#ifndef _BLASR_HDF_CMP_EXPERIMENT_GROUP_HPP_
#define _BLASR_HDF_CMP_EXPERIMENT_GROUP_HPP_

#include <cstdint>
#include <map>
#include <set>
#include <vector>

#include <pbdata/Types.h>
#include <hdf/HDFArray.hpp>
#include <hdf/HDFCmpSupportedFields.hpp>
#include <hdf/HDFGroup.hpp>

class HDFCmpExperimentGroup
{
public:
    HDFCmpSupportedFields supportedFields;
    HDFArray<unsigned int> startTimeOffset;
    HDFArray<HalfWord> ipd;
    HDFArray<HalfWord> preBaseFrames;
    HDFArray<char> deletionTag;
    HDFArray<char> substitutionTag;
    HDFArray<UChar> qualityValue;
    HDFArray<UChar> deletionQV;
    HDFArray<UChar> insertionQV;
    HDFArray<float> classifierQV;
    // ClassifierQV date type is float in cmp.h5
    HDFArray<UChar> substitutionQV;
    HDFArray<UChar> mergeQV;
    HDFArray<HalfWord> light;
    HDFArray<HalfWord> widthInFrames;
    HDFArray<HalfWord> pulseWidth;
    HDFArray<unsigned int> startTime;
    // StartFrame computed from Pulse metrics and Base metric
    HDFArray<unsigned int> startTimeBase;
    HDFArray<unsigned int> startTimePulse;
    HDFArray<float> pkmid;
    HDFArray<float> pkmax;
    HDFArray<float> pkmean;
    HDFArray<uint32_t> numPasses;
    HDFArray<uint32_t> pulseIndex;
    std::map<std::string, HDFData *> fields;
    HDFGroup experimentGroup;
    HDFArray<unsigned char> alignmentArray;

    bool Create(HDFGroup &parent, std::string experimentGroupName);

    void AddAlignment(std::vector<unsigned char> &alignment, unsigned int &offsetBegin,
                      unsigned int &offsetEnd);

    // AddQVs and AddTags are like AddAlignment, but for QVs and Tags,
    // respectively. They are responsible for initializing and writing to the
    // correct member HDFArray, given a vector of values to write and the name
    // of the QV or Tag
    void AddQVs(const std::vector<UChar> &qualityValues, const std::string &fieldName,
                unsigned int *offsetBegin, unsigned int *offsetEnd);
    void AddTags(const std::vector<char> &qualityValues, const std::string &fieldName,
                 unsigned int *offsetBegin, unsigned int *offsetEnd);

    int Initialize(HDFGroup &refGroup, std::string experimentGroupName,
                   std::set<std::string> &fieldNames);

    int Initialize(HDFGroup &refGroup, std::string experimentGroupName);

    void Read();

    HDFCmpExperimentGroup();

    // Return reference alignment AlnArray size in KB.
    UInt GetAlnArraySize();
};
#endif