/**
 ** 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.cpp
 **
 ** \brief Implementation of the SafInput and AnomalyInput classes.
 **
 ** \author Mohamed Zerara
 **/

#include <sstream>
#include <errno.h>
#include <iostream>

#include "SafInput.hh"

namespace cc = casava::common;

namespace casava
{
namespace common
{

SafInput::SafInput() :
    readID_(std::string()), chromosome_(std::string()), nhood_(std::string()),
            position_(0), strand1_(std::string()), strand2_(std::string()),
            type_(std::string()), bestInsert_(0), scoreSingle_(0),
            scorePair_(0), strandOfPair_(), offsetOfPair_(0)
{
}

SafInput::~SafInput()
{
}

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

void SafInput::setChromosome(const std::string& chromosome)
{
    chromosome_ = chromosome;
}

void SafInput::setPosition(const unsigned int position)
{
    position_ = position;
}

void SafInput::setStrand1(const std::string& strand1)
{
    strand1_ = strand1;
}

void SafInput::setStrand2(const std::string& strand2)
{
    strand2_ = strand2;
}

void SafInput::setType(const std::string& type)
{
    type_ = type;
}

void SafInput::setBestInsert(const int bestInsert)
{
    bestInsert_ = bestInsert;
}

void SafInput::setScoreSingle(const double scoreSingle)
{
    scoreSingle_ = scoreSingle;
}

void SafInput::setScorePair(const double scorePair)
{
    scorePair_ = scorePair;
}

void SafInput::setStrandOfPair(const char strandOfPair)
{
    strandOfPair_ = strandOfPair;
}

void SafInput::setOffsetOfPear(const int offsetOfPair)
{
    offsetOfPair_ = offsetOfPair;
}

void SafInput::setNhood(const std::string& nhood)
{
    nhood_ = nhood;
}

std::ostream & operator<<(std::ostream& os, const SafInput& saf)
{
    os << saf.readID_;
    if (saf.chromosome_ != std::string())
        os << "\t" << saf.chromosome_;
    os << "\t" << saf.nhood_;
    if (saf.chromosome_ != std::string())
        os << "\t" << saf.position_ << "\t" << saf.strand1_ << "\t"
                << saf.type_ << "\t" << saf.scoreSingle_ << "\t"
                << saf.strand2_ << "\t" << saf.scorePair_ << "\t"
                << saf.strandOfPair_ << "\t" << saf.offsetOfPair_;
    os << std::endl;

    return os;
}


}
}