SMRTSequence.hpp

#ifndef _BLASR_SMRT_SEQUENCE_HPP_
#define _BLASR_SMRT_SEQUENCE_HPP_

#include <cassert>
#include <iostream>
#include <sstream>

#include "Types.h"
#include "Enumerations.h"
#include "NucConversion.hpp"
#include "FASTQSequence.hpp"
#include "datastructures/reads/RegionTable.hpp"
#include "datastructures/reads/ZMWGroupEntry.hpp"

class SMRTSequence : public FASTQSequence {
public:
    int16_t xy[2];
    int holeNumber;
    ZMWGroupEntry zmwData;
    PlatformType platform;
    HalfWord *preBaseFrames;
    HalfWord *widthInFrames;
    //
    // The following are fields that are read in from the pulse file.
    // Because they are not standard in bas.h5 files, these fields
    // should not be preallocated when resizing a SMRTSequence, and
    // memory should be managed separately.  For now, these fields all
    // have the same length as the number of bases, but this could
    // change so that all pulse values are stored in a SMRTSequence.
    //
    HalfWord *meanSignal, *maxSignal, *midSignal;
    float *classifierQV;
    unsigned int *startFrame;
    int *pulseIndex;
    DNALength lowQualityPrefix, lowQualitySuffix;

    void SetNull(); 

    SMRTSequence();

    void Allocate(DNALength length); 

    void SetSubreadTitle(SMRTSequence &subread, DNALength subreadStart, 
        DNALength subreadEnd); 

    void SetSubreadBoundaries(SMRTSequence &subread, DNALength &subreadStart, 
        int &subreadEnd); 

    void MakeSubreadAsMasked(SMRTSequence &subread, DNALength subreadStart = 0, 
        int subreadEnd = -1); 

    void MakeSubreadAsReference(SMRTSequence &subread, DNALength subreadStart = 0, 
        int subreadEnd = -1); 

    void Copy(const SMRTSequence &rhs); 

    void Copy(const SMRTSequence &rhs, int rhsPos, int rhsLength); 

    void Print(std::ostream &out); 

    SMRTSequence& operator=(const SMRTSequence &rhs); 

    void Free(); 

    bool StoreXY(int16_t xyP[]); 

    bool StorePlatformType(PlatformId pid);

    bool StorePlatformType(PlatformType ptype); 

    bool StoreHoleNumber(int holeNumberP);

    bool StoreHoleStatus(unsigned int s); 

    bool StoreZMWData(ZMWGroupEntry &data); 

    bool GetXY(int xyP[]); 

    bool GetHoleNumber(int& holeNumberP); 
};

#endif  // _BLASR_SMRT_SEQUENCE_HPP_