| abort_(const Seed &seed, const String &reason) | FeatureFinderAlgorithmPicked< PeakType, FeatureType > | inlineprotected |
| abort_reasons_ | FeatureFinderAlgorithmPicked< PeakType, FeatureType > | protected |
| aborts_ | FeatureFinderAlgorithmPicked< PeakType, FeatureType > | protected |
| ChargedIndexSet typedef | FeatureFinderDefs | |
| check_defaults_ | DefaultParamHandler | protected |
| checkFeatureQuality_(TraceFitter< PeakType > *fitter, MassTraces &feature_traces, const DoubleReal &seed_mz, const DoubleReal &min_feature_score, String &error_msg, DoubleReal &fit_score, DoubleReal &correlation, DoubleReal &final_score) | FeatureFinderAlgorithmPicked< PeakType, FeatureType > | inlineprotected |
| chooseTraceFitter_(double &tau) | FeatureFinderAlgorithmPicked< PeakType, FeatureType > | inlineprotected |
| CoordinateType typedef | FeatureFinderAlgorithm< PeakType, FeatureType > | |
| create() | FeatureFinderAlgorithmPicked< PeakType, FeatureType > | inlinestatic |
| cropFeature_(TraceFitter< PeakType > *fitter, const MassTraces &traces, MassTraces &new_traces) | FeatureFinderAlgorithmPicked< PeakType, FeatureType > | inlineprotected |
| debug_ | FeatureFinderAlgorithmPicked< PeakType, FeatureType > | 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, DoubleReal mz, bool increase_rt, Size meta_index_overall, DoubleReal min_rt=0.0, DoubleReal max_rt=0.0) const | FeatureFinderAlgorithmPicked< PeakType, FeatureType > | inlineprotected |
| extendMassTraces_(const IsotopePattern &pattern, MassTraces &traces, Size meta_index_overall) const | FeatureFinderAlgorithmPicked< PeakType, FeatureType > | inlineprotected |
| FeatureFinderAlgorithm() | FeatureFinderAlgorithm< PeakType, FeatureType > | inline |
| FeatureFinderAlgorithmPicked() | FeatureFinderAlgorithmPicked< PeakType, FeatureType > | inline |
| FeatureFinderAlgorithmPicked(const FeatureFinderAlgorithmPicked &) | FeatureFinderAlgorithmPicked< PeakType, FeatureType > | private |
| FeatureMapType typedef | FeatureFinderAlgorithmPicked< PeakType, FeatureType > | |
| features_ | FeatureFinderAlgorithm< PeakType, FeatureType > | protected |
| ff_ | FeatureFinderAlgorithm< PeakType, FeatureType > | protected |
| findBestIsotopeFit_(const Seed ¢er, UInt charge, IsotopePattern &best_pattern) const | FeatureFinderAlgorithmPicked< PeakType, FeatureType > | inlineprotected |
| findIsotope_(DoubleReal pos, Size spectrum_index, IsotopePattern &pattern, Size pattern_index, Size &peak_index) const | FeatureFinderAlgorithmPicked< PeakType, FeatureType > | inlineprotected |
| Flag enum name | FeatureFinderDefs | |
| FloatDataArrays typedef | FeatureFinderAlgorithmPicked< PeakType, FeatureType > | |
| getDefaultParameters() const | FeatureFinderAlgorithm< PeakType, FeatureType > | inlinevirtual |
| getDefaults() const | DefaultParamHandler | |
| getIsotopeDistribution_(DoubleReal mass) const | FeatureFinderAlgorithmPicked< PeakType, FeatureType > | inlineprotected |
| getName() const | DefaultParamHandler | |
| getParameters() const | DefaultParamHandler | |
| getProductName() | FeatureFinderAlgorithmPicked< PeakType, FeatureType > | inlinestatic |
| getSubsections() const | DefaultParamHandler | |
| IndexPair typedef | FeatureFinderDefs | |
| IndexSet typedef | FeatureFinderDefs | |
| intensity_bins_ | FeatureFinderAlgorithmPicked< PeakType, FeatureType > | protected |
| intensity_mz_step_ | FeatureFinderAlgorithmPicked< PeakType, FeatureType > | protected |
| intensity_percentage_ | FeatureFinderAlgorithmPicked< PeakType, FeatureType > | protected |
| intensity_percentage_optional_ | FeatureFinderAlgorithmPicked< PeakType, FeatureType > | protected |
| intensity_rt_step_ | FeatureFinderAlgorithmPicked< PeakType, FeatureType > | protected |
| intensity_thresholds_ | FeatureFinderAlgorithmPicked< PeakType, FeatureType > | protected |
| intensityScore_(Size spectrum, Size peak) const | FeatureFinderAlgorithmPicked< PeakType, FeatureType > | inlineprotected |
| intensityScore_(Size rt_bin, Size mz_bin, DoubleReal intensity) const | FeatureFinderAlgorithmPicked< PeakType, FeatureType > | inlineprotected |
| IntensityType typedef | FeatureFinderAlgorithm< PeakType, FeatureType > | |
| intersection_(const Feature &f1, const Feature &f2) const | FeatureFinderAlgorithmPicked< PeakType, FeatureType > | inlineprotected |
| isotope_distributions_ | FeatureFinderAlgorithmPicked< PeakType, FeatureType > | protected |
| IsotopePattern typedef | FeatureFinderAlgorithmPicked< PeakType, FeatureType > | protected |
| isotopeScore_(const TheoreticalIsotopePattern &isotopes, IsotopePattern &pattern, bool consider_mz_distances) const | FeatureFinderAlgorithmPicked< PeakType, FeatureType > | inlineprotected |
| log_ | FeatureFinderAlgorithmPicked< PeakType, FeatureType > | mutableprotected |
| map_ | FeatureFinderAlgorithmPicked< PeakType, FeatureType > | protected |
| MapType typedef | FeatureFinderAlgorithmPicked< PeakType, FeatureType > | |
| mass_window_width_ | FeatureFinderAlgorithmPicked< PeakType, FeatureType > | protected |
| MassTrace typedef | FeatureFinderAlgorithmPicked< PeakType, FeatureType > | protected |
| MassTraces typedef | FeatureFinderAlgorithmPicked< PeakType, FeatureType > | protected |
| max_feature_intersection_ | FeatureFinderAlgorithmPicked< PeakType, FeatureType > | protected |
| max_missing_trace_peaks_ | FeatureFinderAlgorithmPicked< PeakType, FeatureType > | protected |
| max_rt_span_ | FeatureFinderAlgorithmPicked< PeakType, FeatureType > | protected |
| min_isotope_fit_ | FeatureFinderAlgorithmPicked< PeakType, FeatureType > | protected |
| min_rt_span_ | FeatureFinderAlgorithmPicked< PeakType, FeatureType > | protected |
| min_spectra_ | FeatureFinderAlgorithmPicked< PeakType, FeatureType > | protected |
| min_trace_score_ | FeatureFinderAlgorithmPicked< PeakType, FeatureType > | protected |
| nearest_(DoubleReal pos, const SpectrumType &spec, Size start) const | FeatureFinderAlgorithmPicked< PeakType, FeatureType > | inlineprotected |
| operator=(const FeatureFinderAlgorithmPicked &) | FeatureFinderAlgorithmPicked< PeakType, FeatureType > | private |
| OpenMS::DefaultParamHandler::operator=(const DefaultParamHandler &rhs) | DefaultParamHandler | virtual |
| operator==(const DefaultParamHandler &rhs) const | DefaultParamHandler | virtual |
| optional_fit_improvement_ | FeatureFinderAlgorithmPicked< PeakType, FeatureType > | protected |
| param_ | DefaultParamHandler | protected |
| pattern_tolerance_ | FeatureFinderAlgorithmPicked< PeakType, FeatureType > | protected |
| positionScore_(DoubleReal pos1, DoubleReal pos2, DoubleReal allowed_deviation) const | FeatureFinderAlgorithmPicked< PeakType, FeatureType > | inlineprotected |
| registerChildren() | FeatureFinderAlgorithm< PeakType, FeatureType > | static |
| reported_mz_ | FeatureFinderAlgorithmPicked< PeakType, FeatureType > | protected |
| run() | FeatureFinderAlgorithmPicked< PeakType, FeatureType > | inlinevirtual |
| Seed typedef | FeatureFinderAlgorithmPicked< PeakType, FeatureType > | protected |
| seeds_ | FeatureFinderAlgorithmPicked< PeakType, FeatureType > | protected |
| setData(const MapType &map, FeatureMapType &features, FeatureFinder &ff) | FeatureFinderAlgorithm< PeakType, FeatureType > | inline |
| setName(const String &name) | DefaultParamHandler | |
| setParameters(const Param ¶m) | DefaultParamHandler | |
| setSeeds(const FeatureMapType &seeds) | FeatureFinderAlgorithmPicked< PeakType, FeatureType > | inlinevirtual |
| slope_bound_ | FeatureFinderAlgorithmPicked< PeakType, FeatureType > | protected |
| SpectrumType typedef | FeatureFinderAlgorithmPicked< PeakType, FeatureType > | |
| subsections_ | DefaultParamHandler | protected |
| TheoreticalIsotopePattern typedef | FeatureFinderAlgorithmPicked< PeakType, FeatureType > | protected |
| trace_tolerance_ | FeatureFinderAlgorithmPicked< PeakType, FeatureType > | protected |
| UNUSED enum value | FeatureFinderDefs | |
| updateMembers_() | FeatureFinderAlgorithmPicked< PeakType, FeatureType > | inlineprotectedvirtual |
| USED enum value | FeatureFinderDefs | |
| warn_empty_defaults_ | DefaultParamHandler | protected |
| writeFeatureDebugInfo_(TraceFitter< PeakType > *fitter, const MassTraces &traces, const MassTraces &new_traces, bool feature_ok, const String error_msg, const DoubleReal final_score, const Int plot_nr, const PeakType &peak, const String path="debug/features/") | FeatureFinderAlgorithmPicked< PeakType, FeatureType > | inlineprotected |
| ~DefaultParamHandler() | DefaultParamHandler | virtual |
| ~FeatureFinderAlgorithm() | FeatureFinderAlgorithm< PeakType, FeatureType > | inlinevirtual |