/*
 * Jalview - A Sequence Alignment Editor and Viewer
 * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
 *
 * This program is free software; you can redistribute it and/or
 * modify it under the terms of the GNU General Public License
 * as published by the Free Software Foundation; either version 2
 * of the License, or (at your option) any later version.
 *
 * This program is distributed in the hope that it will be useful,
 * but WITHOUT ANY WARRANTY; without even the implied warranty of
 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 * GNU General Public License for more details.
 *
 * You should have received a copy of the GNU General Public License
 * along with this program; if not, write to the Free Software
 * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
 */
package jalview.bin;

import java.applet.*;

import java.awt.*;
import java.awt.event.*;
import java.util.*;

import jalview.appletgui.*;
import jalview.datamodel.*;
import jalview.io.*;

/**
 * Jalview Applet. Runs in Java 1.18 runtime
 *
 * @author $author$
 * @version $Revision$
 */
public class JalviewLite
    extends Applet
{



  ///////////////////////////////////////////
  //The following public methods maybe called
  //externally, eg via javascript in HTML page
  /**
   * @return String list of selected sequence IDs, each terminated by "¬" (¬)
   */
  public String getSelectedSequences()
  {
    return getSelectedSequencesFrom(getDefaultTargetFrame());
  }
  /**
   * @param sep separator string or null for default
   * @return String list of selected sequence IDs, each terminated by sep or ("¬" as default)
   */
  public String getSelectedSequences(String sep)
  {
    return getSelectedSequencesFrom(getDefaultTargetFrame(), sep);
  }
  /**
   * @param alf alignframe containing selection
   * @return String list of selected sequence IDs, each terminated by "¬"
   *  
   */
  public String getSelectedSequencesFrom(AlignFrame alf)
  {
    return getSelectedSequencesFrom(alf, "¬");
  }
  /**
   * get list of selected sequence IDs separated by given separator 
   * @param alf window containing selection 
   * @param sep separator string to use - default is "¬"
   * @return String list of selected sequence IDs, each terminated by the given separator
   */
  public String getSelectedSequencesFrom(AlignFrame alf, String sep)
  {
    StringBuffer result = new StringBuffer("");
    if (sep==null || sep.length()==0)
    {
      sep = "¬";
    }
    if (alf.viewport.getSelectionGroup() != null)
    {
      SequenceI[] seqs = alf.viewport.getSelectionGroup().
          getSequencesInOrder(
                  alf.viewport.getAlignment());

      for (int i = 0; i < seqs.length; i++)
      {
        result.append(seqs[i].getName());
        result.append(sep); 
      }
    }

    return result.toString();
  }

  /**
   * get sequences selected in current alignFrame and return their alignment in format 'format' either with or without suffix 
   * @param alf - where selection is
   * @param format - format of alignment file
   * @param suffix - "true" to append /start-end string to each sequence ID 
   * @return selected sequences as flat file or empty string if there was no current selection
   */
  public String getSelectedSequencesAsAlignment(String format, String suffix) {
    return getSelectedSequencesAsAlignmentFrom(currentAlignFrame, format, suffix);
  }

  /**
   * get sequences selected in alf and return their alignment in format 'format' either with or without suffix 
   * @param alf - where selection is
   * @param format - format of alignment file
   * @param suffix - "true" to append /start-end string to each sequence ID 
   * @return selected sequences as flat file or empty string if there was no current selection
   */
  public String getSelectedSequencesAsAlignmentFrom(AlignFrame alf, String format, String suffix)
  {
    try
    {
      boolean seqlimits = suffix.equalsIgnoreCase("true");
      if (alf.viewport.getSelectionGroup()!=null)
      {
        String reply = new AppletFormatAdapter().formatSequences(format,
                new Alignment(alf.viewport.getSelectionAsNewSequence()), seqlimits);
        return reply;
      }
    }
    catch (Exception ex)
    {
      ex.printStackTrace();
      return "Error retrieving alignment in " + format + " format. ";
    }
    return "";
  }

  public String getAlignment(String format)
  {
    return getAlignmentFrom(getDefaultTargetFrame(), format, "true");
  }
  public String getAlignmentFrom(AlignFrame alf, String format)
  {
    return getAlignmentFrom(alf, format, "true");
  }
  public String getAlignment(String format, String suffix)
  {
    return getAlignmentFrom(getDefaultTargetFrame(), format, suffix);
  }
  public String getAlignmentFrom(AlignFrame alf, String format, String suffix)
  {
    try
    {
      boolean seqlimits = suffix.equalsIgnoreCase("true");

      String reply = new AppletFormatAdapter().formatSequences(format,
          alf.viewport.getAlignment(), seqlimits);
      return reply;
    }
    catch (Exception ex)
    {
      ex.printStackTrace();
      return "Error retrieving alignment in " + format + " format. ";
    }
  }

  public void loadAnnotation(String annotation)
  {
    loadAnnotationFrom(getDefaultTargetFrame(), annotation);
  }
  public void loadAnnotationFrom(AlignFrame alf, String annotation)
  {
    if (new AnnotationFile().readAnnotationFile(
        alf.getAlignViewport().getAlignment(), annotation,
        AppletFormatAdapter.PASTE))
    {
      alf.alignPanel.fontChanged();
      alf.alignPanel.setScrollValues(0, 0);
    }
    else
    {
      alf.parseFeaturesFile(annotation, AppletFormatAdapter.PASTE);
    }
  }

  public String getFeatures(String format)
  {
    return getFeaturesFrom(getDefaultTargetFrame(), format);
  }
  public String getFeaturesFrom(AlignFrame alf, String format)
  {
    return alf.outputFeatures(false, format);
  }
  public String getAnnotation()
  {
    return getAnnotationFrom(getDefaultTargetFrame());
  }
  public String getAnnotationFrom(AlignFrame alf)
  {
    return alf.outputAnnotations(false);
  }
  public AlignFrame newView()
  {
    return newViewFrom(getDefaultTargetFrame());
  }
  public AlignFrame newView(String name)
  {
    return newViewFrom(getDefaultTargetFrame(), name);
  }

  public AlignFrame newViewFrom(AlignFrame alf)
  {
    return alf.newView(null);
  }
  public AlignFrame newViewFrom(AlignFrame alf, String name)
  {
    return alf.newView(name);
  }
  /**
   * 
   * @param text alignment file as a string
   * @param title window title 
   * @return null or new alignment frame
   */
  public AlignFrame loadAlignment(String text, String title)
  {
    Alignment al = null;
    String format = new IdentifyFile().Identify(text, AppletFormatAdapter.PASTE);
    try
    {
      al = new AppletFormatAdapter().readFile(text,
                                              AppletFormatAdapter.PASTE,
                                              format);
      if (al.getHeight() > 0)
      {
        return new AlignFrame(al, this, title, false);
      }
    }
    catch (java.io.IOException ex)
    {
      ex.printStackTrace();
    }
    return null;
  }

  ////////////////////////////////////////////////
  ////////////////////////////////////////////////



  static int lastFrameX = 200;
  static int lastFrameY = 200;
  boolean fileFound = true;
  String file = "No file";
  Button launcher = new Button("Start Jalview");

  /**
   * The currentAlignFrame is static, it will change
   * if and when the user selects a new window.
   * Note that it will *never* point back to the embedded AlignFrame 
   * if the applet is started as embedded on the page and then afterwards a new view is created.
   */
  public static AlignFrame currentAlignFrame;

  /** 
   * This is the first frame to be displayed, and does not change.
   * API calls will default to this instance if currentAlignFrame is null.
   */
  AlignFrame initialAlignFrame;

  boolean embedded = false;

  public boolean jmolAvailable = false;
  public static boolean debug;

  /**
   * init method for Jalview Applet
   */
  public void init()
  {
    String dbg = getParameter("debug");
    if (dbg!=null)
    {
      debug = dbg.toLowerCase().equals("true");
    }
    /**
     * get the separator parameter if present
     */
    String sep = getParameter("separator");
    if (sep!=null)
    {
      if (sep.length()>0)
      {      separator = sep;
        if (debug)
        {
          System.err.println("Separator set to '"+separator+"'");
        }
      } else {
        throw new Error("Invalid separator parameter - must be non-zero length");
      }
    }
    int r = 255;
    int g = 255;
    int b = 255;
    String param = getParameter("RGB");

    if (param != null)
    {
      try
      {
        r = Integer.parseInt(param.substring(0, 2), 16);
        g = Integer.parseInt(param.substring(2, 4), 16);
        b = Integer.parseInt(param.substring(4, 6), 16);
      }
      catch (Exception ex)
      {
        r = 255;
        g = 255;
        b = 255;
      }
    }

    param = getParameter("label");
    if (param != null)
    {
      launcher.setLabel(param);
    }

    this.setBackground(new Color(r, g, b));

    file = getParameter("file");

    if (file == null)
    {
      //Maybe the sequences are added as parameters
      StringBuffer data = new StringBuffer("PASTE");
      int i = 1;
      while ( (file = getParameter("sequence" + i)) != null)
      {
        data.append(file.toString() + "\n");
        i++;
      }
      if (data.length() > 5)
      {
        file = data.toString();
      }
    }

    LoadJmolThread jmolAvailable = new LoadJmolThread();
    jmolAvailable.start();

    final JalviewLite applet = this;
    if (getParameter("embedded") != null
        && getParameter("embedded").equalsIgnoreCase("true"))
    {
      embedded = true;
      LoadingThread loader = new LoadingThread(file, applet);
      loader.start();
    }
    else if (file != null)
    {
      add(launcher);

      launcher.addActionListener(new java.awt.event.ActionListener()
      {
        public void actionPerformed(ActionEvent e)
        {
          LoadingThread loader = new LoadingThread(file,
              applet);
          loader.start();
        }
      });
    }
    else
    {
      file = "NO FILE";
      fileFound = false;
    }
  }


  /**
   * Initialises and displays a new java.awt.Frame
   *
   * @param frame java.awt.Frame to be displayed
   * @param title title of new frame
   * @param width width if new frame
   * @param height height of new frame
   */
  public static void addFrame(final Frame frame, String title, int width,
                              int height)
  {
    frame.setLocation(lastFrameX, lastFrameY);
    lastFrameX += 40;
    lastFrameY += 40;
    frame.setSize(width, height);
    frame.setTitle(title);
    frame.addWindowListener(new WindowAdapter()
    {
      public void windowClosing(WindowEvent e)
      {
        if (frame instanceof AlignFrame)
        {
          ( (AlignFrame) frame).closeMenuItem_actionPerformed();
        }
        if (currentAlignFrame == frame)
        {
          currentAlignFrame = null;
        }
        lastFrameX -= 40;
        lastFrameY -= 40;
        if (frame instanceof EmbmenuFrame)
        {
          ((EmbmenuFrame) frame).destroyMenus();
        }
        frame.setMenuBar(null);
        frame.dispose();
      }
      
      public void windowActivated(WindowEvent e)
      {
        if (frame instanceof AlignFrame)
        {
          currentAlignFrame = (AlignFrame) frame;
          if (debug)
          {
            System.err.println("Activated window "+frame);
          }
        }
        // be good.
        super.windowActivated(e);
      }
      /* Probably not necessary to do this - see TODO above.
       * (non-Javadoc)
       * @see java.awt.event.WindowAdapter#windowDeactivated(java.awt.event.WindowEvent)
       *
      public void windowDeactivated(WindowEvent e)
      {
        if (currentAlignFrame == frame)
        {
          currentAlignFrame = null;
          if (debug)
          {
            System.err.println("Deactivated window "+frame);
          }
        }
        super.windowDeactivated(e);
      }
       */
    });
    frame.setVisible(true);
  }

  /**
   * This paints the background surrounding the "Launch Jalview button"
   * <br>
   * <br>If file given in parameter not found, displays error message
   *
   * @param g graphics context
   */
  public void paint(Graphics g)
  {
    if (!fileFound)
    {
      g.setColor(new Color(200, 200, 200));
      g.setColor(Color.cyan);
      g.fillRect(0, 0, getSize().width, getSize().height);
      g.setColor(Color.red);
      g.drawString("Jalview can't open file", 5, 15);
      g.drawString("\"" + file + "\"", 5, 30);
    }
    else if (embedded)
    {
      g.setColor(Color.black);
      g.setFont(new Font("Arial", Font.BOLD, 24));
      g.drawString("Jalview Applet", 50, this.getSize().height / 2 - 30);
      g.drawString("Loading Data...", 50, this.getSize().height / 2);
    }
  }


  class LoadJmolThread extends Thread
  {
    public void run()
    {
      try
      {
        if (!System.getProperty("java.version").startsWith("1.1"))
        {
          Class.forName("org.jmol.adapter.smarter.SmarterJmolAdapter");
          jmolAvailable = true;
        }
      }
      catch (java.lang.ClassNotFoundException ex)
      {
        System.out.println("Jmol not available - Using MCview for structures");
      }
    }
  }


  class LoadingThread
      extends Thread
  {
    /**
     * State variable: File source 
     */
    String file; 
    /**
     * State variable: protocol for access to file source
     */
    String protocol;
    /**
     * State variable: format of file source
     */
    String format;
    JalviewLite applet;
    private void dbgMsg(String msg)
    {
      if (applet.debug)
      {
        System.err.println(msg);
      }
    }
    /**
     * update the protocol state variable for accessing the datasource
     * located by file. 
     * @param file
     * @return possibly updated datasource string
     */
    public String setProtocolState(String file)
    {
      if (file.startsWith("PASTE"))
      {
        file = file.substring(5);
        protocol = AppletFormatAdapter.PASTE;
      }
      else if (inArchive(file))
      {
        protocol = AppletFormatAdapter.CLASSLOADER;
      }
      else
      {
        file = addProtocol(file);
        protocol = AppletFormatAdapter.URL;
      }
      dbgMsg("Protocol identified as '"+protocol+"'");
      return file;
    }
    public LoadingThread(String _file,
                         JalviewLite _applet)
    {
      dbgMsg("Loading thread started with:\n>>file\n"+_file+">>endfile");
      file = setProtocolState(_file);
      
      format = new jalview.io.IdentifyFile().Identify(file, protocol);
      dbgMsg("File identified as '"+format+"'");
      applet = _applet;
    }

    public void run()
    {
      startLoading();
    }

    private void startLoading()
    {
      dbgMsg("Loading started.");
      Alignment al = null;
      try
      {
        al = new AppletFormatAdapter().readFile(file, protocol,
                                                format);
      }
      catch (java.io.IOException ex)
      {
        dbgMsg("File load exception.");
        ex.printStackTrace();
      }
      if ( (al != null) && (al.getHeight() > 0))
      {
        dbgMsg("Successfully loaded file.");
        initialAlignFrame =  new AlignFrame(al,
                                           applet,
                                           file,
                                           embedded);
        // update the focus.
        currentAlignFrame = initialAlignFrame;

        if (protocol == jalview.io.AppletFormatAdapter.PASTE)
        {
          currentAlignFrame.setTitle("Sequences from " + getDocumentBase());
        }

        currentAlignFrame.statusBar.setText("Successfully loaded file " + file);

        String treeFile = applet.getParameter("tree");
        if (treeFile == null)
        {
          treeFile = applet.getParameter("treeFile");
        }

        if (treeFile != null)
        {
          try
          {
            treeFile = setProtocolState(treeFile);
            /*if (inArchive(treeFile))
            {
              protocol = AppletFormatAdapter.CLASSLOADER;
            }
            else
            {
              protocol = AppletFormatAdapter.URL;
              treeFile = addProtocol(treeFile);
            }
             */
            jalview.io.NewickFile fin = new jalview.io.NewickFile(treeFile,
                protocol);

            fin.parse();

            if (fin.getTree() != null)
            {
              currentAlignFrame.loadTree(fin, treeFile);
              dbgMsg("Successfuly imported tree.");
            } else {
              dbgMsg("Tree parameter did not resolve to a valid tree.");
            }
          }
          catch (Exception ex)
          {
            ex.printStackTrace();
          }
        }

        String param = getParameter("features");
        if (param != null)
        {
          param = setProtocolState(param);
          
          currentAlignFrame.parseFeaturesFile(param, protocol);
        }

        param = getParameter("showFeatureSettings");
        if (param != null && param.equalsIgnoreCase("true"))
        {
          currentAlignFrame.viewport.showSequenceFeatures(true);
          new FeatureSettings(currentAlignFrame.alignPanel);
        }

        param = getParameter("annotations");
        if (param != null)
        { 
          param = setProtocolState(param);
          
          if (new AnnotationFile().readAnnotationFile(
              currentAlignFrame.viewport.getAlignment(),
              param,
              protocol))
          {
            currentAlignFrame.alignPanel.fontChanged();
            currentAlignFrame.alignPanel.setScrollValues(0, 0);
          } else {
            System.err.println("Annotations were not added from annotation file '"+param+"'");
          }

        }

        param = getParameter("jnetfile");
        if (param != null)
        {
          try
          {
            param = setProtocolState(param);
            jalview.io.JPredFile predictions = new jalview.io.JPredFile(
                param, protocol);
            JnetAnnotationMaker.add_annotation(predictions,
                currentAlignFrame.viewport.getAlignment(),
                0, false); // false==do not add sequence profile from concise output
            currentAlignFrame.alignPanel.fontChanged();
            currentAlignFrame.alignPanel.setScrollValues(0, 0);
          }
          catch (Exception ex)
          {
            ex.printStackTrace();
          }
        }

        /*
         <param name="PDBfile" value="1gaq.txt PDB|1GAQ|1GAQ|A PDB|1GAQ|1GAQ|B PDB|1GAQ|1GAQ|C">

         <param name="PDBfile2" value="1gaq.txt A=SEQA B=SEQB C=SEQB">

         <param name="PDBfile3" value="1q0o Q45135_9MICO">
        */


        int pdbFileCount = 0;
        do{
          if (pdbFileCount > 0)
            param = getParameter("PDBFILE" + pdbFileCount);
          else
            param = getParameter("PDBFILE");

          if (param != null)
          {
            PDBEntry pdb = new PDBEntry();

            String seqstring;
            SequenceI[] seqs = null;
            String [] chains = null;

            StringTokenizer st = new StringTokenizer(param, " ");

            if (st.countTokens() < 2)
            {
              String sequence = applet.getParameter("PDBSEQ");
              if (sequence != null)
                seqs = new SequenceI[]
                    {
                    (Sequence) currentAlignFrame.
                    getAlignViewport().getAlignment().
                    findName(sequence)};

            }
            else
            {
              param = st.nextToken();
              Vector tmp = new Vector();
              Vector tmp2 = new Vector();

              while (st.hasMoreTokens())
              {
                seqstring = st.nextToken();
                StringTokenizer st2 = new StringTokenizer(seqstring,"=");
                if(st2.countTokens()>1)
                {
                  //This is the chain
                  tmp2.addElement(st2.nextToken());
                  seqstring = st2.nextToken();
                }
                tmp.addElement( (Sequence) currentAlignFrame.
                                 getAlignViewport().getAlignment().
                                 findName(seqstring));
              }

              seqs = new SequenceI[tmp.size()];
              tmp.copyInto(seqs);
              if(tmp2.size()==tmp.size())
              {
                chains = new String[tmp2.size()];
                tmp2.copyInto(chains);
              }
            }
            param = setProtocolState(param);
            
            if (!jmolAvailable && protocol==AppletFormatAdapter.CLASSLOADER)
            {
              // TODO: pass PDB file in classloader on to Jmol
              // This exception preserves the current behaviour where, even if the local pdb file was identified in the class loader
              protocol = AppletFormatAdapter.URL; // this is probably NOT CORRECT!
              param = addProtocol(param); // 
            }

            pdb.setFile(param);

            if(seqs!=null)
            {
              for (int i = 0; i < seqs.length; i++)
              {
                if (seqs[i]!=null)
                {
                  ( (Sequence) seqs[i]).addPDBId(pdb);
                } else {
                  if (JalviewLite.debug)
                  {
                    // this may not really be a problem but we give a warning anyway
                    System.err.println("Warning: Possible input parsing error: Null sequence for attachment of PDB (sequence "+i+")");
                  }
                }
              }

              if (jmolAvailable)
              {
                new jalview.appletgui.AppletJmol(pdb,
                                                 seqs,
                                                 chains,
                                                 currentAlignFrame.alignPanel,
                                                 protocol);
                lastFrameX += 40;
                lastFrameY+=40;
              }
              else
                    new MCview.AppletPDBViewer(pdb,
                                           seqs,
                                           chains,
                                           currentAlignFrame.alignPanel,
                                           protocol);
            }
          }

          pdbFileCount++;
        }
        while(pdbFileCount < 10);
        
        /////////////////////////////
        // modify display of features
        //
        // hide specific groups
        param = getParameter("hidefeaturegroups");
        if (param != null)
        {
          applet.setFeatureGroupState(param, false);
        }
        // show specific groups
        param = getParameter("showfeaturegroups");
        if (param != null)
        {
          applet.setFeatureGroupState(param, true);
        }
      }
      else
      {
        fileFound = false;
        remove(launcher);
        repaint();
      }
    }

    /**
     * Discovers whether the given file is in the Applet Archive
     * @param file String
     * @return boolean
     */
    boolean inArchive(String file)
    {
      //This might throw a security exception in certain browsers
      //Netscape Communicator for instance.
      try
      {
        boolean rtn = (getClass().getResourceAsStream("/" + file) != null);
        if (debug)
        {  System.err.println("Resource '"+file+"' was "+(rtn ? "" : "not") +" located by classloader.");
        }
        return rtn;
      }
      catch (Exception ex)
      {
        System.out.println("Exception checking resources: " + file + " " + ex);
        return false;
      }
    }

    String addProtocol(String file)
    {
      if (file.indexOf("://") == -1)
      {
        file = getCodeBase() + file;
        if (debug)
        {
          System.err.println("Prepended codebase for resource: '"+file+"'");
        }
      }

      return file;
    }
  }
  /**
   * @return the default alignFrame acted on by the public applet methods.
   * May return null with an error message on System.err indicating the fact. 
   */
  protected AlignFrame getDefaultTargetFrame()
  {
    if (currentAlignFrame!=null)
    {
      return currentAlignFrame;
    }
    if (initialAlignFrame!=null)
    {
      return initialAlignFrame;
    }
    System.err.println("Implementation error: Jalview Applet API cannot work out which AlignFrame to use.");
    return null;
  }
  /**
   * separator used for separatorList
   */
  protected String separator = "|"; // this is a safe(ish) separator - tabs don't work for firefox
  /**
   * parse the string into a list
   * @param list
   * @return elements separated by separator
   */
  public String[] separatorListToArray(String list)
  {
    int seplen = separator.length();
    if (list==null || list.equals(""))
      return null;
    java.util.Vector jv = new Vector();
    int cp=0,pos;
    while ((pos=list.indexOf(separator,cp))>cp)
    {
      jv.addElement(list.substring(cp,pos));
      cp = pos+seplen;
    }
    if (cp<list.length())
    {
      jv.addElement(list.substring(cp));
    }
    if (jv.size()>0)
    { String[] v = new String[jv.size()];
      for (int i=0; i<v.length; i++)
      {
        v[i] = (String) jv.elementAt(i);
      }
      jv.removeAllElements();
      if (debug)
      {
        System.err.println("Array from '"+separator+"' separated List:\n"+v.length);
        for (int i=0; i<v.length;i++)
        {
          System.err.println("item "+i+" '"+v[i]+"'");
        }
      }
      return v;
    }
    if (debug)
    {
      System.err.println("Empty Array from '"+separator+"' separated List");
    }
    return null;
  }
  /**
   * concatenate the list with separator
   * @param list
   * @return concatenated string
   */
  public String arrayToSeparatorList(String[] list)
  {
    StringBuffer v = new StringBuffer();
    if (list!=null)
    {
      for (int i=0,iSize=list.length-1;i<iSize;i++)
      { 
        if (list[i]!=null)
        {  
          v.append(list[i]); 
        }
        v.append(separator);
      }
      if (list[list.length-1]!=null)
      { v.append(list[list.length-1]);
      }
      if (debug)
      {
        System.err.println("Returning '"+separator+"' separated List:\n");
        System.err.println(v);
      }
      return v.toString();
    }
    if (debug)
    {
      System.err.println("Returning empty '"+separator+"' separated List\n");
    }
    return "";
  }
  /**
   * @return
   * @see jalview.appletgui.AlignFrame#getFeatureGroups()
   */
  public String getFeatureGroups()
  {
    String lst = arrayToSeparatorList(getDefaultTargetFrame().getFeatureGroups());
    return lst;
  }
  /**
   * @param alf alignframe to get feature groups on
   * @return
   * @see jalview.appletgui.AlignFrame#getFeatureGroups()
   */
  public String getFeatureGroupsOn(AlignFrame alf)
  {
    String lst = arrayToSeparatorList(alf.getFeatureGroups());
    return lst;
  }
  /**
   * @param visible
   * @return
   * @see jalview.appletgui.AlignFrame#getFeatureGroupsOfState(boolean)
   */
  public String getFeatureGroupsOfState(boolean visible)
  {
    return arrayToSeparatorList(getDefaultTargetFrame().getFeatureGroupsOfState(visible));
  }
  /**
   * @param alf align frame to get groups of state visible
   * @param visible
   * @return
   * @see jalview.appletgui.AlignFrame#getFeatureGroupsOfState(boolean)
   */
  public String getFeatureGroupsOfStateOn(AlignFrame alf, boolean visible)
  {
    return arrayToSeparatorList(alf.getFeatureGroupsOfState(visible));
  }  /**
   * @param groups tab separated list of group names 
   * @param state true or false
   * @see jalview.appletgui.AlignFrame#setFeatureGroupState(java.lang.String[], boolean)
   */
  public void setFeatureGroupStateOn(AlignFrame alf, String groups, boolean state)
  {
    boolean st = state;//!(state==null || state.equals("") || state.toLowerCase().equals("false"));
    alf.setFeatureGroupState(separatorListToArray(groups), st);
  }
  public void setFeatureGroupState(String groups, boolean state)
  {
    setFeatureGroupStateOn(getDefaultTargetFrame(), groups, state);
  }
  /**
   * List separator string
   * @return the separator
   */
  public String getSeparator()
  {
    return separator;
  }
  /**
   * List separator string
   * @param separator the separator to set
   */
  public void setSeparator(String separator)
  {
    this.separator = separator;
  }
}