OpenMS  2.8.0
MzTabFile Member List

This is the complete list of members for MzTabFile, including all inherited members.

addOptionalColumnsToSectionRow_(const std::vector< String > &column_names, const std::vector< MzTabOptionalColumnEntry > &column_entries, StringList &output)MzTabFileprotectedstatic
createProteinToPeptideLinks_(const std::map< String, std::vector< PeptideIdentification > > &map_run_to_pepids, MapAccPepType &map_run_accession_to_pephits)MzTabFileprotectedstatic
extractIndexPairsFromBrackets_(const String &s)MzTabFileprotectedstatic
extractNumberOfSubSamples_(const std::map< String, std::vector< ProteinIdentification > > &map_run_to_proids)MzTabFileprotectedstatic
extractNumPeptides_(const String &common_identifier, const String &protein_accession, const MapAccPepType &map_run_accession_to_peptides)MzTabFileprotectedstatic
extractNumPeptidesDistinct_(String common_identifier, String protein_accession, const MapAccPepType &map_run_accession_to_peptides)MzTabFileprotectedstatic
extractNumPeptidesUnambiguous_(String common_identifier, String protein_accession, const MapAccPepType &map_run_accession_to_peptides)MzTabFileprotectedstatic
extractPeptideModifications_(const PeptideHit &peptide_hit)MzTabFileprotectedstatic
extractProteinAccession_(const PeptideHit &peptide_hit)MzTabFileprotectedstatic
generateMzTabMetaDataSection_(const MzTabMetaData &map, StringList &sl) constMzTabFileprotected
generateMzTabNucleicAcidHeader_(Size search_ms_runs, Size n_best_search_engine_scores, Size n_search_engine_scores, const std::vector< String > &optional_columns, size_t &n_columns) constMzTabFileprotected
generateMzTabOligonucleotideHeader_(Size search_ms_runs, Size n_best_search_engine_scores, Size n_search_engine_score, const std::vector< String > &optional_columns, size_t &n_columns) constMzTabFileprotected
generateMzTabOSMHeader_(Size n_search_engine_scores, const std::vector< String > &optional_columns, size_t &n_columns) constMzTabFileprotected
generateMzTabPeptideHeader_(Size search_ms_runs, Size n_best_search_engine_scores, Size n_search_engine_score, Size assays, Size study_variables, const std::vector< String > &optional_columns, size_t &n_columns) constMzTabFileprotected
generateMzTabProteinHeader_(const MzTabProteinSectionRow &reference_row, const Size n_best_search_engine_scores, const std::vector< String > &optional_columns, const MzTabMetaData &meta, size_t &n_columns) constMzTabFileprotected
generateMzTabPSMHeader_(Size n_search_engine_scores, const std::vector< String > &optional_columns, size_t &n_columns) constMzTabFileprotected
generateMzTabSection_(const std::vector< SectionRow > &rows, const std::vector< String > &optional_columns, const MzTabMetaData &meta, StringList &output, size_t n_header_columns) constMzTabFileinlineprotected
generateMzTabSectionRow_(const MzTabProteinSectionRow &row, const std::vector< String > &optional_columns, const MzTabMetaData &meta, size_t &n_columns) constMzTabFileprotected
generateMzTabSectionRow_(const MzTabPeptideSectionRow &row, const std::vector< String > &optional_columns, const MzTabMetaData &meta, size_t &n_columns) constMzTabFileprotected
generateMzTabSectionRow_(const MzTabPSMSectionRow &row, const std::vector< String > &optional_columns, const MzTabMetaData &meta, size_t &n_columns) constMzTabFileprotected
generateMzTabSectionRow_(const MzTabSmallMoleculeSectionRow &row, const std::vector< String > &optional_columns, const MzTabMetaData &meta, size_t &n_columns) constMzTabFileprotected
generateMzTabSectionRow_(const MzTabNucleicAcidSectionRow &row, const std::vector< String > &optional_columns, const MzTabMetaData &meta, size_t &n_columns) constMzTabFileprotected
generateMzTabSectionRow_(const MzTabOligonucleotideSectionRow &row, const std::vector< String > &optional_columns, const MzTabMetaData &meta, size_t &n_columns) constMzTabFileprotected
generateMzTabSectionRow_(const MzTabOSMSectionRow &row, const std::vector< String > &optional_columns, const MzTabMetaData &meta, size_t &n_columns) constMzTabFileprotected
generateMzTabSmallMoleculeHeader_(Size search_ms_runs, Size n_best_search_engine_scores, Size n_search_engine_score, Size assays, Size study_variables, const std::vector< String > &optional_columns, size_t &n_columns) constMzTabFileprotected
keepFirstPSM_(std::vector< PeptideIdentification >::iterator begin, std::vector< PeptideIdentification >::iterator end)MzTabFileprotectedstatic
load(const String &filename, MzTab &mz_tab)MzTabFile
MapAccPepType typedefMzTabFile
mapSearchEngineScoreToCvParam_(const String &openms_search_engine_name, double score, String score_type)MzTabFileprotectedstatic
mapSearchEngineToCvParam_(const String &openms_search_engine_name)MzTabFileprotectedstatic
MzTabFile()MzTabFile
MzTabMFile classMzTabFilefriend
partitionIntoRuns_(const std::vector< PeptideIdentification > &pep_ids, const std::vector< ProteinIdentification > &pro_ids, std::map< String, std::vector< PeptideIdentification > > &map_run_to_pepids, std::map< String, std::vector< ProteinIdentification > > &map_run_to_proids)MzTabFileprotectedstatic
sortPSM_(std::vector< PeptideIdentification >::iterator begin, std::vector< PeptideIdentification >::iterator end)MzTabFileprotectedstatic
store(const String &filename, const MzTab &mz_tab) constMzTabFile
store(const String &filename, const std::vector< ProteinIdentification > &protein_identifications, const std::vector< PeptideIdentification > &peptide_identifications, bool first_run_inference_only, bool export_empty_pep_ids=false, bool export_all_psms=false, const String &title="ID export from OpenMS")MzTabFile
store(const String &filename, const ConsensusMap &cmap, 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) constMzTabFile
store_nucleic_acid_goterms_MzTabFileprotected
store_nucleic_acid_reliability_MzTabFileprotected
store_nucleic_acid_uri_MzTabFileprotected
store_oligonucleotide_reliability_MzTabFileprotected
store_oligonucleotide_uri_MzTabFileprotected
store_osm_reliability_MzTabFileprotected
store_osm_uri_MzTabFileprotected
store_peptide_reliability_MzTabFileprotected
store_peptide_uri_MzTabFileprotected
store_protein_goterms_MzTabFileprotected
store_protein_reliability_MzTabFileprotected
store_protein_uri_MzTabFileprotected
store_psm_reliability_MzTabFileprotected
store_psm_uri_MzTabFileprotected
store_smallmolecule_reliability_MzTabFileprotected
store_smallmolecule_uri_MzTabFileprotected
storePeptideReliabilityColumn(bool store)MzTabFile
storePeptideUriColumn(bool store)MzTabFile
storeProteinGoTerms(bool store)MzTabFile
storeProteinReliabilityColumn(bool store)MzTabFile
storeProteinUriColumn(bool store)MzTabFile
storePSMReliabilityColumn(bool store)MzTabFile
storePSMUriColumn(bool store)MzTabFile
storeSmallMoleculeReliabilityColumn(bool store)MzTabFile
storeSmallMoleculeUriColumn(bool store)MzTabFile
writePeptideHeader_(SVOutStream &output, std::map< String, Size > n_sub_samples)MzTabFileprotectedstatic
writeProteinData_(SVOutStream &output, const ProteinIdentification &prot_id, Size run_count, String input_filename, bool has_coverage, const MapAccPepType &map_run_accession_to_peptides, const std::map< String, Size > &map_run_to_num_sub)MzTabFileprotectedstatic
writeProteinHeader_(SVOutStream &output, std::map< String, Size > n_sub_samples)MzTabFileprotectedstatic
~MzTabFile()MzTabFile