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	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) 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	inlineprotected
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	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
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_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