OpenMS
SwathMapMassCorrection.h
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1 // Copyright (c) 2002-present, The OpenMS Team -- EKU Tuebingen, ETH Zurich, and FU Berlin
2 // SPDX-License-Identifier: BSD-3-Clause
3 //
4 // --------------------------------------------------------------------------
5 // $Maintainer: Hannes Roest$
6 // $Authors: Hannes Roest$
7 // --------------------------------------------------------------------------
8 
9 #pragma once
10 
11 #include <vector>
12 
15 
16 namespace OpenMS
17 {
18 
26  class OPENMS_DLLAPI SwathMapMassCorrection :
27  public DefaultParamHandler
28  {
29 
30 public:
31 
35 
37  ~SwathMapMassCorrection() override = default;
39 
41  void updateMembers_() override;
42 
59  void correctMZ(const std::map<String, OpenMS::MRMFeatureFinderScoring::MRMTransitionGroupType *>& transition_group_map,
60  const OpenSwath::LightTargetedExperiment & targeted_exp,
61  std::vector< OpenSwath::SwathMap > & swath_maps, const bool pasef);
62 
78  void correctIM(const std::map<String, OpenMS::MRMFeatureFinderScoring::MRMTransitionGroupType *> & transition_group_map,
79  const OpenSwath::LightTargetedExperiment & targeted_exp,
80  const std::vector< OpenSwath::SwathMap > & swath_maps,
81  const bool pasef,
82  TransformationDescription & im_trafo);
83 
94  std::vector<OpenSwath::SwathMap> findSwathMapsPasef(const OpenMS::MRMFeatureFinderScoring::MRMTransitionGroupType& transition_group,
95  const std::vector< OpenSwath::SwathMap > & swath_maps);
96 
97  private:
100  bool ms1_im_;
106 
107  };
108 }
109 
A base class for all classes handling default parameters.
Definition: DefaultParamHandler.h:66
The representation of a group of transitions in a targeted proteomics experiment.
Definition: MRMTransitionGroup.h:42
A more convenient string class.
Definition: String.h:34
A class containing correction functions for Swath MS maps.
Definition: SwathMapMassCorrection.h:28
std::vector< OpenSwath::SwathMap > findSwathMapsPasef(const OpenMS::MRMFeatureFinderScoring::MRMTransitionGroupType &transition_group, const std::vector< OpenSwath::SwathMap > &swath_maps)
Computes the SwathMaps for PASEF data in which windows can have the same m/z but differ by ion mobili...
bool mz_extraction_window_ppm_
Definition: SwathMapMassCorrection.h:99
double im_extraction_window_
Definition: SwathMapMassCorrection.h:101
String mz_correction_function_
Definition: SwathMapMassCorrection.h:102
~SwathMapMassCorrection() override=default
Destructor.
String debug_mz_file_
Definition: SwathMapMassCorrection.h:105
double mz_extraction_window_
Definition: SwathMapMassCorrection.h:98
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)
Correct the ion mobility values of a SWATH map based on the RT-normalization peptides.
bool ms1_im_
Definition: SwathMapMassCorrection.h:100
String im_correction_function_
Definition: SwathMapMassCorrection.h:103
void updateMembers_() override
Synchronize members with param class.
String debug_im_file_
Definition: SwathMapMassCorrection.h:104
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)
Correct the m/z values of a SWATH map based on the RT-normalization peptides.
Generic description of a coordinate transformation.
Definition: TransformationDescription.h:37
Main OpenMS namespace.
Definition: openswathalgo/include/OpenMS/OPENSWATHALGO/DATAACCESS/ISpectrumAccess.h:19
Definition: TransitionExperiment.h:185