/**
 ** 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.cpp
 **
 ** \brief Class to wrap the fields of the anomaly file.
 **
 **
 ** \author Stephen Allan
 **/
#include <ostream>

#include "AnomalyInput.hh"

namespace casava
{
namespace common
{

    AnomalyInput::AnomalyInput(): 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_(std::string())
    {
    }

    AnomalyInput::~AnomalyInput()
    {
    }

    void AnomalyInput::setReadID(const std::string& readID)
    {
        readID_=readID;
    }

    void AnomalyInput::setRead1(const std::string& read1)
    {
        read1_=read1;
    }

    void AnomalyInput::setRead2(const std::string& read2)
    {
        read2_=read2;
    }

    void AnomalyInput::setQualityValue1(const std::string& qv1)
    {
        qv1_=qv1;
    }

    void AnomalyInput::setQualityValue2(const std::string& qv2)
    {
        qv2_=qv2;
    }

    void AnomalyInput::setDetails1(const std::string& details1)
    {
        details1_=details1;
    }

    void AnomalyInput::setNhood1(const std::string& nhood1)
    {
        nhood1_=nhood1;
    }

    void AnomalyInput::setDetails2(const std::string& details2)
    {
        details2_=details2;
    }

    void AnomalyInput::setNhood2(const std::string& nhood2)
    {
        nhood2_=nhood2;
    }

    std::ostream & operator<<(std::ostream& os, const AnomalyInput& anom)
    {
        os << anom.readID_ << "\t" << anom.read1_ << "\t" <<  anom.read2_ << "\t"
           << anom.qv1_ << "\t" <<  anom.qv2_ << "\t" << anom.details1_ << "\t"
           << anom.nhood1_ << "\t" << anom.details2_ << "\t" << anom.nhood2_ << std::endl;

        return os;
    }

} // common
} // casava