/*
 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
 * Copyright (C) $$Year-Rel$$ The Jalview Authors
 *
 * This file is part of Jalview.
 *
 * Jalview 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 3
 * of the License, or (at your option) any later version.
 *
 * Jalview 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 Jalview.  If not, see <http://www.gnu.org/licenses/>.
 * The Jalview Authors are detailed in the 'AUTHORS' file.
 */
package jalview.io;

import jalview.jsdev.GenericFileAdapter;

import java.io.IOException;

/**
 * DOCUMENT ME!
 *
 * @author $author$
 * @version $Revision$
 */
public class IdentifyFile
{
  public static final String GFF3File = "GFF v2 or v3";

  /**
   * Identify a datasource's file content.
   *
   * @note Do not use this method for stream sources - create a FileParse object
   *       instead.
   *
   * @param file
   *          DOCUMENT ME!
   * @param protocol
   *          DOCUMENT ME!
   * @return ID String
   */
  public String Identify(String file, String protocol)
  {
    String emessage = "UNIDENTIFIED FILE PARSING ERROR";
    FileParse parser = null;
    try
    {
      parser = new FileParse(file, protocol);
      if (parser.isValid())
      {
        return Identify(parser);
      }
    } catch (Exception e)
    {
      System.err.println("Error whilst identifying");
      e.printStackTrace(System.err);
      emessage = e.getMessage();
    }
    if (parser != null)
    {
      return parser.errormessage;
    }
    return emessage;
  }

  public String Identify(FileParse source)
  {
    return Identify(source, true); // preserves original behaviour prior to
    // version 2.3
  }

  /**
   * Identify contents of source, closing it or resetting source to start
   * afterwards.
   *
   * @param source
   * @param closeSource
   * @return filetype string
   */
  public String Identify(FileParse source, boolean closeSource)
  {
    String reply = "PFAM";
    String data;
    int length = 0;
    boolean lineswereskipped = false;
    boolean isBinary = false; // true if length is non-zero and non-printable
    // characters are encountered
    try
    {
      if (!closeSource)
      {
        source.mark();
      }
      while ((data = source.nextLine()) != null)
      {
        length += data.trim().length();
        if (!lineswereskipped)
        {
          for (int i = 0; !isBinary && i < data.length(); i++)
          {
            char c = data.charAt(i);
            isBinary = (c < 32 && c != '\t' && c != '\n' && c != '\r'
                    && c != 5 && c != 27); // nominal binary character filter
            // excluding CR, LF, tab,DEL and ^E
            // for certain blast ids
          }
        }
        if (isBinary)
        {
          // jar files are special - since they contain all sorts of random
          // characters.
          if (source.inFile != null)
          {
            String fileStr = source.inFile.getName();
            // possibly a Jalview archive.
            if (fileStr.lastIndexOf(".jar") > -1
                    || fileStr.lastIndexOf(".zip") > -1)
            {
              reply = "Jalview";
            }
          }
          if (!lineswereskipped && data.startsWith("PK"))
          {
            reply = "Jalview"; // archive.
            break;
          }
        }
        data = data.toUpperCase();

        if (data.startsWith("##GFF-VERSION"))
        {
          reply = GFF3File;
          break;
        }
        if (data.indexOf("# STOCKHOLM") > -1)
        {
          reply = "STH";
          break;
        }
        // if (data.matches("<(\"[^\"]*\"|'[^']*'|[^'\">])*>"))
        if (data.matches("<HTML(\"[^\"]*\"|'[^']*'|[^'\">])*>")) // BH was (?i)rnaml, but JavaScript regex does not support (?i); data is already upper case
        {
          reply = GenericFileAdapter.Html_FILE_DESC;
          break;
        }

        if (data.matches("<RNAML (\"[^\"]*\"|'[^']*'|[^'\">])*>")) // BH was (?i)rnaml, but JavaScript regex does not support (?i); data is already upper case
        {
          reply = "RNAML";
          break;
        }

         if (data.indexOf("{\"") > -1)
         {
         reply = GenericFileAdapter.JSON_FILE_DESC;
         break;
         }
        if ((data.length() < 1) || (data.indexOf("#") == 0))
        {
          lineswereskipped = true;
          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(">") > -1)
        {
          // FASTA, PIR file or BLC file
          boolean checkPIR = false, starterm = false;
          if ((data.indexOf(">P1;") > -1) || (data.indexOf(">DL;") > -1))
          {
            // watch for PIR file attributes
            checkPIR = true;
            reply = "PIR";
          }
          // could also be BLC file, read next line to confirm
          data = source.nextLine();

          if (data.indexOf(">") > -1)
          {
            reply = "BLC";
          }
          else
          {
            // Is this a single line BLC file?
            String data1 = source.nextLine();
            String data2 = source.nextLine();
            int c1;
            if (checkPIR)
            {
              starterm = (data1 != null && data1.indexOf("*") > -1)
                      || (data2 != null && data2.indexOf("*") > -1);
            }
            if (data2 != null && (c1 = data.indexOf("*")) > -1)
            {
              if (c1 == 0 && c1 == data2.indexOf("*"))
              {
                reply = "BLC";
              }
              else
              {
                reply = "FASTA"; // possibly a bad choice - may be recognised as
                // PIR
              }
              // otherwise can still possibly be a PIR file
            }
            else
            {
              reply = "FASTA";
              // TODO : AMSA File is indicated if there is annotation in the
              // FASTA file - but FASTA will automatically generate this at the
              // mo.
              if (!checkPIR)
              {
                break;
              }
            }
          }
          // final check for PIR content. require
          // >P1;title\n<blah>\nterminated sequence to occur at least once.

          // TODO the PIR/fasta ambiguity may be the use case that is needed to
          // have
          // a 'Parse as type XXX' parameter for the applet/application.
          if (checkPIR)
          {
            String dta = null;
            if (!starterm)
            {
              do
              {
                try
                {
                  dta = source.nextLine();
                } catch (IOException ex)
                {
                }
                ;
                if (dta != null && dta.indexOf("*") > -1)
                {
                  starterm = true;
                }
              } while (dta != null && !starterm);
            }
            if (starterm)
            {
              reply = "PIR";
              break;
            }
            else
            {
              reply = "FASTA"; // probably a bad choice!
            }
          }
          // read as a FASTA (probably)
          break;
        }
        else if (data.indexOf("HEADER") == 0 || data.indexOf("ATOM") == 0)
        {
          reply = "PDB";
          break;
        }
        else if (data.matches("\\s*\\d+\\s+\\d+\\s*"))
        {
          reply = GenericFileAdapter.Phylip_FILE_DESC;
          break;
        }


        /*
         * // TODO comment out SimpleBLAST identification for Jalview 2.4.1 else
         * if (!lineswereskipped && data.indexOf("BLAST")<4) { reply =
         * "SimpleBLAST"; break;
         *
         * } // end comments for Jalview 2.4.1
         */
        else if (!lineswereskipped && data.charAt(0) != '*'
                && data.charAt(0) != ' '
                && data.indexOf(":") < data.indexOf(",")) // &&
          // data.indexOf(",")<data.indexOf(",",
          // data.indexOf(",")))
        {
          // file looks like a concise JNet file
          reply = "JnetFile";
          break;
        }

        lineswereskipped = true; // this means there was some junk before any
        // key file signature
      }
      if (closeSource)
      {
        source.close();
      }
      else
      {
        source.reset(); // so the file can be parsed from the beginning again.
      }
    } catch (Exception ex)
    {
      System.err.println("File Identification failed!\n" + ex);
      return source.errormessage;
    }
    if (length == 0)
    {
      System.err
      .println("File Identification failed! - Empty file was read.");
      return "EMPTY DATA FILE";
    }
    return reply;
  }

  /**
   * @j2sIgnore
   * 
   * @param args
   */
  public static void main(String[] args)
  {

    for (int i = 0; args != null && i < args.length; i++)
    {
      IdentifyFile ider = new IdentifyFile();
      String type = ider.Identify(args[i], AppletFormatAdapter.FILE);
      System.out.println("Type of " + args[i] + " is " + type);
    }
    if (args == null || args.length == 0)
    {
      System.err.println("Usage: <Filename> [<Filename> ...]");
    }
  }
}