MSDataSqlConsumer.h

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// Copyright (c) 2002-present, OpenMS Inc. -- EKU Tuebingen, ETH Zurich, and FU Berlin
// SPDX-License-Identifier: BSD-3-Clause
//
// --------------------------------------------------------------------------
// $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 addRun(const String& filename, const UInt64 run_id);
      void setRunId(const UInt64 run_id);
 
      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_;
      bool wrote_any_run_ = false;
    };
 
} //end namespace OpenMS