#ifndef ALIGNCANDINDELREADSIMPL_HH_
#define ALIGNCANDINDELREADSIMPL_HH_
/**
 * Project     : CASAVA
 * Module      : $RCSfile: AlignCandIndelReadsImpl.hh,v $
 * @author     : Bret D. Barnes
 * Copyright   : Copyright (c) Illumina 2008, 2009. All rights reserved.
 *
 ** This software is covered by the "Illumina Genome Analyzer Software
 ** License Agreement" and the "Illumina Source Code License Agreement",
 ** and certain third party copyright/licenses, and any user of this
 ** source file is bound by the terms therein (see accompanying files
 ** Illumina_Genome_Analyzer_Software_License_Agreement.pdf and
 ** Illumina_Source_Code_License_Agreement.pdf and third party
 ** copyright/license notices).
 *
 */

// c++ STL include
#include <string>

// CASAVA Includes
#include "variance/export.h"
#include "variance/tagAligner.h"
//using namespace casava::common;


/**
 * @class AlignCandIndelReadsImpl
 *
 * @brief This implements stage 2 of the indel finder
 *
 * Takes a read (export), genome sequence, insert mean and standard
 *  deviation and realigns the tag (export) to a fragement
 *  of the genome using local alignmnet and updates the export
 *  fields.
 *
 */

// un-comment this to get verbose output
//#define DEBUG_IDF_IMPL



class AlignCandIndelReadsImpl
{
public:
  /*
  AlignCandIndelReadsImpl( const double mc, const double mmc,
			   const double ec, const double oc,
			   const double ast) :
    _matchCost(mc), _misMatchCost(mmc), _gapExtendCost(ec), _gapOpenCost(oc) {}
  */

  AlignCandIndelReadsImpl( const double mc, const double mmc,
			   const double ec, const double oc,
			   const double ast) :
    // Set alignment scoring varaibles
    _matchCost(mc),
    _misMatchCost(mmc),
    _gapExtendCost(ec),
    _gapOpenCost(oc),

    // Set alignment score threshold
    _alignScoreThresh(ast),

    // Initialize align, out-of-bound, un-aligned counts stats variables
    _aCnt(0),
    _oCnt(0),
    _uCnt(0),

    // Initialize number of perfect count stat variable
    _pCnt(0),

    // Intialize align, out-of-bound, un-aligned score-sums stats variables
    _aSum(0.0),
    _oSum(0.0),
    _uSum(0.0),
    align(mc,mmc,ec,oc)

  {}

  void operator()(Export& record, const std::string& refSeq, const unsigned refPos);

  std::string toString() const;

private:
  // Alignment score parameters
  const double _matchCost;
  const double _misMatchCost;
  const double _gapExtendCost;
  const double _gapOpenCost;

  // Alignment score threshold variable
  const double _alignScoreThresh;

  // Align, out-of-bound, un-aligned counts stats varaibles
  unsigned int _aCnt;
  unsigned int _oCnt;
  unsigned int _uCnt;

  // Number of perfect count stat variable
  unsigned int _pCnt;

  // Align, out-of-bound, un-aligned score-sums stats varaibles
  double _aSum;
  double _oSum;
  double _uSum;

  // tagAligner
  TagAligner align;

}; // ~class AlignCandIndelReadsImpl



/**

 */

#endif /*ALIGNCANDINDELREADSIMPL_HH_*/

// End of file