AScore Member List

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

AScore()	AScore
base_match_probability_	AScore	protected
calculatePermutationPeptideScores_(std::vector< PeakSpectrum > &th_spectra, const std::vector< PeakSpectrum > &windows_top10) const	AScore	protected
check_defaults_	DefaultParamHandler	protected
compareMZ_(double mz1, double mz2) const	AScore	protected
compute(const PeptideHit &hit, PeakSpectrum &real_spectrum)	AScore
computeBaseProbability_(double ppm_reference_mz) const	AScore	protected
computeCumulativeScore_(Size N, Size n, double p) const	AScore	protected
computePermutations_(const std::vector< Size > &sites, Int n_phosphorylation_events) const	AScore	protected
computeSiteDeterminingIons_(const std::vector< PeakSpectrum > &th_spectra, const ProbablePhosphoSites &candidates, std::vector< PeakSpectrum > &site_determining_ions) const	AScore	protected
createTheoreticalSpectra_(const std::vector< std::vector< Size >> &permutations, const AASequence &seq_without_phospho) const	AScore	protected
DefaultParamHandler(const String &name)	DefaultParamHandler
DefaultParamHandler(const DefaultParamHandler &rhs)	DefaultParamHandler
DefaultParamHandler()	DefaultParamHandler	private
defaults_	DefaultParamHandler	protected
defaultsToParam_()	DefaultParamHandler	protected
determineHighestScoringPermutations_(const std::vector< std::vector< double >> &peptide_site_scores, std::vector< ProbablePhosphoSites > &sites, const std::vector< std::vector< Size >> &permutations, std::multimap< double, Size > &ranking) const	AScore	protected
error_name_	DefaultParamHandler	protected
fragment_mass_tolerance_	AScore	protected
fragment_tolerance_ppm_	AScore	protected
getDefaults() const	DefaultParamHandler
getName() const	DefaultParamHandler
getParameters() const	DefaultParamHandler
getSites_(const AASequence &without_phospho) const	AScore	protected
getSpectrumDifference_(InputIterator1 first1, InputIterator1 last1, InputIterator2 first2, InputIterator2 last2, OutputIterator result) const	AScore	inlineprotected
getSubsections() const	DefaultParamHandler
max_peptide_length_	AScore	protected
max_permutations_	AScore	protected
numberOfMatchedIons_(const PeakSpectrum &th, const PeakSpectrum &windows, Size depth) const	AScore	protected
numberOfPhosphoEvents_(const String &sequence) const	AScore	protected
operator=(const DefaultParamHandler &rhs)	DefaultParamHandler
operator==(const DefaultParamHandler &rhs) const	DefaultParamHandler	virtual
param_	DefaultParamHandler	protected
peakPickingPerWindowsInSpectrum_(PeakSpectrum &real_spectrum) const	AScore	protected
peptideScore_(const std::vector< double > &scores) const	AScore	protected
PScore	AScore	friend
rankWeightedPermutationPeptideScores_(const std::vector< std::vector< double >> &peptide_site_scores) const	AScore	protected
removePhosphositesFromSequence_(const String &sequence) const	AScore	protected
setName(const String &name)	DefaultParamHandler
setParameters(const Param &param)	DefaultParamHandler
subsections_	DefaultParamHandler	protected
unambiguous_score_	AScore	protected
updateMembers_() override	AScore	protectedvirtual
warn_empty_defaults_	DefaultParamHandler	protected
writeParametersToMetaValues(const Param &write_this, MetaInfoInterface &write_here, const String &key_prefix="")	DefaultParamHandler	static
~AScore() override	AScore
~DefaultParamHandler()	DefaultParamHandler	virtual