| add_up_spectra_ | MRMFeatureFinderScoring | private | 
  | begin_ | ProgressLogger | mutableprotected | 
  | calculateSwathScores_(MRMTransitionGroup< SpectrumT, TransitionT > &transition_group, MRMFeature &mrmfeature_, OpenSwath::SpectrumAccessPtr swath_map, std::vector< double > &normalized_library_intensity, OpenSwath_Scores scores) | MRMFeatureFinderScoring | inlineprivate | 
  | 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 | mutableprotected | 
  | emgscoring_ | MRMFeatureFinderScoring | private | 
  | end_ | ProgressLogger | mutableprotected | 
  | endProgress() const | ProgressLogger |  | 
  | error_name_ | DefaultParamHandler | protected | 
  | getAddedSpectra_(OpenSwath::SpectrumAccessPtr swath_map, double RT, int nr_spectra_to_add) | MRMFeatureFinderScoring | inlineprivate | 
  | 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 |  | 
  | 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(MSExperiment< Peak1D > &chromatograms, FeatureMap< Feature > &output, TargetedExperiment &transition_exp_, TransformationDescription trafo, MSExperiment< Peak1D > &swath_map) | MRMFeatureFinderScoring | inline | 
  | 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 | protectedstatic | 
  | 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 | inlineprivate | 
  | 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 | mutableprotected | 
  | strict_ | MRMFeatureFinderScoring | private | 
  | subsections_ | DefaultParamHandler | protected | 
  | TargetedExpType typedef | MRMFeatureFinderScoring |  | 
  | TransitionGroupMapType typedef | MRMFeatureFinderScoring |  | 
  | TransitionType typedef | MRMFeatureFinderScoring |  | 
  | type_ | ProgressLogger | mutableprotected | 
  | updateMembers_() | MRMFeatureFinderScoring | privatevirtual | 
  | 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 | mutableprotected | 
  | warn_empty_defaults_ | DefaultParamHandler | protected | 
  | write_convex_hull_ | MRMFeatureFinderScoring | private | 
  | ~DefaultParamHandler() | DefaultParamHandler | virtual | 
  | ~MRMFeatureFinderScoring() | MRMFeatureFinderScoring |  | 
  | ~ProgressLogger() | ProgressLogger |  |