PSMExplainedIonCurrent.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.
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// $Maintainer: Tom Waschischeck$
// $Authors: Tom Waschischeck$
// --------------------------------------------------------------------------
 
#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 PSMExplainedIonCurrent : public QCBase
  {
  public:
    PSMExplainedIonCurrent() = default;
 
    virtual ~PSMExplainedIonCurrent() = default;
 
    struct Statistics {
      double average_correctness = 0;
      double variance_correctness = 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 requirements() const override;
 
  private:
    std::vector<Statistics> results_ {};
 
    static double annotatePSMExplainedIonCurrent_(PeptideIdentification& pep_id, const MSExperiment& exp, const QCBase::SpectraMap& map_to_spectrum, WindowMower& filter,
                                                  PSMExplainedIonCurrent::ToleranceUnit tolerance_unit, double tolerance);
  };
 
} // namespace OpenMS