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OpenMS
2.7.0
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This is the complete list of members for MzTab, including all inherited members.
| addMetaInfoToOptionalColumns(const std::set< String > &keys, std::vector< MzTabOptionalColumnEntry > &opt, const String &id, const MetaInfoInterface &meta) | MzTab | static |
| addMSRunMetaData_(const std::map< size_t, String > &msrunindex_2_msfilename, MzTabMetaData &meta_data) | MzTab | protectedstatic |
| addSearchMetaData_(const std::vector< const ProteinIdentification * > &prot_ids, const std::map< std::tuple< String, String, String >, std::set< Size >> &search_engine_to_runs, const std::map< String, std::vector< std::pair< String, String >>> &search_engine_to_settings, MzTabMetaData &meta_data, bool first_run_inference_only) | MzTab | protectedstatic |
| checkSequenceUniqueness_(const std::vector< PeptideIdentification > &curr_pep_ids) | MzTab | protectedstatic |
| comment_rows_ | MzTab | protected |
| empty_rows_ | MzTab | protected |
| exportConsensusMapToMzTab(const ConsensusMap &consensus_map, const String &filename, const bool first_run_inference_only, const bool export_unidentified_features, const bool export_unassigned_ids, const bool export_subfeatures, const bool export_empty_pep_ids=false, const bool export_all_psms=false, const String &title="ConsensusMap export from OpenMS") | MzTab | static |
| exportFeatureMapToMzTab(const FeatureMap &feature_map, const String &filename) | MzTab | static |
| exportIdentificationsToMzTab(const std::vector< ProteinIdentification > &prot_ids, const std::vector< PeptideIdentification > &peptide_ids, const String &filename, bool first_run_inference_only, bool export_empty_pep_ids=false, bool export_all_psms=false, const String &title="ID export from OpenMS") | MzTab | static |
| extractModificationList(const PeptideHit &pep_hit, const std::vector< String > &fixed_mods, const std::vector< String > &localization_mods) | MzTab | static |
| generateMzTabStringFromFixedModifications(const std::vector< String > &mods) | MzTab | static |
| generateMzTabStringFromModifications(const std::vector< String > &mods) | MzTab | static |
| generateMzTabStringFromVariableModifications(const std::vector< String > &mods) | MzTab | static |
| getCommentRows() const | MzTab | |
| getConsensusMapMetaValues_(const ConsensusMap &consensus_map, std::set< String > &consensus_feature_user_value_keys, std::set< String > &peptide_hit_user_value_keys) | MzTab | protectedstatic |
| getEmptyRows() const | MzTab | |
| getFeatureMapMetaValues_(const FeatureMap &feature_map, std::set< String > &feature_user_value_keys, std::set< String > &peptide_hit_user_value_keys) | MzTab | protectedstatic |
| getIdentificationMetaValues_(const std::vector< const ProteinIdentification * > &prot_ids, std::vector< const PeptideIdentification * > &peptide_ids_, std::set< String > &protein_hit_user_value_keys, std::set< String > &peptide_id_user_value_keys, std::set< String > &peptide_hit_user_value_keys) | MzTab | protectedstatic |
| getMetaData() const | MzTab | |
| getModificationIdentifier_(const ResidueModification &r) | MzTab | protectedstatic |
| getMSRunSpectrumIdentifierType_(const std::vector< const PeptideIdentification * > &peptide_ids_) | MzTab | protectedstatic |
| getNucleicAcidOptionalColumnNames() const | MzTab | |
| getNucleicAcidSectionRows() const | MzTab | |
| getOligonucleotideOptionalColumnNames() const | MzTab | |
| getOligonucleotideSectionRows() const | MzTab | |
| getOptionalColumnNames_(const SectionRows &rows) const | MzTab | inlineprotected |
| getOSMOptionalColumnNames() const | MzTab | |
| getOSMSectionRows() const | MzTab | |
| getPeptideOptionalColumnNames() const | MzTab | |
| getPeptideSectionRows() | MzTab | |
| getPeptideSectionRows() const | MzTab | |
| getProteinOptionalColumnNames() const | MzTab | |
| getProteinScoreType_(const ProteinIdentification &prot_id) | MzTab | protectedstatic |
| getProteinSectionRows() | MzTab | |
| getProteinSectionRows() const | MzTab | |
| getPSMOptionalColumnNames() const | MzTab | |
| getPSMSectionRows() | MzTab | |
| getPSMSectionRows() const | MzTab | |
| getQuantStudyVariables_(const ProteinIdentification &pid) | MzTab | protectedstatic |
| getSearchModifications_(const std::vector< const ProteinIdentification * > &prot_ids, StringList &var_mods, StringList &fixed_mods) | MzTab | protectedstatic |
| getSmallMoleculeOptionalColumnNames() const | MzTab | |
| getSmallMoleculeSectionRows() const | MzTab | |
| mapBetweenMSFileNameAndMSRunIndex_(const std::vector< const ProteinIdentification * > &prot_ids, bool skip_first, std::map< String, size_t > &msfilename_2_msrunindex, std::map< size_t, String > &msrunindex_2_msfilename) | MzTab | protectedstatic |
| mapBetweenRunAndSearchEngines_(const std::vector< const ProteinIdentification * > &prot_ids, const std::vector< const PeptideIdentification * > &pep_ids, bool skip_first_run, std::map< std::tuple< String, String, String >, std::set< Size >> &search_engine_to_runs, std::map< Size, std::vector< std::pair< String, String >>> &run_to_search_engines, std::map< Size, std::vector< std::vector< std::pair< String, String >>>> &run_to_search_engines_settings, std::map< String, std::vector< std::pair< String, String >>> &search_engine_to_settings) | MzTab | protectedstatic |
| mapGroupsToProteins_(const std::vector< ProteinIdentification::ProteinGroup > &groups, const std::vector< ProteinHit > &proteins) | MzTab | protectedstatic |
| mapIDRunFileIndex2MSFileIndex_(const std::vector< const ProteinIdentification * > &prot_ids, const std::map< String, size_t > &msfilename_2_msrunindex, bool skip_first_run, std::map< std::pair< size_t, size_t >, size_t > &map_run_fileidx_2_msfileidx) | MzTab | protectedstatic |
| mapIDRunIdentifier2IDRunIndex_(const std::vector< const ProteinIdentification * > &prot_ids) | MzTab | protectedstatic |
| meta_data_ | MzTab | protected |
| MzTab()=default | MzTab | |
| nextProteinSectionRowFromIndistinguishableGroup_(const std::vector< ProteinHit > &protein_hits, const ProteinIdentification::ProteinGroup &group, const size_t g, const std::map< Size, std::set< Size >> &ind2prot, const MzTabString &db, const MzTabString &db_version) | MzTab | protectedstatic |
| nextProteinSectionRowFromProteinGroup_(const ProteinIdentification::ProteinGroup &group, const MzTabString &db, const MzTabString &db_version) | MzTab | protectedstatic |
| nucleic_acid_data_ | MzTab | protected |
| oligonucleotide_data_ | MzTab | protected |
| osm_data_ | MzTab | protected |
| peptide_data_ | MzTab | protected |
| peptideSectionRowFromConsensusFeature_(const ConsensusFeature &c, const ConsensusMap &consensus_map, const StringList &ms_runs, const Size n_study_variables, const std::set< String > &consensus_feature_user_value_keys, const std::set< String > &peptide_hit_user_value_keys, const std::map< String, size_t > &idrun_2_run_index, const std::map< std::pair< size_t, size_t >, size_t > &map_run_fileidx_2_msfileidx, const std::map< std::pair< String, unsigned >, unsigned > &path_label_to_assay, const std::vector< String > &fixed_mods, bool export_subfeatures) | MzTab | protectedstatic |
| peptideSectionRowFromFeature_(const Feature &c, const std::set< String > &feature_user_value_keys, const std::set< String > &peptide_hit_user_value_keys, const std::vector< String > &fixed_mods) | MzTab | protectedstatic |
| protein_data_ | MzTab | protected |
| proteinSectionRowFromProteinHit_(const ProteinHit &hit, const MzTabString &db, const MzTabString &db_version, const std::set< String > &protein_hit_user_value_keys) | MzTab | protectedstatic |
| psm_data_ | MzTab | protected |
| PSMSectionRowFromPeptideID_(PeptideIdentification const &pid, std::vector< ProteinIdentification const * > const &prot_id, std::map< String, size_t > &idrun_2_run_index, std::map< std::pair< size_t, size_t >, size_t > &map_run_fileidx_2_msfileidx, std::map< Size, std::vector< std::pair< String, String >>> &run_to_search_engines, Size const current_psm_idx, Size const psm_id, MzTabString const &db, MzTabString const &db_version, bool const export_empty_pep_ids, bool const export_all_psms) | MzTab | protectedstatic |
| replaceWhiteSpaces_(ForwardIterator first, ForwardIterator last) | MzTab | inlineprotectedstatic |
| replaceWhiteSpaces_(std::set< String > &keys) | MzTab | inlineprotectedstatic |
| setCommentRows(const std::map< Size, String > &com) | MzTab | |
| setEmptyRows(const std::vector< Size > &empty) | MzTab | |
| setMetaData(const MzTabMetaData &md) | MzTab | |
| setNucleicAcidSectionRows(const MzTabNucleicAcidSectionRows &nasd) | MzTab | |
| setOligonucleotideSectionRows(const MzTabOligonucleotideSectionRows &onsd) | MzTab | |
| setOSMSectionRows(const MzTabOSMSectionRows &osd) | MzTab | |
| setPeptideSectionRows(const MzTabPeptideSectionRows &psd) | MzTab | |
| setProteinSectionRows(const MzTabProteinSectionRows &psd) | MzTab | |
| setPSMSectionRows(const MzTabPSMSectionRows &psd) | MzTab | |
| setSmallMoleculeSectionRows(const MzTabSmallMoleculeSectionRows &smsd) | MzTab | |
| small_molecule_data_ | MzTab | protected |
| ~MzTab()=default | MzTab |
1.9.1
