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#ifndef _BLASR_PULSE_FILE_HPP_
#define _BLASR_PULSE_FILE_HPP_
#include <map>
#include <vector>
#include <pbdata/Enumerations.h>
#include <pbdata/Types.h>
#include <pbdata/DNASequence.hpp>
#include <pbdata/SMRTSequence.hpp>
#include <pbdata/reads/PulseBaseCommon.hpp>
#include <pbdata/reads/ScanData.hpp>
class PulseFile : public PulseBaseCommon
{
public:
unsigned int numFrames;
PlatformId platformId;
std::vector<unsigned int> startFrame;
std::vector<uint16_t> plsWidthInFrames;
int midSignalNDims, maxSignalNDims, meanSignalNDims;
std::vector<uint16_t> midSignal;
std::vector<uint16_t> maxSignal;
std::vector<uint16_t> meanSignal;
std::vector<DNALength> numEvent;
std::vector<DSLength> pulseStartPositions;
std::vector<float> classifierQV;
PulseFile()
{
numFrames = 0;
platformId = Springfield;
}
// Copy signals (QVs) from signalData (which has dimension signalNDims)
// starting from position pulseStartPos with length readLength to readData.
// If signal diamension is 2 (2D Array e.g., Chi2), then bases in readSeq at a
// particular location is used to determine which channel to copy the signal from.
// e.g., if basemap is 'GCTA', and base at position 3 is T, each base corresponds
// to 4 channels and then we need to copy signal from channel 2 of position 3.
void CopySignal(HalfWord *signalData, // either a vector or matrix
int signalNDims, // diamension of signal, either 1 or 2.
DSLength pulseStartPos, // 0 if baseToPulseIndex maps to abs position
int *baseToPulseIndex, // Map base to pulse index.
Nucleotide *readSeq,
DNALength readLength, // read length (num of signals to copy)
HalfWord *readData);
// plsReadIndex: index of this hole number in /PulseCalls/ZMW/HoleNumber.
// baseToPulseIndex: index from pulse to base from the beginning of the read.
// read: a SMRTSequence.
void CopyReadAt(UInt plsReadIndex, int *baseToPulseIndex, SMRTSequence &read);
template <typename T_FieldType>
void StoreField(std::vector<T_FieldType> &source, int *basToPlsIndex, T_FieldType *dest,
const DSLength destLength);
template <typename T>
bool Realloc(T *&ptr, const DNALength length);
};
#include "PulseFileImpl.hpp"
#endif
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