| AScore() | AScore | |
| calculatePermutationPeptideScores_(std::vector< PeakSpectrum > &th_spectra, const std::vector< PeakSpectrum > &windows_top10, double fragment_mass_tolerance, bool fragment_mass_unit_ppm) const | AScore | protected |
| compareMZ_(double mz1, double mz2, double fragment_mass_tolerance, bool fragment_mass_unit_ppm) const | AScore | protected |
| compute(const PeptideHit &hit, PeakSpectrum &real_spectrum, double fragment_mass_tolerance, bool fragment_mass_unit_ppm, Size max_peptide_len=60, Size max_num_perm=16384) | AScore | |
| 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, double fragment_mass_tolerance, bool fragment_mass_unit_ppm) const | AScore | protected |
| createTheoreticalSpectra_(const std::vector< std::vector< Size > > &permutations, const AASequence &seq_without_phospho) const | AScore | 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 |
| getSites_(const AASequence &without_phospho) const | AScore | protected |
| getSpectrumDifference_(InputIterator1 first1, InputIterator1 last1, InputIterator2 first2, InputIterator2 last2, OutputIterator result, double fragment_mass_tolerance, bool fragment_mass_unit_ppm) const | AScore | inlineprotected |
| numberOfMatchedIons_(const PeakSpectrum &th, const PeakSpectrum &windows, Size depth, double fragment_mass_tolerance, bool fragment_mass_tolerance_ppm=false) const | AScore | protected |
| numberOfPhosphoEvents_(const String sequence) const | AScore | 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 |
| ~AScore() | AScore | |