OpenMS  3.0.0
FLASHDeconvAlgorithm Member List

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

addExcludedMonoMass(const double m)FLASHDeconvAlgorithm
allowed_iso_error_FLASHDeconvAlgorithmprivate
avg_FLASHDeconvAlgorithmprivate
bin_offsets_FLASHDeconvAlgorithmprivate
bin_width_FLASHDeconvAlgorithmprivate
calculateAveragine(const bool use_RNA_averagine)FLASHDeconvAlgorithm
charge_decoy_FLASHDeconvAlgorithmprivatestatic
check_defaults_DefaultParamHandlerprotected
clearExcludedMonoMasses()FLASHDeconvAlgorithm
current_max_charge_FLASHDeconvAlgorithmprivate
current_max_mass_FLASHDeconvAlgorithmprivate
current_min_charge_FLASHDeconvAlgorithmprivate
current_min_mass_FLASHDeconvAlgorithmprivate
deconvolved_spectrum_FLASHDeconvAlgorithmprivate
decoy_deconvolved_spectrum_FLASHDeconvAlgorithmprivate
decoy_run_flag_FLASHDeconvAlgorithmprivate
DefaultParamHandler(const String &name)DefaultParamHandler
DefaultParamHandler(const DefaultParamHandler &rhs)DefaultParamHandler
DefaultParamHandler()DefaultParamHandlerprivate
defaults_DefaultParamHandlerprotected
defaultsToParam_()DefaultParamHandlerprotected
error_name_DefaultParamHandlerprotected
excluded_mass_bins_FLASHDeconvAlgorithmprivate
excluded_masses_FLASHDeconvAlgorithmprivate
filter_FLASHDeconvAlgorithmprivate
filterMassBins_(const std::vector< float > &mass_intensities)FLASHDeconvAlgorithmprivate
filterPeakGroupsByIsotopeCosine_(const int current_max_mass_count)FLASHDeconvAlgorithmprivate
FLASHDeconvAlgorithm()FLASHDeconvAlgorithm
FLASHDeconvAlgorithm(const FLASHDeconvAlgorithm &)=defaultFLASHDeconvAlgorithm
FLASHDeconvAlgorithm(FLASHDeconvAlgorithm &&other)=defaultFLASHDeconvAlgorithm
generatePeakGroupsFromSpectrum_()FLASHDeconvAlgorithmprivate
getAveragine()FLASHDeconvAlgorithm
getBinNumber_(const double value, const double min_value, const double bin_width)FLASHDeconvAlgorithmprivatestatic
getBinValue_(const Size bin, const double min_value, const 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)FLASHDeconvAlgorithmstatic
getDeconvolvedSpectrum()FLASHDeconvAlgorithm
getDecoyDeconvolvedSpectrum()FLASHDeconvAlgorithm
getDefaults() constDefaultParamHandler
getIsotopeCosineAndDetermineIsotopeIndex(const double mono_mass, const std::vector< float > &per_isotope_intensities, int &offset, int &second_best_iso_offset, const PrecalculatedAveragine &avg, int window_width=-1, int allowed_iso_error=1)FLASHDeconvAlgorithmstatic
getName() constDefaultParamHandler
getNominalMass(const double mass)FLASHDeconvAlgorithmstatic
getParameters() constDefaultParamHandler
getSubsections() constDefaultParamHandler
harmonic_bin_offset_matrix_FLASHDeconvAlgorithmprivate
harmonic_charges_FLASHDeconvAlgorithmprivate
harmonic_filter_matrix_FLASHDeconvAlgorithmprivate
intensity_threshold_FLASHDeconvAlgorithmprivate
is_positive_FLASHDeconvAlgorithmprivate
iso_da_distance_FLASHDeconvAlgorithmprivate
isolation_window_size_FLASHDeconvAlgorithmprivate
isotope_decoy_FLASHDeconvAlgorithmprivatestatic
log_mz_peaks_FLASHDeconvAlgorithmprivate
LogMzPeak typedefFLASHDeconvAlgorithm
low_charge_FLASHDeconvAlgorithmprivate
mass_bin_min_value_FLASHDeconvAlgorithmprivate
mass_bins_FLASHDeconvAlgorithmprivate
max_abs_charge_FLASHDeconvAlgorithmprivate
max_mass_FLASHDeconvAlgorithmprivate
max_mz_FLASHDeconvAlgorithmprivate
max_peak_count_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_FLASHDeconvAlgorithmprivate
ms_level_FLASHDeconvAlgorithmprivate
mz_bin_min_value_FLASHDeconvAlgorithmprivate
mz_bins_FLASHDeconvAlgorithmprivate
mz_bins_for_edge_effect_FLASHDeconvAlgorithmprivate
noise_decoy_FLASHDeconvAlgorithmprivatestatic
operator=(const 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, const int scan_number, const bool write_detail, const std::map< int, std::vector< std::vector< double >>> &precursor_map_for_FLASHIda)FLASHDeconvAlgorithm
PrecalculatedAveragine typedefFLASHDeconvAlgorithm
prev_mass_bins_ms1_FLASHDeconvAlgorithmprivate
prev_mass_bins_ms2_FLASHDeconvAlgorithmprivate
prev_rts_ms1_FLASHDeconvAlgorithmprivate
prev_rts_ms2_FLASHDeconvAlgorithmprivate
registerPrecursor(const std::vector< DeconvolvedSpectrum > &survey_scans, const std::map< int, std::vector< std::vector< double >>> &precursor_map_for_real_time_acquisition)FLASHDeconvAlgorithmprivate
removeHarmonicsPeakGroups_(DeconvolvedSpectrum &dpec)FLASHDeconvAlgorithmprivate
removeOverlappingPeakGroups_(DeconvolvedSpectrum &dpec, const double tol, const int iso_length=1)FLASHDeconvAlgorithmprivate
scoreAndFilterPeakGroups_()FLASHDeconvAlgorithmprivate
setAveragine(const PrecalculatedAveragine &avg)FLASHDeconvAlgorithm
setDecoyFlag(int flag)FLASHDeconvAlgorithm
setFilters_()FLASHDeconvAlgorithmprivate
setName(const String &name)DefaultParamHandler
setParameters(const Param &param)DefaultParamHandler
setTargetMasses(const std::vector< double > &masses)FLASHDeconvAlgorithm
subsections_DefaultParamHandlerprotected
target_mass_bins_FLASHDeconvAlgorithmprivate
target_masses_FLASHDeconvAlgorithmprivate
tolerance_FLASHDeconvAlgorithmprivate
unionPrevMassBins_()FLASHDeconvAlgorithmprivate
updateCandidateMassBins_(std::vector< float > &mass_intensities, const std::vector< float > &mz_intensities)FLASHDeconvAlgorithmprivate
updateLogMzPeaks_(const MSSpectrum *spec)FLASHDeconvAlgorithmprivate
updateMassBins_(const std::vector< float > &mz_intensities)FLASHDeconvAlgorithmprivate
updateMembers_() overrideFLASHDeconvAlgorithmprotectedvirtual
updateMzBins_(const Size bin_number, std::vector< float > &mz_bin_intensities)FLASHDeconvAlgorithmprivate
warn_empty_defaults_DefaultParamHandlerprotected
write_detail_FLASHDeconvAlgorithmprivate
writeParametersToMetaValues(const Param &write_this, MetaInfoInterface &write_here, const String &key_prefix="")DefaultParamHandlerstatic
~DefaultParamHandler()DefaultParamHandlervirtual