| abort_(const Seed &seed, const String &reason) | FeatureFinderAlgorithmPicked | protected |
| abort_reasons_ | FeatureFinderAlgorithmPicked | protected |
| aborts_ | FeatureFinderAlgorithmPicked | protected |
| ChargedIndexSet typedef | FeatureFinderDefs | |
| check_defaults_ | DefaultParamHandler | protected |
| checkFeatureQuality_(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 |
| CoordinateType typedef | FeatureFinderAlgorithm | |
| create() | FeatureFinderAlgorithmPicked | static |
| cropFeature_(TraceFitter *fitter, const MassTraces &traces, MassTraces &new_traces) | FeatureFinderAlgorithmPicked | protected |
| debug_ | FeatureFinderAlgorithmPicked | protected |
| DefaultParamHandler(const String &name) | DefaultParamHandler | |
| DefaultParamHandler(const DefaultParamHandler &rhs) | DefaultParamHandler | |
| defaults_ | DefaultParamHandler | protected |
| defaultsToParam_() | DefaultParamHandler | protected |
| 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 |
| FeatureFinderAlgorithm() | FeatureFinderAlgorithm | inline |
| FeatureFinderAlgorithmPicked() | FeatureFinderAlgorithmPicked | |
| FeatureFinderAlgorithmPicked(const FeatureFinderAlgorithmPicked &) | FeatureFinderAlgorithmPicked | private |
| features_ | FeatureFinderAlgorithm | protected |
| ff_ | FeatureFinderAlgorithm | 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 |
| Flag enum name | FeatureFinderDefs | |
| FloatDataArrays typedef | FeatureFinderAlgorithmPicked | |
| getDefaultParameters() const | FeatureFinderAlgorithm | inlinevirtual |
| getDefaults() const | DefaultParamHandler | |
| getIsotopeDistribution_(double mass) const | FeatureFinderAlgorithmPicked | protected |
| getName() const | DefaultParamHandler | |
| getParameters() const | DefaultParamHandler | |
| getProductName() | FeatureFinderAlgorithmPicked | static |
| getSubsections() const | DefaultParamHandler | |
| IndexPair typedef | FeatureFinderDefs | |
| IndexSet typedef | FeatureFinderDefs | |
| 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 |
| IntensityType typedef | FeatureFinderAlgorithm | |
| 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 |
| log_ | FeatureFinderAlgorithmPicked | mutableprotected |
| 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 |
| operator=(const FeatureFinderAlgorithmPicked &) | FeatureFinderAlgorithmPicked | private |
| OpenMS::DefaultParamHandler::operator=(const DefaultParamHandler &rhs) | DefaultParamHandler | virtual |
| 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 |
| registerChildren() | FeatureFinderAlgorithm | static |
| reported_mz_ | FeatureFinderAlgorithmPicked | protected |
| run() | FeatureFinderAlgorithmPicked | virtual |
| Seed typedef | FeatureFinderAlgorithmPicked | protected |
| seeds_ | FeatureFinderAlgorithmPicked | protected |
| setData(const MapType &map, FeatureMap &features, FeatureFinder &ff) | FeatureFinderAlgorithm | inline |
| setName(const String &name) | DefaultParamHandler | |
| setParameters(const Param ¶m) | DefaultParamHandler | |
| setSeeds(const FeatureMap &seeds) | FeatureFinderAlgorithmPicked | virtual |
| slope_bound_ | FeatureFinderAlgorithmPicked | protected |
| SpectrumType typedef | FeatureFinderAlgorithmPicked | |
| subsections_ | DefaultParamHandler | protected |
| TheoreticalIsotopePattern typedef | FeatureFinderAlgorithmPicked | protected |
| trace_tolerance_ | FeatureFinderAlgorithmPicked | protected |
| UNUSED enum value | FeatureFinderDefs | |
| updateMembers_() | FeatureFinderAlgorithmPicked | protectedvirtual |
| USED enum value | FeatureFinderDefs | |
| warn_empty_defaults_ | DefaultParamHandler | protected |
| writeFeatureDebugInfo_(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 |
| ~DefaultParamHandler() | DefaultParamHandler | virtual |
| ~FeatureFinderAlgorithm() | FeatureFinderAlgorithm | inlinevirtual |