FragmentMassError.h

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// --------------------------------------------------------------------------
//                   OpenMS -- Open-Source Mass Spectrometry
// --------------------------------------------------------------------------
// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
// ETH Zurich, and Freie Universitaet Berlin 2002-2022.
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// $Maintainer: Chris Bielow$
// $Authors: Patricia Scheil, Swenja Wagner$
// --------------------------------------------------------------------------

#pragma once

#include <OpenMS/METADATA/ProteinIdentification.h>
#include <OpenMS/QC/QCBase.h>
#include <vector>

namespace OpenMS
{
  class FeatureMap;
  class MSExperiment;
  class PeptideIdentification;
  class WindowMower;
  
  class OPENMS_DLLAPI FragmentMassError : public QCBase
  {
  public:
    FragmentMassError() = default;

    virtual ~FragmentMassError() = default;

    struct Statistics
    {
      double average_ppm = 0;
      double variance_ppm = 0;
    };

    void compute(FeatureMap& fmap, const MSExperiment& exp, const QCBase::SpectraMap& map_to_spectrum, ToleranceUnit tolerance_unit = ToleranceUnit::AUTO, double tolerance = 20);

    void compute(std::vector<PeptideIdentification>& pep_ids,
                 const ProteinIdentification::SearchParameters& search_params,
                 const MSExperiment& exp,
                 const QCBase::SpectraMap& map_to_spectrum,
                 ToleranceUnit tolerance_unit = ToleranceUnit::AUTO,
                 double tolerance = 20);

    const String& getName() const override;
    
    const std::vector<Statistics>& getResults() const;


    QCBase::Status requires() const override;

  private:
    std::vector<Statistics> results_;

    static void calculateFME_(PeptideIdentification& pep_id, const MSExperiment& exp, const QCBase::SpectraMap& map_to_spectrum, bool& print_warning, double tolerance, FragmentMassError::ToleranceUnit tolerance_unit, double& accumulator_ppm, UInt32& counter_ppm, WindowMower& window_mower_filter);

    static void calculateVariance_(FragmentMassError::Statistics& result, const PeptideIdentification& pep_id, const UInt num_ppm);
  };

} //namespace OpenMS