OpenMS
SwathMapMassCorrection.h
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31 // $Maintainer: Hannes Roest$
32 // $Authors: Hannes Roest$
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34 
35 #pragma once
36 
37 #include <vector>
38 
41 
42 namespace OpenMS
43 {
44 
52  class OPENMS_DLLAPI SwathMapMassCorrection :
53  public DefaultParamHandler
54  {
55 
56 public:
57 
61 
63  ~SwathMapMassCorrection() override = default;
65 
67  void updateMembers_() override;
68 
85  void correctMZ(const std::map<String, OpenMS::MRMFeatureFinderScoring::MRMTransitionGroupType *>& transition_group_map,
86  const OpenSwath::LightTargetedExperiment & targeted_exp,
87  std::vector< OpenSwath::SwathMap > & swath_maps, const bool pasef);
88 
104  void correctIM(const std::map<String, OpenMS::MRMFeatureFinderScoring::MRMTransitionGroupType *> & transition_group_map,
105  const OpenSwath::LightTargetedExperiment & targeted_exp,
106  const std::vector< OpenSwath::SwathMap > & swath_maps,
107  const bool pasef,
108  TransformationDescription & im_trafo);
109 
120  std::vector<OpenSwath::SwathMap> findSwathMapsPasef(const OpenMS::MRMFeatureFinderScoring::MRMTransitionGroupType& transition_group,
121  const std::vector< OpenSwath::SwathMap > & swath_maps);
122 
123  private:
126  bool ms1_im_;
132 
133  };
134 }
135 
A base class for all classes handling default parameters.
Definition: DefaultParamHandler.h:92
The representation of a group of transitions in a targeted proteomics experiment.
Definition: MRMTransitionGroup.h:68
A more convenient string class.
Definition: String.h:60
A class containing correction functions for Swath MS maps.
Definition: SwathMapMassCorrection.h:54
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:125
double im_extraction_window_
Definition: SwathMapMassCorrection.h:127
String mz_correction_function_
Definition: SwathMapMassCorrection.h:128
~SwathMapMassCorrection() override=default
Destructor.
String debug_mz_file_
Definition: SwathMapMassCorrection.h:131
double mz_extraction_window_
Definition: SwathMapMassCorrection.h:124
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:126
String im_correction_function_
Definition: SwathMapMassCorrection.h:129
void updateMembers_() override
Synchronize members with param class.
String debug_im_file_
Definition: SwathMapMassCorrection.h:130
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:63
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:48
Definition: TransitionExperiment.h:219