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IonMobilityScoring.h
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2 // OpenMS -- Open-Source Mass Spectrometry
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31 // $Maintainer: Hannes Roest $
32 // $Authors: Hannes Roest $
33 // --------------------------------------------------------------------------
34
35 #pragma once
36
37 // data access
38 #include <OpenMS/OPENSWATHALGO/DATAACCESS/DataStructures.h>
39 #include <OpenMS/OPENSWATHALGO/DATAACCESS/ISpectrumAccess.h>
40 #include <OpenMS/OPENSWATHALGO/DATAACCESS/ITransition.h>
41 #include <OpenMS/OPENSWATHALGO/DATAACCESS/TransitionExperiment.h>
42 #include <OpenMS/OPENSWATHALGO/DATAACCESS/SwathMap.h>
43
44 #include <OpenMS/ANALYSIS/OPENSWATH/OpenSwathScoring.h>
45
46 // scoring
47 #include <OpenMS/ANALYSIS/OPENSWATH/DIAScoring.h>
48
49 #include <vector>
50
51 namespace OpenMS
52 {
53
59 class OPENMS_DLLAPI IonMobilityScoring
60 {
61 typedef OpenSwath::LightCompound CompoundType;
62 typedef OpenSwath::LightTransition TransitionType;
63
64 public:
65
67 IonMobilityScoring();
68
70 ~IonMobilityScoring();
71
89 static void driftScoring(OpenSwath::SpectrumPtr spectrum,
90 const std::vector<TransitionType> & transitions,
91 OpenSwath_Scores & scores,
92 const double drift_lower,
93 const double drift_upper,
94 const double drift_target,
95 const double dia_extraction_window_,
96 const bool dia_extraction_ppm_,
97 const bool use_spline,
98 const double drift_extra);
99
117 static void driftScoringMS1(OpenSwath::SpectrumPtr spectrum,
118 const std::vector<TransitionType> & transitions,
119 OpenSwath_Scores & scores,
120 const double drift_lower,
121 const double drift_upper,
122 const double drift_target,
123 const double dia_extract_window_,
124 const bool dia_extraction_ppm_,
125 const bool use_spline,
126 const double drift_extra);
127
146 static void driftScoringMS1Contrast(OpenSwath::SpectrumPtr spectrum, OpenSwath::SpectrumPtr ms1spectrum,
147 const std::vector<TransitionType> & transitions,
148 OpenSwath_Scores & scores,
149 const double drift_lower,
150 const double drift_upper,
151 const double dia_extract_window_,
152 const bool dia_extraction_ppm_,
153 const double drift_extra);
154 };
155 }
156
OpenMS::IonMobilityScoring::TransitionType
OpenSwath::LightTransition TransitionType
Definition: IonMobilityScoring.h:62
DataStructures.h
OpenMS::IonMobilityScoring::CompoundType
OpenSwath::LightCompound CompoundType
Definition: IonMobilityScoring.h:61
OpenSwath::LightCompound
Definition: TransitionExperiment.h:149
OpenSwathScoring.h
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
DIAScoring.h
OpenMS::OpenSwath_Scores
A structure to hold the different scores computed by OpenSWATH.
Definition: OpenSwathScores.h:80
OpenMS::IonMobilityScoring
A class that calls the ion mobility scoring routines.
Definition: IonMobilityScoring.h:59
OpenSwath::SpectrumPtr
boost::shared_ptr< Spectrum > SpectrumPtr
Definition: openswathalgo/include/OpenMS/OPENSWATHALGO/DATAACCESS/DataStructures.h:292
SwathMap.h
OpenSwath::LightTransition
Definition: TransitionExperiment.h:46
TransitionExperiment.h
ISpectrumAccess.h
ITransition.h