| add_up_spectra_ | MRMFeatureFinderScoring | private |
| check_defaults_ | DefaultParamHandler | protected |
| CMD enum value | ProgressLogger | |
| current_logger_ | ProgressLogger | mutableprotected |
| 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 | |
| last_invoke_ | ProgressLogger | mutableprotected |
| LogType enum name | ProgressLogger | |
| logTypeToFactoryName_(LogType type) | ProgressLogger | protectedstatic |
| 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 |
| 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 | |
| prepareProteinPeptideMaps_(const OpenSwath::LightTargetedExperiment &transition_exp) | MRMFeatureFinderScoring | |
| ProgressLogger() | ProgressLogger | |
| ProgressLogger(const ProgressLogger &other) | ProgressLogger | |
| ProteinType typedef | MRMFeatureFinderScoring | |
| quantification_cutoff_ | MRMFeatureFinderScoring | private |
| recursion_depth_ | ProgressLogger | protectedstatic |
| 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 sn_win_len_, const unsigned int sn_bin_count_, bool write_log_messages, std::vector< OpenSwath::SwathMap > swath_maps) | MRMFeatureFinderScoring | private |
| scorePeakgroups(MRMTransitionGroupType &transition_group, TransformationDescription &trafo, std::vector< OpenSwath::SwathMap > swath_maps, FeatureMap &output, bool ms1only=false) | MRMFeatureFinderScoring | |
| setLogType(LogType type) const | ProgressLogger | |
| setMS1Map(OpenSwath::SpectrumAccessPtr ms1_map) | MRMFeatureFinderScoring | inline |
| setName(const String &name) | DefaultParamHandler | |
| setParameters(const Param ¶m) | DefaultParamHandler | |
| setProgress(SignedSize value) const | ProgressLogger | |
| setStrictFlag(bool f) | MRMFeatureFinderScoring | inline |
| sonarscoring_ | MRMFeatureFinderScoring | private |
| spacing_for_spectra_resampling_ | MRMFeatureFinderScoring | private |
| splitTransitionGroupsDetection_(MRMTransitionGroupType &transition_group, MRMTransitionGroupType &transition_group_detection) | MRMFeatureFinderScoring | private |
| splitTransitionGroupsIdentification_(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 | mutableprotected |
| uis_threshold_peak_area_ | MRMFeatureFinderScoring | private |
| uis_threshold_sn_ | MRMFeatureFinderScoring | private |
| updateMembers_() | MRMFeatureFinderScoring | privatevirtual |
| warn_empty_defaults_ | DefaultParamHandler | protected |
| write_convex_hull_ | MRMFeatureFinderScoring | private |
| ~DefaultParamHandler() | DefaultParamHandler | virtual |
| ~MRMFeatureFinderScoring() | MRMFeatureFinderScoring | |
| ~ProgressLogger() | ProgressLogger | |