OpenMS
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 
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 
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 
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 
228  const OpenSwath::LightTargetedExperiment& transition_exp,
229  TransitionGroupMapType& transition_group_map,
231  double rt_extraction_window);
232 private:
233 
242  MRMTransitionGroupType& transition_group_detection) const;
243 
254  MRMTransitionGroupType& transition_group_identification,
255  MRMTransitionGroupType& transition_group_identification_decoy) const;
256 
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 
bool SortDoubleDoublePairFirst(const std::pair< double, double > &left, const std::pair< double, double > &right)
Scoring of an spectrum at the peak apex of an chromatographic elution peak.
Definition: DIAScoring.h:84
A base class for all classes handling default parameters.
Definition: DefaultParamHandler.h:92
Scoring of an elution peak using an exponentially modified gaussian distribution model.
Definition: EmgScoring.h:61
A container for features.
Definition: FeatureMap.h:106
The MRMFeatureFinder finds and scores peaks of transitions that co-elute.
Definition: MRMFeatureFinderScoring.h:92
MRMTransitionGroup< MSChromatogram, TransitionType > MRMTransitionGroupType
Definition: MRMFeatureFinderScoring.h:104
OpenSwath_Ind_Scores scoreIdentification_(MRMTransitionGroupType &transition_group_identification, OpenSwathScoring &scorer, const size_t feature_idx, const std::vector< std::string > &native_ids_detection, const double det_intensity_ratio_score, const double det_mi_ratio_score, const std::vector< OpenSwath::SwathMap > &swath_maps) const
Provides scoring for target and decoy identification against detecting transitions.
bool strict_
Definition: MRMFeatureFinderScoring.h:291
OpenSwath::LightProtein ProteinType
Definition: MRMFeatureFinderScoring.h:100
void mapExperimentToTransitionList(const OpenSwath::SpectrumAccessPtr &input, const OpenSwath::LightTargetedExperiment &transition_exp, TransitionGroupMapType &transition_group_map, TransformationDescription trafo, double rt_extraction_window)
Map the chromatograms to the transitions.
int add_up_spectra_
Definition: MRMFeatureFinderScoring.h:296
double sn_win_len_
Definition: MRMFeatureFinderScoring.h:302
double spacing_for_spectra_resampling_
Definition: MRMFeatureFinderScoring.h:298
OpenMS::EmgScoring emgscoring_
Definition: MRMFeatureFinderScoring.h:313
int stop_report_after_feature_
Definition: MRMFeatureFinderScoring.h:289
OpenMS::SONARScoring sonarscoring_
Definition: MRMFeatureFinderScoring.h:312
OpenSwath::LightCompound PeptideType
Definition: MRMFeatureFinderScoring.h:99
OpenMS::DIAScoring diascoring_
Definition: MRMFeatureFinderScoring.h:311
bool write_convex_hull_
Definition: MRMFeatureFinderScoring.h:290
void splitTransitionGroupsIdentification_(const MRMTransitionGroupType &transition_group, MRMTransitionGroupType &transition_group_identification, MRMTransitionGroupType &transition_group_identification_decoy) const
Splits combined transition groups into identification transition groups.
~MRMFeatureFinderScoring() override
Destructor.
std::map< OpenMS::String, const PeptideType * > PeptideRefMap_
Definition: MRMFeatureFinderScoring.h:309
OpenSwath::SpectrumAccessPtr ms1_map_
Definition: MRMFeatureFinderScoring.h:316
OpenSwath::LightTransition TransitionType
Type definitions.
Definition: MRMFeatureFinderScoring.h:97
void pickExperiment(const OpenSwath::SpectrumAccessPtr &input, FeatureMap &output, const OpenSwath::LightTargetedExperiment &transition_exp, const TransformationDescription &trafo, const std::vector< OpenSwath::SwathMap > &swath_maps, TransitionGroupMapType &transition_group_map)
Pick and score features in a single experiment from chromatograms.
void setMS1Map(OpenSwath::SpectrumAccessPtr ms1_map)
Add an MS1 map containing spectra.
Definition: MRMFeatureFinderScoring.h:207
double rt_normalization_factor_
Definition: MRMFeatureFinderScoring.h:295
OpenSwath_Scores_Usage su_
Definition: MRMFeatureFinderScoring.h:310
double uis_threshold_sn_
Definition: MRMFeatureFinderScoring.h:299
double quantification_cutoff_
Definition: MRMFeatureFinderScoring.h:288
void splitTransitionGroupsDetection_(const MRMTransitionGroupType &transition_group, MRMTransitionGroupType &transition_group_detection) const
Splits combined transition groups into detection transition groups.
void setStrictFlag(bool f)
Set the flag for strict mapping.
Definition: MRMFeatureFinderScoring.h:193
unsigned int sn_bin_count_
Definition: MRMFeatureFinderScoring.h:303
double uis_threshold_peak_area_
Definition: MRMFeatureFinderScoring.h:300
String spectrum_addition_method_
Definition: MRMFeatureFinderScoring.h:297
void scorePeakgroups(MRMTransitionGroupType &transition_group, const TransformationDescription &trafo, const std::vector< OpenSwath::SwathMap > &swath_maps, FeatureMap &output, bool ms1only=false) const
Score all peak groups of a transition group.
void pickExperiment(const PeakMap &chromatograms, FeatureMap &output, const TargetedExperiment &transition_exp, const TransformationDescription &trafo, const PeakMap &swath_map)
Picker and prepare functions.
void prepareProteinPeptideMaps_(const OpenSwath::LightTargetedExperiment &transition_exp)
Prepares the internal mappings of peptides and proteins.
OpenSwath::LightTargetedExperiment TargetedExpType
Definition: MRMFeatureFinderScoring.h:98
bool write_log_messages_
Definition: MRMFeatureFinderScoring.h:304
void updateMembers_() override
Synchronize members with param class.
std::map< String, MRMTransitionGroupType > TransitionGroupMapType
Definition: MRMFeatureFinderScoring.h:105
double rt_extraction_window_
Definition: MRMFeatureFinderScoring.h:287
OpenSwath::LightModification ModificationType
Definition: MRMFeatureFinderScoring.h:101
void prepareFeatureOutput_(OpenMS::MRMFeature &mrmfeature, bool ms1only, int charge) const
double im_extra_drift_
Definition: MRMFeatureFinderScoring.h:306
String scoring_model_
Definition: MRMFeatureFinderScoring.h:292
A multi-chromatogram MRM feature.
Definition: MRMFeature.h:52
The representation of a group of transitions in a targeted proteomics experiment.
Definition: MRMTransitionGroup.h:68
In-Memory representation of a mass spectrometry run.
Definition: MSExperiment.h:72
A class that calls the scoring routines.
Definition: OpenSwathScoring.h:60
Base class for all classes that want to report their progress.
Definition: ProgressLogger.h:53
Scoring of an spectrum using SONAR data.
Definition: SONARScoring.h:56
A more convenient string class.
Definition: String.h:60
A description of a targeted experiment containing precursor and production ions.
Definition: TargetedExperiment.h:65
Generic description of a coordinate transformation.
Definition: TransformationDescription.h:63
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:48
A structure to store which scores should be used by the OpenSWATH Algorithm.
Definition: OpenSwathScores.h:51
boost::shared_ptr< ISpectrumAccess > SpectrumAccessPtr
Definition: openswathalgo/include/OpenMS/OPENSWATHALGO/DATAACCESS/ISpectrumAccess.h:87
Definition: TransitionExperiment.h:154
Definition: TransitionExperiment.h:213
Definition: OpenSwathScores.h:198
Definition: TransitionExperiment.h:161
Definition: TransitionExperiment.h:219
Definition: TransitionExperiment.h:46