| OpenMS 2.5.0

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) | MzTabFile | protected static
createProteinToPeptideLinks_(const std::map< String, std::vector< PeptideIdentification > > &map_run_to_pepids, MapAccPepType &map_run_accession_to_pephits) | MzTabFile | protected static
extractIndexPairsFromBrackets_(const String &s) | MzTabFile | protected static
extractNumberOfSubSamples_(const std::map< String, std::vector< ProteinIdentification > > &map_run_to_proids) | MzTabFile | protected static
extractNumPeptides_(const String &common_identifier, const String &protein_accession, const MapAccPepType &map_run_accession_to_peptides) | MzTabFile | protected static
extractNumPeptidesDistinct_(String common_identifier, String protein_accession, const MapAccPepType &map_run_accession_to_peptides) | MzTabFile | protected static
extractNumPeptidesUnambiguous_(String common_identifier, String protein_accession, const MapAccPepType &map_run_accession_to_peptides) | MzTabFile | protected static
extractPeptideModifications_(const PeptideHit &peptide_hit) | MzTabFile | protected static
extractProteinAccession_(const PeptideHit &peptide_hit) | MzTabFile | protected static
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) 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) const | MzTabFile | protected
generateMzTabOSMHeader_(Size n_search_engine_scores, const std::vector< String > &optional_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) const | MzTabFile | protected
generateMzTabProteinHeader_(const MzTabProteinSectionRow &reference_row, const Size n_best_search_engine_scores, const std::vector< String > &optional_columns) const | MzTabFile | protected
generateMzTabPSMHeader_(Size n_search_engine_scores, const std::vector< String > &optional_columns) const | MzTabFile | protected
generateMzTabSection_(const std::vector< SectionRow > &rows, const std::vector< String > &optional_columns, StringList &output) const | MzTabFile | inline protected
generateMzTabSectionRow_(const MzTabProteinSectionRow &row, const std::vector< String > &optional_columns) const | MzTabFile | protected
generateMzTabSectionRow_(const MzTabPeptideSectionRow &row, const std::vector< String > &optional_columns) const | MzTabFile | protected
generateMzTabSectionRow_(const MzTabPSMSectionRow &row, const std::vector< String > &optional_columns) const | MzTabFile | protected
generateMzTabSectionRow_(const MzTabSmallMoleculeSectionRow &row, const std::vector< String > &optional_columns) const | MzTabFile | protected
generateMzTabSectionRow_(const MzTabNucleicAcidSectionRow &row, const std::vector< String > &optional_columns) const | MzTabFile | protected
generateMzTabSectionRow_(const MzTabOligonucleotideSectionRow &row, const std::vector< String > &optional_columns) const | MzTabFile | protected
generateMzTabSectionRow_(const MzTabOSMSectionRow &row, const std::vector< String > &optional_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) const | MzTabFile | protected
keepFirstPSM_(std::vector< PeptideIdentification >::iterator begin, std::vector< PeptideIdentification >::iterator end) | MzTabFile | protected static
load(const String &filename, MzTab &mz_tab) | MzTabFile |
MapAccPepType typedef | MzTabFile |
mapSearchEngineScoreToCvParam_(const String &openms_search_engine_name, double score, String score_type) | MzTabFile | protected static
mapSearchEngineToCvParam_(const String &openms_search_engine_name) | MzTabFile | protected static
MzTabFile() | MzTabFile |
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 | protected static
sortPSM_(std::vector< PeptideIdentification >::iterator begin, std::vector< PeptideIdentification >::iterator end) | MzTabFile | protected static
store(const String &filename, const MzTab &mz_tab) 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 | protected static
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 | protected static
writeProteinHeader_(SVOutStream &output, std::map< String, Size > n_sub_samples) | MzTabFile | protected static
~MzTabFile() | MzTabFile |