abort_(const String &reason) | FeatureFinderAlgorithmPicked | [inline, protected] |
aborts_ | FeatureFinderAlgorithmPicked | [protected] |
ChargedIndexSet typedef | FeatureFinderDefs | |
check_defaults_ | DefaultParamHandler | [protected] |
CoordinateType typedef | FeatureFinderAlgorithmPicked | |
create() | FeatureFinderAlgorithmPicked | [inline, static] |
DefaultParamHandler(const String &name) | DefaultParamHandler | |
DefaultParamHandler(const DefaultParamHandler &rhs) | DefaultParamHandler | |
defaults_ | DefaultParamHandler | [protected] |
defaultsToParam_() | DefaultParamHandler | [protected] |
error_name_ | DefaultParamHandler | [protected] |
extendMassTrace_(MassTrace &trace, Int spectrum_index, DoubleReal mz, bool inc_rt, DoubleReal min_rt=0.0, DoubleReal max_rt=0.0) | FeatureFinderAlgorithmPicked | [inline, protected] |
extendMassTraces_(const IsotopePattern &pattern, MassTraces &traces) | FeatureFinderAlgorithmPicked | [inline, protected] |
FactoryProduct(const String &name) | FactoryProduct | |
FactoryProduct(const FactoryProduct &source) | FactoryProduct | |
FeatureFinderAlgorithm() | FeatureFinderAlgorithm | [inline] |
FeatureFinderAlgorithmPicked() | FeatureFinderAlgorithmPicked | [inline] |
FeatureFinderAlgorithmPicked(const FeatureFinderAlgorithmPicked &) | FeatureFinderAlgorithmPicked | [private] |
FeatureMapType typedef | FeatureFinderAlgorithm | |
features_ | FeatureFinderAlgorithm | [protected] |
ff_ | FeatureFinderAlgorithm | [protected] |
findBestIsotopeFit_(const Seed ¢er, UInt charge, IsotopePattern &best_pattern) | FeatureFinderAlgorithmPicked | [inline, protected] |
findIsotope_(CoordinateType pos, UInt spectrum_index, IsotopePattern &pattern, UInt pattern_index, bool debug, UInt &peak_index) | FeatureFinderAlgorithmPicked | [inline, protected] |
Flag enum name | FeatureFinderDefs | |
gaussDF_(const gsl_vector *param, void *data, gsl_matrix *J) | FeatureFinderAlgorithmPicked | [inline, protected, static] |
gaussF_(const gsl_vector *param, void *data, gsl_vector *f) | FeatureFinderAlgorithmPicked | [inline, protected, static] |
gaussFDF_(const gsl_vector *param, void *data, gsl_vector *f, gsl_matrix *J) | FeatureFinderAlgorithmPicked | [inline, protected, static] |
getDefaultParameters() const | FeatureFinderAlgorithm | [inline, virtual] |
getDefaults() const | DefaultParamHandler | |
getIsotopeDistribution_(DoubleReal mass) | FeatureFinderAlgorithmPicked | [inline, protected] |
getName() const | DefaultParamHandler | |
getParameters() const | DefaultParamHandler | |
getProductName() | FeatureFinderAlgorithmPicked | [inline, static] |
getSubsections() const | DefaultParamHandler | |
IndexPair typedef | FeatureFinderDefs | |
IndexSet typedef | FeatureFinderDefs | |
info_ | FeatureFinderAlgorithmPicked | [protected] |
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_(DoubleReal intensity, UInt spectrum, UInt peak) | FeatureFinderAlgorithmPicked | [inline, protected] |
intensityScore_(UInt rt_bin, UInt mz_bin, DoubleReal intensity) | FeatureFinderAlgorithmPicked | [inline, protected] |
IntensityType typedef | FeatureFinderAlgorithmPicked | |
intersection_(const Feature &f1, const Feature &f2) | FeatureFinderAlgorithmPicked | [inline, protected] |
isotope_distributions_ | FeatureFinderAlgorithmPicked | [protected] |
isotopeScore_(const TheoreticalIsotopePattern &isotopes, IsotopePattern &pattern, bool consider_mz_distances, bool debug) | FeatureFinderAlgorithmPicked | [inline, protected] |
log_ | FeatureFinderAlgorithmPicked | [protected] |
map_ | FeatureFinderAlgorithm | [protected] |
MapType typedef | FeatureFinderAlgorithmPicked | |
mass_window_width_ | FeatureFinderAlgorithmPicked | [protected] |
max_missing_trace_peaks_ | FeatureFinderAlgorithmPicked | [protected] |
min_isotope_fit_ | FeatureFinderAlgorithmPicked | [protected] |
min_spectra_ | FeatureFinderAlgorithmPicked | [protected] |
min_trace_score_ | FeatureFinderAlgorithmPicked | [protected] |
nearest_(CoordinateType pos, const SpectrumType &spec, UInt start) const | FeatureFinderAlgorithmPicked | [inline, protected] |
operator=(const FeatureFinderAlgorithmPicked &) | FeatureFinderAlgorithmPicked | [private] |
OpenMS::FactoryProduct::operator=(const FactoryProduct &source) | FactoryProduct | [virtual] |
OpenMS::DefaultParamHandler::operator=(const DefaultParamHandler &rhs) | DefaultParamHandler | [virtual] |
operator==(const FactoryProduct &rhs) const | FactoryProduct | [virtual] |
OpenMS::DefaultParamHandler::operator==(const DefaultParamHandler &rhs) const | DefaultParamHandler | [virtual] |
optional_fit_improvement_ | FeatureFinderAlgorithmPicked | [protected] |
param_ | DefaultParamHandler | [protected] |
pattern_tolerance_ | FeatureFinderAlgorithmPicked | [protected] |
positionScore_(CoordinateType pos1, CoordinateType pos2, DoubleReal allowed_deviation) const | FeatureFinderAlgorithmPicked | [inline, protected] |
registerChildren() | FeatureFinderAlgorithm | [inline, static] |
run() | FeatureFinderAlgorithmPicked | [inline, virtual] |
setData(const MapType &map, FeatureMapType &features, FeatureFinder &ff) | FeatureFinderAlgorithm | [inline] |
setName(const String &name) | DefaultParamHandler | |
setParameters(const Param ¶m) | DefaultParamHandler | |
slope_bound_ | FeatureFinderAlgorithmPicked | [protected] |
SpectrumType typedef | FeatureFinderAlgorithmPicked | |
subsections_ | DefaultParamHandler | [protected] |
trace_tolerance_ | FeatureFinderAlgorithmPicked | [protected] |
UNUSED enum value | FeatureFinderDefs | |
updateMembers_() | FeatureFinderAlgorithmPicked | [inline, protected, virtual] |
USED enum value | FeatureFinderDefs | |
~DefaultParamHandler() | DefaultParamHandler | [virtual] |
~FeatureFinderAlgorithm() | FeatureFinderAlgorithm | [inline, virtual] |