, including all inherited members.
| add_up_spectra_ | MRMFeatureFinderScoring | [private] |
| begin_ | ProgressLogger | [mutable, protected] |
| calculateSwathScores_(MRMTransitionGroup< SpectrumT, TransitionT > &transition_group, MRMFeature &mrmfeature_, OpenSwath::SpectrumAccessPtr swath_map, std::vector< double > &normalized_library_intensity, OpenSwath_Scores scores) | MRMFeatureFinderScoring | [inline, private] |
| check_defaults_ | DefaultParamHandler | [protected] |
| CMD enum value | ProgressLogger | |
| DefaultParamHandler(const String &name) | DefaultParamHandler | |
| DefaultParamHandler(const DefaultParamHandler &rhs) | DefaultParamHandler | |
| defaults_ | DefaultParamHandler | [protected] |
| defaultsToParam_() | DefaultParamHandler | [protected] |
| diascoring_ | MRMFeatureFinderScoring | [private] |
| dlg_ | ProgressLogger | [mutable, protected] |
| emgscoring_ | MRMFeatureFinderScoring | [private] |
| end_ | ProgressLogger | [mutable, protected] |
| endProgress() const | ProgressLogger | |
| error_name_ | DefaultParamHandler | [protected] |
| getAddedSpectra_(OpenSwath::SpectrumAccessPtr swath_map, double RT, int nr_spectra_to_add) | MRMFeatureFinderScoring | [inline, private] |
| getDefaults() const | DefaultParamHandler | |
| getLogType() const | ProgressLogger | |
| getName() const | DefaultParamHandler | |
| getParameters() const | DefaultParamHandler | |
| getSubsections() const | DefaultParamHandler | |
| GUI enum value | ProgressLogger | |
| last_invoke_ | ProgressLogger | [mutable, protected] |
| LogType enum name | ProgressLogger | |
| mapExperimentToTransitionList(OpenSwath::SpectrumAccessPtr input, OpenSwath::LightTargetedExperiment &transition_exp, TransitionGroupMapType &transition_group_map, TransformationDescription trafo, double rt_extraction_window) | MRMFeatureFinderScoring | |
| ModificationType typedef | MRMFeatureFinderScoring | |
| MRMFeatureFinderScoring() | MRMFeatureFinderScoring | |
| mrmscore_ | MRMFeatureFinderScoring | [private] |
| MRMTransitionGroupType typedef | MRMFeatureFinderScoring | |
| NONE enum value | ProgressLogger | |
| operator=(const DefaultParamHandler &rhs) | DefaultParamHandler | [virtual] |
| operator==(const DefaultParamHandler &rhs) const | DefaultParamHandler | [virtual] |
| param_ | DefaultParamHandler | [protected] |
| PeptideRefMap_ | MRMFeatureFinderScoring | [private] |
| PeptideRTMap_ | MRMFeatureFinderScoring | [private] |
| PeptideType typedef | MRMFeatureFinderScoring | |
| pickExperiment(OpenSwath::SpectrumAccessPtr input, FeatureMap< Feature > &output, OpenSwath::LightTargetedExperiment &transition_exp, TransformationDescription trafo, OpenSwath::SpectrumAccessPtr swath_map, TransitionGroupMapType &transition_group_map) | MRMFeatureFinderScoring | [inline] |
| ProgressLogger() | ProgressLogger | |
| ProteinRefMap_ | MRMFeatureFinderScoring | [private] |
| ProteinType typedef | MRMFeatureFinderScoring | |
| quantification_cutoff_ | MRMFeatureFinderScoring | [private] |
| recursion_depth_ | ProgressLogger | [protected, static] |
| RichPeakChromatogram typedef | MRMFeatureFinderScoring | |
| rt_extraction_window_ | MRMFeatureFinderScoring | [private] |
| rt_normalization_factor_ | MRMFeatureFinderScoring | [private] |
| scorePeakgroups_(MRMTransitionGroup< SpectrumT, TransitionT > &transition_group, TransformationDescription &trafo, OpenSwath::SpectrumAccessPtr swath_map, FeatureMap< Feature > &output) | MRMFeatureFinderScoring | [inline, private] |
| setLogType(LogType type) const | ProgressLogger | |
| setName(const String &name) | DefaultParamHandler | |
| setParameters(const Param ¶m) | DefaultParamHandler | |
| setProgress(SignedSize value) const | ProgressLogger | |
| setStrictFlag(bool f) | MRMFeatureFinderScoring | [inline] |
| spacing_for_spectra_resampling_ | MRMFeatureFinderScoring | [private] |
| startProgress(SignedSize begin, SignedSize end, const String &label) const | ProgressLogger | |
| stop_report_after_feature_ | MRMFeatureFinderScoring | [private] |
| stop_watch_ | ProgressLogger | [mutable, protected] |
| strict_ | MRMFeatureFinderScoring | [private] |
| subsections_ | DefaultParamHandler | [protected] |
| TargetedExpType typedef | MRMFeatureFinderScoring | |
| TransitionGroupMapType typedef | MRMFeatureFinderScoring | |
| TransitionType typedef | MRMFeatureFinderScoring | |
| type_ | ProgressLogger | [mutable, protected] |
| updateMembers_() | MRMFeatureFinderScoring | [private] |
| OpenMS::DefaultParamHandler::updateMembers_() | DefaultParamHandler | [protected, virtual] |
| use_coelution_score_ | MRMFeatureFinderScoring | [private] |
| use_elution_model_score_ | MRMFeatureFinderScoring | [private] |
| use_intensity_score_ | MRMFeatureFinderScoring | [private] |
| use_library_score_ | MRMFeatureFinderScoring | [private] |
| use_nr_peaks_score_ | MRMFeatureFinderScoring | [private] |
| use_rt_score_ | MRMFeatureFinderScoring | [private] |
| use_shape_score_ | MRMFeatureFinderScoring | [private] |
| use_sn_score_ | MRMFeatureFinderScoring | [private] |
| use_total_xic_score_ | MRMFeatureFinderScoring | [private] |
| value_ | ProgressLogger | [mutable, protected] |
| warn_empty_defaults_ | DefaultParamHandler | [protected] |
| write_convex_hull_ | MRMFeatureFinderScoring | [private] |
| ~DefaultParamHandler() | DefaultParamHandler | [virtual] |
| ~MRMFeatureFinderScoring() | MRMFeatureFinderScoring | |
| ~ProgressLogger() | ProgressLogger | |