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 |