FragmentMassError.h

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// Copyright (c) 2002-present, OpenMS Inc. -- EKU Tuebingen, ETH Zurich, and FU Berlin
// SPDX-License-Identifier: BSD-3-Clause
//
// --------------------------------------------------------------------------
// $Maintainer: Chris Bielow$
// $Authors: Patricia Scheil, Swenja Wagner$
// --------------------------------------------------------------------------
 
#pragma once
 
#include <OpenMS/METADATA/ProteinIdentification.h>
#include <OpenMS/QC/QCBase.h>
#include <OpenMS/METADATA/PeptideIdentificationList.h>
#include <vector>
 
namespace OpenMS
{
  class FeatureMap;
  class MSExperiment;
  class PeptideIdentification;
  class WindowMower;
 
  class 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(PeptideIdentificationList& 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 std::string& getName() const override;
 
    const std::vector<Statistics>& getResults() const;
 
 
    QCBase::Status requirements() 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