/**
 ** 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 AlignStatsXmlWriter.hh
 **
 ** \brief Alignment data statistics into an Xml file.
 **
 ** \author Roman Petrovski
 **/

#include <boost/foreach.hpp>
#include <boost/lexical_cast.hpp>
#include <boost/property_tree/xml_parser.hpp>

#include "common/Exceptions.hh"
#include "io/PtreeXml.hh"

#include "statistics/AlignStatsXmlWriter.hh"


namespace casava
{
namespace statistics
{

namespace cc=casava::common;

AlignStatsXmlWriter::AlignStatsXmlWriter(const fs::path &statsFilePath) :
    statsFilePath_(statsFilePath), os_(statsFilePath.string().c_str()){
    if (!os_) {
        BOOST_THROW_EXCEPTION(cc::IoException(errno, "ERROR: Unable to open file for writing: " + statsFilePath_.string()));
    }
}

void AlignStatsXmlWriter::addTile(const std::string &sampleName, const std::string &barcode,
                                  const unsigned int lane, const unsigned int read, const unsigned int tile,
                                  const Stats_Set& tileStats)
{
    const std::string tileValuePrefix("Stats"
                                      ".<indexed>Sample.<index>" + sampleName
                                      +".<indexed>Barcode.<index>" + barcode
                                      +".<indexed>Read.<index>" + boost::lexical_cast<std::string>(read)
                                      +".<indexed>Lane.<index>" + boost::lexical_cast<std::string>(lane)
                                      +".<indexed>Tile.<index>" + boost::lexical_cast<std::string>(tile)
                                      +".<value>.");

    tree_.add(tileValuePrefix + "Yield", tileStats.basesTotal());
    tree_.add(tileValuePrefix + "YieldQ20", tileStats.q20BasesTotal());
    tree_.add(tileValuePrefix + "YieldQ30", tileStats.q30BasesTotal());
    tree_.add(tileValuePrefix + "QualityScoreSum", tileStats.qualityScoreSum());
    tree_.add(tileValuePrefix + "ClusterCount", tileStats.clustersTotal());
    tree_.add(tileValuePrefix + "UniquelyAlignedClusterCount", tileStats.uniqueAligns());
    tree_.add(tileValuePrefix + "AlignScoreSum", tileStats.alignScoreSum());
    tree_.add(tileValuePrefix + "UniquelyAlignedBasesOutsideIndels", tileStats.basesAligned());
    tree_.add(tileValuePrefix + "AlignMismatches", tileStats.alignMismatches());
}

void AlignStatsXmlWriter::close()
{
    using namespace casava::io;
    os_ << tree_;
    if (!os_) {
        BOOST_THROW_EXCEPTION(cc::IoException(errno, "ERROR: failed to store alignment statistics: " + statsFilePath_.string()));
    }
}


} //namespace statistics
} //namespace casava