libpbihdf-dev 0~20161219-2 / usr / include / pbseq / hdf / HDFScanDataWriter.hpp

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// Author: Yuan Li

#ifndef DATA_HDF_HDF_SCAN_DATA_WRITER_H_
#define DATA_HDF_HDF_SCAN_DATA_WRITER_H_

#include <string>
#include <iostream>
#include "HDFFile.hpp"
#include "HDFGroup.hpp"
#include "HDFAtom.hpp"
// pbdata/
#include "../pbdata/Enumerations.h"
#include "../pbdata/reads/ScanData.hpp"
#include "../pbdata/reads/AcqParams.hpp"


class HDFScanDataWriter {
private:
    HDFGroup * rootGroupPtr;
	HDFGroup scanDataGroup;
	HDFGroup acqParamsGroup;
    HDFGroup dyeSetGroup;
	HDFGroup runInfoGroup;

	HDFAtom<std::string> whenStartedAtom;
	HDFAtom<float> frameRateAtom;
	HDFAtom<unsigned int> numFramesAtom;

    HDFAtom<std::string> baseMapAtom;
    HDFAtom<uint16_t> numAnalogAtom;

	HDFAtom<std::string> movieNameAtom;
	HDFAtom<std::string> runCodeAtom;

	HDFAtom<std::string> bindingKitAtom;
	HDFAtom<std::string> sequencingKitAtom;

	HDFAtom<unsigned int> platformIdAtom;
	HDFAtom<std::string> platformNameAtom;
    HDFAtom<std::string> instrumentNameAtom;

    void CreateAcqParamsGroup();

    void CreateDyeSetGroup();

    void CreateRunInfoGroup();

public:
	HDFScanDataWriter(HDFFile & _outFile);

    HDFScanDataWriter(HDFGroup & _rootGroup);

    ~HDFScanDataWriter();
    
    int Initialize(HDFGroup & _rootGroup);
      
    void Write(const ScanData & scanData);

    void Write(const ScanData & scanData, 
               const AcqParams & acqParam);
   
	void WriteFrameRate(const float frameRate);

    void WriteNumFrames(const unsigned int numFrames);

    void WriteWhenStarted(const std::string whenStarted);

	void Close();
  
private:
    void WriteBaseMap(const std::string baseMapStr);
   
    void WriteNumAnalog(const uint16_t numAnalog);

    void WritePlatformId(const PlatformId id);
   
    void WriteMovieName(const std::string movieName);

    void WriteRunCode(const std::string runCode);

    void WriteBindingKit(const std::string & bindingKit);

    void WriteSequencingKit(const std::string & sequencingKit);

private:
    /// Write attributes to /ScanData/AcqParams
    void _WriteAcqParams(const AcqParams & acqParams);

    void _WriteAduGain(const float aduGain);

    void _WriteCameraGain(const float cameraGain);

    void _WriteCameraType(const int cameraType);

    void _WriteHotStartFrame(const UInt hotStartFrame);

    void _WriteLaserOnFrame(const UInt laserOnFrame);

};

#endif

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