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
binLogMzPeaks_(Size bin_number, std::vector< float > &binned_log_mz_peak_intensities)	SpectralDeconvolution	private
binned_harmonic_patterns	SpectralDeconvolution	private
binned_log_masses_	SpectralDeconvolution	private
binned_log_mz_peaks_	SpectralDeconvolution	private
binned_universal_pattern_	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_mass_bins_for_decoy_runs_	SpectralDeconvolution	private
excluded_masses_	SpectralDeconvolution	private
excluded_masses_for_decoy_runs_	SpectralDeconvolution	private
excluded_peak_masses_for_decoy_runs_	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_len)	SpectralDeconvolution	static
getDeconvolvedSpectrum()	SpectralDeconvolution
getDefaults() const	DefaultParamHandler
getIsotopeCosineAndIsoOffset(double mono_mass, const std::vector< float > &per_isotope_intensities, int &offset, const PrecalculatedAveragine &avg, int iso_int_shift, int window_width, const std::vector< double > &excluded_masses)	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_pattern_matrix_	SpectralDeconvolution	private
is_positive_	SpectralDeconvolution	private
iso_da_distance_	SpectralDeconvolution	private
isPeakGroupInExcludedMassForDecoyRuns_(const PeakGroup &peak_group, double tol, int offset=0) const	SpectralDeconvolution	private
log_mz_peaks_	SpectralDeconvolution	private
LogMzPeak typedef	SpectralDeconvolution
mass_bin_min_value_	SpectralDeconvolution	private
max_abs_charge_	SpectralDeconvolution	private
max_mass_	SpectralDeconvolution	private
max_mass_dalton_tolerance_	SpectralDeconvolution	private
min_abs_charge_	SpectralDeconvolution	private
min_iso_size	SpectralDeconvolution	static
min_isotope_cosine_	SpectralDeconvolution	private
min_mass_	SpectralDeconvolution	private
min_qscore_	SpectralDeconvolution	private
min_snr_	SpectralDeconvolution	private
min_support_peak_count_	SpectralDeconvolution	privatestatic
ms_level_	SpectralDeconvolution	private
mz_bin_min_value_	SpectralDeconvolution	private
noise_iso_delta_	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
prepareNoiseDecoySpectrum_(const MSSpectrum &spec)	SpectralDeconvolution	private
prepareSignalDecoyExclusions_()	SpectralDeconvolution	private
registerPrecursorForMSn_(const PeakGroup &precursor_peak_group)	SpectralDeconvolution	private
removeChargeErrorPeakGroups_(DeconvolvedSpectrum &dspec, const PeakGroup::TargetDecoyType &target_decoy_type) const	SpectralDeconvolution	private
removeExcludedMasses_(DeconvolvedSpectrum &dspec, std::vector< double > excluded_masses, double tol) const	SpectralDeconvolution	private
removeOverlappingPeakGroups_(DeconvolvedSpectrum &dspec, double tol, PeakGroup::TargetDecoyType target_decoy_type=PeakGroup::TargetDecoyType::target)	SpectralDeconvolution	privatestatic
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
setToleranceEstimation()	SpectralDeconvolution	inline
SpectralDeconvolution()	SpectralDeconvolution
SpectralDeconvolution(const SpectralDeconvolution &)=default	SpectralDeconvolution
SpectralDeconvolution(SpectralDeconvolution &&other)=default	SpectralDeconvolution
subsections_	DefaultParamHandler	protected
target_decoy_type_	SpectralDeconvolution	private
target_dspec_for_decoy_calculation_	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
universal_pattern_	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
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