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OpenSwathScoring.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 // 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 // scoring
45 #include <OpenMS/ANALYSIS/OPENSWATH/OpenSwathScores.h>
46 #include <OpenMS/ANALYSIS/OPENSWATH/DIAScoring.h>
47
48 #include <vector>
49 #include <boost/shared_ptr.hpp>
50 #include <boost/make_shared.hpp>
51
52 namespace OpenMS
53 {
59 class OPENMS_DLLAPI OpenSwathScoring
60 {
61 typedef OpenSwath::LightCompound CompoundType;
62 typedef OpenSwath::LightTransition TransitionType;
63
64 double rt_normalization_factor_;
65 double spacing_for_spectra_resampling_;
66 int add_up_spectra_;
67 std::string spectra_addition_method_;
68 double im_drift_extra_pcnt_;
69 OpenSwath_Scores_Usage su_;
70
71 public:
72
74 OpenSwathScoring();
75
77 ~OpenSwathScoring();
78
90 void initialize(double rt_normalization_factor,
91 int add_up_spectra,
92 double spacing_for_spectra_resampling,
93 const double drift_extra,
94 const OpenSwath_Scores_Usage & su,
95 const std::string& spectrum_addition_method);
96
115 void calculateChromatographicScores(OpenSwath::IMRMFeature* imrmfeature,
116 const std::vector<std::string>& native_ids,
117 const std::vector<std::string>& precursor_ids,
118 const std::vector<double>& normalized_library_intensity,
119 std::vector<OpenSwath::ISignalToNoisePtr>& signal_noise_estimators,
120 OpenSwath_Scores & scores);
121
140 void calculateChromatographicIdScores(OpenSwath::IMRMFeature* imrmfeature,
141 const std::vector<std::string>& native_ids_identification,
142 const std::vector<std::string>& native_ids_detection,
143 std::vector<OpenSwath::ISignalToNoisePtr>& signal_noise_estimators,
144 OpenSwath_Ind_Scores & scores);
145
161 void calculateLibraryScores(OpenSwath::IMRMFeature* imrmfeature,
162 const std::vector<TransitionType> & transitions,
163 const CompoundType& compound,
164 const double normalized_feature_rt,
165 OpenSwath_Scores & scores);
166
183 void calculateDIAScores(OpenSwath::IMRMFeature* imrmfeature,
184 const std::vector<TransitionType>& transitions,
185 const std::vector<OpenSwath::SwathMap>& swath_maps,
186 OpenSwath::SpectrumAccessPtr ms1_map,
187 OpenMS::DIAScoring& diascoring,
188 const CompoundType& compound,
189 OpenSwath_Scores& scores,
190 std::vector<double>& mzerror_ppm,
191 const double drift_lower,
192 const double drift_upper,
193 const double drift_target);
194
208 void calculatePrecursorDIAScores(OpenSwath::SpectrumAccessPtr ms1_map,
209 OpenMS::DIAScoring& diascoring,
210 double precursor_mz,
211 double rt,
212 const CompoundType& compound,
213 OpenSwath_Scores& scores,
214 double drift_lower,
215 double drift_upper);
216
230 void calculateDIAIdScores(OpenSwath::IMRMFeature* imrmfeature,
231 const TransitionType & transition,
232 const std::vector<OpenSwath::SwathMap> swath_maps,
233 OpenMS::DIAScoring & diascoring,
234 OpenSwath_Scores & scores,
235 double drift_lower,
236 double drift_upper);
237
246 void getNormalized_library_intensities_(const std::vector<TransitionType> & transitions,
247 std::vector<double>& normalized_library_intensity);
248
265 OpenSwath::SpectrumPtr fetchSpectrumSwath(std::vector<OpenSwath::SwathMap> swath_maps,
266 double RT,
267 int nr_spectra_to_add,
268 const double drift_lower,
269 const double drift_upper);
270
286 OpenSwath::SpectrumPtr fetchSpectrumSwath(OpenSwath::SpectrumAccessPtr swath_map,
287 double RT,
288 int nr_spectra_to_add,
289 const double drift_lower,
290 const double drift_upper);
291
292 protected:
293
308 OpenSwath::SpectrumPtr getAddedSpectra_(OpenSwath::SpectrumAccessPtr swath_map,
309 double RT,
310 int nr_spectra_to_add,
311 const double drift_lower,
312 const double drift_upper);
313
314 };
315 }
316
OpenMS::OpenSwathScoring::spacing_for_spectra_resampling_
double spacing_for_spectra_resampling_
Definition: OpenSwathScoring.h:65
DataStructures.h
OpenMS::OpenSwathScoring::TransitionType
OpenSwath::LightTransition TransitionType
Definition: OpenSwathScoring.h:62
OpenMS::OpenSwathScoring::su_
OpenSwath_Scores_Usage su_
Definition: OpenSwathScoring.h:69
OpenMS::OpenSwath_Scores_Usage
A structure to store which scores should be used by the OpenSWATH Algorithm.
Definition: OpenSwathScores.h:50
OpenSwath::IMRMFeature
Definition: ITransition.h:56
OpenSwath::SpectrumAccessPtr
boost::shared_ptr< ISpectrumAccess > SpectrumAccessPtr
Definition: openswathalgo/include/OpenMS/OPENSWATHALGO/DATAACCESS/ISpectrumAccess.h:89
OpenMS::OpenSwathScoring
A class that calls the scoring routines.
Definition: OpenSwathScoring.h:59
OpenMS::OpenSwathScoring::spectra_addition_method_
std::string spectra_addition_method_
Definition: OpenSwathScoring.h:67
OpenMS::OpenSwathScoring::im_drift_extra_pcnt_
double im_drift_extra_pcnt_
Definition: OpenSwathScoring.h:68
OpenSwathScores.h
OpenSwath::LightCompound
Definition: TransitionExperiment.h:149
OpenMS::DIAScoring
Scoring of an spectrum at the peak apex of an chromatographic elution peak.
Definition: DIAScoring.h:83
OpenMS::OpenSwathScoring::rt_normalization_factor_
double rt_normalization_factor_
Definition: OpenSwathScoring.h:64
OpenMS::OpenSwath_Ind_Scores
Definition: OpenSwathScores.h:192
OpenMS::OpenSwathScoring::CompoundType
OpenSwath::LightCompound CompoundType
Definition: OpenSwathScoring.h:61
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
DIAScoring.h
OpenMS::OpenSwathScoring::add_up_spectra_
int add_up_spectra_
Definition: OpenSwathScoring.h:66
OpenMS::OpenSwath_Scores
A structure to hold the different scores computed by OpenSWATH.
Definition: OpenSwathScores.h:80
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