SwathQC.h

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//                   OpenMS -- Open-Source Mass Spectrometry
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// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
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// $Maintainer: Chris Bielow $
// $Authors: Chris Bielow $
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#pragma once

#include <OpenMS/OPENSWATHALGO/DATAACCESS/SwathMap.h>
#include <OpenMS/OpenMSConfig.h>

#include <functional>
#include <map>
#include <vector>

namespace OpenMS
{
  class String;
  class MSSpectrum;
  class ExperimentalSettings;

}

namespace OpenSwath
{

  class OPENMS_DLLAPI SwathQC
  {
  public:
    typedef std::map<int,int> ChargeDistribution;
    
    SwathQC() = delete;

    SwathQC(const size_t cd_spectra, const double decon_ms1_mz_tol);


    std::function<void(const OpenMS::ExperimentalSettings& es)> getExpSettingsFunc();

    std::function<void (const OpenMS::MSSpectrum&)> getSpectraProcessingFunc();


    static ChargeDistribution getChargeDistribution(const std::vector<SwathMap>& swath_maps, const size_t nr_samples, const double mz_tol);


    void storeJSON(const OpenMS::String& filename);

    const ChargeDistribution& getChargeDistribution() const;

    void setNrMS1Spectra(size_t nr);


   protected: 

    static bool isSubsampledSpectrum_(const size_t total_spec_count, const size_t subsample_count, const size_t idx);
   
   private: 

    ChargeDistribution cd_;

    size_t nr_ms1_spectra_;
    size_t cd_spectra_;
    double decon_ms1_mz_tol_;

    size_t ms1_spectra_seen_;
  };
    
}