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MRMFeatureFinderScoring.h
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2 // OpenMS -- Open-Source Mass Spectrometry
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4 // Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
5 // ETH Zurich, and Freie Universitaet Berlin 2002-2020.
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30 // --------------------------------------------------------------------------
31 // $Maintainer: Hannes Roest $
32 // $Authors: Hannes Roest $
33 // --------------------------------------------------------------------------
34
35 #pragma once
36
37 #define USE_SP_INTERFACE
38
39 // Actual scoring
40 #include <OpenMS/ANALYSIS/OPENSWATH/OpenSwathScoring.h>
41
42 #include <OpenMS/ANALYSIS/OPENSWATH/DIAScoring.h>
43 #include <OpenMS/ANALYSIS/OPENSWATH/SONARScoring.h>
44 #include <OpenMS/TRANSFORMATIONS/FEATUREFINDER/EmgScoring.h>
45
46 // Kernel classes
47 #include <OpenMS/KERNEL/StandardTypes.h>
48 #include <OpenMS/ANALYSIS/MAPMATCHING/TransformationDescription.h>
49 #include <OpenMS/KERNEL/FeatureMap.h>
50 #include <OpenMS/KERNEL/MRMTransitionGroup.h>
51 #include <OpenMS/KERNEL/MRMFeature.h>
52 #include <OpenMS/KERNEL/MSSpectrum.h>
53 #include <OpenMS/KERNEL/MSChromatogram.h>
54 #include <OpenMS/ANALYSIS/TARGETED/TargetedExperiment.h>
55
56 #include <OpenMS/OPENSWATHALGO/DATAACCESS/SwathMap.h>
57
58 #include <boost/shared_ptr.hpp>
59 #include <boost/make_shared.hpp>
60 #include <boost/unordered_map.hpp>
61
62 #ifdef _OPENMP
63 #include <omp.h>
64 #endif
65
66 bool SortDoubleDoublePairFirst(const std::pair<double, double>& left, const std::pair<double, double>& right);
67
68 namespace OpenMS
69 {
70
93 class OPENMS_DLLAPI MRMFeatureFinderScoring :
94 public DefaultParamHandler,
95 public ProgressLogger
96 {
97
98 public:
100
101 typedef OpenSwath::LightTransition TransitionType;
102 typedef OpenSwath::LightTargetedExperiment TargetedExpType;
103 typedef OpenSwath::LightCompound PeptideType;
104 typedef OpenSwath::LightProtein ProteinType;
105 typedef OpenSwath::LightModification ModificationType;
106 // a transition group holds the chromatographic data and peaks across
107 // multiple chromatograms from the same compound
108 typedef MRMTransitionGroup< MSChromatogram, TransitionType> MRMTransitionGroupType;
109 typedef std::map<String, MRMTransitionGroupType> TransitionGroupMapType;
110
112
114 MRMFeatureFinderScoring();
115
117 ~MRMFeatureFinderScoring() override;
118
120
121
134 void pickExperiment(PeakMap & chromatograms, FeatureMap& output, TargetedExperiment& transition_exp,
135 TransformationDescription trafo, PeakMap& swath_map);
136
151 void pickExperiment(OpenSwath::SpectrumAccessPtr input,
152 FeatureMap& output,
153 OpenSwath::LightTargetedExperiment& transition_exp,
154 TransformationDescription trafo,
155 std::vector<OpenSwath::SwathMap> swath_maps,
156 TransitionGroupMapType& transition_group_map);
157
165 void prepareProteinPeptideMaps_(const OpenSwath::LightTargetedExperiment& transition_exp);
167
185 void scorePeakgroups(MRMTransitionGroupType& transition_group,
186 const TransformationDescription & trafo,
187 const std::vector<OpenSwath::SwathMap>& swath_maps,
188 FeatureMap& output,
189 bool ms1only = false);
190
193 void setStrictFlag(bool f)
194 {
195 strict_ = f;
196 }
197
207 void setMS1Map(OpenSwath::SpectrumAccessPtr ms1_map)
208 {
209 ms1_map_ = ms1_map;
210 }
211
227 void mapExperimentToTransitionList(OpenSwath::SpectrumAccessPtr input,
228 OpenSwath::LightTargetedExperiment& transition_exp,
229 TransitionGroupMapType& transition_group_map,
230 TransformationDescription trafo,
231 double rt_extraction_window);
232 private:
233
241 void splitTransitionGroupsDetection_(const MRMTransitionGroupType& transition_group,
242 MRMTransitionGroupType& transition_group_detection);
243
253 void splitTransitionGroupsIdentification_(const MRMTransitionGroupType& transition_group,
254 MRMTransitionGroupType& transition_group_identification,
255 MRMTransitionGroupType& transition_group_identification_decoy);
256
273 OpenSwath_Ind_Scores scoreIdentification_(MRMTransitionGroupType& transition_group_identification,
274 OpenSwathScoring& scorer,
275 const size_t feature_idx,
276 const std::vector<std::string> & native_ids_detection,
277 const double det_intensity_ratio_score,
278 const double det_mi_ratio_score,
279 const std::vector<OpenSwath::SwathMap>& swath_maps);
280
281 void prepareFeatureOutput_(OpenMS::MRMFeature& mrmfeature, bool ms1only, int charge);
282
284 void updateMembers_() override;
285
286 // parameters
287 double rt_extraction_window_;
288 double quantification_cutoff_;
289 int stop_report_after_feature_;
290 bool write_convex_hull_;
291 bool strict_;
292 String scoring_model_;
293
294 // scoring parameters
295 double rt_normalization_factor_;
296 int add_up_spectra_;
297 String spectrum_addition_method_ ;
298 double spacing_for_spectra_resampling_;
299 double uis_threshold_sn_;
300 double uis_threshold_peak_area_;
301
302 double sn_win_len_;
303 unsigned int sn_bin_count_;
304 bool write_log_messages_;
305
306 double im_extra_drift_;
307
308 // members
309 std::map<OpenMS::String, const PeptideType*> PeptideRefMap_;
310 OpenSwath_Scores_Usage su_;
311 OpenMS::DIAScoring diascoring_;
312 OpenMS::SONARScoring sonarscoring_;
313 OpenMS::EmgScoring emgscoring_;
314
315 // data
316 OpenSwath::SpectrumAccessPtr ms1_map_;
317
318 };
319 }
320
321 #undef run_identifier
322
OpenMS::EmgScoring
Scoring of an elution peak using an exponentially modified gaussian distribution model.
Definition: EmgScoring.h:59
OpenMS::String
A more convenient string class.
Definition: String.h:58
OpenMS::MRMFeatureFinderScoring::spectrum_addition_method_
String spectrum_addition_method_
Definition: MRMFeatureFinderScoring.h:297
OpenMS::MRMFeatureFinderScoring::setStrictFlag
void setStrictFlag(bool f)
Set the flag for strict mapping.
Definition: MRMFeatureFinderScoring.h:193
OpenMS::DefaultParamHandler
A base class for all classes handling default parameters.
Definition: DefaultParamHandler.h:91
TargetedExperiment.h
OpenMS::MRMFeatureFinderScoring::im_extra_drift_
double im_extra_drift_
Definition: MRMFeatureFinderScoring.h:306
OpenMS::OpenSwath_Scores_Usage
A structure to store which scores should be used by the OpenSWATH Algorithm.
Definition: OpenSwathScores.h:50
OpenMS::SONARScoring
Scoring of an spectrum using SONAR data.
Definition: SONARScoring.h:54
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::MSExperiment
In-Memory representation of a mass spectrometry experiment.
Definition: MSExperiment.h:77
OpenMS::MRMFeatureFinderScoring::TargetedExpType
OpenSwath::LightTargetedExperiment TargetedExpType
Definition: MRMFeatureFinderScoring.h:102
OpenMS::MRMTransitionGroup
The representation of a group of transitions in a targeted proteomics experiment. ...
Definition: MRMTransitionGroup.h:67
OpenMS::MRMFeatureFinderScoring::add_up_spectra_
int add_up_spectra_
Definition: MRMFeatureFinderScoring.h:296
OpenMS::FeatureMap
A container for features.
Definition: FeatureMap.h:95
OpenMS::MRMFeatureFinderScoring::sn_bin_count_
unsigned int sn_bin_count_
Definition: MRMFeatureFinderScoring.h:303
OpenMS::MRMFeatureFinderScoring::setMS1Map
void setMS1Map(OpenSwath::SpectrumAccessPtr ms1_map)
Add an MS1 map containing spectra.
Definition: MRMFeatureFinderScoring.h:207
StandardTypes.h
OpenMS::MRMFeatureFinderScoring::rt_extraction_window_
double rt_extraction_window_
Definition: MRMFeatureFinderScoring.h:287
OpenMS::MRMFeatureFinderScoring::rt_normalization_factor_
double rt_normalization_factor_
Definition: MRMFeatureFinderScoring.h:295
OpenMS::MRMFeatureFinderScoring::stop_report_after_feature_
int stop_report_after_feature_
Definition: MRMFeatureFinderScoring.h:289
OpenMS::MRMFeatureFinderScoring::PeptideRefMap_
std::map< OpenMS::String, const PeptideType * > PeptideRefMap_
Definition: MRMFeatureFinderScoring.h:309
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
SONARScoring.h
OpenMS::TransformationDescription
Generic description of a coordinate transformation.
Definition: TransformationDescription.h:61
OpenMS::MRMFeatureFinderScoring::MRMTransitionGroupType
MRMTransitionGroup< MSChromatogram, TransitionType > MRMTransitionGroupType
Definition: MRMFeatureFinderScoring.h:108
OpenMS::MRMFeatureFinderScoring::quantification_cutoff_
double quantification_cutoff_
Definition: MRMFeatureFinderScoring.h:288
SortDoubleDoublePairFirst
bool SortDoubleDoublePairFirst(const std::pair< double, double > &left, const std::pair< double, double > &right)
OpenMS::MRMFeatureFinderScoring::scoring_model_
String scoring_model_
Definition: MRMFeatureFinderScoring.h:292
FeatureMap.h
OpenMS::MRMFeatureFinderScoring::su_
OpenSwath_Scores_Usage su_
Definition: MRMFeatureFinderScoring.h:310
OpenMS::MRMFeatureFinderScoring::PeptideType
OpenSwath::LightCompound PeptideType
Definition: MRMFeatureFinderScoring.h:103
OpenMS::OpenSwath_Ind_Scores
Definition: OpenSwathScores.h:192
OpenSwathScoring.h
OpenMS::TargetedExperiment
A description of a targeted experiment containing precursor and production ions.
Definition: TargetedExperiment.h:64
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
OpenMS::MRMFeatureFinderScoring::uis_threshold_peak_area_
double uis_threshold_peak_area_
Definition: MRMFeatureFinderScoring.h:300
EmgScoring.h
DIAScoring.h
OpenMS::ProgressLogger
Base class for all classes that want to report their progress.
Definition: ProgressLogger.h:54
OpenMS::MRMFeatureFinderScoring::strict_
bool strict_
Definition: MRMFeatureFinderScoring.h:291
TransformationDescription.h
OpenMS::MRMFeatureFinderScoring
The MRMFeatureFinder finds and scores peaks of transitions that co-elute.
Definition: MRMFeatureFinderScoring.h:93
OpenMS::MRMFeatureFinderScoring::ProteinType
OpenSwath::LightProtein ProteinType
Definition: MRMFeatureFinderScoring.h:104
OpenMS::MRMFeatureFinderScoring::uis_threshold_sn_
double uis_threshold_sn_
Definition: MRMFeatureFinderScoring.h:299
OpenMS::MRMFeatureFinderScoring::diascoring_
OpenMS::DIAScoring diascoring_
Definition: MRMFeatureFinderScoring.h:311
OpenSwath::LightModification
Definition: TransitionExperiment.h:142
OpenSwath::LightProtein
Definition: TransitionExperiment.h:201
MSSpectrum.h
OpenSwath::LightTargetedExperiment
Definition: TransitionExperiment.h:207
MRMFeature.h
OpenMS::MRMFeatureFinderScoring::sn_win_len_
double sn_win_len_
Definition: MRMFeatureFinderScoring.h:302
OpenMS::MRMFeatureFinderScoring::ms1_map_
OpenSwath::SpectrumAccessPtr ms1_map_
Definition: MRMFeatureFinderScoring.h:316
OpenMS::MRMFeatureFinderScoring::spacing_for_spectra_resampling_
double spacing_for_spectra_resampling_
Definition: MRMFeatureFinderScoring.h:298
SwathMap.h
MSChromatogram.h
OpenSwath::LightTransition
Definition: TransitionExperiment.h:46
OpenMS::MRMFeatureFinderScoring::TransitionGroupMapType
std::map< String, MRMTransitionGroupType > TransitionGroupMapType
Definition: MRMFeatureFinderScoring.h:109
OpenMS::MRMFeature
A multi-chromatogram MRM feature.
Definition: MRMFeature.h:50
OpenMS::MRMFeatureFinderScoring::ModificationType
OpenSwath::LightModification ModificationType
Definition: MRMFeatureFinderScoring.h:105
OpenMS::MRMFeatureFinderScoring::write_log_messages_
bool write_log_messages_
Definition: MRMFeatureFinderScoring.h:304
MRMTransitionGroup.h
OpenMS::MRMFeatureFinderScoring::emgscoring_
OpenMS::EmgScoring emgscoring_
Definition: MRMFeatureFinderScoring.h:313
OpenMS::MRMFeatureFinderScoring::TransitionType
OpenSwath::LightTransition TransitionType
Type definitions.
Definition: MRMFeatureFinderScoring.h:101
OpenMS::MRMFeatureFinderScoring::sonarscoring_
OpenMS::SONARScoring sonarscoring_
Definition: MRMFeatureFinderScoring.h:312
OpenMS::MRMFeatureFinderScoring::write_convex_hull_
bool write_convex_hull_
Definition: MRMFeatureFinderScoring.h:290