MSDataCachedConsumer.h

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// --------------------------------------------------------------------------
//                   OpenMS -- Open-Source Mass Spectrometry
// --------------------------------------------------------------------------
// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
// ETH Zurich, and Freie Universitaet Berlin 2002-2017.
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// $Maintainer: Hannes Roest $
// $Authors: Hannes Roest $
// --------------------------------------------------------------------------

#ifndef OPENMS_FORMAT_DATAACCESS_MSDATACACHEDCONSUMER_H
#define OPENMS_FORMAT_DATAACCESS_MSDATACACHEDCONSUMER_H

#include <OpenMS/INTERFACES/IMSDataConsumer.h>

#include <OpenMS/KERNEL/StandardTypes.h>
#include <OpenMS/KERNEL/MSSpectrum.h>
#include <OpenMS/KERNEL/MSChromatogram.h>

#include <OpenMS/FORMAT/CachedMzML.h>

namespace OpenMS
{
    class OPENMS_DLLAPI MSDataCachedConsumer :
      public CachedmzML,
      public Interfaces::IMSDataConsumer
    {
      typedef MSSpectrum SpectrumType;
      typedef MSChromatogram ChromatogramType;

    public:

      MSDataCachedConsumer(String filename, bool clearData=true) :
        ofs_(filename.c_str(), std::ios::binary),
        clearData_(clearData),
        spectra_written_(0),
        chromatograms_written_(0)
      {
        int file_identifier = CACHED_MZML_FILE_IDENTIFIER;
        ofs_.write((char*)&file_identifier, sizeof(file_identifier));
      }

      ~MSDataCachedConsumer()
      {
        // Write size of file (to the end of the file)
        ofs_.write((char*)&spectra_written_, sizeof(spectra_written_));
        ofs_.write((char*)&chromatograms_written_, sizeof(chromatograms_written_));

        // Close file stream: close() _should_ call flush() but it might not in
        // all cases. To be sure call flush() first.
        ofs_.flush();
        ofs_.close();
      }

      void consumeSpectrum(SpectrumType & s)
      {
        if (chromatograms_written_ > 0)
        {
          throw Exception::IllegalArgument(__FILE__, __LINE__, OPENMS_PRETTY_FUNCTION,
            "Cannot write spectra after writing chromatograms.");
        }
        writeSpectrum_(s, ofs_);
        spectra_written_++;
        if (clearData_) {s.clear(false);}
      }

      void consumeChromatogram(ChromatogramType & c)
      {
        writeChromatogram_(c, ofs_);
        chromatograms_written_++;
        if (clearData_) {c.clear(false);}
      }

      void setExpectedSize(Size /* expectedSpectra */, Size /* expectedChromatograms */) {;}

      void setExperimentalSettings(const ExperimentalSettings& /* exp */) {;}

    protected:
      std::ofstream ofs_;
      bool clearData_;
      Size spectra_written_;
      Size chromatograms_written_;

    };

} //end namespace OpenMS

#endif