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FLASHDeconvAlgorithm Member List

This is the complete list of members for FLASHDeconvAlgorithm, including all inherited members.

addMZsToExcludsionList(const DeconvolvedSpectrum &dspec, std::unordered_set< double > &excluded_mzs)FLASHDeconvAlgorithmstatic
allowed_iso_error_FLASHDeconvAlgorithmprivate
avg_FLASHDeconvAlgorithmprivate
bin_mul_factors_FLASHDeconvAlgorithmprivate
bin_offsets_FLASHDeconvAlgorithmprivate
calculateAveragine(bool use_RNA_averagine)FLASHDeconvAlgorithm
check_defaults_DefaultParamHandlerprotected
current_max_charge_FLASHDeconvAlgorithmprivate
current_max_mass_FLASHDeconvAlgorithmprivate
current_min_mass_FLASHDeconvAlgorithmprivate
deconvolved_spectrum_FLASHDeconvAlgorithmprivate
DefaultParamHandler(const String &name)DefaultParamHandler
DefaultParamHandler(const DefaultParamHandler &rhs)DefaultParamHandler
DefaultParamHandler()DefaultParamHandlerprivate
defaults_DefaultParamHandlerprotected
defaultsToParam_()DefaultParamHandlerprotected
error_name_DefaultParamHandlerprotected
excluded_masses_FLASHDeconvAlgorithmprivate
excluded_peak_mzs_FLASHDeconvAlgorithmprivate
filter_FLASHDeconvAlgorithmprivate
filterMassBins_(const std::vector< float > &mass_intensities)FLASHDeconvAlgorithmprivate
FLASHDeconvAlgorithm()FLASHDeconvAlgorithm
FLASHDeconvAlgorithm(const FLASHDeconvAlgorithm &)=defaultFLASHDeconvAlgorithm
FLASHDeconvAlgorithm(FLASHDeconvAlgorithm &&other)=defaultFLASHDeconvAlgorithm
generatePeakGroupsFromSpectrum_()FLASHDeconvAlgorithmprivate
getAveragine()FLASHDeconvAlgorithm
getBinNumber_(double value, double min_value, double bin_mul_factor)FLASHDeconvAlgorithmprivatestatic
getBinValue_(Size bin, double min_value, double bin_mul_factor)FLASHDeconvAlgorithmprivatestatic
getCandidatePeakGroups_(const Matrix< int > &per_mass_abs_charge_ranges)FLASHDeconvAlgorithmprivate
getCosine(const std::vector< float > &a, int a_start, int a_end, const IsotopeDistribution &b, int b_size, int offset, int min_iso_size)FLASHDeconvAlgorithmstatic
getDeconvolvedSpectrum()FLASHDeconvAlgorithm
getDefaults() constDefaultParamHandler
getIsotopeCosineAndDetermineIsotopeIndex(double mono_mass, const std::vector< float > &per_isotope_intensities, int &offset, const PrecalculatedAveragine &avg, int iso_int_shift=0, int window_width=-1, int allowed_iso_error_for_second_best_cos=0, PeakGroup::TargetDummyType target_dummy_type=PeakGroup::TargetDummyType::target)FLASHDeconvAlgorithmstatic
getMassFromMassBin_(Size mass_bin, double bin_mul_factor) constFLASHDeconvAlgorithmprivate
getMzFromMzBin_(Size mass_bin, double bin_mul_factor) constFLASHDeconvAlgorithmprivate
getName() constDefaultParamHandler
getNominalMass(double mass)FLASHDeconvAlgorithmstatic
getParameters() constDefaultParamHandler
getSubsections() constDefaultParamHandler
harmonic_bin_offset_matrix_FLASHDeconvAlgorithmprivate
harmonic_filter_matrix_FLASHDeconvAlgorithmprivate
intensity_threshold_FLASHDeconvAlgorithmprivate
is_positive_FLASHDeconvAlgorithmprivate
iso_da_distance_FLASHDeconvAlgorithmprivate
isolation_window_size_FLASHDeconvAlgorithmprivate
log_mz_peaks_FLASHDeconvAlgorithmprivate
LogMzPeak typedefFLASHDeconvAlgorithm
mass_bin_min_value_FLASHDeconvAlgorithmprivate
mass_bins_FLASHDeconvAlgorithmprivate
max_abs_charge_FLASHDeconvAlgorithmprivate
max_mass_FLASHDeconvAlgorithmprivate
max_mz_FLASHDeconvAlgorithmprivate
max_rt_FLASHDeconvAlgorithmprivate
min_abs_charge_FLASHDeconvAlgorithmprivate
min_iso_size_FLASHDeconvAlgorithmprivatestatic
min_isotope_cosine_FLASHDeconvAlgorithmprivate
min_mass_FLASHDeconvAlgorithmprivate
min_mz_FLASHDeconvAlgorithmprivate
min_rt_FLASHDeconvAlgorithmprivate
min_support_peak_count_FLASHDeconvAlgorithmprivatestatic
ms_level_FLASHDeconvAlgorithmprivate
mz_bin_min_value_FLASHDeconvAlgorithmprivate
mz_bins_FLASHDeconvAlgorithmprivate
operator=(const FLASHDeconvAlgorithm &fd)=defaultFLASHDeconvAlgorithm
operator=(FLASHDeconvAlgorithm &&fd)=defaultFLASHDeconvAlgorithm
OpenMS::DefaultParamHandler::operator=(const DefaultParamHandler &rhs)DefaultParamHandler
operator==(const DefaultParamHandler &rhs) constDefaultParamHandlervirtual
param_DefaultParamHandlerprotected
performSpectrumDeconvolution(const MSSpectrum &spec, const std::vector< DeconvolvedSpectrum > &survey_scans, int scan_number, const std::map< int, std::vector< std::vector< float >>> &precursor_map_for_FLASHIda)FLASHDeconvAlgorithm
PrecalculatedAveragine typedefFLASHDeconvAlgorithm
previously_deconved_mass_bins_for_dummy_FLASHDeconvAlgorithmprivate
previously_deconved_mono_masses_for_dummy_FLASHDeconvAlgorithmprivate
registerPrecursor_(const std::vector< DeconvolvedSpectrum > &survey_scans, const std::map< int, std::vector< std::vector< float >>> &precursor_map_for_real_time_acquisition)FLASHDeconvAlgorithmprivate
removeChargeErrorPeakGroups_(DeconvolvedSpectrum &dspec) constFLASHDeconvAlgorithmprivate
removeOverlappingPeakGroups_(DeconvolvedSpectrum &dspec, double tol)FLASHDeconvAlgorithmprivate
scoreAndFilterPeakGroups_()FLASHDeconvAlgorithmprivate
setAveragine(const PrecalculatedAveragine &avg)FLASHDeconvAlgorithm
setFilters_()FLASHDeconvAlgorithmprivate
setName(const String &name)DefaultParamHandler
setParameters(const Param &param)DefaultParamHandler
setTargetDummyType(PeakGroup::TargetDummyType target_dummy_type, DeconvolvedSpectrum &target_dspec_for_dummy_calcualtion)FLASHDeconvAlgorithm
setTargetMasses(const std::vector< double > &masses, bool exclude=false)FLASHDeconvAlgorithm
subsections_DefaultParamHandlerprotected
target_dspec_for_dummy_calcualtion_FLASHDeconvAlgorithmprivate
target_dummy_type_FLASHDeconvAlgorithmprivate
target_mass_bins_FLASHDeconvAlgorithmprivate
target_mono_masses_FLASHDeconvAlgorithmprivate
tolerance_FLASHDeconvAlgorithmprivate
updateCandidateMassBins_(std::vector< float > &mass_intensities, const std::vector< float > &mz_intensities)FLASHDeconvAlgorithmprivate
updateLogMzPeaks_()FLASHDeconvAlgorithmprivate
updateMassBins_(const std::vector< float > &mz_intensities)FLASHDeconvAlgorithmprivate
updateMembers_() overrideFLASHDeconvAlgorithmprotectedvirtual
updateMzBins_(Size bin_number, std::vector< float > &mz_bin_intensities)FLASHDeconvAlgorithmprivate
warn_empty_defaults_DefaultParamHandlerprotected
writeParametersToMetaValues(const Param &write_this, MetaInfoInterface &write_here, const String &key_prefix="")DefaultParamHandlerstatic
~DefaultParamHandler()DefaultParamHandlervirtual
~FLASHDeconvAlgorithm()=defaultFLASHDeconvAlgorithm