/*
* 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 jalview.io.*;

import org.apache.log4j.*;

import java.awt.event.*;

import javax.swing.*;


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());
        } 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);
            }
        }
    }
}