35 #ifndef OPENMS_ANALYSIS_OPENSWATH_MRMFEATUREFINDERSCORING_H 36 #define OPENMS_ANALYSIS_OPENSWATH_MRMFEATUREFINDERSCORING_H 38 #define USE_SP_INTERFACE 55 #include <boost/shared_ptr.hpp> 56 #include <boost/make_shared.hpp> 224 void updateMembers_();
250 #undef run_identifier 251 #endif // OPENMS_ANALYSIS_OPENSWATH_MRMFEATUREFINDERSCORING_H double spacing_for_spectra_resampling_
Definition: MRMFeatureFinderScoring.h:236
OpenSwath::LightPeptide PeptideType
Definition: MRMFeatureFinderScoring.h:105
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
MRMTransitionGroup< MSSpectrum< ChromatogramPeak >, TransitionType > MRMTransitionGroupType
Definition: MRMFeatureFinderScoring.h:109
OpenMS::DIAScoring diascoring_
Definition: MRMFeatureFinderScoring.h:241
A container for features.
Definition: FeatureMap.h:93
OpenSwath::LightTransition TransitionType
Definition: MRMFeatureFinderScoring.h:103
The MRMFeatureFinder finds and scores peaks of transitions that co-elute.
Definition: MRMFeatureFinderScoring.h:89
bool write_convex_hull_
Definition: MRMFeatureFinderScoring.h:230
int add_up_spectra_
Definition: MRMFeatureFinderScoring.h:235
std::map< String, MRMTransitionGroupType > TransitionGroupMapType
Definition: MRMFeatureFinderScoring.h:110
double rt_extraction_window_
Definition: MRMFeatureFinderScoring.h:227
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:47
void setMS1Map(OpenSwath::SpectrumAccessPtr ms1_map)
Add an MS1 map containing spectra.
Definition: MRMFeatureFinderScoring.h:199
OpenMS::EmgScoring emgscoring_
Definition: MRMFeatureFinderScoring.h:242
The representation of a transition group that has information about the individual chromatograms as w...
Definition: MRMTransitionGroup.h:56
int stop_report_after_feature_
Definition: MRMFeatureFinderScoring.h:229
OpenSwath::LightProtein ProteinType
Definition: MRMFeatureFinderScoring.h:106
Definition: TransitionExperiment.h:155
The representation of a 1D spectrum.
Definition: MSSpectrum.h:66
OpenSwath::SpectrumAccessPtr ms1_map_
Definition: MRMFeatureFinderScoring.h:245
Scoring of an spectrum at the peak apex of an chromatographic elution peak.
Definition: DIAScoring.h:82
double quantification_cutoff_
Definition: MRMFeatureFinderScoring.h:228
std::map< OpenMS::String, const PeptideType * > PeptideRefMap_
Definition: MRMFeatureFinderScoring.h:239
void setStrictFlag(bool f)
Set the flag for strict mapping.
Definition: MRMFeatureFinderScoring.h:185
Definition: TransitionExperiment.h:47
A structure to store which scores should be used by the Algorithm.
Definition: OpenSwathScoring.h:57
OpenSwath::LightTargetedExperiment TargetedExpType
Definition: MRMFeatureFinderScoring.h:104
Base class for all classes that want to report their progress.
Definition: ProgressLogger.h:55
This class stores an prediction of an SRM/MRM transition.
Definition: TargetedExperiment.h:53
bool SortDoubleDoublePairFirst(const std::pair< double, double > &left, const std::pair< double, double > &right)
OpenSwath::LightModification ModificationType
Definition: MRMFeatureFinderScoring.h:107
double rt_normalization_factor_
Definition: MRMFeatureFinderScoring.h:234
A base class for all classes handling default parameters.
Definition: DefaultParamHandler.h:92
Definition: TransitionExperiment.h:173
Definition: TransitionExperiment.h:179
OpenSwath_Scores_Usage su_
Definition: MRMFeatureFinderScoring.h:240
MSSpectrum< ChromatogramPeak > RichPeakChromatogram
Type definitions.
Definition: MRMFeatureFinderScoring.h:102
bool strict_
Definition: MRMFeatureFinderScoring.h:231
Definition: TransitionExperiment.h:149