OpenMS
MRMFeatureFinderScoring Member List

This is the complete list of members for MRMFeatureFinderScoring, including all inherited members.

add_up_spectra_MRMFeatureFinderScoringprivate
apply_im_peak_picking_MRMFeatureFinderScoringprivate
check_defaults_DefaultParamHandlerprotected
CMD enum valueProgressLogger
current_logger_ProgressLoggermutableprotected
DefaultParamHandler(const String &name)DefaultParamHandler
DefaultParamHandler(const DefaultParamHandler &rhs)DefaultParamHandler
DefaultParamHandler()DefaultParamHandlerprivate
defaults_DefaultParamHandlerprotected
defaultsToParam_()DefaultParamHandlerprotected
diascoring_MRMFeatureFinderScoringprivate
emgscoring_MRMFeatureFinderScoringprivate
endProgress(UInt64 bytes_processed=0) constProgressLogger
error_name_DefaultParamHandlerprotected
getDefaults() constDefaultParamHandler
getLogType() constProgressLogger
getName() constDefaultParamHandler
getParameters() constDefaultParamHandler
getSubsections() constDefaultParamHandler
GUI enum valueProgressLogger
im_extra_drift_MRMFeatureFinderScoringprivate
last_invoke_ProgressLoggermutableprotected
LogType enum nameProgressLogger
mapExperimentToTransitionList(const OpenSwath::SpectrumAccessPtr &input, const OpenSwath::LightTargetedExperiment &transition_exp, TransitionGroupMapType &transition_group_map, TransformationDescription trafo, double rt_extraction_window)MRMFeatureFinderScoring
merge_spectra_by_peak_width_fraction_MRMFeatureFinderScoringprivate
ModificationType typedefMRMFeatureFinderScoring
MRMFeatureFinderScoring()MRMFeatureFinderScoring
MRMTransitionGroupType typedefMRMFeatureFinderScoring
ms1_map_MRMFeatureFinderScoringprivate
nextProgress() constProgressLogger
NONE enum valueProgressLogger
OpenMS::operator=(const DefaultParamHandler &rhs)DefaultParamHandler
OpenMS::ProgressLogger::operator=(const ProgressLogger &other)ProgressLogger
operator==(const DefaultParamHandler &rhs) constDefaultParamHandlervirtual
param_DefaultParamHandlerprotected
PeptideRefMap_MRMFeatureFinderScoringprivate
PeptideType typedefMRMFeatureFinderScoring
pickExperiment(const PeakMap &chromatograms, FeatureMap &output, const TargetedExperiment &transition_exp, const TransformationDescription &trafo, const PeakMap &swath_map)MRMFeatureFinderScoring
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)MRMFeatureFinderScoring
prepareFeatureOutput_(OpenMS::MRMFeature &mrmfeature, bool ms1only, int charge) constMRMFeatureFinderScoringprivate
prepareProteinPeptideMaps_(const OpenSwath::LightTargetedExperiment &transition_exp)MRMFeatureFinderScoring
ProgressLogger()ProgressLogger
ProgressLogger(const ProgressLogger &other)ProgressLogger
ProteinType typedefMRMFeatureFinderScoring
quantification_cutoff_MRMFeatureFinderScoringprivate
recursion_depth_ProgressLoggerprotectedstatic
rt_extraction_window_MRMFeatureFinderScoringprivate
rt_normalization_factor_MRMFeatureFinderScoringprivate
scoreIdentification_(MRMTransitionGroupType &transition_group_identification, MRMTransitionGroupType &transition_group_detection, 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 double drift_target, RangeMobility &im_range) constMRMFeatureFinderScoringprivate
scorePeakgroups(MRMTransitionGroupType &transition_group, const TransformationDescription &trafo, const std::vector< OpenSwath::SwathMap > &swath_maps, FeatureMap &output, bool ms1only=false) constMRMFeatureFinderScoring
scoring_model_MRMFeatureFinderScoringprivate
setLogger(ProgressLoggerImpl *logger)ProgressLogger
setLogType(LogType type) constProgressLogger
setMS1Map(OpenSwath::SpectrumAccessPtr ms1_map)MRMFeatureFinderScoringinline
setName(const String &name)DefaultParamHandler
setParameters(const Param &param)DefaultParamHandler
setProgress(SignedSize value) constProgressLogger
setStrictFlag(bool f)MRMFeatureFinderScoringinline
sn_bin_count_MRMFeatureFinderScoringprivate
sn_win_len_MRMFeatureFinderScoringprivate
spacing_for_spectra_resampling_MRMFeatureFinderScoringprivate
spectrum_addition_method_MRMFeatureFinderScoringprivate
spectrum_merge_method_type_MRMFeatureFinderScoringprivate
splitTransitionGroupsDetection_(const MRMTransitionGroupType &transition_group, MRMTransitionGroupType &transition_group_detection) constMRMFeatureFinderScoringprivate
splitTransitionGroupsIdentification_(const MRMTransitionGroupType &transition_group, MRMTransitionGroupType &transition_group_identification, MRMTransitionGroupType &transition_group_identification_decoy) constMRMFeatureFinderScoringprivate
startProgress(SignedSize begin, SignedSize end, const String &label) constProgressLogger
stop_report_after_feature_MRMFeatureFinderScoringprivate
strict_MRMFeatureFinderScoringprivate
su_MRMFeatureFinderScoringprivate
subsections_DefaultParamHandlerprotected
TargetedExpType typedefMRMFeatureFinderScoring
TransitionGroupMapType typedefMRMFeatureFinderScoring
TransitionType typedefMRMFeatureFinderScoring
type_ProgressLoggermutableprotected
uis_threshold_peak_area_MRMFeatureFinderScoringprivate
uis_threshold_sn_MRMFeatureFinderScoringprivate
updateMembers_() overrideMRMFeatureFinderScoringprivatevirtual
use_ms1_ion_mobility_MRMFeatureFinderScoringprivate
warn_empty_defaults_DefaultParamHandlerprotected
write_convex_hull_MRMFeatureFinderScoringprivate
write_log_messages_MRMFeatureFinderScoringprivate
writeParametersToMetaValues(const Param &write_this, MetaInfoInterface &write_here, const String &key_prefix="")DefaultParamHandlerstatic
~DefaultParamHandler()DefaultParamHandlervirtual
~MRMFeatureFinderScoring() overrideMRMFeatureFinderScoring
~ProgressLogger()ProgressLoggervirtual