/*
* Jalview - A Sequence Alignment Editor and Viewer
* Copyright (C) 2005 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.TreePanel;


/**
 * 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");

    static AlignFrame currentAlignFrame;
    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.indexOf("://")==-1)
               file = getCodeBase() + file;

        final JalviewLite applet = this;
        if(getParameter("embedded")!=null
           && getParameter("embedded").equalsIgnoreCase("true"))
        {
          embedded = true;
          LoadingThread loader = new LoadingThread(file,
                            "URL",
                            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,
                            "URL",
                            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 = jalview.io.IdentifyFile.Identify(args[0],"File");
      SequenceI[] sequences = null;
     try{
       sequences = new AppletFormatAdapter().readFile(args[0], "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]);
        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(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 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,
                             String protocol,
                             JalviewLite applet)
        {
            this.file = file;
            this.protocol = protocol;
            format = jalview.io.IdentifyFile.Identify(file, "URL");
            this.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);
              if (embedded)
                currentAlignFrame.setEmbedded();

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


                String treeFile = applet.getParameter("treeFile");
                if (treeFile != null)
                {
                  if (treeFile.indexOf("://") == -1)
                    treeFile = getCodeBase() + treeFile;

                  try
                  {
                    jalview.io.NewickFile fin = new jalview.io.NewickFile(treeFile, "URL");
                    fin.parse();

                    if (fin.getTree() != null)
                    {
                      TreePanel tp = null;
                      tp = new TreePanel(currentAlignFrame.viewport,
                                         currentAlignFrame.viewport.getAlignment().getSequences(),
                                         fin, "FromFile", treeFile);
                      addFrame(tp, treeFile, 600, 500);
                      currentAlignFrame.addTreeMenuItem(tp, treeFile);
                    }
                  }
                  catch (Exception ex)
                  {
                    ex.printStackTrace();
                  }
              }

              String param = getParameter("features");
              if (param != null)
              {
                if (param.indexOf("://") == -1)
                  param = getCodeBase() + param;

                currentAlignFrame.parseFeaturesFile(param);
              }

             param = getParameter("annotations");
             if (param != null)
             {
               if (param.indexOf("://") == -1)
                 param = getCodeBase() + param;

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

               currentAlignFrame.alignPanel.fontChanged();
             }


                String pdbfile = applet.getParameter("PDBFILE");
                if(pdbfile!=null)
                {
                  if(pdbfile.indexOf("://")==-1)
                       pdbfile = getCodeBase() + pdbfile;

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

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

                }
            }
            else
            {
                fileFound = false;
                remove(launcher);
                repaint();
            }
        }
    }
}