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#ifndef _BLASR_HDF_ARRAY_HPP_
#define _BLASR_HDF_ARRAY_HPP_
#include <cassert>
#include <iostream>
#include <H5Cpp.h>
#include <hdf/BufferedHDFArray.hpp>
#include <hdf/HDFConfig.hpp>
#include <hdf/HDFData.hpp>
#include <pbdata/DNASequence.hpp>
#include <pbdata/FASTQSequence.hpp>
/*
*
* Implementation of a 1-D array for IO from an HDF array.
* This is templated, but specialized for a few data types, so that
* the HDF data types do not need to be specified by anybody.
*
* Two examples of the usage of this class follow:
*
* HDFArray<int> nElemArray;
* nElemArray.Initialize(hdfFile, "PulseData/BaseCalls/ZMW/NumEvent");
* nElemArray.Read(i, i+1, &nElem);
*
* HDFArray<unsigned char> qualArray;
* qualArray.Initialize(hdfFile, "PulseData/BaseCalls/QualityValue");
* qualArray.Read(cur, cur + nElem, qual);
*
*/
template <typename T>
class HDFArray : public BufferedHDFArray<T>
{
public:
HDFArray() : BufferedHDFArray<T>() {}
HDFArray(H5::Group* _container, std::string _datasetName)
: BufferedHDFArray<T>(_container, _datasetName)
{
}
/*
* An unbuffered write is simply a write immediately followed by a flush.
*/
void WriteToPos(const T* data, int dataLength, UInt writePos)
{
this->writeBuffer = (T*)data;
this->bufferIndex = dataLength;
this->bufferSize = dataLength;
this->Flush(false, writePos);
ResetBuffer();
}
void ResetBuffer()
{
this->writeBuffer = NULL;
this->bufferIndex = 0;
this->bufferSize = 0;
}
void Write(const T* data, int dataLength)
{
this->writeBuffer = (T*)data;
this->bufferIndex = dataLength;
this->bufferSize = dataLength;
this->Flush();
//
// Reset status of buffer so that no methods are tricked into
// thinking this is a valid pointer.
//
ResetBuffer();
}
~HDFArray() {}
};
class HDFStringArray : public HDFArray<std::string>
{
public:
void Read(DSLength start, DSLength end, std::string* dest)
{
std::vector<char*> tmpDestCharPtrs;
if (end == start) return;
assert(end > start);
tmpDestCharPtrs.resize(end - start);
// ReadCharArray(start, end, (char**) &tmpDestCharPtrs[0]);
ReadCharArray(start, end, dest);
}
};
#endif
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