/**
 ** Copyright (c) 2007-2010 Illumina, Inc.
 **
 ** 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).
 **
 ** This file is part of the Consensus Assessment of Sequence And VAriation
 ** (CASAVA) software package.
 **
 **/

#ifndef TRIMMER_PROCESS_H
#define TRIMMER_PROCESS_H

#include <cstdio>
#include <climits>

#include <string>
#include <map>

#include "TrimmerResult.h"

class CTrimmerInput;
class CTrimmer;

class CTrimmerProcess
{
public:
    CTrimmerProcess()
      : m_FpIn(0)
      , m_FpOut(0)
      , m_Threshold(INT_MIN)
      , m_nPadLen(0)
      , m_nExtraBases(0)
    {};

    CTrimmerProcess(CTrimmerInput & trimmerInput);

    virtual ~CTrimmerProcess();

    void Run(CTrimmer & trimmer);

private:
    FILE *                      m_FpIn;
    FILE *                      m_FpOut;
    FILE *                      m_FpReport;
    int                         m_Threshold;
    int                         m_nPadLen;
    int                         m_nExtraBases;

    char                        m_Buffer[MAX_BUF_SIZE];
    char                        m_ReadString[MAX_BUF_SIZE];
    char                        m_PreString[MAX_BUF_SIZE];

    std::map<std::string, CTrimmerResult> m_ResultHolder;

    void runFromFile(CTrimmer & trimmer);

    void runFromFastqFile(CTrimmer & trimmer);

    void runFromConsole(CTrimmer & trimmer);

    void deallocateHolder();

    void parse();

    void parse(const char delimiter,
               const int  startColumn,       // Columns are indexed from 1
               const int  endColumn);
};

#endif // TRIMMER_PROCESS_H