// Author: Yuan Li

#ifndef _BLASR_HDF_HDFZMWMETRICSWriter_HPP_
#define _BLASR_HDF_HDFZMWMETRICSWriter_HPP_

#include <hdf/BufferedHDF2DArray.hpp>
#include <hdf/BufferedHDFArray.hpp>
#include <hdf/HDFWriterBase.hpp>
#include <pbdata/SMRTSequence.hpp>

class HDFBaseCallerWriter;

class HDFZMWMetricsWriter : public HDFWriterBase
{

    friend class HDFBaseCallerWriter;

private:
    /// \name Private variable
    /// \{
    HDFGroup& parentGroup_;

    HDFGroup zmwMetricsGroup_;

    /// HDF2DArray for writing average SNR within HQRegion.
    BufferedHDF2DArray<float> hqRegionSNRArray_;

    /// HDFArray for writing read raw accuracy prediction.
    BufferedHDFArray<float> readScoreArray_;

    /// HDFArray for writing Productivity
    BufferedHDFArray<unsigned char> productivityArray_;

    /// Map bases (e.g., ACGT) to indices
    std::map<char, size_t> baseMap_;

    int curRow_;

    static const int SNRNCOLS = 4;
    /// \}

public:
    /// \name Constructors and Destructors
    /// \{
    HDFZMWMetricsWriter(const std::string& filename, HDFGroup& parentGroup,
                        const std::map<char, size_t>& baseMap);

    ~HDFZMWMetricsWriter(void);
    /// \}

    /// \name Public Methods
    /// \{

    /// \note Write info of a SMRTSequence to ZMWMetrics,
    ///       (1) add average signal to noise ratio in HQRegion to HQRegionSNR
    ///       (2) add read raw accuracy prediction to ReadScore
    bool WriteOneZmw(const SMRTSequence& read);

    /// \note Flushes all data from cache to disc.
    void Flush(void);

    /// \note Closes this zmw group as well as child hdf groups.
    void Close(void);
    /// \}

private:
    /// \name Private Methods
    /// \{

    /// \note Initialize child hdf groups under ZMWMetrics, including
    ///       HQRegionSNR and ReadScore
    /// \reutrns bool, whether or not child hdf groups successfully initialized.
    bool InitializeChildHDFGroups(void);

    /// \note Write Attributes.
    bool WriteAttributes(void);
    /// \}
};

#endif
