/**
 ** 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).
 **
 ** \file AnomalyInput.hh
 **
 ** \brief Class to wrap the fields of the anomaly file.
 **
 **
 ** \author Stephen Allan
 **/
#ifndef ANOMALY_INPUT_HH_
#define ANOMALY_INPUT_HH_

#include <string>
#include <iosfwd>

namespace casava
{
namespace common
{

//TODO move AnomalyInput to separate declaration and implementation files
class AnomalyInput
{
public:
    /**
     * \brief default constructor
     */
    AnomalyInput();

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

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

    /**
     * \brief set first read
     */
    void setRead1(const std::string&);

    /**
     * \brief set second read
     */
    void setRead2(const std::string&);

    /**
     * \brief set quality value of first read
     */
    void setQualityValue1(const std::string&);

    /**
     * \brief set quality value of second read
     */
    void setQualityValue2(const std::string&);

    /**
     * \brief set details for first read
     */
    void setDetails1(const std::string&);

    /**
     * \brief set first neighborhood
     */
    void setNhood1(const std::string&);

    /**
     * \brief set details for second read
     */
    void setDetails2(const std::string&);

    /**
     * \brief set second neighborhood
     */
    void setNhood2(const std::string&);

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

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

    std::string readID_;
    std::string read1_;
    std::string read2_;
    std::string qv1_;
    std::string qv2_;
    std::string details1_;
    std::string nhood1_;
    std::string details2_;
    std::string nhood2_;
};

} // common
} // casava

#endif // ANOMALY_INPUT_HH_