/*****************************************************************************
#   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.c **/

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

#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include <math.h>
// #include "phred.h"
#include "typeDef.h"
#include "ourMalloc.h"
#include "ourFree.h"
#include "chromatData.h"



/*
** ChromatData allocate/free.
*/
#ifdef ANSI_C
ChromatData *allocChromatData( int numPoint, int numBase )
#else
ChromatData *allocChromatData( numPoint, numBase )
int numPoint;
int numBase;
#endif
{
  int j;
  int numByte;
  ChromatData *chromatData;

  numByte = sizeof( ChromatData );
  chromatData = (ChromatData *)ourMalloc( numByte );

  for( j = 0; j < 4; ++j )
  {
    chromatData->trace[j] = NULL;
  }
  chromatData->base     = NULL;
  chromatData->baseLoc  = NULL;
  chromatData->baseQual = NULL;

  if( numPoint > 0 )
  {
    numByte = numPoint * sizeof( FLOAT );
  }
  else
  {
    numByte = sizeof( FLOAT );
  }

  for( j = 0; j < 4; ++j )
  {
    chromatData->trace[j] = (FLOAT *)ourMalloc( numByte );
  }

  if( numBase > 0 )
  {
    numByte = numBase * sizeof( char );
  }
  else
  {
    numByte = sizeof( char );
  }
  chromatData->base = (char *)ourMalloc( numByte );

  if( numBase > 0 )
  {
    numByte = numBase * sizeof( int );
  }
  else
  {
    numByte = sizeof( int );
  }
  chromatData->baseLoc = (int *)ourMalloc( numByte );

  if( numBase > 0 )
  {
    numByte = numBase * sizeof( int );
  }
  else
  {
    numByte = sizeof( int );
  }
  chromatData->baseQual = (int *)ourMalloc( numByte );

  /*
  ** Initialize values.
  */
  chromatData->fileName[0]    = '\0';
  chromatData->fileType       = -1;
  chromatData->numPoint       = numPoint;
  chromatData->maxTraceValue  = 0.0;
  chromatData->numBase        = numBase;
  chromatData->primerLoc      = 0;
  chromatData->avgSpacing     = 0.0;
  chromatData->sampleName[0]  = '\0';
  chromatData->machineName[0] = '\0';
  chromatData->primerID[0]    = '\0'; 

  for( j = 0; j < 4; ++j )
  {
    chromatData->signalStrength[j] = 0;
  }

  return( chromatData );
}

#ifdef ANSI_C
int freeChromatData( ChromatData *chromatData )
#else
int freeChromatData( chromatData )
ChromatData *chromatData;
#endif
{
  int j;

  for( j = 0; j < 4; ++j )
  {
    if( chromatData->trace[j] != NULL )
    {
      ourFree( (char *)chromatData->trace[j] );
    }
  }

  if( chromatData->base != NULL )
  {
    ourFree( (char *)chromatData->base );
  }

  if( chromatData->baseLoc != NULL )
  {
    ourFree( (char *)chromatData->baseLoc );
  }

  if( chromatData->baseQual != NULL )
  {
    ourFree( (char *)chromatData->baseQual );
  }

  ourFree( (char *)chromatData );

  return( OK );
}