/**
 ** 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_INPUT_H
#define TRIMMER_INPUT_H

#include <cstdio>
#include "TrimmerErrors.h"

class CTrimmerInput
{
public:
    CTrimmerInput();

    CTrimmerInput(int    argc,
                  char * argv[],
                  int &  status);

    virtual ~CTrimmerInput();

    static void PrintHelp(const char * command);

    void WriteBanner();

    FILE * & GetInFilePtr() {return m_FpIn;}
    FILE * & GetOutFilePtr() {return m_FpOut;}
    FILE * & GetReportFilePtr() {return m_FpReport;}
    int GetThreshold() const {return m_Threshold;}
    int GetNpad() const {return m_padLength;}
    int GetNextraBases() const {return m_nExtraBases;}

    char   adaptorString[MAX_READ_SIZE];
    int    simmatrix[NSYMBOLS][NSYMBOLS];

private:
    char   m_InputFilename[MAX_BUF_SIZE];
    char   m_OutputFilename[MAX_BUF_SIZE];
    char   m_ReportFilename[MAX_BUF_SIZE];
    char   m_SimMatFilename[MAX_BUF_SIZE];
    int    m_Threshold;
    FILE * m_FpIn;
    FILE * m_FpOut;
    FILE * m_FpReport;
    int    m_padLength;
    int    m_nExtraBases;

    void createDefaultAdaptorString();
    void createDefaultSimilarityMatrix();
};

#endif // TRIMMER_INPUT_H