/*
* 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.gui.*;
import javax.swing.*;
import java.awt.event.*;
import jalview.io.*;

import org.apache.log4j.*;

public class Jalview extends JApplet
{
  public static JApplet applet;
  Desktop frame;
  public void init()
  {
    applet = this;
    Cache.loadProperties();
    jalview.gui.Preferences.initPreferences();

    frame = new Desktop();
    frame.setResizable(true);
    frame.setVisible(true);
    frame.setDefaultCloseOperation(JFrame.DO_NOTHING_ON_CLOSE);
    frame.addWindowListener(new WindowAdapter()
    {
      public void windowClosing(WindowEvent e)
      {
          applet.stop();
          applet.destroy();
      }
    });

    String file = getParameter("alignment");

    if(file!=null)
    {
      jalview.bin.Cache.setProperty("LAST_DIRECTORY", file);
      String protocol = "File";
      if (file.indexOf("http:") > -1)
        protocol = "URL";

      String format = jalview.io.IdentifyFile.Identify(file, protocol);

      frame.LoadFile(file, protocol, format);
    }
  }

  public void destroy()
  {
    if(applet!=null)
      applet.stop();
    else
      System.exit(0);
    frame.setVisible(false);
  }

  private static void initLogger() {
    Logger l = Logger.getLogger("org.apache.axis");
    if (Cache.getProperty("logs.Axis.Level")==null) {
      Cache.setProperty("logs.Axis.Level", Level.INFO.toString());
    }

    l.setLevel(Level.toLevel(Cache.getProperty("logs.Axis.Level")));
    ConsoleAppender ap = new ConsoleAppender(new SimpleLayout(),"System.err");
    ap.setName("Axis");
    l.addAppender(ap);
  }
   public static void main(String[] args) {

    Cache.loadProperties();
    jalview.gui.Preferences.initPreferences();
    try {
      initLogger();
    } catch (Exception e) {
      System.err.println("Problems initializing the log4j system\n");
      e.printStackTrace();
    }
    try{
       UIManager.setLookAndFeel(
   //   "javax.swing.plaf.metal.MetalLookAndFeel"
    //  "javax.swing.plaf.multi.MultiLookAndFeel"
         UIManager.getSystemLookAndFeelClassName()
     //    UIManager.getCrossPlatformLookAndFeelClassName()
       // "com.sun.java.swing.plaf.gtk.GTKLookAndFeel"
       //   "com.sun.java.swing.plaf.windows.WindowsLookAndFeel"
       //  "com.sun.java.swing.plaf.motif.MotifLookAndFeel"
     );
     }
     catch (Exception ex)
     {}

     Desktop frame = new Desktop();
     frame.setResizable(true);
     frame.setVisible(true);



     if(args!=null && args.length>0)
     {
         String file=null;
         if(args[0].equals("-open"))
           file = args[1];
         else
           file = args[0];

         String protocol = "File";
         if(file.indexOf("http:")>-1)
           protocol = "URL";

         String format = jalview.io.IdentifyFile.Identify(file, protocol);

         frame.LoadFile(file, protocol, format);
     }

     if(jalview.gui.Preferences.showStartupFile &&
         jalview.gui.Preferences.startupFile!=null)
     {
       String file = jalview.gui.Preferences.startupFile;
       String protocol = "File";
       if (file.indexOf("http:") > -1)
         protocol = "URL";

       if(file.endsWith(".jar"))
         Jalview2XML.LoadJalviewAlign(file);
       else
       {
         String format = jalview.io.IdentifyFile.Identify(file, protocol);
         frame.LoadFile(file, protocol, format);
       }
     }



   }

}