/*
* 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.*;


/**
 * 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");
    public static boolean AWT1 = false;

    AlignFrame currentAlignFrame;


    /**
     * init method for Jalview Applet
     */
    public void init()
    {
        String version = System.getProperty("java.version");
        if (version.indexOf("1.1") == 0)
          AWT1 = true;

        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;
            }
        }

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


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

        file = getParameter("file");
        final JalviewLite applet = this;
        if (file != null)
        {
            add(launcher);
            if(file.indexOf("://")==-1)
               file = getCodeBase() + file;

            launcher.addActionListener(new java.awt.event.ActionListener()
                {
                    public void actionPerformed(ActionEvent e)
                    {
                        String format = jalview.io.IdentifyFile.Identify(file,
                                "URL");
                        LoadingThread loader = new LoadingThread(file,
                            "URL",
                            format,
                            featuresFile,
                            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 = new AppletFormatAdapter().readFile(args[0], "File", format);

      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)
                {
                    frame.dispose();
                }
            });
        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(),
            true, 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);
        }
    }

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

        public LoadingThread(String file,
                             String protocol,
                             String format,
                             String features,
                             JalviewLite applet)
        {
            this.file = file;
            this.protocol = protocol;
            this.format = format;
            featuresFile = features;
            this.applet = applet;
        }

        public void run()
        {
            SequenceI[] sequences = null;
            sequences = new AppletFormatAdapter().readFile(file, protocol, format);

            if ((sequences != null) && (sequences.length > 0))
            {
                currentAlignFrame = new AlignFrame(new Alignment(sequences),
                        applet, file);
                currentAlignFrame.statusBar.setText("Successfully loaded file " + file);

                if(featuresFile!=null)
                  currentAlignFrame.parseFeaturesFile(featuresFile);
            }
            else
            {
                fileFound = false;
                remove(launcher);
                repaint();
            }
        }
    }
}