/*****************************************************************************
#   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.
#
#*****************************************************************************/
/** chromatData.h **/

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

/*
** Data from chromat file.
*/

#ifndef CHROMATDATA_DEFINED
#define CHROMATDATA_DEFINED


#ifndef FLOAT
#define FLOAT		double
#endif

/*
** This should be only in typeDef.h but is
** repeated here for David's convenience.
** The same applies to DOUBLE above.
*/
#ifdef PHRED_PATH_MAX
#undef PHRED_PATH_MAX
#endif

#define PHRED_PATH_MAX	4096

#ifndef SCFFormat
#define SCFFormat	1
#endif

#ifndef ABIFormat
#define ABIFormat	2
#endif

#ifndef MD1Format
#define MD1Format       3
#endif

#ifndef MD2Format
#define MD2Format       4
#endif

typedef struct
{
  char   fileName[PHRED_PATH_MAX];
  int    fileType;                                 /* SCFFormat=1,  ABIFormat=2 */

  int    numPoint;
  FLOAT *trace[4];
  FLOAT  maxTraceValue;
  FLOAT  minTraceValue;

  int    numBase;
  char  *base;
  int   *baseLoc;
  int   *baseQual;

  int    laneNumber;
  int    primerLoc;
  int    signalStrength[4];
  FLOAT  avgSpacing;
  char   comment[256];
  char   convProg[256];
  char   gelName[256];
  char   machineName[256];
  char   primerID[256];
  char   processing[256];
  char   reTracker[256];
  char   sampleName[256];
  char   source[256];

  char   thumbPrint[10];

} ChromatData;

#ifdef ANSI_C
ChromatData *allocChromatData( int numPoint, int numBase );
int freeChromatData( ChromatData *chromatData );
#else
ChromatData *allocChromatData();
int freeChromatData();
#endif

#endif