FragmentIonLikelihoodModel Member List

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

absentOutcome() const	FragmentIonLikelihoodModel	inline
addObservations(const std::vector< Ion > &ions, bool noise)	FragmentIonLikelihoodModel
CLEAVAGE_SITES	FragmentIonLikelihoodModel	static
complement_	FragmentIonLikelihoodModel	private
COMPLEMENT_STATES	FragmentIonLikelihoodModel	static
context_set_	FragmentIonLikelihoodModel	private
contexts() const	FragmentIonLikelihoodModel	inline
contexts_	FragmentIonLikelihoodModel	private
ContextSet enum name	FragmentIonLikelihoodModel
contextSet() const	FragmentIonLikelihoodModel	inline
ERROR_BINS	FragmentIonLikelihoodModel	static
errorBin(double relative_error)	FragmentIonLikelihoodModel	static
errors_	FragmentIonLikelihoodModel	private
finalize()	FragmentIonLikelihoodModel
finalized_	FragmentIonLikelihoodModel	private
FRAGMENT_CHARGES	FragmentIonLikelihoodModel	static
FragmentIonLikelihoodModel(ContextSet context_set=ContextSet::RICH, double pseudo_count=20.0)	FragmentIonLikelihoodModel	explicit
isTrained() const	FragmentIonLikelihoodModel	inline
level1Context_(Size context) const	FragmentIonLikelihoodModel	private
level2Context_(Size context) const	FragmentIonLikelihoodModel	private
logLikelihoodRatio(Size context, Size outcome) const	FragmentIonLikelihoodModel
matchIons(const PeakLists &peaks, Size index, const MSSpectrum &theoretical, const AASequence &peptide, int precursor_charge, double tolerance, bool ppm, std::vector< Ion > &ions) const	FragmentIonLikelihoodModel
matchIons(const PeakLists &peaks, Size index, const MSSpectrum &theoretical, const std::vector< Residue::ResidueType > &ion_types, const std::vector< UInt > &ion_ordinals, const std::vector< Int > &ion_charges, const AASequence &peptide, int precursor_charge, double tolerance, bool ppm, std::vector< Ion > &ions) const	FragmentIonLikelihoodModel
matchIons_(const PeakLists &peaks, Size index, const MSSpectrum &theoretical, IonOf &&ion_of, ChargeOf &&charge_of, const AASequence &peptide, int precursor_charge, double tolerance, bool ppm, std::vector< Ion > &ions) const	FragmentIonLikelihoodModel	private
noise_counts_	FragmentIonLikelihoodModel	private
noise_logp_	FragmentIonLikelihoodModel	private
noise_psms_	FragmentIonLikelihoodModel	private
noisePsms() const	FragmentIonLikelihoodModel	inline
outcomes() const	FragmentIonLikelihoodModel	inline
outcomes_	FragmentIonLikelihoodModel	private
parseIonName(const std::string &name, bool &prefix, Size &ordinal)	FragmentIonLikelihoodModel	static
parseIonSeries(const std::string &name, Size &series, Size &ordinal)	FragmentIonLikelihoodModel	static
POSITION_BINS	FragmentIonLikelihoodModel	static
PRECURSOR_BUCKETS	FragmentIonLikelihoodModel	static
presenceProbability(Size context) const	FragmentIonLikelihoodModel
pseudo_count_	FragmentIonLikelihoodModel	private
pseudoCount() const	FragmentIonLikelihoodModel	inline
RANK_BINS	FragmentIonLikelihoodModel	static
rankBin(Size rank)	FragmentIonLikelihoodModel	static
requireTrained_() const	FragmentIonLikelihoodModel	private
score(const std::vector< Ion > &ions, Size top_k=6) const	FragmentIonLikelihoodModel
SERIES	FragmentIonLikelihoodModel	static
seriesOf(Residue::ResidueType type)	FragmentIonLikelihoodModel	static
signal_counts_	FragmentIonLikelihoodModel	private
signal_logp_	FragmentIonLikelihoodModel	private
signal_psms_	FragmentIonLikelihoodModel	private
signalPsms() const	FragmentIonLikelihoodModel	inline
sites_	FragmentIonLikelihoodModel	private
smooth_(const std::vector< double > &counts) const	FragmentIonLikelihoodModel	private