/*
* Jalview - A Sequence Alignment Editor and Viewer
* Copyright (C) 2006 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 jalview.appletgui.AlignFrame;

import jalview.datamodel.*;

import jalview.io.*;

import java.applet.*;

import java.awt.*;
import java.awt.event.*;
import jalview.appletgui.FeatureSettings;


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

    //This is the first frame to be displayed, and does not change
    AlignFrame initialAlignFrame;

    boolean embedded = false;


    /**
     * init method for Jalview Applet
     */
    public void init()
    {
        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();
        }

        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;
        }
    }


    public static void main(String [] args)
    {
      if(args.length!=1)
      {
        System.out.println("\nUsage: java -jar jalviewApplet.jar fileName\n");
        System.exit(1);
      }

      String format = new jalview.io.IdentifyFile().Identify(args[0],AppletFormatAdapter.FILE);

      SequenceI[] sequences = null;
     try{
       sequences = new AppletFormatAdapter().readFile(args[0], AppletFormatAdapter.FILE, format);
     }catch(java.io.IOException ex)
     {
       ex.printStackTrace();
     }
      if ( (sequences != null) && (sequences.length > 0))
      {
        AlignFrame af = new AlignFrame(new Alignment(sequences), null, args[0], false);
        af.statusBar.setText("Successfully loaded file " + args[0]);
      }
    }


    /**
     * 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;
                    frame.setMenuBar(null);
                    frame.dispose();
                }
                public void windowActivated(WindowEvent e)
                {
                  if(frame instanceof AlignFrame)
                    currentAlignFrame = (AlignFrame)frame;
                }

            });
        frame.setVisible(true);
    }

    public String getSelectedSequences()
    {
      StringBuffer result = new StringBuffer("");

      if(initialAlignFrame.viewport.getSelectionGroup()!=null)
      {
        SequenceI[] seqs = initialAlignFrame.viewport.getSelectionGroup().
            getSequencesInOrder(
                initialAlignFrame.viewport.getAlignment());

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

      return result.toString();
    }

    public String getAlignment(String format)
    {
      return getAlignment(format, "true");
    }

    public String getAlignment(String format, String suffix)
    {
      try
      {
        boolean seqlimits = suffix.equalsIgnoreCase("true");

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

    /**
     * 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.size().height/2 -30);
          g.drawString("Loading Data...", 50, this.size().height/2);
        }


    }

    class LoadingThread extends Thread
    {
        String file;
        String protocol;
        String format;
        JalviewLite applet;

        public LoadingThread(String _file,
                             JalviewLite _applet)
        {
            file = _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;
            }
            format = new jalview.io.IdentifyFile().Identify(file, protocol);
            applet = _applet;
        }

        public void run()
        {
            SequenceI[] sequences = null;
            try{
              sequences = new AppletFormatAdapter().readFile(file, protocol,
                  format);
            }catch(java.io.IOException ex)
            {
              ex.printStackTrace();
            }
            if ((sequences != null) && (sequences.length > 0))
            {
              currentAlignFrame = new AlignFrame(new Alignment(sequences),
                                                 applet,
                                                 file,
                                                 embedded);

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

              initialAlignFrame = currentAlignFrame;

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


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

                if (treeFile != null)
                {
                  try
                  {
                    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);
                    }
                  }
                  catch (Exception ex)
                  {
                    ex.printStackTrace();
                  }
              }

              String param = getParameter("features");
              if (param != null)
              {
                if( !inArchive(param) )
                  param = addProtocol( 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)
             {
               if( !inArchive(param) )
                  param = addProtocol( param );

               new AnnotationFile().readAnnotationFile(
                   currentAlignFrame.viewport.getAlignment(),
                   param);

               currentAlignFrame.alignPanel.fontChanged();
               currentAlignFrame.alignPanel.setScrollValues(0,0);

             }

             param = getParameter("jnetfile");
             if (param != null)
             {
               try
               {
                 if (inArchive(param))
                   protocol = AppletFormatAdapter.CLASSLOADER;
                 else
                 {
                   protocol = AppletFormatAdapter.URL;
                   param = addProtocol(param);
                 }

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


                String pdbfile = applet.getParameter("PDBFILE");
                if(pdbfile!=null)
                {
                  if( inArchive(pdbfile) )
                    protocol = AppletFormatAdapter.CLASSLOADER;
                  else
                  {
                    protocol = AppletFormatAdapter.URL;
                    pdbfile = addProtocol(pdbfile);
                  }

                  String sequence = applet.getParameter("PDBSEQ");

                  if(sequence!=null)
                  {
                    new MCview.AppletPDBViewer(pdbfile, protocol,
                                               (Sequence)currentAlignFrame.getAlignViewport().getAlignment().findName(sequence),
                                               currentAlignFrame.getSeqcanvas());
                  }

                }
            }
            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{
            return (getClass().getResourceAsStream("/" + file) != null);
          }catch(Exception ex)
          {
            System.out.println("Exception checking resources: "+file+" "+ex);
            return false;
          }
        }

        String addProtocol(String file)
        {
          if (file.indexOf("://") == -1)
             file = getCodeBase() + file;

          return file;
        }

    }
}