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FeatureFinderAlgorithmPicked< PeakType, FeatureType > Member List

This is the complete list of members for FeatureFinderAlgorithmPicked< PeakType, FeatureType >, including all inherited members.

abort_(const Seed &seed, const String &reason)FeatureFinderAlgorithmPicked< PeakType, FeatureType >inlineprotected
abort_reasons_FeatureFinderAlgorithmPicked< PeakType, FeatureType >protected
aborts_FeatureFinderAlgorithmPicked< PeakType, FeatureType >protected
ChargedIndexSet typedefFeatureFinderDefs
check_defaults_DefaultParamHandlerprotected
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 typedefFeatureFinderAlgorithm< 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_DefaultParamHandlerprotected
defaultsToParam_()DefaultParamHandlerprotected
error_name_DefaultParamHandlerprotected
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 typedefFeatureFinderAlgorithmPicked< PeakType, FeatureType >
features_FeatureFinderAlgorithm< PeakType, FeatureType >protected
ff_FeatureFinderAlgorithm< PeakType, FeatureType >protected
findBestIsotopeFit_(const Seed &center, 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 nameFeatureFinderDefs
FloatDataArrays typedefFeatureFinderAlgorithmPicked< 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 typedefFeatureFinderDefs
IndexSet typedefFeatureFinderDefs
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 typedefFeatureFinderAlgorithm< PeakType, FeatureType >
intersection_(const Feature &f1, const Feature &f2) const FeatureFinderAlgorithmPicked< PeakType, FeatureType >inlineprotected
isotope_distributions_FeatureFinderAlgorithmPicked< PeakType, FeatureType >protected
IsotopePattern typedefFeatureFinderAlgorithmPicked< 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 typedefFeatureFinderAlgorithmPicked< PeakType, FeatureType >
mass_window_width_FeatureFinderAlgorithmPicked< PeakType, FeatureType >protected
MassTrace typedefFeatureFinderAlgorithmPicked< PeakType, FeatureType >protected
MassTraces typedefFeatureFinderAlgorithmPicked< 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)DefaultParamHandlervirtual
operator==(const DefaultParamHandler &rhs) const DefaultParamHandlervirtual
optional_fit_improvement_FeatureFinderAlgorithmPicked< PeakType, FeatureType >protected
param_DefaultParamHandlerprotected
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 typedefFeatureFinderAlgorithmPicked< 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 &param)DefaultParamHandler
setSeeds(const FeatureMapType &seeds)FeatureFinderAlgorithmPicked< PeakType, FeatureType >inlinevirtual
slope_bound_FeatureFinderAlgorithmPicked< PeakType, FeatureType >protected
SpectrumType typedefFeatureFinderAlgorithmPicked< PeakType, FeatureType >
subsections_DefaultParamHandlerprotected
TheoreticalIsotopePattern typedefFeatureFinderAlgorithmPicked< PeakType, FeatureType >protected
trace_tolerance_FeatureFinderAlgorithmPicked< PeakType, FeatureType >protected
UNUSED enum valueFeatureFinderDefs
updateMembers_()FeatureFinderAlgorithmPicked< PeakType, FeatureType >inlineprotectedvirtual
USED enum valueFeatureFinderDefs
warn_empty_defaults_DefaultParamHandlerprotected
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()DefaultParamHandlervirtual
~FeatureFinderAlgorithm()FeatureFinderAlgorithm< PeakType, FeatureType >inlinevirtual

OpenMS / TOPP release 1.11.1 Documentation generated on Thu Nov 14 2013 11:19:34 using doxygen 1.8.5