/*****************************************************************************
#   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.
#
#*****************************************************************************/
/** readSCF.h **/

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

#ifndef READSCF_DEFINED
#define READSCF_DEFINED

#include    "chromatData.h"

/* ---- Constants ---- */
#define SCF_MAGIC (((((int4)'.'<<8)+(int4)'s'<<8)+(int4)'c'<<8)+(int4)'f')
#define scale(V,OLDMAX,NEWMAX) (int2)( (FLOAT) V * (FLOAT) NEWMAX / (FLOAT) OLDMAX )

/*
** Type definition for the Header structure.
*/
typedef struct
{
  uint4 magic_number;
  uint4 samples;
  uint4 samples_offset;
  uint4 bases;
  uint4 bases_left_clip;
  uint4 bases_right_clip;
  uint4 bases_offset;
  uint4 comments_size;
  uint4 comments_offset;
  char  version[4];
  uint4 sample_size;
  uint4 code_set;
  uint4 private_size;
  uint4 private_offset;
  uint4 spare[18];
} SCFHeader;

/*
** Type definition for the Sample data
*/
typedef struct
{
  uint1 sample_A;
  uint1 sample_C;
  uint1 sample_G;
  uint1 sample_T;
} Samples1;

typedef struct
{
  uint2 sample_A;
  uint2 sample_C;
  uint2 sample_G;
  uint2 sample_T;
} Samples2;

/*
** Type definition for the sequence data
*/
typedef struct
{
  uint4 peak_index;
  uint1 prob_A;
  uint1 prob_C;
  uint1 prob_G;
  uint1 prob_T;
  uint1 base;
  uint1 spare[3];
} Bases;


typedef struct
{
  char *label;
  char *value;
  int  used;
} CommentEntry;


#ifdef ANSI_C
ChromatData *readSCF( char *fn, int *status );
uint2 swpBytU2( char *ptr );
uint4 swpBytU4( char *ptr );
char *findValue( int len, char *comment, char *target, int *ipos );
char *findSignal( char *src, char target );
CommentEntry *parseSCFComment( int len, char *comment, int *numEntry );
int readSCF2( char *fn, FILE *fp, SCFHeader *header, ChromatData *chromatData, int numPoint, int numBase, int *status );
int readSCF3( char *fn, FILE *fp, SCFHeader *header, ChromatData *chromatData, int numPoint, int numBase, int *status );
#else
ChromatData *readSCF();
uint2 inSwpUint2();
uint4 inSwpUint4();
char *findValue();
char *findSignal();
CommentEntry *parseSCFComment();
int readSCF2();
int readSCF3();
#endif

#endif