| abort_(const Seed &seed, const String &reason) | FeatureFinderAlgorithmPicked | protected |
| abort_reasons_ | FeatureFinderAlgorithmPicked | protected |
| aborts_ | FeatureFinderAlgorithmPicked | protected |
| check_defaults_ | DefaultParamHandler | protected |
| checkFeatureQuality_(const std::shared_ptr< TraceFitter > &fitter, MassTraces &feature_traces, const double &seed_mz, const double &min_feature_score, String &error_msg, double &fit_score, double &correlation, double &final_score) | FeatureFinderAlgorithmPicked | protected |
| chooseTraceFitter_(double &tau) | FeatureFinderAlgorithmPicked | protected |
| CMD enum value | ProgressLogger | |
| cropFeature_(const std::shared_ptr< TraceFitter > &fitter, const MassTraces &traces, MassTraces &new_traces) | FeatureFinderAlgorithmPicked | protected |
| current_logger_ | ProgressLogger | mutableprotected |
| debug_ | FeatureFinderAlgorithmPicked | protected |
| DefaultParamHandler(const String &name) | DefaultParamHandler | |
| DefaultParamHandler(const DefaultParamHandler &rhs) | DefaultParamHandler | |
| DefaultParamHandler() | DefaultParamHandler | private |
| defaults_ | DefaultParamHandler | protected |
| defaultsToParam_() | DefaultParamHandler | protected |
| endProgress(UInt64 bytes_processed=0) const | ProgressLogger | |
| error_name_ | DefaultParamHandler | protected |
| extendMassTrace_(MassTrace &trace, SignedSize spectrum_index, double mz, bool increase_rt, Size meta_index_overall, double min_rt=0.0, double max_rt=0.0) const | FeatureFinderAlgorithmPicked | protected |
| extendMassTraces_(const IsotopePattern &pattern, MassTraces &traces, Size meta_index_overall) const | FeatureFinderAlgorithmPicked | protected |
| FeatureFinderAlgorithmPicked() | FeatureFinderAlgorithmPicked | |
| FeatureFinderAlgorithmPicked(const FeatureFinderAlgorithmPicked &) | FeatureFinderAlgorithmPicked | private |
| features_ | FeatureFinderAlgorithmPicked | protected |
| findBestIsotopeFit_(const Seed ¢er, UInt charge, IsotopePattern &best_pattern) const | FeatureFinderAlgorithmPicked | protected |
| findIsotope_(double pos, Size spectrum_index, IsotopePattern &pattern, Size pattern_index, Size &peak_index) const | FeatureFinderAlgorithmPicked | protected |
| FloatDataArrays typedef | FeatureFinderAlgorithmPicked | |
| getDefaultParameters() const | FeatureFinderAlgorithmPicked | inlinevirtual |
| getDefaults() const | DefaultParamHandler | |
| getIsotopeDistribution_(double mass) const | FeatureFinderAlgorithmPicked | protected |
| getLogType() const | ProgressLogger | |
| getName() const | DefaultParamHandler | |
| getParameters() const | DefaultParamHandler | |
| getSubsections() const | DefaultParamHandler | |
| GUI enum value | ProgressLogger | |
| intensity_bins_ | FeatureFinderAlgorithmPicked | protected |
| intensity_mz_step_ | FeatureFinderAlgorithmPicked | protected |
| intensity_percentage_ | FeatureFinderAlgorithmPicked | protected |
| intensity_percentage_optional_ | FeatureFinderAlgorithmPicked | protected |
| intensity_rt_step_ | FeatureFinderAlgorithmPicked | protected |
| intensity_thresholds_ | FeatureFinderAlgorithmPicked | protected |
| intensityScore_(Size spectrum, Size peak) const | FeatureFinderAlgorithmPicked | protected |
| intensityScore_(Size rt_bin, Size mz_bin, double intensity) const | FeatureFinderAlgorithmPicked | protected |
| intersection_(const Feature &f1, const Feature &f2) const | FeatureFinderAlgorithmPicked | protected |
| isotope_distributions_ | FeatureFinderAlgorithmPicked | protected |
| IsotopePattern typedef | FeatureFinderAlgorithmPicked | protected |
| isotopeScore_(const TheoreticalIsotopePattern &isotopes, IsotopePattern &pattern, bool consider_mz_distances) const | FeatureFinderAlgorithmPicked | protected |
| last_invoke_ | ProgressLogger | mutableprotected |
| log_ | FeatureFinderAlgorithmPicked | mutableprotected |
| LogType enum name | ProgressLogger | |
| map_ | FeatureFinderAlgorithmPicked | protected |
| MapType typedef | FeatureFinderAlgorithmPicked | |
| mass_window_width_ | FeatureFinderAlgorithmPicked | protected |
| MassTrace typedef | FeatureFinderAlgorithmPicked | protected |
| MassTraces typedef | FeatureFinderAlgorithmPicked | protected |
| max_feature_intersection_ | FeatureFinderAlgorithmPicked | protected |
| max_missing_trace_peaks_ | FeatureFinderAlgorithmPicked | protected |
| max_rt_span_ | FeatureFinderAlgorithmPicked | protected |
| min_isotope_fit_ | FeatureFinderAlgorithmPicked | protected |
| min_rt_span_ | FeatureFinderAlgorithmPicked | protected |
| min_spectra_ | FeatureFinderAlgorithmPicked | protected |
| min_trace_score_ | FeatureFinderAlgorithmPicked | protected |
| nearest_(double pos, const MSSpectrum &spec, Size start) const | FeatureFinderAlgorithmPicked | protected |
| nextProgress() const | ProgressLogger | |
| NONE enum value | ProgressLogger | |
| operator=(const FeatureFinderAlgorithmPicked &) | FeatureFinderAlgorithmPicked | private |
| OpenMS::DefaultParamHandler::operator=(const DefaultParamHandler &rhs) | DefaultParamHandler | |
| OpenMS::ProgressLogger::operator=(const ProgressLogger &other) | ProgressLogger | |
| operator==(const DefaultParamHandler &rhs) const | DefaultParamHandler | virtual |
| optional_fit_improvement_ | FeatureFinderAlgorithmPicked | protected |
| param_ | DefaultParamHandler | protected |
| pattern_tolerance_ | FeatureFinderAlgorithmPicked | protected |
| PeakType typedef | FeatureFinderAlgorithmPicked | protected |
| positionScore_(double pos1, double pos2, double allowed_deviation) const | FeatureFinderAlgorithmPicked | protected |
| ProgressLogger() | ProgressLogger | |
| ProgressLogger(const ProgressLogger &other) | ProgressLogger | |
| recursion_depth_ | ProgressLogger | protectedstatic |
| reported_mz_ | FeatureFinderAlgorithmPicked | protected |
| run(PeakMap &input_map, FeatureMap &features, const Param ¶m, const FeatureMap &seeds) | FeatureFinderAlgorithmPicked | |
| run() | FeatureFinderAlgorithmPicked | protected |
| Seed typedef | FeatureFinderAlgorithmPicked | protected |
| seeds_ | FeatureFinderAlgorithmPicked | protected |
| setData(const MSExperiment &map, FeatureMap &features) | FeatureFinderAlgorithmPicked | |
| setLogger(ProgressLoggerImpl *logger) | ProgressLogger | |
| setLogType(LogType type) const | ProgressLogger | |
| setName(const String &name) | DefaultParamHandler | |
| setParameters(const Param ¶m) | DefaultParamHandler | |
| setProgress(SignedSize value) const | ProgressLogger | |
| setSeeds(const FeatureMap &seeds) | FeatureFinderAlgorithmPicked | |
| slope_bound_ | FeatureFinderAlgorithmPicked | protected |
| SpectrumType typedef | FeatureFinderAlgorithmPicked | |
| startProgress(SignedSize begin, SignedSize end, const String &label) const | ProgressLogger | |
| subsections_ | DefaultParamHandler | protected |
| TheoreticalIsotopePattern typedef | FeatureFinderAlgorithmPicked | protected |
| trace_tolerance_ | FeatureFinderAlgorithmPicked | protected |
| type_ | ProgressLogger | mutableprotected |
| updateMembers_() override | FeatureFinderAlgorithmPicked | protectedvirtual |
| warn_empty_defaults_ | DefaultParamHandler | protected |
| writeFeatureDebugInfo_(const std::shared_ptr< TraceFitter > &fitter, const MassTraces &traces, const MassTraces &new_traces, bool feature_ok, const String &error_msg, const double final_score, const Int plot_nr, const PeakType &peak, const String &path="debug/features/") | FeatureFinderAlgorithmPicked | protected |
| writeParametersToMetaValues(const Param &write_this, MetaInfoInterface &write_here, const String &key_prefix="") | DefaultParamHandler | static |
| ~DefaultParamHandler() | DefaultParamHandler | virtual |
| ~ProgressLogger() | ProgressLogger | virtual |
1.9.1 
