MSDataSqlConsumer.h

Go to the documentation of this file.

// --------------------------------------------------------------------------
//                   OpenMS -- Open-Source Mass Spectrometry
// --------------------------------------------------------------------------
// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
// ETH Zurich, and Freie Universitaet Berlin 2002-2021.
//
// This software is released under a three-clause BSD license:
//  * Redistributions of source code must retain the above copyright
//    notice, this list of conditions and the following disclaimer.
//  * Redistributions in binary form must reproduce the above copyright
//    notice, this list of conditions and the following disclaimer in the
//    documentation and/or other materials provided with the distribution.
//  * Neither the name of any author or any participating institution
//    may be used to endorse or promote products derived from this software
//    without specific prior written permission.
// For a full list of authors, refer to the file AUTHORS.
// --------------------------------------------------------------------------
// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
// ARE DISCLAIMED. IN NO EVENT SHALL ANY OF THE AUTHORS OR THE CONTRIBUTING
// INSTITUTIONS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
// EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
// PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
// OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
// WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
// OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
// ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
//
// --------------------------------------------------------------------------
// $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