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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 <hdf/HDF2DArray.hpp>
#include <hdf/HDFArray.hpp>
#include <hdf/HDFAtom.hpp>
#include <hdf/HDFFile.hpp>
#include <pbdata/reads/RegionTable.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 ®ionTableFileName,
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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