String pdbFile)
   {
-    // TODO Auto-generated method stub
-
+    return appLoader.addPdbFile(alFrame, sequenceId, pdbEntryString,
+            pdbFile);
   }
 
   @Override
-  public void setMouseoverListener(jalview.appletgui.AlignFrame af,
-          String listener)
+  public void scrollViewToIn(AlignFrameI alf, String topRow,
+          String leftHandColumn)
   {
-    // TODO Auto-generated method stub
-
+    appLoader.scrollViewToIn(alf, topRow, leftHandColumn);
   }
 
   @Override
-  public void setSelectionListener(String listener)
+  public void scrollViewToRowIn(AlignFrameI alf, String topRow)
   {
-    // TODO Auto-generated method stub
-
+    appLoader.scrollViewToRowIn(alf, topRow);
   }
 
   @Override
-  public void setSelectionListener(jalview.appletgui.AlignFrame af,
-          String listener)
+  public void scrollViewToColumnIn(AlignFrameI alf, String leftHandColumn)
   {
-    // TODO Auto-generated method stub
+    appLoader.scrollViewToColumnIn(alf, leftHandColumn);
+  }
 
+  @Override
+  public String getFeatureGroups()
+  {
+    return getFeatureGroupsOn(getCurrentAlignFrame());
   }
 
   @Override
-  public void setStructureListener(String listener, String modelSet)
+  public String getFeatureGroupsOn(AlignFrameI alf)
   {
-    // TODO Auto-generated method stub
+    return appLoader.getFeatureGroupsOn(alf);
+  }
 
+  @Override
+  public String getFeatureGroupsOfState(boolean visible)
+  {
+    return getFeatureGroupsOfStateOn(getCurrentAlignFrame(), visible);
   }
 
   @Override
-  public void removeJavascriptListener(jalview.appletgui.AlignFrame af,
-          String listener)
+  public String getFeatureGroupsOfStateOn(AlignFrameI alf, boolean visible)
   {
-    // TODO Auto-generated method stub
+    return appLoader.getFeatureGroupsOfStateOn(alf, visible);
+  }
 
+  @Override
+  public void setFeatureGroupStateOn(AlignFrameI alf, String groups,
+          boolean state)
+  {
+    setFeatureGroupStateOn(alf, groups, state);
   }
 
   @Override
-  public void mouseOverStructure(String pdbResNum, String chain,
-          String pdbfile)
+  public void setFeatureGroupState(String groups, boolean state)
   {
-    // TODO Auto-generated method stub
+    appLoader.setFeatureGroupStateOn(getCurrentAlignFrame(), groups, state);
+  }
 
+  @Override
+  public String getSeparator()
+  {
+    return appLoader.getSeparator();
   }
 
   @Override
-  public boolean addPdbFile(jalview.appletgui.AlignFrame alFrame,
-          String sequenceId, String pdbEntryString, String pdbFile)
+  public void setSeparator(String separator)
   {
-    // TODO Auto-generated method stub
-    return false;
+    appLoader.setSeparator(separator);
   }
 
   @Override
-  public void scrollViewToIn(jalview.appletgui.AlignFrame alf,
-          String topRow, String leftHandColumn)
+  public String getJsMessage(String messageclass, String viewId)
   {
-    // TODO Auto-generated method stub
+    // see http://www.jalview.org/examples/jalviewLiteJs.html
+    return null;
+  }
 
+  /**
+   * Open a new Tree panel on the desktop statically. Params are standard (not
+   * set by Groovy). No dialog is opened.
+   * 
+   * @param af
+   * @param treeType
+   * @param modelName
+   * @return null, or the string "label.you_need_at_least_n_sequences" if number
+   *         of sequences selected is inappropriate
+   */
+  @Override
+  public Object openTreePanel(AlignFrame af, String treeType,
+          String modelName)
+  {
+    return CalculationChooser.openTreePanel(af, treeType, modelName, null);
   }
 
+  /**
+   * public static method for JalviewJS API to open a PCAPanel without
+   * necessarily using a dialog.
+   * 
+   * @param af
+   * @param modelName
+   * @return the PCAPanel, or the string "label.you_need_at_least_n_sequences"
+   *         if number of sequences selected is inappropriate
+   */
   @Override
-  public void scrollViewToRowIn(jalview.appletgui.AlignFrame alf,
-          String topRow)
+  public Object openPcaPanel(AlignFrame af, String modelName)
   {
-    // TODO Auto-generated method stub
+    return CalculationChooser.openPcaPanel(af, modelName, null);
+  }
 
+  @Override
+  public String getSelectedSequencesAsAlignment(String format,
+          boolean suffix)
+  {
+    return getSelectedSequencesAsAlignmentFrom(getCurrentAlignFrame(),
+            format, suffix);
   }
 
   @Override
-  public void scrollViewToColumnIn(jalview.appletgui.AlignFrame alf,
-          String leftHandColumn)
+  public String getSelectedSequencesAsAlignmentFrom(AlignFrameI alf,
+          String format, boolean suffix)
   {
-    // TODO Auto-generated method stub
+    return appLoader.getSelectedSequencesAsAlignmentFrom(alf, format,
+            "" + suffix);
+  }
 
+  @Override
+  public String arrayToSeparatorList(String[] array)
+  {
+    return appLoader.arrayToSeparatorList(array);
   }
 
   @Override
-  public String getFeatureGroups()
+  public String[] separatorListToArray(String list)
   {
-    // TODO Auto-generated method stub
-    return null;
+    return appLoader.separatorListToArray(list);
   }
 
+  //// probably not needed in JalviewJS -- From when Jmol and Jalview did not
+  //// have a direct connection?
+
   @Override
-  public String getFeatureGroupsOn(jalview.appletgui.AlignFrame alf)
+  public void setMouseoverListener(String listener)
   {
     // TODO Auto-generated method stub
-    return null;
+
   }
 
   @Override
-  public String getFeatureGroupsOfState(boolean visible)
+  public void setMouseoverListener(AlignFrameI af, String listener)
   {
     // TODO Auto-generated method stub
-    return null;
+
   }
 
   @Override
-  public String getFeatureGroupsOfStateOn(jalview.appletgui.AlignFrame alf,
-          boolean visible)
+  public void setSelectionListener(String listener)
   {
     // TODO Auto-generated method stub
-    return null;
+
   }
 
   @Override
-  public void setFeatureGroupStateOn(jalview.appletgui.AlignFrame alf,
-          String groups, boolean state)
+  public void setSelectionListener(AlignFrameI af, String listener)
   {
     // TODO Auto-generated method stub
 
   }
 
   @Override
-  public void setFeatureGroupState(String groups, boolean state)
+  public void setStructureListener(String listener, String modelSet)
   {
     // TODO Auto-generated method stub
 
   }
 
   @Override
-  public String getSeparator()
+  public void removeJavascriptListener(AlignFrameI af, String listener)
   {
     // TODO Auto-generated method stub
-    return null;
+
   }
 
   @Override
-  public void setSeparator(String separator)
+  public void mouseOverStructure(String pdbResNum, String chain,
+          String pdbfile)
   {
     // TODO Auto-generated method stub
 
   }
 
   @Override
-  public String getJsMessage(String messageclass, String viewId)
+  public void showOverview()
   {
-    // TODO Auto-generated method stub
-    return null;
+    currentAlignFrame.overviewMenuItem_actionPerformed(null);
+  }
+
+  public void notifyWorker(AlignCalcWorkerI worker, String status)
+  {
+    // System.out.println("Jalview worker " + worker.getClass().getSimpleName()
+    // + " " + status);
   }
 
 }
+