OpenMS  3.0.0
MRMFeatureFinderScoring.h
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31 // $Maintainer: Hannes Roest $
32 // $Authors: Hannes Roest $
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34 
35 #pragma once
36 
37 #define USE_SP_INTERFACE
38 
39 // Actual scoring
41 
45 
46 // Kernel classes
55 
57 
58 #ifdef _OPENMP
59 #include <omp.h>
60 #endif
61 
62 bool SortDoubleDoublePairFirst(const std::pair<double, double>& left, const std::pair<double, double>& right);
63 
64 namespace OpenMS
65 {
66 
89  class OPENMS_DLLAPI MRMFeatureFinderScoring :
90  public DefaultParamHandler,
91  public ProgressLogger
92  {
93 
94 public:
96 
102  // a transition group holds the chromatographic data and peaks across
103  // multiple chromatograms from the same compound
105  typedef std::map<String, MRMTransitionGroupType> TransitionGroupMapType;
106 
108 
111 
113  ~MRMFeatureFinderScoring() override;
114 
116 
117 
131  void pickExperiment(const PeakMap & chromatograms,
132  FeatureMap& output,
133  const TargetedExperiment& transition_exp,
134  const TransformationDescription& trafo,
135  const PeakMap& swath_map);
136 
151  void pickExperiment(const OpenSwath::SpectrumAccessPtr input,
152  FeatureMap& output,
153  const OpenSwath::LightTargetedExperiment& transition_exp,
154  const TransformationDescription& trafo,
155  const 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) const;
190 
193  void setStrictFlag(bool f)
194  {
195  strict_ = f;
196  }
197 
208  {
209  ms1_map_ = ms1_map;
210  }
211 
227  void mapExperimentToTransitionList(const OpenSwath::SpectrumAccessPtr input,
228  const OpenSwath::LightTargetedExperiment& transition_exp,
229  TransitionGroupMapType& transition_group_map,
231  double rt_extraction_window);
232 private:
233 
241  void splitTransitionGroupsDetection_(const MRMTransitionGroupType& transition_group,
242  MRMTransitionGroupType& transition_group_detection) const;
243 
253  void splitTransitionGroupsIdentification_(const MRMTransitionGroupType& transition_group,
254  MRMTransitionGroupType& transition_group_identification,
255  MRMTransitionGroupType& transition_group_identification_decoy) const;
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) const;
280 
281  void prepareFeatureOutput_(OpenMS::MRMFeature& mrmfeature, bool ms1only, int charge) const;
282 
284  void updateMembers_() override;
285 
286  // parameters
291  bool strict_;
293 
294  // scoring parameters
301 
302  double sn_win_len_;
303  unsigned int sn_bin_count_;
305 
307 
308  // members
309  std::map<OpenMS::String, const PeptideType*> PeptideRefMap_;
314 
315  // data
317 
318  };
319 }
320 
321 #undef run_identifier
322 
OpenMS::MRMFeatureFinderScoring::ms1_map_
OpenSwath::SpectrumAccessPtr ms1_map_
Definition: MRMFeatureFinderScoring.h:316
TargetedExperiment.h
OpenMS::MRMFeatureFinderScoring::quantification_cutoff_
double quantification_cutoff_
Definition: MRMFeatureFinderScoring.h:288
OpenMS::MRMFeatureFinderScoring::uis_threshold_peak_area_
double uis_threshold_peak_area_
Definition: MRMFeatureFinderScoring.h:300
OpenSwathScoring.h
OpenMS::MRMFeatureFinderScoring::su_
OpenSwath_Scores_Usage su_
Definition: MRMFeatureFinderScoring.h:310
DIAScoring.h
OpenMS::MRMFeatureFinderScoring::PeptideRefMap_
std::map< OpenMS::String, const PeptideType * > PeptideRefMap_
Definition: MRMFeatureFinderScoring.h:309
OpenMS::MRMFeatureFinderScoring::scoring_model_
String scoring_model_
Definition: MRMFeatureFinderScoring.h:292
OpenMS::MRMFeatureFinderScoring::strict_
bool strict_
Definition: MRMFeatureFinderScoring.h:291
OpenMS::DIAScoring
Scoring of an spectrum at the peak apex of an chromatographic elution peak.
Definition: DIAScoring.h:82
SwathMap.h
OpenMS::MRMFeatureFinderScoring::im_extra_drift_
double im_extra_drift_
Definition: MRMFeatureFinderScoring.h:306
OpenMS::MRMFeatureFinderScoring::sn_bin_count_
unsigned int sn_bin_count_
Definition: MRMFeatureFinderScoring.h:303
OpenMS::MRMFeatureFinderScoring
The MRMFeatureFinder finds and scores peaks of transitions that co-elute.
Definition: MRMFeatureFinderScoring.h:89
SortDoubleDoublePairFirst
bool SortDoubleDoublePairFirst(const std::pair< double, double > &left, const std::pair< double, double > &right)
OpenMS::MRMFeatureFinderScoring::MRMTransitionGroupType
MRMTransitionGroup< MSChromatogram, TransitionType > MRMTransitionGroupType
Definition: MRMFeatureFinderScoring.h:104
OpenMS::String
A more convenient string class.
Definition: String.h:58
OpenMS::MRMFeatureFinderScoring::emgscoring_
OpenMS::EmgScoring emgscoring_
Definition: MRMFeatureFinderScoring.h:313
OpenMS::MSExperiment
In-Memory representation of a mass spectrometry run.
Definition: MSExperiment.h:70
OpenMS::MRMFeatureFinderScoring::sn_win_len_
double sn_win_len_
Definition: MRMFeatureFinderScoring.h:302
OpenSwath::LightModification
Definition: TransitionExperiment.h:153
OpenMS::OpenSwath_Ind_Scores
Definition: OpenSwathScores.h:194
TransformationDescription.h
OpenMS::MRMFeatureFinderScoring::PeptideType
OpenSwath::LightCompound PeptideType
Definition: MRMFeatureFinderScoring.h:99
OpenSwath::LightTargetedExperiment
Definition: TransitionExperiment.h:218
OpenMS::MRMFeatureFinderScoring::uis_threshold_sn_
double uis_threshold_sn_
Definition: MRMFeatureFinderScoring.h:299
OpenMS::MRMFeatureFinderScoring::ModificationType
OpenSwath::LightModification ModificationType
Definition: MRMFeatureFinderScoring.h:101
OpenMS::MRMFeature
A multi-chromatogram MRM feature.
Definition: MRMFeature.h:50
OpenMS::MRMFeatureFinderScoring::TransitionGroupMapType
std::map< String, MRMTransitionGroupType > TransitionGroupMapType
Definition: MRMFeatureFinderScoring.h:105
OpenMS::DefaultParamHandler
A base class for all classes handling default parameters.
Definition: DefaultParamHandler.h:92
MRMTransitionGroup.h
OpenMS::MRMFeatureFinderScoring::write_log_messages_
bool write_log_messages_
Definition: MRMFeatureFinderScoring.h:304
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:47
OpenSwath::LightCompound
Definition: TransitionExperiment.h:160
OpenMS::ProgressLogger
Base class for all classes that want to report their progress.
Definition: ProgressLogger.h:52
MRMFeature.h
FeatureMap.h
OpenMS::MRMFeatureFinderScoring::setStrictFlag
void setStrictFlag(bool f)
Set the flag for strict mapping.
Definition: MRMFeatureFinderScoring.h:193
OpenMS::MRMFeatureFinderScoring::spacing_for_spectra_resampling_
double spacing_for_spectra_resampling_
Definition: MRMFeatureFinderScoring.h:298
OpenMS::MRMFeatureFinderScoring::ProteinType
OpenSwath::LightProtein ProteinType
Definition: MRMFeatureFinderScoring.h:100
OpenMS::OpenSwathScoring
A class that calls the scoring routines.
Definition: OpenSwathScoring.h:59
SONARScoring.h
EmgScoring.h
OpenMS::MRMFeatureFinderScoring::setMS1Map
void setMS1Map(OpenSwath::SpectrumAccessPtr ms1_map)
Add an MS1 map containing spectra.
Definition: MRMFeatureFinderScoring.h:207
OpenMS::MRMFeatureFinderScoring::sonarscoring_
OpenMS::SONARScoring sonarscoring_
Definition: MRMFeatureFinderScoring.h:312
OpenMS::EmgScoring
Scoring of an elution peak using an exponentially modified gaussian distribution model.
Definition: EmgScoring.h:60
OpenMS::MRMFeatureFinderScoring::spectrum_addition_method_
String spectrum_addition_method_
Definition: MRMFeatureFinderScoring.h:297
OpenMS::FeatureMap
A container for features.
Definition: FeatureMap.h:98
OpenMS::MRMFeatureFinderScoring::add_up_spectra_
int add_up_spectra_
Definition: MRMFeatureFinderScoring.h:296
OpenMS::MRMFeatureFinderScoring::write_convex_hull_
bool write_convex_hull_
Definition: MRMFeatureFinderScoring.h:290
OpenMS::MRMFeatureFinderScoring::rt_normalization_factor_
double rt_normalization_factor_
Definition: MRMFeatureFinderScoring.h:295
OpenMS::MRMFeatureFinderScoring::rt_extraction_window_
double rt_extraction_window_
Definition: MRMFeatureFinderScoring.h:287
MSChromatogram.h
OpenSwath::LightProtein
Definition: TransitionExperiment.h:212
OpenSwath::SpectrumAccessPtr
boost::shared_ptr< ISpectrumAccess > SpectrumAccessPtr
Definition: openswathalgo/include/OpenMS/OPENSWATHALGO/DATAACCESS/ISpectrumAccess.h:87
OpenMS::MRMTransitionGroup
The representation of a group of transitions in a targeted proteomics experiment.
Definition: MRMTransitionGroup.h:67
OpenMS::SONARScoring
Scoring of an spectrum using SONAR data.
Definition: SONARScoring.h:54
OpenMS::MRMFeatureFinderScoring::TargetedExpType
OpenSwath::LightTargetedExperiment TargetedExpType
Definition: MRMFeatureFinderScoring.h:98
OpenMS::MRMFeatureFinderScoring::diascoring_
OpenMS::DIAScoring diascoring_
Definition: MRMFeatureFinderScoring.h:311
OpenMS::TargetedExperiment
A description of a targeted experiment containing precursor and production ions.
Definition: TargetedExperiment.h:64
OpenMS::MRMFeatureFinderScoring::TransitionType
OpenSwath::LightTransition TransitionType
Type definitions.
Definition: MRMFeatureFinderScoring.h:97
OpenMS::MRMFeatureFinderScoring::stop_report_after_feature_
int stop_report_after_feature_
Definition: MRMFeatureFinderScoring.h:289
OpenSwath::LightTransition
Definition: TransitionExperiment.h:45
OpenMS::TransformationDescription
Generic description of a coordinate transformation.
Definition: TransformationDescription.h:62
StandardTypes.h
OpenMS::OpenSwath_Scores_Usage
A structure to store which scores should be used by the OpenSWATH Algorithm.
Definition: OpenSwathScores.h:50
MSSpectrum.h