/*
* 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.io;

import java.io.*;

import java.net.*;


/**
 * DOCUMENT ME!
 *
 * @author $author$
 * @version $Revision$
 */
public class IdentifyFile
{
    /**
     * DOCUMENT ME!
     *
     * @param file DOCUMENT ME!
     * @param protocol DOCUMENT ME!
     *
     * @return DOCUMENT ME!
     */
    public String Identify(String file, String protocol)
    {
        String reply = "PFAM";
        String error =  "FILE NOT FOUND";
        try
        {
            BufferedReader reader = null;

            if (protocol.equals(AppletFormatAdapter.FILE))
            {
              reader = new BufferedReader(new FileReader(file));
            }
            else if (protocol.equals(AppletFormatAdapter.URL))
            {
              error = "URL NOT FOUND";
              URL url = new URL(file);
              reader = new BufferedReader(new InputStreamReader(
                  url.openStream()));

            }
            else if (protocol.equals(AppletFormatAdapter.PASTE))
            {
              reader = new BufferedReader(new StringReader(file));
            }
            else if (protocol.equals(AppletFormatAdapter.CLASSLOADER))
            {
              java.io.InputStream is = getClass().getResourceAsStream("/" +
                  file);
              reader = new BufferedReader(new java.io.InputStreamReader(is));
            }

            String data;

            while ((data = reader.readLine()) != null)
            {
                data = data.toUpperCase();

                if ((data.indexOf("#") == 0) || (data.length() < 1))
                {
                    continue;
                }

                if (data.indexOf("PILEUP") > -1)
                {
                    reply = "PileUp";

                    break;
                }

                if ((data.indexOf("//") == 0) ||
                        ((data.indexOf("!!") > -1) &&
                        (data.indexOf("!!") < data.indexOf(
                            "_MULTIPLE_ALIGNMENT "))))
                {
                    reply = "MSF";

                    break;
                }
                else if (data.indexOf("CLUSTAL") > -1)
                {
                    reply = "CLUSTAL";

                    break;
                }
                else if ((data.indexOf(">P1;") > -1) ||
                        (data.indexOf(">DL;") > -1))
                {
                    reply = "PIR";

                    break;
                }
                else if (data.indexOf(">") > -1)
                {
                    // could be BLC file, read next line to confirm
                    data = reader.readLine();

                    if (data.indexOf(">") > -1 || data.indexOf("*") >-1 )
                    {
                        reply = "BLC";
                    }
                    else
                    {
                        reply = "FASTA";
                    }

                    break;
                }
                else if (data.indexOf(":")<data.indexOf(",")) //  && data.indexOf(",")<data.indexOf(",", data.indexOf(",")))
                {
                  // file looks like a concise JNet file
                  reply="JnetFile";
                  break;
                }
            }

            reader.close();
        }
        catch (Exception ex)
        {
            System.err.println("File Identification failed!\n" + ex);
            return error;
        }
        return reply;
    }
}