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void | registerOptionsAndFlags_ () |
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vector< ResidueModification > | getModifications_ (StringList modNames) |
| Query ResidueModifications (given as strings) from ModificationsDB. More...
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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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vector< FragmentAdductDefinition_ > | getFeasibleFragmentAdducts_ (const String &exp_pc_adduct, const String &exp_pc_formula, const PrecursorToFragmentAdductMapType &precursor_to_fragment_adducts) |
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map< String, vector< FragmentAdductDefinition_ > > | getAllFeasibleFragmentAdducts_ (const RNPxlModificationMassesResult &precursor_adducts, const PrecursorToFragmentAdductMapType &precursor_to_fragment_adducts) |
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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, TheoreticalSpectrumGenerator spectrum_generator, double fragment_mass_tolerance, bool fragment_mass_tolerance_unit_ppm, const map< String, vector< FragmentAdductDefinition_ > > &all_feasible_fragment_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 | normalizeAdductName_ (String &name) |
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map< String, set< FragmentAdductDefinition_ > > | getPrecursorToFragmentAdducts_ (StringList fragment_adducts) |
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ExitCodes | main_ (int, const char **) |
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