SpectralDeconvolution Member List

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

allowed_iso_error_	SpectralDeconvolution	private
avg_	SpectralDeconvolution	private
bin_mul_factors_	SpectralDeconvolution	private
bin_offsets_	SpectralDeconvolution	private
calculateAveragine(bool use_RNA_averagine)	SpectralDeconvolution
check_defaults_	DefaultParamHandler	protected
current_max_charge_	SpectralDeconvolution	private
current_max_mass_	SpectralDeconvolution	private
current_min_mass_	SpectralDeconvolution	private
deconvolved_spectrum_	SpectralDeconvolution	private
DefaultParamHandler(const String &name)	DefaultParamHandler
DefaultParamHandler(const DefaultParamHandler &rhs)	DefaultParamHandler
DefaultParamHandler()	DefaultParamHandler	private
defaults_	DefaultParamHandler	protected
defaultsToParam_()	DefaultParamHandler	protected
error_name_	DefaultParamHandler	protected
excluded_masses_	SpectralDeconvolution	private
filter_	SpectralDeconvolution	private
filterMassBins_(const std::vector< float > &mass_intensities)	SpectralDeconvolution	private
generatePeakGroupsFromSpectrum_()	SpectralDeconvolution	private
getAveragine()	SpectralDeconvolution
getBinNumber_(double value, double min_value, double bin_mul_factor)	SpectralDeconvolution	privatestatic
getBinValue_(Size bin, double min_value, double bin_mul_factor)	SpectralDeconvolution	privatestatic
getCandidatePeakGroups_(const Matrix< int > &per_mass_abs_charge_ranges)	SpectralDeconvolution	private
getCosine(const std::vector< float > &a, int a_start, int a_end, const IsotopeDistribution &b, int offset, int min_iso_size, bool decoy=false)	SpectralDeconvolution	static
getDeconvolvedSpectrum()	SpectralDeconvolution
getDefaults() const	DefaultParamHandler
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::TargetDecoyType target_decoy_type=PeakGroup::TargetDecoyType::target)	SpectralDeconvolution	static
getMassFromMassBin_(Size mass_bin, double bin_mul_factor) const	SpectralDeconvolution	private
getMzFromMzBin_(Size mass_bin, double bin_mul_factor) const	SpectralDeconvolution	private
getName() const	DefaultParamHandler
getNominalMass(double mass)	SpectralDeconvolution	static
getParameters() const	DefaultParamHandler
getSubsections() const	DefaultParamHandler
harmonic_bin_offset_matrix_	SpectralDeconvolution	private
harmonic_filter_matrix_	SpectralDeconvolution	private
is_positive_	SpectralDeconvolution	private
iso_da_distance_	SpectralDeconvolution	private
log_mz_peaks_	SpectralDeconvolution	private
LogMzPeak typedef	SpectralDeconvolution
mass_bin_min_value_	SpectralDeconvolution	private
mass_bins_	SpectralDeconvolution	private
max_abs_charge_	SpectralDeconvolution	private
max_mass_	SpectralDeconvolution	private
max_qvalue_	SpectralDeconvolution	private
min_abs_charge_	SpectralDeconvolution	private
min_iso_size_	SpectralDeconvolution	privatestatic
min_isotope_cosine_	SpectralDeconvolution	private
min_mass_	SpectralDeconvolution	private
min_snr_	SpectralDeconvolution	private
min_support_peak_count_	SpectralDeconvolution	privatestatic
ms_level_	SpectralDeconvolution	private
mz_bin_min_value_	SpectralDeconvolution	private
mz_bins_	SpectralDeconvolution	private
operator=(const SpectralDeconvolution &fd)=default	SpectralDeconvolution
operator=(SpectralDeconvolution &&fd)=default	SpectralDeconvolution
OpenMS::DefaultParamHandler::operator=(const DefaultParamHandler &rhs)	DefaultParamHandler
operator==(const DefaultParamHandler &rhs) const	DefaultParamHandler	virtual
param_	DefaultParamHandler	protected
performSpectrumDeconvolution(const MSSpectrum &spec, int scan_number, const PeakGroup &precursor_peak_group)	SpectralDeconvolution
PrecalculatedAveragine typedef	SpectralDeconvolution
previously_deconved_mass_bins_for_decoy_	SpectralDeconvolution	private
previously_deconved_mono_masses_for_decoy_	SpectralDeconvolution	private
removeChargeErrorPeakGroups_(DeconvolvedSpectrum &dspec, const PeakGroup::TargetDecoyType &target_decoy_type) const	SpectralDeconvolution	private
removeExcludedMasses_(DeconvolvedSpectrum &dspec) const	SpectralDeconvolution	private
removeOverlappingPeakGroups(DeconvolvedSpectrum &dspec, double tol, PeakGroup::TargetDecoyType target_decoy_type=PeakGroup::TargetDecoyType::target)	SpectralDeconvolution	static
scoreAndFilterPeakGroups_()	SpectralDeconvolution	private
setAveragine(const PrecalculatedAveragine &avg)	SpectralDeconvolution
setFilters_()	SpectralDeconvolution	private
setName(const String &name)	DefaultParamHandler
setParameters(const Param &param)	DefaultParamHandler
setTargetDecoyType(PeakGroup::TargetDecoyType target_decoy_type, const DeconvolvedSpectrum &target_dspec_for_decoy_calcualtion)	SpectralDeconvolution
setTargetMasses(const std::vector< double > &masses, bool exclude=false)	SpectralDeconvolution
setTargetPrecursorCharge_()	SpectralDeconvolution	private
SpectralDeconvolution()	SpectralDeconvolution
SpectralDeconvolution(SpectralDeconvolution &&other)=default	SpectralDeconvolution
subsections_	DefaultParamHandler	protected
target_decoy_type_	SpectralDeconvolution	private
target_dspec_for_decoy_calcualtion_	SpectralDeconvolution	private
target_mass_bins_	SpectralDeconvolution	private
target_mono_masses_	SpectralDeconvolution	private
target_precursor_charge_	SpectralDeconvolution	private
target_precursor_mz_	SpectralDeconvolution	private
tolerance_	SpectralDeconvolution	private
updateCandidateMassBins_(std::vector< float > &mass_intensities, const std::vector< float > &mz_intensities)	SpectralDeconvolution	private
updateLogMzPeaks_()	SpectralDeconvolution	private
updateMassBins_(const std::vector< float > &mz_intensities)	SpectralDeconvolution	private
updateMembers_() override	SpectralDeconvolution	protectedvirtual
updateMzBins_(Size bin_number, std::vector< float > &mz_bin_intensities)	SpectralDeconvolution	private
warn_empty_defaults_	DefaultParamHandler	protected
writeParametersToMetaValues(const Param &write_this, MetaInfoInterface &write_here, const String &key_prefix="")	DefaultParamHandler	static
~DefaultParamHandler()	DefaultParamHandler	virtual
~SpectralDeconvolution()=default	SpectralDeconvolution