|
OpenMS
2.6.0
|
Go to the documentation of this file.
37 #define USE_SP_INTERFACE
58 #include <boost/shared_ptr.hpp>
59 #include <boost/make_shared.hpp>
60 #include <boost/unordered_map.hpp>
155 std::vector<OpenSwath::SwathMap> swath_maps,
187 const std::vector<OpenSwath::SwathMap>& swath_maps,
189 bool ms1only =
false);
229 TransitionGroupMapType& transition_group_map,
231 double rt_extraction_window);
241 void splitTransitionGroupsDetection_(
const MRMTransitionGroupType& transition_group,
242 MRMTransitionGroupType& transition_group_detection);
253 void splitTransitionGroupsIdentification_(
const MRMTransitionGroupType& transition_group,
254 MRMTransitionGroupType& transition_group_identification,
255 MRMTransitionGroupType& transition_group_identification_decoy);
273 OpenSwath_Ind_Scores scoreIdentification_(MRMTransitionGroupType& transition_group_identification,
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);
284 void updateMembers_()
override;
321 #undef run_identifier
OpenSwath::SpectrumAccessPtr ms1_map_
Definition: MRMFeatureFinderScoring.h:316
double quantification_cutoff_
Definition: MRMFeatureFinderScoring.h:288
double uis_threshold_peak_area_
Definition: MRMFeatureFinderScoring.h:300
OpenSwath_Scores_Usage su_
Definition: MRMFeatureFinderScoring.h:310
std::map< OpenMS::String, const PeptideType * > PeptideRefMap_
Definition: MRMFeatureFinderScoring.h:309
String scoring_model_
Definition: MRMFeatureFinderScoring.h:292
bool strict_
Definition: MRMFeatureFinderScoring.h:291
Scoring of an spectrum at the peak apex of an chromatographic elution peak.
Definition: DIAScoring.h:83
double im_extra_drift_
Definition: MRMFeatureFinderScoring.h:306
unsigned int sn_bin_count_
Definition: MRMFeatureFinderScoring.h:303
The MRMFeatureFinder finds and scores peaks of transitions that co-elute.
Definition: MRMFeatureFinderScoring.h:93
bool SortDoubleDoublePairFirst(const std::pair< double, double > &left, const std::pair< double, double > &right)
MRMTransitionGroup< MSChromatogram, TransitionType > MRMTransitionGroupType
Definition: MRMFeatureFinderScoring.h:108
A more convenient string class.
Definition: String.h:59
OpenMS::EmgScoring emgscoring_
Definition: MRMFeatureFinderScoring.h:313
In-Memory representation of a mass spectrometry experiment.
Definition: MSExperiment.h:77
double sn_win_len_
Definition: MRMFeatureFinderScoring.h:302
Definition: TransitionExperiment.h:142
Definition: OpenSwathScores.h:192
OpenSwath::LightCompound PeptideType
Definition: MRMFeatureFinderScoring.h:103
Definition: TransitionExperiment.h:207
double uis_threshold_sn_
Definition: MRMFeatureFinderScoring.h:299
OpenSwath::LightModification ModificationType
Definition: MRMFeatureFinderScoring.h:105
A multi-chromatogram MRM feature.
Definition: MRMFeature.h:50
std::map< String, MRMTransitionGroupType > TransitionGroupMapType
Definition: MRMFeatureFinderScoring.h:109
A base class for all classes handling default parameters.
Definition: DefaultParamHandler.h:92
bool write_log_messages_
Definition: MRMFeatureFinderScoring.h:304
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
Definition: TransitionExperiment.h:149
Base class for all classes that want to report their progress.
Definition: ProgressLogger.h:54
void setStrictFlag(bool f)
Set the flag for strict mapping.
Definition: MRMFeatureFinderScoring.h:193
double spacing_for_spectra_resampling_
Definition: MRMFeatureFinderScoring.h:298
OpenSwath::LightProtein ProteinType
Definition: MRMFeatureFinderScoring.h:104
A class that calls the scoring routines.
Definition: OpenSwathScoring.h:59
void setMS1Map(OpenSwath::SpectrumAccessPtr ms1_map)
Add an MS1 map containing spectra.
Definition: MRMFeatureFinderScoring.h:207
OpenMS::SONARScoring sonarscoring_
Definition: MRMFeatureFinderScoring.h:312
Scoring of an elution peak using an exponentially modified gaussian distribution model.
Definition: EmgScoring.h:59
String spectrum_addition_method_
Definition: MRMFeatureFinderScoring.h:297
A container for features.
Definition: FeatureMap.h:97
int add_up_spectra_
Definition: MRMFeatureFinderScoring.h:296
bool write_convex_hull_
Definition: MRMFeatureFinderScoring.h:290
double rt_normalization_factor_
Definition: MRMFeatureFinderScoring.h:295
double rt_extraction_window_
Definition: MRMFeatureFinderScoring.h:287
Definition: TransitionExperiment.h:201
boost::shared_ptr< ISpectrumAccess > SpectrumAccessPtr
Definition: openswathalgo/include/OpenMS/OPENSWATHALGO/DATAACCESS/ISpectrumAccess.h:89
The representation of a group of transitions in a targeted proteomics experiment.
Definition: MRMTransitionGroup.h:67
Scoring of an spectrum using SONAR data.
Definition: SONARScoring.h:54
OpenSwath::LightTargetedExperiment TargetedExpType
Definition: MRMFeatureFinderScoring.h:102
OpenMS::DIAScoring diascoring_
Definition: MRMFeatureFinderScoring.h:311
A description of a targeted experiment containing precursor and production ions.
Definition: TargetedExperiment.h:64
OpenSwath::LightTransition TransitionType
Type definitions.
Definition: MRMFeatureFinderScoring.h:101
int stop_report_after_feature_
Definition: MRMFeatureFinderScoring.h:289
Definition: TransitionExperiment.h:46
A structure to store which scores should be used by the OpenSWATH Algorithm.
Definition: OpenSwathScores.h:50