/**
 ** Copyright (c) 2007-2009 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.
 **
 ** \file SafInput.hh
 **
 ** \brief Declarations of the SafInput and AnomalyInput classes.
 **
 ** \author Mohamed Zerara
 **/

#ifndef CASAVA_COMMON_SAF_INPUT_HH
#define CASAVA_COMMON_SAF_INPUT_HH

#include <string>
#include "common/ParameterTypes.hh"

namespace casava
{
namespace common
{

class SafInput
{
public:
    /**
     * \brief default constructor
     */
    SafInput();

    /**
     * \brief destructor
     */
    virtual ~SafInput();

    /**
     * \brief set read ID
     */
    void setReadID(const std::string&);

    /**
     * \brief get read ID
     */
    const std::string getReadID(){ return readID_; }

    /**
     * \brief set chromosome
     */
    void setChromosome(const std::string&);

    /**
     * \brief set position
     */
    void setPosition(const unsigned int);

    /**
     * \brief set first strand
     */
    void setStrand1(const std::string&);

    /**
     * \brief set second strand
     */
    void setStrand2(const std::string&);

    /**
     * \brief set type
     */
    void setType(const std::string&);

    /**
     * \brief set single read alignment score
     */
    void setScoreSingle(const double);

    /**
     * \brief set best insert
     */
    void setBestInsert(const int bestInsert);

    /**
     * \brief set score paired read alignment score
     */
    void setScorePair(const double);

    /**
     * \brief set strand of pair
     */
    void setStrandOfPair(const char);

    /**
     * \brief set offset of pear
     */
    void setOffsetOfPear(const int);

    /**
     * \brief set neighborhood
     */
    void setNhood(const std::string&);

    friend std::ostream & operator<<(std::ostream& os, const SafInput&);

private:
    SafInput(const SafInput&);
    SafInput& operator=(const SafInput&);

    std::string readID_, chromosome_;
    std::string nhood_;
    unsigned int position_;
    std::string strand1_, strand2_;
    std::string type_;
    int bestInsert_;
    double scoreSingle_, scorePair_;
    char strandOfPair_;
    int offsetOfPair_;
};


} // namespace common
} // namespace casava

#endif // #ifndef CASAVA_COMMON_SAF_INPUT_HH