MSDataWritingConsumer.h

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// --------------------------------------------------------------------------
//                   OpenMS -- Open-Source Mass Spectrometry
// --------------------------------------------------------------------------
// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
// ETH Zurich, and Freie Universitaet Berlin 2002-2023.
//
// 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
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// EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
// PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
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//
// --------------------------------------------------------------------------
// $Maintainer: Hannes Roest $
// $Authors: Hannes Roest $
// --------------------------------------------------------------------------
 
#pragma once
 
#include <OpenMS/INTERFACES/IMSDataConsumer.h>
 
#include <OpenMS/FORMAT/MzMLFile.h>
#include <OpenMS/FORMAT/HANDLERS/MzMLHandler.h>
#include <OpenMS/CONCEPT/ProgressLogger.h>
 
#include <vector>
#include <string>
#include <fstream>
#include <boost/shared_ptr.hpp>
 
namespace OpenMS
{
    class OPENMS_DLLAPI MSDataWritingConsumer : 
      public Internal::MzMLHandler,
      public Interfaces::IMSDataConsumer
    {
 
    public:
      typedef PeakMap MapType;
      typedef MapType::SpectrumType SpectrumType;
      typedef MapType::ChromatogramType ChromatogramType;
 
      explicit MSDataWritingConsumer(const String& filename);
 
      ~MSDataWritingConsumer() override;
 
 
 
      void setExperimentalSettings(const ExperimentalSettings& exp) override;
 
      void setExpectedSize(Size expectedSpectra, Size expectedChromatograms) override;
 
      void consumeSpectrum(SpectrumType & s) override;
 
      void consumeChromatogram(ChromatogramType & c) override;
 
      virtual void addDataProcessing(DataProcessing d);
 
      virtual Size getNrSpectraWritten();
 
      virtual Size getNrChromatogramsWritten();
 
    private:
 
 
 
      virtual void processSpectrum_(SpectrumType & s) = 0;
 
      virtual void processChromatogram_(ChromatogramType & c) = 0;
 
      virtual void doCleanup_();
 
    protected:
 
      std::ofstream ofs_;
 
      bool started_writing_;
      bool writing_spectra_;
      bool writing_chromatograms_;
      Size spectra_written_;
      Size chromatograms_written_;
      Size spectra_expected_;
      Size chromatograms_expected_;
      bool add_dataprocessing_;
 
      Internal::MzMLValidator * validator_;
 
      ExperimentalSettings settings_;
      std::vector<std::vector< ConstDataProcessingPtr > > dps_;
      DataProcessingPtr additional_dataprocessing_;
    };
 
    class OPENMS_DLLAPI PlainMSDataWritingConsumer :
      public MSDataWritingConsumer 
    {
      void processSpectrum_(MapType::SpectrumType & /* s */) override {}
      void processChromatogram_(MapType::ChromatogramType & /* c */) override {}
 
    public:
 
      explicit PlainMSDataWritingConsumer(String filename) : MSDataWritingConsumer(filename) {}
    };
 
    class OPENMS_DLLAPI NoopMSDataWritingConsumer :
      public MSDataWritingConsumer 
    {
    public:
 
      explicit NoopMSDataWritingConsumer(String filename) : MSDataWritingConsumer(filename) {}
      void setExperimentalSettings(const ExperimentalSettings& /* exp */) override {}
      void consumeSpectrum(SpectrumType & /* s */) override {}
      void consumeChromatogram(ChromatogramType & /* c */) override {}
 
    private:
 
      void doCleanup_() override {}
      void processSpectrum_(MapType::SpectrumType & /* s */) override {}
      void processChromatogram_(MapType::ChromatogramType & /* c */) override {}
    };
 
 
} //end namespace OpenMS