/**
 ** 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.
 **
 ** \file ReadState.cpp
 **
 ** \brief
 **
 ** 
 **
 ** \author
 **/

#include "ReadState.hh"

namespace casava
{
namespace alignment
{
    
    ReadState::ReadState()
        : bestScore_(0),
          exactScore_(0),
          restOfGenomeCorrection_(0),
          scoreSingle_(0),
          addShadowToSingletonThreshold_(0),
          alignmentOk_(0),
          alignmentPoor_(0),
          numberResolved_(0),
          numberUnique_(0),
          positionOfMatch_(0),
          readLength_(0),
          singleReadAlignmentPosition_(0),
          numberWithNoMatchPosition_(0),
          bestInsert_(""),
          chromosomeName_(""),
          elandDetails_(""),
          matchStrand_(""),
          matchType_(""),
          matchNeighbourhood_(""),
          qualityValue_(""),
          read_(""),
          readId_(""),
          singleReadAlignmentMatchChromosome_(""),
          singleReadAlignmentStrand_(""),
          typeSingle_(""),
          elandExtendedFile_(""),
          elandExtendedFilePath_(""),
          shortAlignmentFormatFile_(""),
          shortAlignmentFormatFilePath_("")
    {
    }



    std::ostream & operator<<(std::ostream &os, ReadState &rs)
    {
        os << "ReadState object state:- "
           << "\n\t\tbestScore_\t\t\t- " << rs.bestScore_
           << ";\n\t\texactScore_\t\t\t- " << rs.exactScore_
           << ";\n\t\trestOfGenomeCorrection_\t\t- " << rs.restOfGenomeCorrection_
           << ";\n\t\tscoreSingle_\t\t\t- " << rs.scoreSingle_
           << ";\n\t\taddShadowToSingletonThreshold_\t- " << rs.addShadowToSingletonThreshold_
           << ";\n\t\talignmentOk_\t\t\t- " << rs.alignmentOk_
           << ";\n\t\talignmentPoor_\t\t\t- " << rs.alignmentPoor_
           << ";\n\t\tnumberResolved_\t\t\t- " << rs.numberResolved_
           << ";\n\t\tnumberUnique\t\t\t- " << rs.numberUnique_
           << ";\n\t\tpositionOfMatch_\t\t- " << rs.positionOfMatch_
           << ";\n\t\treadLength_\t\t\t- " << rs.readLength_
           << ";\n\t\tsingleReadAlignmentPosition_\t- " << rs.singleReadAlignmentPosition_
           << ";\n\t\tnumberWithNoMatchPosition_\t- " << rs.numberWithNoMatchPosition_
           << ";\n\t\tbestInsert_\t\t\t- " << rs.bestInsert_
           << ";\n\t\tchromosomeName_\t\t\t- " << rs.chromosomeName_
           << ";\n\t\telandDetails_\t\t\t- " << rs.elandDetails_
           << ";\n\t\tmatchStrand_\t\t\t- " << rs.matchStrand_
           << ";\n\t\tmatchType_\t\t\t- " << rs.matchType_
           << ";\n\t\tmatchNeighbourhood_\t\t- " << rs.matchNeighbourhood_
           << ";\n\t\tqualityValue_\t\t\t- " << rs.qualityValue_
           << ";\n\t\tread_\t\t\t\t- " << rs.read_
           << ";\n\t\treadId_\t\t\t\t- " << rs.readId_
           << ";\n\t\tsingleReadAlignmentMatchChromosome_\t- " << rs.singleReadAlignmentMatchChromosome_
           << ";\n\t\tsingleReadAlignmentStrand_\t- " << rs.singleReadAlignmentStrand_
           << ";\n\t\ttypeSingle_\t\t\t- " << rs.typeSingle_
           << ";\n\t\telandExtendedFile_\t\t- " << rs.elandExtendedFile_
           << ";\n\t\telandExtendedFilePath_\t\t- " << rs.elandExtendedFilePath_
           << ";\n\t\tshortAlignmentFormatFile_\t- " << rs.shortAlignmentFormatFile_
           << ";\n\t\tshortAlignmentFormatFilePath_\t- " << rs.shortAlignmentFormatFilePath_
           << ";" << std::endl;
        return os;
    }


} // alignment
} // casava