/*****************************************************************************
#   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.
#
#*****************************************************************************/
/** readESD.h **/

/*
*|***************************************************************************|*
*|                                                                           |*
*|   phred * NOT FOR DISTRIBUTION                                            |*
*|   Copyright (C) 1995-2000 by Phil Green and Brent Ewing.                  |*
*|   All rights reserved.                                                    |*
*|                                                                           |*
*|***************************************************************************|*
*/

#include "chromatData.h"

typedef unsigned int4           DWORD;
typedef unsigned char           TCHAR;
typedef char                    BYTE;
typedef int4                    BOOL;
typedef unsigned int            UINT;
typedef int                     ScanRate;
typedef int4                    l_time_t;

#define INSTRUMENT_NAME_LEN     ((10*2+2)/sizeof(TCHAR))
#define SAMPLE_NAME_LEN         (24 / sizeof(TCHAR))
#define SPLITTER_NAME_LEN       (30 / sizeof(TCHAR))
#define FILTER_NAME_LEN         (30 / sizeof(TCHAR))
#define OPERATOR_NAME_LEN       (30 / sizeof(TCHAR))
#define DYE_NAME_LEN            (10 / sizeof(TCHAR))
#define PAR_SET_NAME_LEN        (30 / sizeof(TCHAR))
#define PLATE_NAME_LEN          (18 / sizeof(TCHAR))
#define RUN_ID_LEN              (6  / sizeof(TCHAR))
#define CHEM_NAME_LEN           (32 / sizeof(TCHAR))

#define ORDER_A                 0
#define ORDER_C                 1
#define ORDER_G                 2
#define ORDER_T                 3

#define ES_FOUR_CHAN            4

#define ESD_STR_MAX		256

typedef struct
{
  int4 capillaryCurrent;
  float channel1Intensity;
  float channel2Intensity;
  float channel3Intensity;
  float channel4Intensity;
} ProcessedScan;


typedef struct
{
  TCHAR         m_tcSampleName[SAMPLE_NAME_LEN];
  TCHAR         m_tcOperator[OPERATOR_NAME_LEN];

  float         m_fRunVoltage;
  float         m_fRunTime;
  float         m_fInjectionTime;
  float         m_fInjectionVoltage;
  float         m_fTemperature;

  int           m_nLazerIndex;
  float         m_fPMTVoltage1;
  float         m_fPMTVoltage2;
  TCHAR         m_csBeamSplitterA[SPLITTER_NAME_LEN];
  TCHAR         m_csBeamSplitterB[SPLITTER_NAME_LEN];
  TCHAR         m_csFilter1[FILTER_NAME_LEN];
  TCHAR         m_csFilter2[FILTER_NAME_LEN];
  TCHAR         m_csFilter3[FILTER_NAME_LEN];
  TCHAR         m_csFilter4[FILTER_NAME_LEN];

  float         m_fFillTime;
  float         m_fFlushTime1;
  float         m_fFlushTime2;
  float         m_fFlushTime3;
  float         m_fPrerunVoltage;
  float         m_fRelaxationTime;
  float         m_fPrerunTime;
  float         m_fSpecSepMx[ES_FOUR_CHAN][ES_FOUR_CHAN];

  TCHAR         m_csBaseOrder[ES_FOUR_CHAN][DYE_NAME_LEN];
  TCHAR         m_InstID[INSTRUMENT_NAME_LEN];

  TCHAR         m_csParamSetName[PAR_SET_NAME_LEN];

  DWORD         m_dMagicNumber;                 /* 826561349 */
  DWORD         m_dExtHeaderOffset;
  DWORD         m_dExtHeaderLen;

  float         m_fPreinjectionTime;
  float         m_fPreinjectionVoltage;
  float         m_fLowPressureTime;
  float         m_fUserInputTime;
  float         m_fSleepTime;
  float         m_fSleepTemperature;

  BYTE          m_byReserved[82];

  TCHAR         m_csRunID[RUN_ID_LEN];
  TCHAR         m_csPlateID[PLATE_NAME_LEN];
  DWORD         m_dwPrevRunID;

  BOOL          m_bDWORDFile;

  BOOL          m_bSaturated;
  float         m_fVersion;
  l_time_t      m_tRunStartTime;
  l_time_t      m_tRunStopTime;

  DWORD         m_dwNumberOfLines;

  ScanRate      m_nScanRate;

  BYTE          m_byFileType;

  BYTE          m_byNumberOfCapillaries;

  BYTE          m_byCapUsage;
  BYTE          m_byDummy;

  UINT          m_uiSecurityCode;

} ESDTrailer;

typedef struct
{
  char primerName[ESD_STR_MAX];
  char sampleName[ESD_STR_MAX];
  char plateID[ESD_STR_MAX];
  char comment[ESD_STR_MAX];
  char machineName[ESD_STR_MAX];
  char wellID[ESD_STR_MAX];
  char baseMap[4];
  int  numBase;
  char *base;
  int  *baseLoc;
  int  baseLocOffset;
} ESDExtHeader;


#ifdef ANSI_C
ChromatData *readESD( char *filename, int version, int *status );
#else
ChromatData *readESD();
#endif