SwathMapMassCorrection.h

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//                   OpenMS -- Open-Source Mass Spectrometry
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// $Maintainer: Hannes Roest$
// $Authors: Hannes Roest$
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#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<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<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);

  private:
    double mz_extraction_window_;
    bool mz_extraction_window_ppm_;
    bool ms1_im_;
    double im_extraction_window_;
    String mz_correction_function_;
    String im_correction_function_;
    String debug_im_file_;
    String debug_mz_file_;

  };
}