OpenMS  2.7.0
MzTab Member List

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)MzTabstatic
addMSRunMetaData_(const std::map< size_t, String > &msrunindex_2_msfilename, MzTabMetaData &meta_data)MzTabprotectedstatic
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)MzTabprotectedstatic
checkSequenceUniqueness_(const std::vector< PeptideIdentification > &curr_pep_ids)MzTabprotectedstatic
comment_rows_MzTabprotected
empty_rows_MzTabprotected
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")MzTabstatic
exportFeatureMapToMzTab(const FeatureMap &feature_map, const String &filename)MzTabstatic
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")MzTabstatic
extractModificationList(const PeptideHit &pep_hit, const std::vector< String > &fixed_mods, const std::vector< String > &localization_mods)MzTabstatic
generateMzTabStringFromFixedModifications(const std::vector< String > &mods)MzTabstatic
generateMzTabStringFromModifications(const std::vector< String > &mods)MzTabstatic
generateMzTabStringFromVariableModifications(const std::vector< String > &mods)MzTabstatic
getCommentRows() constMzTab
getConsensusMapMetaValues_(const ConsensusMap &consensus_map, std::set< String > &consensus_feature_user_value_keys, std::set< String > &peptide_hit_user_value_keys)MzTabprotectedstatic
getEmptyRows() constMzTab
getFeatureMapMetaValues_(const FeatureMap &feature_map, std::set< String > &feature_user_value_keys, std::set< String > &peptide_hit_user_value_keys)MzTabprotectedstatic
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)MzTabprotectedstatic
getMetaData() constMzTab
getModificationIdentifier_(const ResidueModification &r)MzTabprotectedstatic
getMSRunSpectrumIdentifierType_(const std::vector< const PeptideIdentification * > &peptide_ids_)MzTabprotectedstatic
getNucleicAcidOptionalColumnNames() constMzTab
getNucleicAcidSectionRows() constMzTab
getOligonucleotideOptionalColumnNames() constMzTab
getOligonucleotideSectionRows() constMzTab
getOptionalColumnNames_(const SectionRows &rows) constMzTabinlineprotected
getOSMOptionalColumnNames() constMzTab
getOSMSectionRows() constMzTab
getPeptideOptionalColumnNames() constMzTab
getPeptideSectionRows()MzTab
getPeptideSectionRows() constMzTab
getProteinOptionalColumnNames() constMzTab
getProteinScoreType_(const ProteinIdentification &prot_id)MzTabprotectedstatic
getProteinSectionRows()MzTab
getProteinSectionRows() constMzTab
getPSMOptionalColumnNames() constMzTab
getPSMSectionRows()MzTab
getPSMSectionRows() constMzTab
getQuantStudyVariables_(const ProteinIdentification &pid)MzTabprotectedstatic
getSearchModifications_(const std::vector< const ProteinIdentification * > &prot_ids, StringList &var_mods, StringList &fixed_mods)MzTabprotectedstatic
getSmallMoleculeOptionalColumnNames() constMzTab
getSmallMoleculeSectionRows() constMzTab
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)MzTabprotectedstatic
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)MzTabprotectedstatic
mapGroupsToProteins_(const std::vector< ProteinIdentification::ProteinGroup > &groups, const std::vector< ProteinHit > &proteins)MzTabprotectedstatic
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)MzTabprotectedstatic
mapIDRunIdentifier2IDRunIndex_(const std::vector< const ProteinIdentification * > &prot_ids)MzTabprotectedstatic
meta_data_MzTabprotected
MzTab()=defaultMzTab
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)MzTabprotectedstatic
nextProteinSectionRowFromProteinGroup_(const ProteinIdentification::ProteinGroup &group, const MzTabString &db, const MzTabString &db_version)MzTabprotectedstatic
nucleic_acid_data_MzTabprotected
oligonucleotide_data_MzTabprotected
osm_data_MzTabprotected
peptide_data_MzTabprotected
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)MzTabprotectedstatic
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)MzTabprotectedstatic
protein_data_MzTabprotected
proteinSectionRowFromProteinHit_(const ProteinHit &hit, const MzTabString &db, const MzTabString &db_version, const std::set< String > &protein_hit_user_value_keys)MzTabprotectedstatic
psm_data_MzTabprotected
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)MzTabprotectedstatic
replaceWhiteSpaces_(ForwardIterator first, ForwardIterator last)MzTabinlineprotectedstatic
replaceWhiteSpaces_(std::set< String > &keys)MzTabinlineprotectedstatic
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_MzTabprotected
~MzTab()=defaultMzTab