 |
OpenMS
|
This is the complete list of members for FragmentIndex, including all inherited members.
| 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 |
| add_zp1_ions_ | FragmentIndex | private |
| bucket_min_mz_ | FragmentIndex | protected |
| bucket_skip_ | FragmentIndex | private |
| bucketsize_ | FragmentIndex | protected |
| build(const std::vector< FASTAFile::FASTAEntry > &fasta_entries) | FragmentIndex | |
| build(const std::vector< FASTAFile::FASTAEntry > &fasta_entries, const std::function< const MSExperiment *(Size)> &searched_spectra) | 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 |
| buildSkipTables_() | FragmentIndex | private |
| check_defaults_ | DefaultParamHandler | protected |
| checkFixedModifications(const StringList &fixed_modifications, const std::string &name_prefix="") | FragmentIndex | static |
| checkSearchParameters(const Param ¶m, const std::string &name_prefix="") | FragmentIndex | static |
| clear() | FragmentIndex | |
| clip_nterm_methionine_ | FragmentIndex | private |
| computeMassWindow_(float precursor_mass) const | FragmentIndex | private |
| computeSigmaDeltaSet_(bool include_prot_nterm_mods, bool include_prot_cterm_mods) const | FragmentIndex | protected |
| deduplicate_ | FragmentIndex | private |
| deduplicateByString_(const std::vector< FASTAFile::FASTAEntry > &fasta_entries) | 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 |
| electron_bucket_min_mz_ | FragmentIndex | protected |
| electron_bucket_skip_ | FragmentIndex | private |
| electron_fragments_ | FragmentIndex | protected |
| electron_ions_ | FragmentIndex | private |
| entry_lengths_ | FragmentIndex | protected |
| ENTRY_MAX_SITES_ | FragmentIndex | protectedstatic |
| ENTRY_MOTHER_MASK_ | FragmentIndex | protectedstatic |
| entry_sites_ | FragmentIndex | protected |
| ENTRY_SITES_SHIFT_ | FragmentIndex | protectedstatic |
| entry_words_ | FragmentIndex | protected |
| 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_mod_residues_ | FragmentIndex | protected |
| fixed_nterm_delta_ | FragmentIndex | protected |
| fixed_nterm_mod_ptr_ | FragmentIndex | protected |
| fixed_residue_masses_ | FragmentIndex | protected |
| forEachPrefixMass_(const char *sequence, size_t len, F &&f) const | 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 | |
| FragmentIndex(const FragmentIndex &)=default | FragmentIndex | |
| FragmentIndex(FragmentIndex &&)=default | FragmentIndex | |
| generateFragmentsForSeries_(FragmentSink &fragments, const char *sequence, size_t seq_len, UInt32 peptide_idx, double n_term_mod_mass, double c_term_mod_mass, const double *residue_masses, const double *residue_mod_masses, bool add_b, bool add_a, bool add_c, bool add_y, bool add_x, bool add_z, bool add_zp1) const | FragmentIndex | protected |
| generateFragmentsLightweight_(FragmentSink &fragments, FragmentSink &electron_fragments, const char *sequence, size_t seq_len, UInt32 peptide_idx, double n_term_mod_mass, double c_term_mod_mass, const double *residue_masses, const double *residue_mod_masses) const | FragmentIndex | protected |
| generateMothers_(const std::vector< FASTAFile::FASTAEntry > &fasta_entries) | FragmentIndex | protected |
| generatePeptides(const std::vector< FASTAFile::FASTAEntry > &fasta_entries) | FragmentIndex | protected |
| generatePeptidoformFragments_(FragmentSink &fragments, FragmentSink &electron_fragments, const char *sequence, size_t seq_len, UInt32 peptide_idx, uint32_t slot_bits, const ModSlot *slots, size_t n_slots, std::vector< double > &mod_masses) const | 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 | |
| getProteinOccurrences(Size peptide_idx, const std::vector< FASTAFile::FASTAEntry > &fasta_entries, std::vector< std::pair< UInt32, UInt32 > > &occurrences) const | FragmentIndex | |
| getRemovedOccurrences() const noexcept | FragmentIndex | inline |
| getSubsections() const | DefaultParamHandler | |
| hasProteinOccurrences(const std::vector< FASTAFile::FASTAEntry > &fasta_entries) const | FragmentIndex | |
| initModificationTables_() | FragmentIndex | protected |
| initResidueMassTable_() | FragmentIndex | protectedstatic |
| ion_offsets_ | FragmentIndex | protectedstatic |
| is_build_ | FragmentIndex | protected |
| is_peptide_mass_mode_ | FragmentIndex | protected |
| isBuild() const | FragmentIndex | |
| isBuiltFrom(const std::vector< FASTAFile::FASTAEntry > &fasta_entries) const | FragmentIndex | |
| isOpenSearchMode(double lower_magnitude, double upper_magnitude, bool unit_ppm) noexcept | FragmentIndex | inlinestatic |
| isOpenSearchMode_() const noexcept | FragmentIndex | inlineprivate |
| isPeptideMassMode() const noexcept | FragmentIndex | inline |
| isProteinNTerminal_(const std::string &protein, Size start) const | FragmentIndex | private |
| keepPeptidesInPrecursorWindows_(const MSExperiment &spectra) | FragmentIndex | private |
| mass_table_once_flag_ | FragmentIndex | protectedstatic |
| matchesMotif_(const char *sequence, size_t length) const | FragmentIndex | private |
| max_fragment_charge_ | FragmentIndex | private |
| max_isotope_error_ | FragmentIndex | private |
| max_mod_shift_ | FragmentIndex | protected |
| 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_mod_shift_ | FragmentIndex | protected |
| min_precursor_charge_ | FragmentIndex | private |
| missed_cleavages_ | FragmentIndex | private |
| mod_shifts_ | FragmentIndex | protected |
| mod_tables_initialized_ | FragmentIndex | protected |
| modifications_fixed_ | FragmentIndex | private |
| modifications_variable_ | FragmentIndex | private |
| modShiftLevels_(bool include_prot_nterm_mods, bool include_prot_cterm_mods) const | FragmentIndex | protected |
| nonemptyZeroSigmaSubsetExists_() const | FragmentIndex | protected |
| operator=(const FragmentIndex &)=default | FragmentIndex | |
| operator=(FragmentIndex &&)=default | FragmentIndex | |
| OpenMS::DefaultParamHandler::operator=(const DefaultParamHandler &rhs) | DefaultParamHandler | |
| operator==(const DefaultParamHandler &rhs) const | DefaultParamHandler | virtual |
| packed_entries_ | FragmentIndex | protected |
| packedEntryMz_(size_t e, const std::vector< FASTAFile::FASTAEntry > &fasta_entries) const | FragmentIndex | private |
| param_ | DefaultParamHandler | protected |
| peptide_max_length_ | FragmentIndex | private |
| peptide_max_mass_ | FragmentIndex | private |
| peptide_min_length_ | FragmentIndex | private |
| peptide_min_mass_ | FragmentIndex | private |
| peptide_motif_ | FragmentIndex | private |
| peptidoformRendering_() const | FragmentIndex | protected |
| precursor_mass_tolerance_lower_ | FragmentIndex | protected |
| precursor_mass_tolerance_unit_ppm_ | FragmentIndex | protected |
| precursor_mass_tolerance_upper_ | FragmentIndex | protected |
| precursorCharges(const Precursor &precursor, int min_charge, int max_charge, std::vector< uint16_t > &charges, bool search_outside_range=false) | FragmentIndex | static |
| precursorWindows_(const MSExperiment &spectra, bool with_margin, std::vector< std::pair< float, float > > &windows) const | FragmentIndex | private |
| prefixMass_(const char *sequence, size_t length) const | FragmentIndex | private |
| 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::vector< CandidateBlock_ > &blocks, const uint16_t precursor_charge, const bool with_electron_ions) | FragmentIndex | private |
| querySpectrum(const MSSpectrum &spectrum, SpectrumMatchesTopN &sms) | FragmentIndex | |
| querySpectrum(const MSSpectrum &spectrum, const std::vector< FASTAFile::FASTAEntry > &fasta_entries, SpectrumMatchesTopN &sms) | FragmentIndex | |
| querySpectrum(const MSSpectrum &spectrum, const std::vector< FASTAFile::FASTAEntry > &fasta_entries, SpectrumMatchesTopN &sms, bool with_electron_ions) | FragmentIndex | |
| querySpectrumPeptideMasses_(const MSSpectrum &spectrum, const std::vector< FASTAFile::FASTAEntry > &fasta_entries, SpectrumMatchesTopN &sms, bool with_electron_ions) | FragmentIndex | private |
| realizePrefixLength(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 | |
| removed_occurrences_ | FragmentIndex | protected |
| renderPeptidoform_(const Peptide &peptide, const std::vector< FASTAFile::FASTAEntry > &fasta_entries, const PeptidoformRendering_ &rendering, std::vector< uint32_t > &tokens) const | FragmentIndex | protected |
| residue_mass_table_ | FragmentIndex | protectedstatic |
| restrictSearchParameters(Param ¶m) | FragmentIndex | static |
| samePeptidoform_(const Peptide &a, const Peptide &b, const std::vector< FASTAFile::FASTAEntry > &fasta_entries, const PeptidoformRendering_ &rendering, std::vector< uint32_t > &tokens_a, std::vector< uint32_t > &tokens_b) const | FragmentIndex | protected |
| search_outside_charges_ | FragmentIndex | private |
| searchDifferentPrecursorRanges(const MSSpectrum &spectrum, float precursor_mass, SpectrumMatchesTopN &sms, uint16_t charge, bool with_electron_ions) | FragmentIndex | private |
| setName(const std::string &name) | DefaultParamHandler | |
| setParameters(const Param ¶m) | DefaultParamHandler | |
| shadowedVariableResidueModifications(const StringList &fixed_modifications, const StringList &variable_modifications) | FragmentIndex | static |
| shadowedVariableTerminalModifications(const StringList &fixed_modifications, const StringList &variable_modifications) | FragmentIndex | static |
| sigma_delta_set_ | FragmentIndex | protected |
| sigma_delta_set_with_prot_cterm_ | FragmentIndex | protected |
| sigma_delta_set_with_prot_nterm_ | FragmentIndex | protected |
| skip_per_bucket_ | FragmentIndex | private |
| SKIP_STRIDE_ | FragmentIndex | privatestatic |
| sortAndBucketFragments_(std::vector< Fragment > &fragments, std::vector< float > &bucket_min_mz, int num_threads) | FragmentIndex | private |
| sortPackedEntries_(const std::vector< FASTAFile::FASTAEntry > &fasta_entries, const std::vector< size_t > &bin_start, uint32_t first_bin) | FragmentIndex | private |
| sortPeptides_(std::vector< Peptide > &peptides, size_t min_task_size=8192, size_t min_parallel_partition=size_t(1)<< 18) | FragmentIndex | protectedstatic |
| 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 |
| zero_sigma_subsets_ | FragmentIndex | protected |
| ~DefaultParamHandler() | DefaultParamHandler | virtual |
| ~FragmentIndex() override=default | FragmentIndex |
1.9.8 