| OpenMS 2.5.0

MRMFeatureFinderScoring Member List

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

add_up_spectra_ | MRMFeatureFinderScoring | private
check_defaults_ | DefaultParamHandler | protected
CMD enum value | ProgressLogger |
current_logger_ | ProgressLogger | mutable protected
DefaultParamHandler(const String &name) | DefaultParamHandler |
DefaultParamHandler(const DefaultParamHandler &rhs) | DefaultParamHandler |
defaults_ | DefaultParamHandler | protected
defaultsToParam_() | DefaultParamHandler | protected
diascoring_ | MRMFeatureFinderScoring | private
emgscoring_ | MRMFeatureFinderScoring | private
endProgress() const | ProgressLogger |
error_name_ | DefaultParamHandler | protected
getDefaults() const | DefaultParamHandler |
getLogType() const | ProgressLogger |
getName() const | DefaultParamHandler |
getParameters() const | DefaultParamHandler |
getSubsections() const | DefaultParamHandler |
GUI enum value | ProgressLogger |
im_extra_drift_ | MRMFeatureFinderScoring | private
last_invoke_ | ProgressLogger | mutable protected
LogType enum name | ProgressLogger |
logTypeToFactoryName_(LogType type) | ProgressLogger | protected static
mapExperimentToTransitionList(OpenSwath::SpectrumAccessPtr input, OpenSwath::LightTargetedExperiment &transition_exp, TransitionGroupMapType &transition_group_map, TransformationDescription trafo, double rt_extraction_window) | MRMFeatureFinderScoring |
ModificationType typedef | MRMFeatureFinderScoring |
MRMFeatureFinderScoring() | MRMFeatureFinderScoring |
MRMTransitionGroupType typedef | MRMFeatureFinderScoring |
ms1_map_ | MRMFeatureFinderScoring | private
nextProgress() const | ProgressLogger |
NONE enum value | ProgressLogger |
OpenMS::operator=(const DefaultParamHandler &rhs) | DefaultParamHandler | virtual
OpenMS::ProgressLogger::operator=(const ProgressLogger &other) | ProgressLogger |
operator==(const DefaultParamHandler &rhs) const | DefaultParamHandler | virtual
param_ | DefaultParamHandler | protected
PeptideRefMap_ | MRMFeatureFinderScoring | private
PeptideType typedef | MRMFeatureFinderScoring |
pickExperiment(PeakMap &chromatograms, FeatureMap &output, TargetedExperiment &transition_exp, TransformationDescription trafo, PeakMap &swath_map) | MRMFeatureFinderScoring |
pickExperiment(OpenSwath::SpectrumAccessPtr input, FeatureMap &output, OpenSwath::LightTargetedExperiment &transition_exp, TransformationDescription trafo, std::vector< OpenSwath::SwathMap > swath_maps, TransitionGroupMapType &transition_group_map) | MRMFeatureFinderScoring |
prepareFeatureOutput_(OpenMS::MRMFeature &mrmfeature, bool ms1only, int charge) | MRMFeatureFinderScoring | private
prepareProteinPeptideMaps_(const OpenSwath::LightTargetedExperiment &transition_exp) | MRMFeatureFinderScoring |
ProgressLogger() | ProgressLogger |
ProgressLogger(const ProgressLogger &other) | ProgressLogger |
ProteinType typedef | MRMFeatureFinderScoring |
quantification_cutoff_ | MRMFeatureFinderScoring | private
recursion_depth_ | ProgressLogger | protected static
rt_extraction_window_ | MRMFeatureFinderScoring | private
rt_normalization_factor_ | MRMFeatureFinderScoring | private
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) | MRMFeatureFinderScoring | private
scorePeakgroups(MRMTransitionGroupType &transition_group, const TransformationDescription &trafo, const std::vector< OpenSwath::SwathMap > &swath_maps, FeatureMap &output, bool ms1only=false) | MRMFeatureFinderScoring |
scoring_model_ | MRMFeatureFinderScoring | private
setLogType(LogType type) const | ProgressLogger |
setMS1Map(OpenSwath::SpectrumAccessPtr ms1_map) | MRMFeatureFinderScoring | inline
setName(const String &name) | DefaultParamHandler |
setParameters(const Param &param) | DefaultParamHandler |
setProgress(SignedSize value) const | ProgressLogger |
setStrictFlag(bool f) | MRMFeatureFinderScoring | inline
sn_bin_count_ | MRMFeatureFinderScoring | private
sn_win_len_ | MRMFeatureFinderScoring | private
sonarscoring_ | MRMFeatureFinderScoring | private
spacing_for_spectra_resampling_ | MRMFeatureFinderScoring | private
spectrum_addition_method_ | MRMFeatureFinderScoring | private
splitTransitionGroupsDetection_(const MRMTransitionGroupType &transition_group, MRMTransitionGroupType &transition_group_detection) | MRMFeatureFinderScoring | private
splitTransitionGroupsIdentification_(const MRMTransitionGroupType &transition_group, MRMTransitionGroupType &transition_group_identification, MRMTransitionGroupType &transition_group_identification_decoy) | MRMFeatureFinderScoring | private
startProgress(SignedSize begin, SignedSize end, const String &label) const | ProgressLogger |
stop_report_after_feature_ | MRMFeatureFinderScoring | private
strict_ | MRMFeatureFinderScoring | private
su_ | MRMFeatureFinderScoring | private
subsections_ | DefaultParamHandler | protected
TargetedExpType typedef | MRMFeatureFinderScoring |
TransitionGroupMapType typedef | MRMFeatureFinderScoring |
TransitionType typedef | MRMFeatureFinderScoring |
type_ | ProgressLogger | mutable protected
uis_threshold_peak_area_ | MRMFeatureFinderScoring | private
uis_threshold_sn_ | MRMFeatureFinderScoring | private
updateMembers_() override | MRMFeatureFinderScoring | private virtual
warn_empty_defaults_ | DefaultParamHandler | protected
write_convex_hull_ | MRMFeatureFinderScoring | private
write_log_messages_ | MRMFeatureFinderScoring | private
~DefaultParamHandler() | DefaultParamHandler | virtual
~MRMFeatureFinderScoring() override | MRMFeatureFinderScoring |
~ProgressLogger() | ProgressLogger |