libpbihdf-dev 0~20161219-2 / usr / include / pbseq / hdf / HDFRegionTableReader.hpp

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#ifndef _BLASR_HDF_REGION_TABLE_READER_HPP_
#define _BLASR_HDF_REGION_TABLE_READER_HPP_

#include <string>
#include <vector>

#include <H5Cpp.h>

#include "../pbdata/reads/RegionTable.hpp"
#include "HDFFile.hpp"
#include "HDFArray.hpp"
#include "HDF2DArray.hpp"
#include "HDFAtom.hpp"


class HDFRegionTableReader {
private:
    HDFFile regionTableFile;
    HDFGroup pulseDataGroup;
    HDF2DArray<int> regions;

    HDFAtom<std::vector<std::string> > regionTypes;
    HDFAtom<std::vector<std::string> > regionDescriptions;
    HDFAtom<std::vector<std::string> > regionSources;
    HDFAtom<std::vector<std::string> > columnNames;

    int curRow;

    bool isInitialized_; // whether or not this reader is initialized.

    int nRows;

    bool fileContainsRegionTable;

public:

    HDFRegionTableReader(void)
    : curRow(0), isInitialized_(false), nRows(0) 
    , fileContainsRegionTable(false) {}

    int Initialize(std::string &regionTableFileName, 
                   const H5::FileAccPropList & fileAccPropList = H5::FileAccPropList::DEFAULT);

    bool IsInitialized(void) const;

    bool HasRegionTable(void) const;

    void GetMinMaxHoleNumber(UInt &minHole, UInt &maxHole);

    void ReadTable(RegionTable &table);

    void Close();

private:
    int GetNext(RegionAnnotation &annotation);
};


#endif

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