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// Author: Yuan Li
#ifndef _HDF_REGIONS_WRITER_HPP_
#define _HDF_REGIONS_WRITER_HPP_
#include <string>
#include <pbdata/Enumerations.h>
#include <hdf/HDF2DArray.hpp>
#include <hdf/HDFArray.hpp>
#include <hdf/HDFAtom.hpp>
#include <hdf/HDFFile.hpp>
#include <hdf/HDFWriterBase.hpp>
#include <pbdata/reads/RegionTable.hpp>
using namespace H5;
class HDFRegionsWriter : public HDFWriterBase
{
public:
/// \name Constructor and destructor
/// \{
/// \param[in] filename, hdf file name
/// \param[in] parentGroup, parent hdf group in hirarchy
HDFRegionsWriter(const std::string &filename, HDFGroup &parentGroup,
const std::vector<std::string> ®ionTypes =
PacBio::AttributeValues::Regions::regiontypes);
~HDFRegionsWriter(void);
/// \}
private:
/// \name Private variables for hdf IO.
/// \{
HDFGroup &parentGroup_; //< parent hdf group
/// A vector of std::string's of region types for RegionTypeIndex to look up. Order matters!
std::vector<std::string> regionTypes_;
HDF2DArray<int> regionsArray_; //< HDF2DArray for writing regions to hdf
int curRow_; //< which row to write
static const int NCOLS = 5; //< number of columns in Regions table.
/// \brief Write attributes of the 'regions' group
bool WriteAttributes(void);
/// \}
public:
/// \name Method to write region annotations.
/// \{
/// \brief Append a vector of region annotations to 'regions'
/// \param[in] annotations - region annotations to append.
/// \returns true if succeeded.
bool Write(const std::vector<RegionAnnotation> &annotations);
/// \brief Append a region annotation to 'regions'
/// \param[in] annotation - region annotation to append
/// \returns true if succeeded.
bool Write(const RegionAnnotation &annotation);
void Flush(void);
void Close(void);
};
#endif
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