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AScore Member List

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

AScore()AScore
base_match_probability_AScoreprotected
calculatePermutationPeptideScores_(std::vector< PeakSpectrum > &th_spectra, const std::vector< PeakSpectrum > &windows_top10) constAScoreprotected
check_defaults_DefaultParamHandlerprotected
compareMZ_(double mz1, double mz2) constAScoreprotected
compute(const PeptideHit &hit, PeakSpectrum &real_spectrum)AScore
computeBaseProbability_(double ppm_reference_mz) constAScoreprotected
computeCumulativeScore_(Size N, Size n, double p) constAScoreprotected
computePermutations_(const std::vector< Size > &sites, Int n_phosphorylation_events) constAScoreprotected
computeSiteDeterminingIons_(const std::vector< PeakSpectrum > &th_spectra, const ProbablePhosphoSites &candidates, std::vector< PeakSpectrum > &site_determining_ions) constAScoreprotected
createTheoreticalSpectra_(const std::vector< std::vector< Size >> &permutations, const AASequence &seq_without_phospho) constAScoreprotected
DefaultParamHandler(const String &name)DefaultParamHandler
DefaultParamHandler(const DefaultParamHandler &rhs)DefaultParamHandler
DefaultParamHandler()DefaultParamHandlerprivate
defaults_DefaultParamHandlerprotected
defaultsToParam_()DefaultParamHandlerprotected
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) constAScoreprotected
error_name_DefaultParamHandlerprotected
fragment_mass_tolerance_AScoreprotected
fragment_tolerance_ppm_AScoreprotected
getDefaults() constDefaultParamHandler
getName() constDefaultParamHandler
getParameters() constDefaultParamHandler
getSites_(const String &unmodified_sequence) constAScoreprotected
getSpectrumDifference_(InputIterator1 first1, InputIterator1 last1, InputIterator2 first2, InputIterator2 last2, OutputIterator result) constAScoreinlineprotected
getSubsections() constDefaultParamHandler
max_peptide_length_AScoreprotected
max_permutations_AScoreprotected
numberOfMatchedIons_(const PeakSpectrum &th, const PeakSpectrum &windows, Size depth) constAScoreprotected
numberOfPhosphoEvents_(const String &sequence) constAScoreprotected
operator=(const DefaultParamHandler &rhs)DefaultParamHandler
operator==(const DefaultParamHandler &rhs) constDefaultParamHandlervirtual
param_DefaultParamHandlerprotected
peakPickingPerWindowsInSpectrum_(PeakSpectrum &real_spectrum) constAScoreprotected
peptideScore_(const std::vector< double > &scores) constAScoreprotected
PScoreAScorefriend
rankWeightedPermutationPeptideScores_(const std::vector< std::vector< double >> &peptide_site_scores) constAScoreprotected
removePhosphositesFromSequence_(const String &sequence) constAScoreprotected
setName(const String &name)DefaultParamHandler
setParameters(const Param &param)DefaultParamHandler
subsections_DefaultParamHandlerprotected
unambiguous_score_AScoreprotected
updateMembers_() overrideAScoreprotectedvirtual
warn_empty_defaults_DefaultParamHandlerprotected
writeParametersToMetaValues(const Param &write_this, MetaInfoInterface &write_here, const String &key_prefix="")DefaultParamHandlerstatic
~AScore() overrideAScore
~DefaultParamHandler()DefaultParamHandlervirtual