Ms2SpectrumStats.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: Juliane Schmachtenberg, Chris Bielow $
// --------------------------------------------------------------------------

#pragma once

#include <OpenMS/QC/QCBase.h>

#include <OpenMS/KERNEL/Peak1D.h>
#include <OpenMS/KERNEL/MSSpectrum.h>


namespace OpenMS
{
  class FeatureMap;
  class MSExperiment;
  class PeptideIdentification;
  class TransformationDescription;

  class OPENMS_DLLAPI Ms2SpectrumStats : public QCBase
  {
  public:
    struct ScanEvent
    {
      ScanEvent(UInt32 sem, bool ms2)
        : scan_event_number(sem), ms2_presence(ms2) 
      {}
      UInt32 scan_event_number;
      bool ms2_presence;
    };

    Ms2SpectrumStats() = default;

    virtual ~Ms2SpectrumStats() = default;

    std::vector<PeptideIdentification> compute(const MSExperiment& exp, FeatureMap& features, const QCBase::SpectraMap& map_to_spectrum);

    const String& getName() const override;
    Status requires() const override;

  private:
    const String name_ = "Ms2SpectrumStats";
    
    std::vector<ScanEvent> ms2_included_{};

    void setScanEventNumber_(const MSExperiment& exp);

    void setPresenceAndScanEventNumber_(PeptideIdentification& peptide_ID, const MSExperiment& exp, const QCBase::SpectraMap& map_to_spectrum);

    std::vector<PeptideIdentification> getUnassignedPeptideIdentifications_(const MSExperiment& exp);

    static MSSpectrum::PeakType::IntensityType getBPI_(const MSSpectrum& spec);
  };
}