CachedMzML.h

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//                   OpenMS -- Open-Source Mass Spectrometry
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// $Maintainer: Hannes Roest $
// $Authors: Hannes Roest $
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#ifndef OPENMS_FORMAT_CACHEDMZML_H
#define OPENMS_FORMAT_CACHEDMZML_H

#include <OpenMS/ANALYSIS/OPENSWATH/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 8093

namespace OpenMS
{

  class OPENMS_DLLAPI CachedmzML :
    public ProgressLogger
  {
    int int_field_;
    double dbl_field_;

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;

    CachedmzML();

    ~CachedmzML();

    CachedmzML& operator=(const CachedmzML& rhs);


    void writeMemdump(MapType& exp, String out);

    void writeMetadata(MapType exp, 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)
    {
      Size spec_size = -1;
      ifs.read((char*) &spec_size, sizeof(spec_size));
      ifs.read((char*) &ms_level, sizeof(ms_level));
      ifs.read((char*) &rt, sizeof(rt));

      if ( static_cast<int>(spec_size) < 0)
      {
        throw Exception::ParseError(__FILE__, __LINE__, OPENMS_PRETTY_FUNCTION, 
          "Read an invalid spectrum length, something is wrong here. Aborting.", "filestream");
      }

      data1->data.resize(spec_size);
      data2->data.resize(spec_size);

      if (spec_size > 0)
      {
        ifs.read((char*) &(data1->data)[0], spec_size * sizeof(double));
        ifs.read((char*) &(data2->data)[0], spec_size * sizeof(double));
      }
    }

    static inline void readChromatogramFast(OpenSwath::BinaryDataArrayPtr data1,
                                            OpenSwath::BinaryDataArrayPtr data2, std::ifstream& ifs)
    {
      Size spec_size = -1;
      ifs.read((char*) &spec_size, sizeof(spec_size));

      if ( static_cast<int>(spec_size) < 0)
      {
        throw Exception::ParseError(__FILE__, __LINE__, OPENMS_PRETTY_FUNCTION, 
          "Read an invalid chromatogram length, something is wrong here. Aborting.", "filestream");
      }

      data1->data.resize(spec_size);
      data2->data.resize(spec_size);
      ifs.read((char*) &(data1->data)[0], spec_size * sizeof(double));
      ifs.read((char*) &(data2->data)[0], spec_size * sizeof(double));
    }

protected:

    void readSpectrum_(Datavector& data1, Datavector& data2, std::ifstream& ifs, int& ms_level, double& rt) const;

    void readChromatogram_(Datavector& data1, Datavector& data2, std::ifstream& ifs) const;

    void readSpectrum_(SpectrumType& spectrum, std::ifstream& ifs) const;

    void readChromatogram_(ChromatogramType& chromatogram, std::ifstream& ifs) const;

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

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

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

  };
}
#endif // OPENMS_FORMAT_CACHEDMZML_H