| add_a_ions_ | FragmentIndex | private |
| add_b_ions_ | FragmentIndex | private |
| add_c_ions_ | FragmentIndex | private |
| add_x_ions_ | FragmentIndex | private |
| add_y_ions_ | FragmentIndex | private |
| add_z_ions_ | FragmentIndex | private |
| bucket_min_mz_ | FragmentIndex | protected |
| bucketsize_ | FragmentIndex | protected |
| build(const std::vector< FASTAFile::FASTAEntry > &fasta_entries) | FragmentIndex | |
| buildModSlots_(const char *sequence, size_t seq_len, ModSlot *out_slots, bool is_protein_nterm=false, bool is_protein_cterm=false) const | FragmentIndex | protected |
| check_defaults_ | DefaultParamHandler | protected |
| clear() | FragmentIndex | |
| computeMassWindow_(float precursor_mass) const | FragmentIndex | private |
| computeSnesSigmaDeltaSet_(bool include_prot_nterm_mods, bool include_prot_cterm_mods) const | FragmentIndex | protected |
| DefaultParamHandler(const std::string &name) | DefaultParamHandler | |
| DefaultParamHandler(const DefaultParamHandler &rhs) | DefaultParamHandler | |
| DefaultParamHandler() | DefaultParamHandler | private |
| defaults_ | DefaultParamHandler | protected |
| defaultsToParam_() | DefaultParamHandler | protected |
| digestion_enzyme_ | FragmentIndex | private |
| enzyme_specificity_ | FragmentIndex | private |
| error_name_ | DefaultParamHandler | protected |
| fi_fragments_ | FragmentIndex | protected |
| fi_peptides_ | FragmentIndex | protected |
| fixed_cterm_delta_ | FragmentIndex | protected |
| fixed_cterm_mod_ptr_ | FragmentIndex | protected |
| fixed_mod_deltas_ | FragmentIndex | protected |
| fixed_mod_ptrs_ | FragmentIndex | protected |
| fixed_nterm_delta_ | FragmentIndex | protected |
| fixed_nterm_mod_ptr_ | FragmentIndex | protected |
| fragment_max_mz_ | FragmentIndex | protected |
| fragment_min_mz_ | FragmentIndex | protected |
| fragment_mz_tolerance_ | FragmentIndex | protected |
| fragment_mz_tolerance_unit_ppm_ | FragmentIndex | protected |
| FragmentIndex() | FragmentIndex | |
| generateFragmentsForSeries_(std::vector< Fragment > &fragments, const char *sequence, size_t seq_len, UInt32 peptide_idx, double n_term_mod_mass, double c_term_mod_mass, const double *residue_mod_masses, bool add_b, bool add_a, bool add_c, bool add_y, bool add_x, bool add_z) const | FragmentIndex | protected |
| generateFragmentsLightweight_(std::vector< Fragment > &fragments, const char *sequence, size_t seq_len, UInt32 peptide_idx, double n_term_mod_mass, double c_term_mod_mass, const double *residue_mod_masses) const | FragmentIndex | protected |
| generatePeptides(const std::vector< FASTAFile::FASTAEntry > &fasta_entries) | FragmentIndex | protected |
| generateSNESMothers_(const std::vector< FASTAFile::FASTAEntry > &fasta_entries) | FragmentIndex | protected |
| getDefaults() const | DefaultParamHandler | |
| getName() const | DefaultParamHandler | |
| getNumFragments() const noexcept | FragmentIndex | inline |
| getParameters() const | DefaultParamHandler | |
| getPeptides() const | FragmentIndex | |
| getPeptidesInMassWindow(float precursor_mass, const std::pair< float, float > &window) const | FragmentIndex | |
| getSubsections() const | DefaultParamHandler | |
| initModificationTables_() | FragmentIndex | protected |
| initResidueMassTable_() | FragmentIndex | protectedstatic |
| ion_offsets_ | FragmentIndex | protectedstatic |
| is_build_ | FragmentIndex | protected |
| is_snes_mode_ | FragmentIndex | protected |
| isBuild() const | FragmentIndex | |
| isOpenSearchMode(double lower_magnitude, double upper_magnitude, bool unit_ppm) noexcept | FragmentIndex | inlinestatic |
| isOpenSearchMode_() const noexcept | FragmentIndex | inlineprivate |
| isSingleCMother(uint32_t mod_bitmask) noexcept | FragmentIndex | inlinestatic |
| isSingleNMother(uint32_t mod_bitmask) noexcept | FragmentIndex | inlinestatic |
| isSnesMode() const noexcept | FragmentIndex | inline |
| mass_table_once_flag_ | FragmentIndex | protectedstatic |
| max_fragment_charge_ | FragmentIndex | private |
| max_isotope_error_ | FragmentIndex | private |
| MAX_MOD_SLOTS | FragmentIndex | protectedstatic |
| max_precursor_charge_ | FragmentIndex | private |
| max_processed_hits_ | FragmentIndex | private |
| max_variable_mods_per_peptide_ | FragmentIndex | private |
| min_ion_index_ | FragmentIndex | protected |
| min_isotope_error_ | FragmentIndex | private |
| min_matched_peaks_ | FragmentIndex | private |
| min_precursor_charge_ | FragmentIndex | private |
| missed_cleavages_ | FragmentIndex | private |
| mod_tables_initialized_ | FragmentIndex | protected |
| modifications_fixed_ | FragmentIndex | private |
| modifications_variable_ | FragmentIndex | private |
| operator=(const DefaultParamHandler &rhs) | DefaultParamHandler | |
| operator==(const DefaultParamHandler &rhs) const | DefaultParamHandler | virtual |
| param_ | DefaultParamHandler | protected |
| peptide_max_length_ | FragmentIndex | private |
| peptide_max_mass_ | FragmentIndex | private |
| peptide_min_length_ | FragmentIndex | private |
| peptide_min_mass_ | FragmentIndex | private |
| precursor_mass_tolerance_lower_ | FragmentIndex | protected |
| precursor_mass_tolerance_unit_ppm_ | FragmentIndex | protected |
| precursor_mass_tolerance_upper_ | FragmentIndex | protected |
| protein_lengths_ | FragmentIndex | protected |
| query(const Peak1D &peak, const std::pair< size_t, size_t > &peptide_idx_range, uint16_t peak_charge) | FragmentIndex | |
| queryPeaks(SpectrumMatchesTopN &candidates, const MSSpectrum &spectrum, const std::pair< size_t, size_t > &candidates_range, const int16_t isotope_error, const uint16_t precursor_charge) | FragmentIndex | private |
| querySpectrum(const MSSpectrum &spectrum, SpectrumMatchesTopN &sms) | FragmentIndex | |
| querySpectrum(const MSSpectrum &spectrum, const std::vector< FASTAFile::FASTAEntry > &fasta_entries, SpectrumMatchesTopN &sms) | FragmentIndex | |
| querySpectrumSNES_(const MSSpectrum &spectrum, const std::vector< FASTAFile::FASTAEntry > &fasta_entries, SpectrumMatchesTopN &sms) | FragmentIndex | private |
| realizeSNESLength(const Peptide &mother, const std::vector< FASTAFile::FASTAEntry > &fasta_entries, double target_mh_plus, double tolerance_lower_magnitude, double tolerance_upper_magnitude, bool tolerance_ppm) const | FragmentIndex | |
| reconstructModifiedSequence(const Peptide &peptide, const std::vector< FASTAFile::FASTAEntry > &fasta_entries) const | FragmentIndex | |
| reconstructRealizedSubSequence(const Peptide &mother, const std::vector< FASTAFile::FASTAEntry > &fasta_entries, size_t realized_length, uint32_t subset_bitmask=0) const | FragmentIndex | |
| residue_mass_table_ | FragmentIndex | protectedstatic |
| searchDifferentPrecursorRanges(const MSSpectrum &spectrum, float precursor_mass, SpectrumMatchesTopN &sms, uint16_t charge) | FragmentIndex | private |
| setName(const std::string &name) | DefaultParamHandler | |
| setParameters(const Param ¶m) | DefaultParamHandler | |
| snes_enabled_ | FragmentIndex | protected |
| SNES_KIND_BIT_MASK | FragmentIndex | static |
| snes_sigma_delta_set_ | FragmentIndex | protected |
| snes_sigma_delta_set_with_prot_cterm_ | FragmentIndex | protected |
| snes_sigma_delta_set_with_prot_nterm_ | FragmentIndex | protected |
| SNES_SLOT_MASK | FragmentIndex | static |
| SnesAnchor enum name | FragmentIndex | |
| subsections_ | DefaultParamHandler | protected |
| trimHits(SpectrumMatchesTopN &init_hits) const | FragmentIndex | private |
| updateMembers_() override | FragmentIndex | protectedvirtual |
| variable_cterm_mods_ | FragmentIndex | protected |
| variable_mod_table_ | FragmentIndex | protected |
| variable_nterm_mods_ | FragmentIndex | protected |
| warn_empty_defaults_ | DefaultParamHandler | protected |
| writeParametersToMetaValues(const Param &write_this, MetaInfoInterface &write_here, const std::string &key_prefix="") | DefaultParamHandler | static |
| ~DefaultParamHandler() | DefaultParamHandler | virtual |
| ~FragmentIndex() override=default | FragmentIndex | |
1.9.8 