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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 > [inline, protected]
abort_reasons_FeatureFinderAlgorithmPicked< PeakType, FeatureType > [protected]
aborts_FeatureFinderAlgorithmPicked< PeakType, FeatureType > [protected]
ChargedIndexSet typedefFeatureFinderDefs
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 > [inline, protected]
chooseTraceFitter_(double &tau)FeatureFinderAlgorithmPicked< PeakType, FeatureType > [inline, protected]
CoordinateType typedefFeatureFinderAlgorithm< PeakType, FeatureType >
create()FeatureFinderAlgorithmPicked< PeakType, FeatureType > [inline, static]
cropFeature_(TraceFitter< PeakType > *fitter, const MassTraces &traces, MassTraces &new_traces)FeatureFinderAlgorithmPicked< PeakType, FeatureType > [inline, protected]
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 > [inline, protected]
extendMassTraces_(const IsotopePattern &pattern, MassTraces &traces, Size meta_index_overall) const FeatureFinderAlgorithmPicked< PeakType, FeatureType > [inline, protected]
FeatureFinderAlgorithm()FeatureFinderAlgorithm< PeakType, FeatureType > [inline]
FeatureFinderAlgorithmPicked()FeatureFinderAlgorithmPicked< PeakType, FeatureType > [inline]
FeatureFinderAlgorithmPicked(const FeatureFinderAlgorithmPicked &)FeatureFinderAlgorithmPicked< PeakType, FeatureType > [private]
FeatureMapType typedefFeatureFinderAlgorithmPicked< PeakType, FeatureType >
OpenMS::FeatureFinderAlgorithm::FeatureMapType typedefFeatureFinderAlgorithm< 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 > [inline, protected]
findIsotope_(DoubleReal pos, Size spectrum_index, IsotopePattern &pattern, Size pattern_index, Size &peak_index) const FeatureFinderAlgorithmPicked< PeakType, FeatureType > [inline, protected]
Flag enum nameFeatureFinderDefs
FloatDataArrays typedefFeatureFinderAlgorithmPicked< PeakType, FeatureType >
getDefaultParameters() const FeatureFinderAlgorithm< PeakType, FeatureType > [inline, virtual]
getDefaults() const DefaultParamHandler
getIsotopeDistribution_(DoubleReal mass) const FeatureFinderAlgorithmPicked< PeakType, FeatureType > [inline, protected]
getName() const DefaultParamHandler
getParameters() const DefaultParamHandler
getProductName()FeatureFinderAlgorithmPicked< PeakType, FeatureType > [inline, static]
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 > [inline, protected]
intensityScore_(Size rt_bin, Size mz_bin, DoubleReal intensity) const FeatureFinderAlgorithmPicked< PeakType, FeatureType > [inline, protected]
IntensityType typedefFeatureFinderAlgorithm< PeakType, FeatureType >
intersection_(const Feature &f1, const Feature &f2) const FeatureFinderAlgorithmPicked< PeakType, FeatureType > [inline, protected]
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 > [inline, protected]
log_FeatureFinderAlgorithmPicked< PeakType, FeatureType > [mutable, protected]
map_FeatureFinderAlgorithmPicked< PeakType, FeatureType > [protected]
OpenMS::FeatureFinderAlgorithm::map_FeatureFinderAlgorithm< PeakType, FeatureType > [protected]
MapType typedefFeatureFinderAlgorithmPicked< PeakType, FeatureType >
OpenMS::FeatureFinderAlgorithm::MapType typedefFeatureFinderAlgorithm< 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 > [inline, protected]
operator=(const FeatureFinderAlgorithmPicked &)FeatureFinderAlgorithmPicked< PeakType, FeatureType > [private]
OpenMS::FeatureFinderAlgorithm::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 > [inline, protected]
registerChildren()FeatureFinderAlgorithm< PeakType, FeatureType > [static]
reported_mz_FeatureFinderAlgorithmPicked< PeakType, FeatureType > [protected]
run()FeatureFinderAlgorithmPicked< PeakType, FeatureType > [inline, virtual]
OpenMS::FeatureFinderAlgorithm::run()=0FeatureFinderAlgorithm< PeakType, FeatureType > [pure virtual]
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 > [inline, virtual]
OpenMS::FeatureFinderAlgorithm::setSeeds(const FeatureMapType &seeds)FeatureFinderAlgorithm< PeakType, FeatureType > [inline, virtual]
slope_bound_FeatureFinderAlgorithmPicked< PeakType, FeatureType > [protected]
SpectrumType typedefFeatureFinderAlgorithmPicked< PeakType, FeatureType >
subsections_DefaultParamHandler [protected]
TheoreticalIsotopePattern typedefFeatureFinderAlgorithmPicked< PeakType, FeatureType > [protected]
trace_tolerance_FeatureFinderAlgorithmPicked< PeakType, FeatureType > [protected]
UNUSED enum valueFeatureFinderDefs
updateMembers_()FeatureFinderAlgorithmPicked< PeakType, FeatureType > [inline, protected, virtual]
OpenMS::FeatureFinderAlgorithm::updateMembers_()DefaultParamHandler [protected, virtual]
USED enum valueFeatureFinderDefs
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 > [inline, protected]
~DefaultParamHandler()DefaultParamHandler [virtual]
~FeatureFinderAlgorithm()FeatureFinderAlgorithm< PeakType, FeatureType > [inline, virtual]
OpenMS / TOPP release 1.10.0 Documentation generated on Thu Mar 7 2013 09:42:56 using doxygen 1.7.1