/********************
 * 2004 Jalview Reengineered
 * Barton Group
 * Dundee University
 *
 * AM Waterhouse
 *******************/

package jalview.io;

import java.io.*;
import java.net.*;

public class IdentifyFile
{
  public static String Identify(String file, String protocol)
  {
    String reply = "PFAM";
    try{

      BufferedReader reader = null;

      if(protocol.equals("File"))
        reader = new BufferedReader(new FileReader(file));

      else if (protocol.equals("URL"))
      {
        reply = "URL NOT FOUND";
        URL url = new URL(file);
        reader = new BufferedReader(new InputStreamReader( url.openStream() ) );
        reply = "error";
      }
      else if( protocol.equals("Paste"))
        reader = new BufferedReader( new StringReader(file) );


      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)
            reply = "BLC";
          else
            reply = "FASTA";

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

    return reply;
  }


}