CachedMzMLHandler.h

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//                   OpenMS -- Open-Source Mass Spectrometry
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// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
// ETH Zurich, and Freie Universitaet Berlin 2002-2018.
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//    may be used to endorse or promote products derived from this software
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// $Maintainer: Hannes Roest $
// $Authors: Hannes Roest $
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#pragma once

#include <OpenMS/OPENSWATHALGO/DATAACCESS/ISpectrumAccess.h>

#include <OpenMS/KERNEL/StandardDeclarations.h>
#include <OpenMS/CONCEPT/Types.h>
#include <OpenMS/CONCEPT/Exception.h>
#include <OpenMS/CONCEPT/Macros.h>

#include <OpenMS/KERNEL/StandardTypes.h>
#include <OpenMS/CONCEPT/ProgressLogger.h>

#include <fstream>

#define CACHED_MZML_FILE_IDENTIFIER 8094

namespace OpenMS
{

namespace Internal
{

  class OPENMS_DLLAPI CachedMzMLHandler :
    public ProgressLogger
  {
    typedef int IntType;
    typedef double DoubleType;

public:

    typedef PeakMap MapType;
    typedef MSSpectrum SpectrumType;
    typedef MSChromatogram ChromatogramType;

    // using double precision to store all data (has to agree with type of BinaryDataArrayPtr)
    typedef double DatumSingleton;

    typedef std::vector<DatumSingleton> Datavector;

    CachedMzMLHandler();

    ~CachedMzMLHandler();

    CachedMzMLHandler& operator=(const CachedMzMLHandler& rhs);


    void writeMemdump(const MapType& exp, const String& out) const;

    void writeMetadata(MapType exp, String out_meta, bool addCacheMetaValue=false);

    void writeMetadata_x(const MapType& exp, const String& out_meta, bool addCacheMetaValue=false);

    void readMemdump(MapType& exp_reading, String filename) const;

    void createMemdumpIndex(String filename);

    const std::vector<std::streampos>& getSpectraIndex() const;

    const std::vector<std::streampos>& getChromatogramIndex() const;


    static inline void readSpectrumFast(OpenSwath::BinaryDataArrayPtr& data1,
                                        OpenSwath::BinaryDataArrayPtr& data2,
                                        std::ifstream& ifs, 
                                        int& ms_level,
                                        double& rt)
    {
      std::vector<OpenSwath::BinaryDataArrayPtr> data = readSpectrumFast(ifs, ms_level, rt);
      data1 = data[0];
      data2 = data[1];
    }

    static std::vector<OpenSwath::BinaryDataArrayPtr> readSpectrumFast(std::ifstream& ifs, int& ms_level, double& rt);

    static inline void readChromatogramFast(OpenSwath::BinaryDataArrayPtr& data1,
                                            OpenSwath::BinaryDataArrayPtr& data2, std::ifstream& ifs)
    {
      std::vector<OpenSwath::BinaryDataArrayPtr> data = readChromatogramFast(ifs);
      data1 = data[0];
      data2 = data[1];
    }

    static std::vector<OpenSwath::BinaryDataArrayPtr> readChromatogramFast(std::ifstream& ifs);

    static void readSpectrum(SpectrumType& spectrum, std::ifstream& ifs);

    static void readChromatogram(ChromatogramType& chromatogram, std::ifstream& ifs);

protected:

    void writeSpectrum_(const SpectrumType& spectrum, std::ofstream& ofs) const;

    void writeChromatogram_(const ChromatogramType& chromatogram, std::ofstream& ofs) const;

    static inline void readDataFast_(std::ifstream& ifs, std::vector<OpenSwath::BinaryDataArrayPtr>& data, const Size& data_size, 
      const Size& nr_float_arrays);

    std::vector<std::streampos> spectra_index_;
    std::vector<std::streampos> chrom_index_;

  };
}
}