/*****************************************************************************
#   Copyright (C) 1994-2008 by David Gordon.
#   All rights reserved.                           
#                                                                           
#   This software is part of a beta-test version of the Consed/Autofinish
#   package.  It should not be redistributed or
#   used for any commercial purpose, including commercially funded
#   sequencing, without written permission from the author and the
#   University of Washington.
#   
#   This software is provided ``AS IS'' and any express or implied
#   warranties, including, but not limited to, the implied warranties of
#   merchantability and fitness for a particular purpose, are disclaimed.
#   In no event shall the authors or the University of Washington be
#   liable for any direct, indirect, incidental, special, exemplary, or
#   consequential damages (including, but not limited to, procurement of
#   substitute goods or services; loss of use, data, or profits; or
#   business interruption) however caused and on any theory of liability,
#   whether in contract, strict liability, or tort (including negligence
#   or otherwise) arising in any way out of the use of this software, even
#   if advised of the possibility of such damage.
#
#   Building Consed from source is error prone and not simple which is
#   why I provide executables.  Due to time limitations I cannot
#   provide any assistance in building Consed.  Even if you do not
#   modify the source, you may introduce errors due to using a
#   different version of the compiler, a different version of motif,
#   different versions of other libraries than I used, etc.  For this
#   reason, if you discover Consed bugs, I can only offer help with
#   those bugs if you first reproduce those bugs with an executable
#   provided by me--not an executable you have built.
# 
#   Modifying Consed is also difficult.  Although Consed is modular,
#   some modules are used by many other modules.  Thus making a change
#   in one place can have unforeseen effects on many other features.
#   It may takes months for you to notice these other side-effects
#   which may not seen connected at all.  It is not feasable for me to
#   provide help with modifying Consed sources because of the
#   potentially huge amount of time involved.
#
#*****************************************************************************/
/** readData.c **/

/*
*|***************************************************************************|*
*|                                                                           |*
*|   phred * NOT FOR DISTRIBUTION                                            |*
*|   Copyright (C) 1995-1999 by Phil Green and Brent Ewing.                  |*
*|   All rights reserved.                                                    |*
*|                                                                           |*
*|***************************************************************************|*
*/

/*
*******************************************************************************
**                                                                           **
**    * readData.c                                                     *     **
**    * benefits from ideas in code written by LaDeana Hillier and     *     **
**    * Tim Gleeson.                                                   *     **
**                                                                           **
*******************************************************************************
*/

/*
** Note: try to have phred write a 'empty' output files
**       on error.
*/

#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include <math.h>
// #include "phred.h"
#include "typeDef.h"
#include "readType.h"
#include "readSCF.h"
#include "readABI.h"
#include "readESD.h"

/*
** Read sequence data.
*/
#ifdef ANSI_C
ChromatData *readData( char *filename, int *status )
#else
ChromatData *readData( filename, status )
char *filename;
int *status;
#endif
{
  int inType;
  int lstat;
  ChromatData *chromatData;

  inType = readType( filename );
  if( inType == -1 )
  {
    fprintf( stderr, "error: file not found > %s\n", filename );
    *status = 1;
    return( NULL );
  }

  /*
  ** read data
  */ 
  switch( inType )
  {
    case SCFFormat:
      /*
      ** SCF
      */

      chromatData = readSCF( filename, &lstat );
      *status = lstat;
      break;

    case ABIFormat:
      /*
      ** ABI
      */

      chromatData = readABI( filename, &lstat );
      *status = lstat;
      break;

    case MD1Format:
      /*
      ** ESD format one (old ESD file)
      */

      chromatData = readESD( filename, MD1Format, &lstat );
      *status = lstat;
      break;

    case MD2Format:
      /*
      ** ESD format two (new ESD file)
      */

      chromatData = readESD( filename, MD2Format, &lstat );
      *status = lstat;
      break;

    default:
      fprintf( stderr, "  readData: unknown file type\n" );
      *status = 1;
      return( NULL );
  }

  return( chromatData );
}