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void | registerOptionsAndFlags_ () override |
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void | preprocessSpectra_ (PeakMap &exp, double fragment_mass_tolerance, bool fragment_mass_tolerance_unit_ppm, bool single_charge_spectra, bool annotate_charge=false) |
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void | postScoreHits_ (const PeakMap &exp, vector< vector< AnnotatedHit > > &annotated_hits, Size top_hits, const RNPxlModificationMassesResult &mm, const vector< ResidueModification > &fixed_modifications, const vector< ResidueModification > &variable_modifications, Size max_variable_mods_per_peptide, const TheoreticalSpectrumGenerator &partial_loss_spectrum_generator, double fragment_mass_tolerance, bool fragment_mass_tolerance_unit_ppm, const RNPxlParameterParsing::PrecursorsToMS2Adducts &all_feasible_adducts) |
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void | postProcessHits_ (const PeakMap &exp, vector< vector< AnnotatedHit > > &annotated_hits, vector< ProteinIdentification > &protein_ids, vector< PeptideIdentification > &peptide_ids, Size top_hits, const RNPxlModificationMassesResult &mm, const vector< ResidueModification > &fixed_modifications, const vector< ResidueModification > &variable_modifications, Size max_variable_mods_per_peptide) |
| Filter by top scoring hits, reconstruct original peptide from memory efficient structure, and add additional meta information. More...
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void | mapPrecursorMassesToScans (const Int min_precursor_charge, const Int max_precursor_charge, const IntList &precursor_isotopes, const double small_peptide_mass_filter_threshold, const Size peptide_min_size, const PeakMap &spectra, multimap< double, pair< Size, int >> &multimap_mass_2_scan_index) const |
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void | initializeSpectrumGenerators (TheoreticalSpectrumGenerator &total_loss_spectrum_generator, TheoreticalSpectrumGenerator &partial_loss_spectrum_generator, TheoreticalSpectrumGenerator &a_ion_sub_score_spectrum_generator, TheoreticalSpectrumGenerator &immonium_ion_sub_score_spectrum_generator, TheoreticalSpectrumGenerator &precursor_ion_sub_score_spectrum_generator) const |
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ExitCodes | main_ (int, const char **) override |
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void | scoreTotalLossFragments_ (const PeakSpectrum &exp_spectrum, const PeakSpectrum &total_loss_spectrum, double fragment_mass_tolerance, bool fragment_mass_tolerance_unit_ppm, const PeakSpectrum &a_ion_sub_score_spectrum, const PeakSpectrum &precursor_sub_score_spectrum, const PeakSpectrum &immonium_sub_score_spectrum, float &total_loss_score, float &tlss_MIC, float &tlss_err, float &tlss_Morph, float &immonium_sub_score, float &precursor_sub_score, float &a_ion_sub_score) const |
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void | scorePartialLossFragments_ (const PeakSpectrum &exp_spectrum, double fragment_mass_tolerance, bool fragment_mass_tolerance_unit_ppm, const PeakSpectrum &partial_loss_spectrum_z1, const PeakSpectrum &partial_loss_spectrum_z2, const PeakSpectrum &marker_ions_sub_score_spectrum_z1, float &partial_loss_sub_score, float &marker_ions_sub_score, float &plss_MIC, float &plss_err, float &plss_Morph) const |
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