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SwathMapMassCorrection.h
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2 // OpenMS -- Open-Source Mass Spectrometry
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30 // --------------------------------------------------------------------------
31 // $Maintainer: Hannes Roest$
32 // $Authors: Hannes Roest$
33 // --------------------------------------------------------------------------
34
35 #pragma once
36
37 #include <vector>
38
39 #include <OpenMS/OPENSWATHALGO/DATAACCESS/SwathMap.h>
40 #include <OpenMS/ANALYSIS/OPENSWATH/MRMFeatureFinderScoring.h>
41
42 namespace OpenMS
43 {
44
52 class OPENMS_DLLAPI SwathMapMassCorrection :
53 public DefaultParamHandler
54 {
55
56 public:
57
59 SwathMapMassCorrection();
61
63 ~SwathMapMassCorrection() = default;
65
67 void updateMembers_() override;
68
84 void correctMZ(const std::map<String, OpenMS::MRMFeatureFinderScoring::MRMTransitionGroupType *>& transition_group_map,
85 std::vector< OpenSwath::SwathMap > & swath_maps, const OpenSwath::LightTargetedExperiment& targeted_exp);
86
100 void correctIM(const std::map<String, OpenMS::MRMFeatureFinderScoring::MRMTransitionGroupType *> & transition_group_map,
101 const std::vector< OpenSwath::SwathMap > & swath_maps,
102 TransformationDescription& im_trafo,
103 const OpenSwath::LightTargetedExperiment& targeted_exp);
104
105 private:
106 double mz_extraction_window_;
107 bool mz_extraction_window_ppm_;
108 bool ms1_im_;
109 double im_extraction_window_;
110 String mz_correction_function_;
111 String im_correction_function_;
112 String debug_im_file_;
113 String debug_mz_file_;
114
115 };
116 }
117
OpenMS::String
A more convenient string class.
Definition: String.h:58
OpenMS::DefaultParamHandler
A base class for all classes handling default parameters.
Definition: DefaultParamHandler.h:91
OpenMS::SwathMapMassCorrection::im_correction_function_
String im_correction_function_
Definition: SwathMapMassCorrection.h:111
OpenMS::SwathMapMassCorrection
A class containing correction functions for Swath MS maps.
Definition: SwathMapMassCorrection.h:52
OpenMS::SwathMapMassCorrection::ms1_im_
bool ms1_im_
Definition: SwathMapMassCorrection.h:108
OpenMS::TransformationDescription
Generic description of a coordinate transformation.
Definition: TransformationDescription.h:61
MRMFeatureFinderScoring.h
OpenMS::SwathMapMassCorrection::im_extraction_window_
double im_extraction_window_
Definition: SwathMapMassCorrection.h:109
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
OpenMS::SwathMapMassCorrection::debug_mz_file_
String debug_mz_file_
Definition: SwathMapMassCorrection.h:113
OpenSwath::LightTargetedExperiment
Definition: TransitionExperiment.h:207
OpenMS::SwathMapMassCorrection::debug_im_file_
String debug_im_file_
Definition: SwathMapMassCorrection.h:112
SwathMap.h
OpenMS::SwathMapMassCorrection::mz_extraction_window_ppm_
bool mz_extraction_window_ppm_
Definition: SwathMapMassCorrection.h:107
OpenMS::SwathMapMassCorrection::mz_correction_function_
String mz_correction_function_
Definition: SwathMapMassCorrection.h:110
OpenMS::SwathMapMassCorrection::mz_extraction_window_
double mz_extraction_window_
Definition: SwathMapMassCorrection.h:106