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MRMFeatureFinderScoring.h
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34 
35 #ifndef OPENMS_ANALYSIS_OPENSWATH_MRMFEATUREFINDERSCORING_H
36 #define OPENMS_ANALYSIS_OPENSWATH_MRMFEATUREFINDERSCORING_H
37 
38 #define USE_SP_INTERFACE
39 
40 // Actual scoring
42 
46 
47 // Kernel classes
56 
58 
59 #include <boost/shared_ptr.hpp>
60 #include <boost/make_shared.hpp>
61 #include <boost/unordered_map.hpp>
62 
63 #ifdef _OPENMP
64 #include <omp.h>
65 #endif
66 
67 bool SortDoubleDoublePairFirst(const std::pair<double, double>& left, const std::pair<double, double>& right);
68 
69 namespace OpenMS
70 {
71 
94  class OPENMS_DLLAPI MRMFeatureFinderScoring :
95  public DefaultParamHandler,
96  public ProgressLogger
97  {
98 
99 public:
101 
107  // a transition group holds the chromatographic data and peaks across
108  // multiple chromatograms from the same compound
110  typedef std::map<String, MRMTransitionGroupType> TransitionGroupMapType;
111 
113 
116 
119 
121 
122 
135  void pickExperiment(PeakMap & chromatograms, FeatureMap& output, TargetedExperiment& transition_exp,
136  TransformationDescription trafo, PeakMap& swath_map);
137 
152  void pickExperiment(OpenSwath::SpectrumAccessPtr input,
153  FeatureMap& output,
154  OpenSwath::LightTargetedExperiment& transition_exp,
156  std::vector<OpenSwath::SwathMap> swath_maps,
157  TransitionGroupMapType& transition_group_map);
158 
166  void prepareProteinPeptideMaps_(const OpenSwath::LightTargetedExperiment& transition_exp);
168 
186  void scorePeakgroups(MRMTransitionGroupType& transition_group,
188  std::vector<OpenSwath::SwathMap> swath_maps,
189  FeatureMap& output,
190  bool ms1only=false);
191 
194  void setStrictFlag(bool f)
195  {
196  strict_ = f;
197  }
198 
209  {
210  ms1_map_ = ms1_map;
211  }
212 
228  void mapExperimentToTransitionList(OpenSwath::SpectrumAccessPtr input, OpenSwath::LightTargetedExperiment& transition_exp,
229  TransitionGroupMapType& transition_group_map, TransformationDescription trafo, double rt_extraction_window);
230 private:
231 
239  void splitTransitionGroupsDetection_(MRMTransitionGroupType& transition_group, MRMTransitionGroupType& transition_group_detection);
240 
250  void splitTransitionGroupsIdentification_(MRMTransitionGroupType& transition_group, MRMTransitionGroupType& transition_group_identification, MRMTransitionGroupType& transition_group_identification_decoy);
251 
267  OpenSwath_Scores scoreIdentification_(MRMTransitionGroupType& transition_group_identification,
268  OpenSwathScoring& scorer,
269  const size_t feature_idx,
270  const std::vector<std::string> native_ids_detection,
271  const double sn_win_len_,
272  const unsigned int sn_bin_count_,
273  bool write_log_messages,
274  std::vector<OpenSwath::SwathMap> swath_maps);
275 
277  void updateMembers_();
278 
279  // parameters
284  bool strict_;
285 
286  // scoring parameters
292 
293  // members
294  std::map<OpenMS::String, const PeptideType*> PeptideRefMap_;
299 
300  // data
302 
303  };
304 }
305 
306 #undef run_identifier
307 #endif // OPENMS_ANALYSIS_OPENSWATH_MRMFEATUREFINDERSCORING_H
308 
double spacing_for_spectra_resampling_
Definition: MRMFeatureFinderScoring.h:289
boost::shared_ptr< ISpectrumAccess > SpectrumAccessPtr
Definition: openswathalgo/include/OpenMS/ANALYSIS/OPENSWATH/OPENSWATHALGO/DATAACCESS/ISpectrumAccess.h:90
Scoring of an elution peak using an exponentially modified gaussian distribution model.
Definition: EmgScoring.h:60
OpenMS::DIAScoring diascoring_
Definition: MRMFeatureFinderScoring.h:296
OpenSwath::LightCompound PeptideType
Definition: MRMFeatureFinderScoring.h:104
double uis_threshold_peak_area_
Definition: MRMFeatureFinderScoring.h:291
A container for features.
Definition: FeatureMap.h:94
OpenSwath::LightTransition TransitionType
Type definitions.
Definition: MRMFeatureFinderScoring.h:102
A class that calls the scoring routines.
Definition: OpenSwathScoring.h:442
The MRMFeatureFinder finds and scores peaks of transitions that co-elute.
Definition: MRMFeatureFinderScoring.h:94
bool write_convex_hull_
Definition: MRMFeatureFinderScoring.h:283
int add_up_spectra_
Definition: MRMFeatureFinderScoring.h:288
std::map< String, MRMTransitionGroupType > TransitionGroupMapType
Definition: MRMFeatureFinderScoring.h:110
double rt_extraction_window_
Definition: MRMFeatureFinderScoring.h:280
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:47
void setMS1Map(OpenSwath::SpectrumAccessPtr ms1_map)
Add an MS1 map containing spectra.
Definition: MRMFeatureFinderScoring.h:208
OpenMS::EmgScoring emgscoring_
Definition: MRMFeatureFinderScoring.h:298
The representation of a group of transitions in a targeted proteomics experiment. ...
Definition: MRMTransitionGroup.h:68
int stop_report_after_feature_
Definition: MRMFeatureFinderScoring.h:282
OpenSwath::LightProtein ProteinType
Definition: MRMFeatureFinderScoring.h:105
OpenSwath::SpectrumAccessPtr ms1_map_
Definition: MRMFeatureFinderScoring.h:301
Scoring of an spectrum at the peak apex of an chromatographic elution peak.
Definition: DIAScoring.h:82
double quantification_cutoff_
Definition: MRMFeatureFinderScoring.h:281
std::map< OpenMS::String, const PeptideType * > PeptideRefMap_
Definition: MRMFeatureFinderScoring.h:294
void setStrictFlag(bool f)
Set the flag for strict mapping.
Definition: MRMFeatureFinderScoring.h:194
Definition: TransitionExperiment.h:150
Definition: TransitionExperiment.h:47
MRMTransitionGroup< MSChromatogram, TransitionType > MRMTransitionGroupType
Definition: MRMFeatureFinderScoring.h:109
In-Memory representation of a mass spectrometry experiment.
Definition: MSExperiment.h:82
A structure to store which scores should be used by the Algorithm.
Definition: OpenSwathScoring.h:59
A structure to hold the different scores computed by OpenSWATH.
Definition: OpenSwathScoring.h:104
OpenSwath::LightTargetedExperiment TargetedExpType
Definition: MRMFeatureFinderScoring.h:103
OpenMS::SONARScoring sonarscoring_
Definition: MRMFeatureFinderScoring.h:297
Base class for all classes that want to report their progress.
Definition: ProgressLogger.h:55
A description of a targeted experiment containing precursor and production ions.
Definition: TargetedExperiment.h:62
bool SortDoubleDoublePairFirst(const std::pair< double, double > &left, const std::pair< double, double > &right)
double uis_threshold_sn_
Definition: MRMFeatureFinderScoring.h:290
OpenSwath::LightModification ModificationType
Definition: MRMFeatureFinderScoring.h:106
double rt_normalization_factor_
Definition: MRMFeatureFinderScoring.h:287
Scoring of an spectrum using SONAR data.
Definition: SONARScoring.h:55
Generic description of a coordinate transformation.
Definition: TransformationDescription.h:61
A base class for all classes handling default parameters.
Definition: DefaultParamHandler.h:92
Definition: TransitionExperiment.h:189
Definition: TransitionExperiment.h:195
OpenSwath_Scores_Usage su_
Definition: MRMFeatureFinderScoring.h:295
bool strict_
Definition: MRMFeatureFinderScoring.h:284
Definition: TransitionExperiment.h:143

OpenMS / TOPP release 2.3.0 Documentation generated on Tue Jan 9 2018 18:22:02 using doxygen 1.8.13