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OpenMS
2.8.0
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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) | MzTabFile | protectedstatic |
| createProteinToPeptideLinks_(const std::map< String, std::vector< PeptideIdentification > > &map_run_to_pepids, MapAccPepType &map_run_accession_to_pephits) | MzTabFile | protectedstatic |
| extractIndexPairsFromBrackets_(const String &s) | MzTabFile | protectedstatic |
| extractNumberOfSubSamples_(const std::map< String, std::vector< ProteinIdentification > > &map_run_to_proids) | MzTabFile | protectedstatic |
| extractNumPeptides_(const String &common_identifier, const String &protein_accession, const MapAccPepType &map_run_accession_to_peptides) | MzTabFile | protectedstatic |
| extractNumPeptidesDistinct_(String common_identifier, String protein_accession, const MapAccPepType &map_run_accession_to_peptides) | MzTabFile | protectedstatic |
| extractNumPeptidesUnambiguous_(String common_identifier, String protein_accession, const MapAccPepType &map_run_accession_to_peptides) | MzTabFile | protectedstatic |
| extractPeptideModifications_(const PeptideHit &peptide_hit) | MzTabFile | protectedstatic |
| extractProteinAccession_(const PeptideHit &peptide_hit) | MzTabFile | protectedstatic |
| generateMzTabMetaDataSection_(const MzTabMetaData &map, StringList &sl) const | MzTabFile | protected |
| 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) const | MzTabFile | protected |
| 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) const | MzTabFile | protected |
| generateMzTabOSMHeader_(Size n_search_engine_scores, const std::vector< String > &optional_columns, size_t &n_columns) const | MzTabFile | protected |
| 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) const | MzTabFile | protected |
| 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) const | MzTabFile | protected |
| generateMzTabPSMHeader_(Size n_search_engine_scores, const std::vector< String > &optional_columns, size_t &n_columns) const | MzTabFile | protected |
| generateMzTabSection_(const std::vector< SectionRow > &rows, const std::vector< String > &optional_columns, const MzTabMetaData &meta, StringList &output, size_t n_header_columns) const | MzTabFile | inlineprotected |
| generateMzTabSectionRow_(const MzTabProteinSectionRow &row, const std::vector< String > &optional_columns, const MzTabMetaData &meta, size_t &n_columns) const | MzTabFile | protected |
| generateMzTabSectionRow_(const MzTabPeptideSectionRow &row, const std::vector< String > &optional_columns, const MzTabMetaData &meta, size_t &n_columns) const | MzTabFile | protected |
| generateMzTabSectionRow_(const MzTabPSMSectionRow &row, const std::vector< String > &optional_columns, const MzTabMetaData &meta, size_t &n_columns) const | MzTabFile | protected |
| generateMzTabSectionRow_(const MzTabSmallMoleculeSectionRow &row, const std::vector< String > &optional_columns, const MzTabMetaData &meta, size_t &n_columns) const | MzTabFile | protected |
| generateMzTabSectionRow_(const MzTabNucleicAcidSectionRow &row, const std::vector< String > &optional_columns, const MzTabMetaData &meta, size_t &n_columns) const | MzTabFile | protected |
| generateMzTabSectionRow_(const MzTabOligonucleotideSectionRow &row, const std::vector< String > &optional_columns, const MzTabMetaData &meta, size_t &n_columns) const | MzTabFile | protected |
| generateMzTabSectionRow_(const MzTabOSMSectionRow &row, const std::vector< String > &optional_columns, const MzTabMetaData &meta, size_t &n_columns) const | MzTabFile | protected |
| 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) const | MzTabFile | protected |
| keepFirstPSM_(std::vector< PeptideIdentification >::iterator begin, std::vector< PeptideIdentification >::iterator end) | MzTabFile | protectedstatic |
| load(const String &filename, MzTab &mz_tab) | MzTabFile | |
| MapAccPepType typedef | MzTabFile | |
| mapSearchEngineScoreToCvParam_(const String &openms_search_engine_name, double score, String score_type) | MzTabFile | protectedstatic |
| mapSearchEngineToCvParam_(const String &openms_search_engine_name) | MzTabFile | protectedstatic |
| MzTabFile() | MzTabFile | |
| MzTabMFile class | MzTabFile | friend |
| 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) | MzTabFile | protectedstatic |
| sortPSM_(std::vector< PeptideIdentification >::iterator begin, std::vector< PeptideIdentification >::iterator end) | MzTabFile | protectedstatic |
| store(const String &filename, const MzTab &mz_tab) const | MzTabFile | |
| 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) const | MzTabFile | |
| store_nucleic_acid_goterms_ | MzTabFile | protected |
| store_nucleic_acid_reliability_ | MzTabFile | protected |
| store_nucleic_acid_uri_ | MzTabFile | protected |
| store_oligonucleotide_reliability_ | MzTabFile | protected |
| store_oligonucleotide_uri_ | MzTabFile | protected |
| store_osm_reliability_ | MzTabFile | protected |
| store_osm_uri_ | MzTabFile | protected |
| store_peptide_reliability_ | MzTabFile | protected |
| store_peptide_uri_ | MzTabFile | protected |
| store_protein_goterms_ | MzTabFile | protected |
| store_protein_reliability_ | MzTabFile | protected |
| store_protein_uri_ | MzTabFile | protected |
| store_psm_reliability_ | MzTabFile | protected |
| store_psm_uri_ | MzTabFile | protected |
| store_smallmolecule_reliability_ | MzTabFile | protected |
| store_smallmolecule_uri_ | MzTabFile | protected |
| 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) | MzTabFile | protectedstatic |
| 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) | MzTabFile | protectedstatic |
| writeProteinHeader_(SVOutStream &output, std::map< String, Size > n_sub_samples) | MzTabFile | protectedstatic |
| ~MzTabFile() | MzTabFile |
1.9.1
