MSDataSqlConsumer.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 2002-2022.
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// $Maintainer: Hannes Roest $
// $Authors: Hannes Roest $
// --------------------------------------------------------------------------

#pragma once

#include <OpenMS/INTERFACES/IMSDataConsumer.h>

#include <OpenMS/KERNEL/MSExperiment.h>

namespace OpenMS
{

    namespace Internal
    {
      class MzMLSqliteHandler;
    }

    class OPENMS_DLLAPI MSDataSqlConsumer :
      public Interfaces::IMSDataConsumer
    {
      typedef MSExperiment MapType;
      typedef MapType::SpectrumType SpectrumType;
      typedef MapType::ChromatogramType ChromatogramType;

    public:

      MSDataSqlConsumer(const String& sql_filename, UInt64 run_id, int buffer_size = 500, bool full_meta = true, bool lossy_compression=false, double linear_mass_acc=1e-4);

      ~MSDataSqlConsumer() override;

      void flush();

      void consumeSpectrum(SpectrumType & s) override;

      void consumeChromatogram(ChromatogramType & c) override;

      void setExpectedSize(Size /* expectedSpectra */, Size /* expectedChromatograms */) override;

      void setExperimentalSettings(const ExperimentalSettings& /* exp */) override;

    protected:

      String filename_;
      OpenMS::Internal::MzMLSqliteHandler * handler_;

      size_t flush_after_;
      bool full_meta_;
      std::vector<SpectrumType> spectra_;
      std::vector<ChromatogramType> chromatograms_;

      MSExperiment peak_meta_;
    };

} //end namespace OpenMS