SwathMapMassCorrection.h

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// Copyright (c) 2002-present, OpenMS Inc. -- EKU Tuebingen, ETH Zurich, and FU Berlin
// SPDX-License-Identifier: BSD-3-Clause
//
// --------------------------------------------------------------------------
// $Maintainer: Hannes Roest$
// $Authors: Hannes Roest$
// --------------------------------------------------------------------------
 
#pragma once
 
#include <vector>
 
#include <OpenMS/OPENSWATHALGO/DATAACCESS/SwathMap.h>
#include <OpenMS/ANALYSIS/OPENSWATH/MRMFeatureFinderScoring.h>
 
namespace OpenMS
{
 
  class OPENMS_DLLAPI SwathMapMassCorrection :
    public DefaultParamHandler
  {
 
public:
 
 
    SwathMapMassCorrection();
 
    ~SwathMapMassCorrection() override = default;
 
    void updateMembers_() override;
 
    void correctMZ(const std::map<std::string, OpenMS::MRMFeatureFinderScoring::MRMTransitionGroupType *>& transition_group_map,
                   const OpenSwath::LightTargetedExperiment & targeted_exp,
                   std::vector< OpenSwath::SwathMap > & swath_maps, const bool pasef);
 
    void correctIM(const std::map<std::string, OpenMS::MRMFeatureFinderScoring::MRMTransitionGroupType *> & transition_group_map,
                   const OpenSwath::LightTargetedExperiment & targeted_exp,
                   const std::vector< OpenSwath::SwathMap > & swath_maps,
                   const bool pasef,
                   TransformationDescription & im_trafo);
 
    std::vector<OpenSwath::SwathMap> findSwathMapsPasef(const OpenMS::MRMFeatureFinderScoring::MRMTransitionGroupType& transition_group,
                                                         const std::vector< OpenSwath::SwathMap > & swath_maps);
 
    static double estimateWindow(
      std::vector<double> residuals,
      double quantile = 0.99,
      bool full_width = true,
      double padding_factor = 1.0
    );
 
    double getFragmentMzWindow() const;
 
    void setFragmentMzWindow(double fragmentMzWindow);
 
    double getFragmentImWindow() const;
 
    void setFragmentImWindow(double fragmentImWindow);
 
    double getPrecursorMzWindow() const;
 
    void setPrecursorMzWindow(double precursorMzWindow);
 
    double getPrecursorImWindow() const;
 
    void setPrecursorImWindow(double precursorImWindow);
 
  private:
    double mz_extraction_window_;
    bool mz_extraction_window_ppm_;
    bool ms1_im_;
    double im_extraction_window_;
    std::string mz_correction_function_;
    std::string im_correction_function_;
    std::string debug_im_file_;
    std::string debug_mz_file_;
 
    double mz_estimation_padding_factor_ = 1.0;
    double im_estimation_padding_factor_ = 1.0;
    double mz_estimation_percentile_ = 99.0;
    double im_estimation_percentile_ = 99.0;
    double fragment_mz_window_ = -1;
    double fragment_im_window_ = -1;
    double precursor_mz_window_ = -1;
    double precursor_im_window_ = -1;
  };
}