OpenMS  3.0.0
FLASHDeconvAlgorithm Member List

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

allowed_iso_error_FLASHDeconvAlgorithmprivate
avg_FLASHDeconvAlgorithmprivate
bin_offsets_FLASHDeconvAlgorithmprivate
bin_width_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
decoy_flag_FLASHDeconvAlgorithmprivate
DefaultParamHandler(const String &name)DefaultParamHandler
DefaultParamHandler(const DefaultParamHandler &rhs)DefaultParamHandler
defaults_DefaultParamHandlerprotected
defaultsToParam_()DefaultParamHandlerprotected
error_name_DefaultParamHandlerprotected
excluded_integer_mzs_FLASHDeconvAlgorithmprivate
excluded_masses_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_width)FLASHDeconvAlgorithmprivatestatic
getBinValue_(Size bin, double min_value, double bin_width)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 window_width=-1, int allowed_iso_error_for_second_best_cos=0, PeakGroup::DecoyFlag decoyFlag=PeakGroup::DecoyFlag::target)FLASHDeconvAlgorithmstatic
getMassFromMassBin_(Size mass_bin, double bin_width) constFLASHDeconvAlgorithmprivate
getMzFromMzBin_(Size mass_bin, double bin_width) 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)DefaultParamHandlervirtual
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_decoyFLASHDeconvAlgorithmprivate
previously_deconved_mono_masses_for_decoyFLASHDeconvAlgorithmprivate
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)FLASHDeconvAlgorithmprivate
removeOverlappingPeakGroups_(DeconvolvedSpectrum &dspec)FLASHDeconvAlgorithmprivatestatic
scoreAndFilterPeakGroups_()FLASHDeconvAlgorithmprivate
setAveragine(const PrecalculatedAveragine &avg)FLASHDeconvAlgorithm
setDecoyFlag(PeakGroup::DecoyFlag flag, FLASHDeconvAlgorithm &targetFD)FLASHDeconvAlgorithm
setFilters_()FLASHDeconvAlgorithmprivate
setName(const String &name)DefaultParamHandler
setParameters(const Param &param)DefaultParamHandler
setTargetMasses(const std::vector< double > &masses, bool exclude=false)FLASHDeconvAlgorithm
subsections_DefaultParamHandlerprotected
target_mass_bins_FLASHDeconvAlgorithmprivate
target_mono_masses_FLASHDeconvAlgorithmprivate
targetFD_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