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OpenMS
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This is the complete list of members for ProSEAlgorithm, including all inherited members.
| accessionHasDecoyMarker_(const std::string &accession, const std::string &marker, bool is_prefix) | ProSEAlgorithm | protectedstatic |
| add_a_ions_ | ProSEAlgorithm | protected |
| add_b_ions_ | ProSEAlgorithm | protected |
| add_c_ions_ | ProSEAlgorithm | protected |
| add_x_ions_ | ProSEAlgorithm | protected |
| add_y_ions_ | ProSEAlgorithm | protected |
| add_z_ions_ | ProSEAlgorithm | protected |
| add_zp1_ions_ | ProSEAlgorithm | protected |
| annotate_psm_ | ProSEAlgorithm | protected |
| annotateIonPriors_(const PeakMap &spectra, const FragmentIonLikelihoodModel::PeakLists &evidence, std::vector< ProteinIdentification > &protein_ids, PeptideIdentificationList &peptide_ids) const | ProSEAlgorithm | protected |
| annotatePeptDeepFeatures_(const PeakMap &spectra, std::vector< ProteinIdentification > &protein_ids, PeptideIdentificationList &peptide_ids) const | ProSEAlgorithm | protected |
| annotatePsmQValues(PeptideIdentificationList &peptide_ids) const | ProSEAlgorithm | |
| applyCompleteSetProteinFDR(std::vector< ProteinIdentification > &protein_ids, PeptideIdentificationList &peptide_ids, const std::string &decoy_string, bool decoy_is_prefix, double protein_fdr) | ProSEAlgorithm | static |
| applyDeferredPsmFDR(const std::vector< ProteinIdentification > &protein_ids, PeptideIdentificationList &peptide_ids, bool rescored, double psm_fdr) const | ProSEAlgorithm | |
| applyProteinMapping_(const ProteinMapping_ &mapping, const std::vector< FASTAFile::FASTAEntry > &db, const Param &indexer_parameters, std::vector< ProteinIdentification > &protein_ids, PeptideIdentificationList &peptide_ids, std::string &fallback_reason) | ProSEAlgorithm | protectedstatic |
| applyPsmFDR_(std::vector< ProteinIdentification > &protein_ids, PeptideIdentificationList &peptide_ids, bool has_decoys, RunStatistics &stats, PeptideIdentificationList *pre_fdr_psms=nullptr) const | ProSEAlgorithm | protected |
| buildCalibrationSample_(const std::vector< FASTAFile::FASTAEntry > &full_db) const | ProSEAlgorithm | protected |
| buildDecoyAugmentedDB_(const std::vector< FASTAFile::FASTAEntry > &fasta_db, const DecoyStrategy_ &strategy) const | ProSEAlgorithm | protected |
| buildDecoyAugmentedDB_(std::vector< FASTAFile::FASTAEntry > &&fasta_db, const DecoyStrategy_ &strategy) const | ProSEAlgorithm | protected |
| buildProteinMapping_(const FragmentIndex &index, const std::vector< FASTAFile::FASTAEntry > &db, std::vector< UInt32 > candidates, const Param &indexer_parameters) | ProSEAlgorithm | protectedstatic |
| calibration_enabled_ | ProSEAlgorithm | protected |
| calibration_min_psms_ | ProSEAlgorithm | protected |
| calibration_subset_ratio_ | ProSEAlgorithm | protected |
| capturePreFdrStats_(const PeptideIdentificationList &peptide_ids, RunStatistics &stats) | ProSEAlgorithm | protectedstatic |
| check_defaults_ | DefaultParamHandler | protected |
| CMD enum value | ProgressLogger | |
| collectRunStatistics_(const PeakMap &spectra, const std::vector< ProteinIdentification > &protein_ids, const PeptideIdentificationList &peptide_ids, RunStatistics &stats) const | ProSEAlgorithm | protected |
| computeModMatchTolerance_() const | ProSEAlgorithm | inlineprotected |
| countElectronActivated_(const PeakMap &spectra) const | ProSEAlgorithm | protected |
| current_logger_ | ProgressLogger | mutableprotected |
| database_chunk_size_ | ProSEAlgorithm | protected |
| decoy_mode_ | ProSEAlgorithm | protected |
| decoy_prefix_ | ProSEAlgorithm | protected |
| DecoyMode_ enum name | ProSEAlgorithm | protected |
| DefaultParamHandler(const std::string &name) | DefaultParamHandler | |
| DefaultParamHandler(const DefaultParamHandler &rhs) | DefaultParamHandler | |
| DefaultParamHandler() | DefaultParamHandler | private |
| defaults_ | DefaultParamHandler | protected |
| defaultsToParam_() | DefaultParamHandler | protected |
| deisotope_requested_ | ProSEAlgorithm | protected |
| deisotoping_ | ProSEAlgorithm | protected |
| endProgress(UInt64 bytes_processed=0) const | ProgressLogger | |
| enzyme_ | ProSEAlgorithm | protected |
| error_name_ | DefaultParamHandler | protected |
| ExitCodes enum name | ProSEAlgorithm | |
| fdr_protein_ | ProSEAlgorithm | protected |
| fdr_psm_ | ProSEAlgorithm | protected |
| fdr_psm_by_scored_charges_ | ProSEAlgorithm | protected |
| filterLocalPeaks_(MSSpectrum &spectrum, Size peaks_per_window) | ProSEAlgorithm | protectedstatic |
| fragment_mass_tolerance_ | ProSEAlgorithm | protected |
| fragment_mass_tolerance_unit_ | ProSEAlgorithm | protected |
| fragmentIndexParameters_(bool electron_ions=false) const | ProSEAlgorithm | protected |
| getDefaults() const | DefaultParamHandler | |
| getLogType() const | ProgressLogger | |
| getName() const | DefaultParamHandler | |
| getParameters() const | DefaultParamHandler | |
| getSubsections() const | DefaultParamHandler | |
| GUI enum value | ProgressLogger | |
| ion_prior_feature_explained_ | ProSEAlgorithm | protected |
| ion_prior_feature_llr_ | ProSEAlgorithm | protected |
| ion_prior_feature_topk_ | ProSEAlgorithm | protected |
| ion_prior_max_fragment_charge_ | ProSEAlgorithm | protected |
| ion_prior_min_psms_ | ProSEAlgorithm | protected |
| ion_prior_model_ | ProSEAlgorithm | protected |
| ion_prior_scored_peaks_ | ProSEAlgorithm | protected |
| ion_prior_train_fdr_ | ProSEAlgorithm | protected |
| ions_by_activation_ | ProSEAlgorithm | protected |
| isElectronActivated_(const MSSpectrum &spectrum) | ProSEAlgorithm | protectedstatic |
| isOpenSearchMode_() const | ProSEAlgorithm | inlineprivate |
| isotope_error_observed_minus_theoretical_ | ProSEAlgorithm | protected |
| keep_pre_fdr_psms_ | ProSEAlgorithm | protected |
| last_calibration_result_ | ProSEAlgorithm | mutableprotected |
| last_invoke_ | ProgressLogger | mutableprotected |
| last_mod_match_tolerance_used_ | ProSEAlgorithm | mutableprotected |
| last_percolator_ | ProSEAlgorithm | mutableprotected |
| last_run_stats_ | ProSEAlgorithm | mutableprotected |
| localFragmentEvidence_(const MSSpectrum &spectrum, const MSSpectrum &theoretical, const std::vector< double > &densities, double tolerance, bool ppm) | ProSEAlgorithm | protectedstatic |
| localFragmentEvidence_(const MSSpectrum &spectrum, const MSSpectrum &theoretical, int max_charge, const std::vector< double > &densities, double tolerance, bool ppm, std::vector< double > &alternatives) | ProSEAlgorithm | protectedstatic |
| localPeakDensities_(const MSSpectrum &spectrum) | ProSEAlgorithm | protectedstatic |
| LogType enum name | ProgressLogger | |
| mass_accuracy_score_ | ProSEAlgorithm | protected |
| mass_error_sd_ppm_ | ProSEAlgorithm | protected |
| maxRetainedScore_(const PeptideIdentificationList &peptide_ids) | ProSEAlgorithm | protectedstatic |
| mergeFileResults(MultiFileSearchResult &result, const StringList &in_spectra_files, bool remove_decoys=true) const | ProSEAlgorithm | |
| modifications_fixed_ | ProSEAlgorithm | protected |
| modifications_max_variable_mods_per_peptide_ | ProSEAlgorithm | protected |
| modifications_variable_ | ProSEAlgorithm | protected |
| nextProgress() const | ProgressLogger | |
| NONE enum value | ProgressLogger | |
| OpenMS::operator=(const DefaultParamHandler &rhs) | DefaultParamHandler | |
| OpenMS::ProgressLogger::operator=(const ProgressLogger &other) | ProgressLogger | |
| operator==(const DefaultParamHandler &rhs) const | DefaultParamHandler | virtual |
| param_ | DefaultParamHandler | protected |
| peaks_keep_n_ | ProSEAlgorithm | protected |
| peaks_window_top_ | ProSEAlgorithm | protected |
| peaks_window_type_ | ProSEAlgorithm | protected |
| peptdeep_batch_size_ | ProSEAlgorithm | protected |
| peptdeep_enable_ | ProSEAlgorithm | protected |
| peptdeep_instrument_ | ProSEAlgorithm | protected |
| peptdeep_ms2_model_ | ProSEAlgorithm | protected |
| peptdeep_nce_ | ProSEAlgorithm | protected |
| peptdeep_rt_model_ | ProSEAlgorithm | protected |
| peptdeep_rt_model_type_ | ProSEAlgorithm | protected |
| peptide_enzyme_specificity_ | ProSEAlgorithm | protected |
| peptide_max_size_ | ProSEAlgorithm | protected |
| peptide_min_size_ | ProSEAlgorithm | protected |
| peptide_missed_cleavages_ | ProSEAlgorithm | protected |
| peptide_motif_ | ProSEAlgorithm | protected |
| poolSearchedFiles_(std::vector< SearchResult > &per_file, bool move_psms, const StringList &in_spectra_files, std::vector< ProteinIdentification > &protein_ids, PeptideIdentificationList &peptide_ids) | ProSEAlgorithm | protectedstatic |
| postProcessHits_(const PeakMap &exp, std::vector< std::vector< ProSEAlgorithm::AnnotatedHit_ > > &annotated_hits, const std::vector< CandidatePoolStats_ > &pool_stats, std::vector< ProteinIdentification > &protein_ids, PeptideIdentificationList &peptide_ids, Size top_hits, const StringList &modifications_fixed, const StringList &modifications_variable, Int peptide_missed_cleavages, double precursor_mass_tolerance, double fragment_mass_tolerance, const std::string &precursor_mass_tolerance_unit_ppm, const std::string &fragment_mass_tolerance_unit_ppm, const Int precursor_min_charge, const Int precursor_max_charge, const std::string &enzyme, const std::string &database_name, const PeakMap *evidence_spectra=nullptr) const | ProSEAlgorithm | protected |
| pre_fdr_peptide_ids_ | ProSEAlgorithm | mutableprotected |
| precursor_mass_tolerance_lower_ | ProSEAlgorithm | mutableprotected |
| precursor_mass_tolerance_unit_ | ProSEAlgorithm | protected |
| precursor_mass_tolerance_upper_ | ProSEAlgorithm | mutableprotected |
| precursor_max_charge_ | ProSEAlgorithm | protected |
| precursor_min_charge_ | ProSEAlgorithm | protected |
| prepareContext(const std::vector< FASTAFile::FASTAEntry > &fasta_db) const | ProSEAlgorithm | |
| prepareContext(const std::vector< FASTAFile::FASTAEntry > &fasta_db, bool electron_ions) const | ProSEAlgorithm | |
| prepareContext_(std::vector< FASTAFile::FASTAEntry > &&fasta_db, bool electron_ions, const std::function< const PeakMap *(Size)> &searched_spectra={}) const | ProSEAlgorithm | protected |
| preprocessSpectra_(PeakMap &exp, double fragment_mass_tolerance, bool fragment_mass_tolerance_unit_ppm, bool deisotope_requested, Size peaks_keep_n, Int peaks_window_top, const std::string &window_type, const DeisotopingSettings_ &deisotoping, FragmentIonLikelihoodModel::PeakLists *ion_evidence=nullptr, bool ion_evidence_scored_peaks=false, PeakMap *evidence_spectra=nullptr, PeakMap *query_spectra=nullptr) | ProSEAlgorithm | protectedstatic |
| preprocessSpectra_(PeakMap &exp, double fragment_mass_tolerance, bool fragment_mass_tolerance_unit_ppm, bool deisotope_requested, Size peaks_keep_n, Int peaks_window_top, const std::string &window_type="auto") | ProSEAlgorithm | protectedstatic |
| ProgressLogger() | ProgressLogger | |
| ProgressLogger(const ProgressLogger &other) | ProgressLogger | |
| ProSEAlgorithm() | ProSEAlgorithm | |
| protein_mapping_from_index_ | ProSEAlgorithm | protected |
| query_raw_spectrum_ | ProSEAlgorithm | protected |
| recursion_depth_ | ProgressLogger | protectedstatic |
| renderModificationSummary(const OpenSearchModificationAnalysis::OpenSearchAnalysisResult &mod_analysis, std::ostream &os) | ProSEAlgorithm | static |
| renderRunSummary(const RunStatistics &stats, const SharedSearchStats &shared, const OpenSearchModificationAnalysis::OpenSearchAnalysisResult &mod_analysis, bool is_open_search, std::ostream &os) | ProSEAlgorithm | static |
| renderRunSummaryYaml(const MultiFileSearchResult &mfres, const std::vector< std::pair< std::string, std::vector< std::string > > > &manifest, Size files_failed, Size files_total) | ProSEAlgorithm | static |
| report_top_hits_ | ProSEAlgorithm | protected |
| rescore_ | ProSEAlgorithm | protected |
| rescoreWithPercolator(std::vector< ProteinIdentification > &protein_ids, PeptideIdentificationList &peptide_ids, int threads) | ProSEAlgorithm | static |
| resolveDecoyStrategy_(const std::vector< FASTAFile::FASTAEntry > &db) const | ProSEAlgorithm | protected |
| restrictIndexToSpectra_() const | ProSEAlgorithm | inlineprotected |
| reversedNoiseSequence_(const AASequence &sequence) | ProSEAlgorithm | protectedstatic |
| runCalibrationPass_(PeakMap &spectra, FragmentIndex &fragment_index, const std::vector< FASTAFile::FASTAEntry > &db, const PeakMap *query_spectra=nullptr) const | ProSEAlgorithm | protected |
| scoreSpectraAgainstIndex_(const PeakMap &spectra, FragmentIndex &fi, const std::vector< FASTAFile::FASTAEntry > &db, const SpectrumGenerators_ &generators, double effective_fragment_tol, bool fragment_mass_tolerance_unit_ppm, bool open_search_mode, std::vector< std::vector< AnnotatedHit_ > > &annotated_hits, std::vector< CandidatePoolStats_ > &pool_stats, const std::string &progress_label, const PeakMap *query_spectra=nullptr) const | ProSEAlgorithm | protected |
| scoring_max_charge_ | ProSEAlgorithm | protected |
| scoring_multiple_charges_ | ProSEAlgorithm | protected |
| scoringMaxCharge_(int precursor_charge) const | ProSEAlgorithm | inlineprotected |
| search(const std::string &in_spectra, const std::string &in_db, std::vector< ProteinIdentification > &prot_ids, PeptideIdentificationList &pep_ids) const | ProSEAlgorithm | |
| search(PeakMap &spectra, const std::vector< FASTAFile::FASTAEntry > &fasta_db, std::vector< ProteinIdentification > &prot_ids, PeptideIdentificationList &pep_ids) const | ProSEAlgorithm | |
| search(PeakMap &spectra, SearchContext &ctx, std::vector< ProteinIdentification > &prot_ids, PeptideIdentificationList &pep_ids) const | ProSEAlgorithm | |
| searchChunked_(PeakMap &spectra, std::vector< FASTAFile::FASTAEntry > &full_db, const DecoyStrategy_ &strategy, std::vector< ProteinIdentification > &protein_ids, PeptideIdentificationList &peptide_ids) const | ProSEAlgorithm | protected |
| searchWithModificationAnalysis(const std::string &in_spectra, const std::string &in_db, const std::string &output_base_name="") const | ProSEAlgorithm | |
| searchWithModificationAnalysis(PeakMap &spectra, const std::vector< FASTAFile::FASTAEntry > &fasta_db, const std::string &output_base_name="") const | ProSEAlgorithm | |
| searchWithModificationAnalysis(const std::vector< std::string > &in_spectra_files, const std::vector< FASTAFile::FASTAEntry > &fasta_db, const std::vector< std::string > &output_base_names={}, const std::string &aggregate_base_name="", bool build_pooled_aggregate=true) const | ProSEAlgorithm | |
| searchWithModificationAnalysis(const std::vector< std::string > &in_spectra_files, const std::string &in_db, const std::vector< std::string > &output_base_names={}, const std::string &aggregate_base_name="", bool build_pooled_aggregate=true) const | ProSEAlgorithm | |
| self_trained_ion_priors_ | ProSEAlgorithm | protected |
| setKeepPreFdrPsms(bool keep) | ProSEAlgorithm | inline |
| setLogger(ProgressLoggerImpl *logger) | ProgressLogger | |
| setLogType(LogType type) const | ProgressLogger | |
| setName(const std::string &name) | DefaultParamHandler | |
| setParameters(const Param ¶m) | DefaultParamHandler | |
| setProgress(SignedSize value) const | ProgressLogger | |
| spectrumGenerators_() const | ProSEAlgorithm | protected |
| startProgress(SignedSize begin, SignedSize end, const std::string &label) const | ProgressLogger | |
| subsections_ | DefaultParamHandler | protected |
| type_ | ProgressLogger | mutableprotected |
| updateFinalStats(RunStatistics &stats, const PeptideIdentificationList &peptide_ids, const std::string &enzyme, bool fdr_applied) | ProSEAlgorithm | static |
| updateMembers_() override | ProSEAlgorithm | protectedvirtual |
| warn_empty_defaults_ | DefaultParamHandler | protected |
| writeParametersToMetaValues(const Param &write_this, MetaInfoInterface &write_here, const std::string &key_prefix="") | DefaultParamHandler | static |
| ~DefaultParamHandler() | DefaultParamHandler | virtual |
| ~ProgressLogger() | ProgressLogger | virtual |
1.9.8 