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#ifndef _BLASR_HDF_PULSE_DATA_FILE_HPP_
#define _BLASR_HDF_PULSE_DATA_FILE_HPP_
#include <string>
#include <vector>
#include <H5Cpp.h>
#include <hdf/HDFGroup.hpp>
#include <hdf/HDFScanDataReader.hpp>
#include <hdf/HDFZMWReader.hpp>
class HDFPulseDataFile
{
public:
H5::H5File hdfBasFile;
HDFGroup pulseDataGroup;
HDFGroup rootGroup;
HDFGroup *rootGroupPtr;
std::string pulseDataGroupName;
HDFScanDataReader scanDataReader;
bool useScanData;
bool closeFileOnExit;
// Max number of rows allowed to read into memory at a time.
DSLength maxAllocNElements;
HDFZMWReader zmwReader;
std::vector<DSLength> eventOffset;
UInt nReads;
bool preparedForRandomAccess;
DSLength GetAllReadLengths(std::vector<DNALength> &readLengths);
void CheckMemoryAllocation(long allocSize, long allocLimit, const char *fieldName = NULL);
HDFPulseDataFile();
void PrepareForRandomAccess();
int OpenHDFFile(std::string fileName,
const H5::FileAccPropList &fileAccPropList = H5::FileAccPropList::DEFAULT);
//
// All pulse data files contain the "PulseData" group name.
//
//
int InitializePulseDataFile(std::string fileName, const H5::FileAccPropList &fileAccPropList =
H5::FileAccPropList::DEFAULT);
int Initialize(std::string fileName,
const H5::FileAccPropList &fileAccPropList = H5::FileAccPropList::DEFAULT);
//
// Initialize inside another open group.
//
int Initialize(HDFGroup *rootGroupP);
//
// Initialize all fields
//
int Initialize();
int InitializePulseGroup();
size_t GetAllHoleNumbers(std::vector<unsigned int> &holeNumbers);
void Close();
};
#endif
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