OpenMS  2.4.0
MzTabFile Member List

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

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
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) constMzTabFileprotected
generateMzTabPeptideSection_(const MzTabPeptideSectionRows &rows, StringList &sl, const std::vector< String > &optional_columns) constMzTabFileprotected
generateMzTabPeptideSectionRow_(const MzTabPeptideSectionRow &row, const std::vector< String > &optional_columns) constMzTabFileprotected
generateMzTabProteinHeader_(const MzTabProteinSectionRow &reference_row, const Size n_best_search_engine_scores, const std::vector< String > &optional_columns) constMzTabFileprotected
generateMzTabProteinSection_(const MzTabProteinSectionRows &rows, StringList &sl, const std::vector< String > &optional_columns) constMzTabFileprotected
generateMzTabProteinSectionRow_(const MzTabProteinSectionRow &row, const std::vector< String > &optional_columns) constMzTabFileprotected
generateMzTabPSMHeader_(Size n_search_engine_scores, const std::vector< String > &optional_columns) constMzTabFileprotected
generateMzTabPSMSection_(const MzTabPSMSectionRows &rows, StringList &sl, const std::vector< String > &optional_columns) constMzTabFileprotected
generateMzTabPSMSectionRow_(const MzTabPSMSectionRow &row, const std::vector< String > &optional_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) constMzTabFileprotected
generateMzTabSmallMoleculeSection_(const MzTabSmallMoleculeSectionRows &map, StringList &sl, const std::vector< String > &optional_columns) constMzTabFileprotected
generateMzTabSmallMoleculeSectionRow_(const MzTabSmallMoleculeSectionRow &row, const std::vector< String > &optional_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
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_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