/**
 ** Copyright (c) 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 PairStats.hh
 **
 ** \brief Encapsulation of pair statistics XML file.
 **
 ** Encapsulation of pair statistics XML file.
 **
 ** \author Richard Shaw
 **/

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#ifndef PAIR_STATS_HH
#define PAIR_STATS_HH

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#include <string>
#include <map>

#include <boost/filesystem.hpp>

#include "common/RelOrient.hh"

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namespace casava
{
namespace common
{

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class LaneBarcodePairStats
{
public:
    LaneBarcodePairStats();
    LaneBarcodePairStats(const std::string &goodPairs, const std::string &read1Len, const std::string &read2Len,
                  const RelOrient &relOrient, const std::string &fragmentLenMedian,
                  const std::string &fragmentLenLowSd, const std::string &fragmentLenHighSd);

    unsigned int getReadLen(unsigned int readNum) const;

    void setNumSds(float numLowSds, float numHighSds);
    void getBounds(RelOrient& relOrient,
                   double& minSize, double& maxSize) const;
    void getSds(double& lowSd, double& highSd) const;

    double mostLikelyInsertSize() const { return fragmentLenMedian_; }

    bool isCompatible(const LaneBarcodePairStats& that);
    LaneBarcodePairStats & operator |= (const LaneBarcodePairStats& that);
    LaneBarcodePairStats & assign(LaneBarcodePairStats that);

private:
    // configuration
    float numLowSds_;
    float numHighSds_;

    // data
    unsigned int goodPairs_;
    unsigned int read1Len_;
    unsigned int read2Len_;
    RelOrient relOrient_;
    double fragmentLenMedian_;
    double fragmentLenLowSd_;
    double fragmentLenHighSd_;

    //derived
    double fragmentLenSizeMin_;
    double fragmentLenSizeMax_;

    void updateDerived();
};

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class PairStats
{
public:
    // Expects to find *pair.xml according to the run.conf.xml for this proj.
    PairStats(const boost::filesystem::path& projDirPath);
    bool isValid(const std::string &instrument,
                 const int run,
                 const int lane,
                 const std::string &barcode) const {
        return myLaneBarcodePairStatsMap.end() != getLaneBarcodePairStats(instrument, run, lane, barcode, "isValid"); }

    unsigned int getReadLen(const std::string &instrument,
                            const int run,
                            const int lane,
                            const std::string &barcode,
                            unsigned int readNum) const;
    void setNumSds(float numLowSds, float numHighSds);
    void getBounds(const std::string &instrument,
                   const int run,
                   const int lane,
                   const std::string &barcode,
                   RelOrient& relOrient,
                   double& minSize, double& maxSize) const;
    void getSds(const std::string &instrument,
                const int run,
                const int lane,
                const std::string &barcode,
                double& lowSd, double& highSd) const;

    double mostLikelyInsertSize(const std::string &instrument,
                                const int run,
                                const int lane,
                                const std::string &barcode) const;

private:
    // Prevent other forms of construction and copying.
    PairStats();
    PairStats(const PairStats&);
    PairStats& operator=(const PairStats&);

    typedef std::map<std::string, LaneBarcodePairStats> LaneBarcodePairStatsMap;
    typedef LaneBarcodePairStatsMap::iterator LaneBarcodePairStatsMapIter;
    typedef LaneBarcodePairStatsMap::const_iterator LaneBarcodePairStatsMapCIter;
    LaneBarcodePairStatsMap myLaneBarcodePairStatsMap;

    LaneBarcodePairStatsMap::const_iterator getLaneBarcodePairStats(const std::string &instrument,
                                                      const int run,
                                                      const int lane,
                                                      const std::string &barcode,
                                                      const std::string &label) const;
};

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} // namespace common
} // namespace casava

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#endif // #ifndef PAIR_STATS_HH

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