#ifndef _BLASR_HDF_CMP_DATA_HPP_
#define _BLASR_HDF_CMP_DATA_HPP_

#include <hdf/HDFAtom.hpp>
#include <hdf/HDFCmpRefAlignmentGroup.hpp>

class HDFCmpData
{
public:
    HDFAtom<std::string> commandLine;
    H5::H5File hdfCmpFile;
    HDFArray<int> movieNameIdArray;
    HDFStringArray movieNameArray;

    HDFStringArray readGroupPathArray;
    HDFArray<int> readGroupPathIdArray;

    HDFArray<int> refSeqNameIdArray;
    HDFStringArray refSeqNameArray;
    static const int NCols = 22;
    std::vector<HDFAtom<std::string> > colNameAtoms;
    std::vector<HDFCmpRefAlignmentGroup *> refAlignGroups;
    std::map<std::string, int> nameToAlignmentGroupIndex;
    static const char *colNameIds[];

    void Close() { hdfCmpFile.close(); }
};

const char *HDFCmpData::colNameIds[] = {"00", "01", "02", "03", "04", "05", "06", "07",
                                        "08", "09", "10", "11", "12", "13", "14", "15",
                                        "16", "17", "18", "19", "20", "21"};

#endif