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void | generateMzTabMetaDataSection_ (const MzTabMetaData &map, StringList &sl) const |
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String | generateMzTabProteinHeader_ (const MzTabProteinSectionRow &reference_row, const Size n_best_search_engine_scores, const std::vector< String > &optional_columns) const |
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String | generateMzTabSectionRow_ (const MzTabProteinSectionRow &row, const std::vector< String > &optional_columns) const |
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String | 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 |
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String | generateMzTabSectionRow_ (const MzTabPeptideSectionRow &row, const std::vector< String > &optional_columns) const |
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String | generateMzTabPSMHeader_ (Size n_search_engine_scores, const std::vector< String > &optional_columns) const |
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String | generateMzTabSectionRow_ (const MzTabPSMSectionRow &row, const std::vector< String > &optional_columns) const |
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String | 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 |
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String | generateMzTabSectionRow_ (const MzTabSmallMoleculeSectionRow &row, const std::vector< String > &optional_columns) const |
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String | generateMzTabNucleicAcidHeader_ (Size search_ms_runs, Size n_best_search_engine_scores, Size n_search_engine_scores, const std::vector< String > &optional_columns) const |
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String | generateMzTabSectionRow_ (const MzTabNucleicAcidSectionRow &row, const std::vector< String > &optional_columns) const |
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String | generateMzTabOligonucleotideHeader_ (Size search_ms_runs, Size n_best_search_engine_scores, Size n_search_engine_score, const std::vector< String > &optional_columns) const |
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String | generateMzTabSectionRow_ (const MzTabOligonucleotideSectionRow &row, const std::vector< String > &optional_columns) const |
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String | generateMzTabOSMHeader_ (Size n_search_engine_scores, const std::vector< String > &optional_columns) const |
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String | generateMzTabSectionRow_ (const MzTabOSMSectionRow &row, const std::vector< String > &optional_columns) const |
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template<typename SectionRow > |
void | generateMzTabSection_ (const std::vector< SectionRow > &rows, const std::vector< String > &optional_columns, StringList &output) const |
| Generate an mzTab section comprising multiple rows of the same type. More...
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static void | addOptionalColumnsToSectionRow_ (const std::vector< String > &column_names, const std::vector< MzTabOptionalColumnEntry > &column_entries, StringList &output) |
| Helper function for "generateMzTabSectionRow_" functions. More...
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static std::pair< int, int > | extractIndexPairsFromBrackets_ (const String &s) |
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static void | sortPSM_ (std::vector< PeptideIdentification >::iterator begin, std::vector< PeptideIdentification >::iterator end) |
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static void | keepFirstPSM_ (std::vector< PeptideIdentification >::iterator begin, std::vector< PeptideIdentification >::iterator end) |
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static void | 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) |
| Extract protein and peptide identifications for each run. maps are assumed empty. More...
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static void | createProteinToPeptideLinks_ (const std::map< String, std::vector< PeptideIdentification > > &map_run_to_pepids, MapAccPepType &map_run_accession_to_pephits) |
| create links from protein to peptides More...
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static String | extractProteinAccession_ (const PeptideHit &peptide_hit) |
| Extracts, if possible a unique protein accession for a peptide hit in mzTab format. Otherwise NA is returned. More...
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static String | extractPeptideModifications_ (const PeptideHit &peptide_hit) |
| Extracts, modifications and positions of a peptide hit in mzTab format. More...
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static String | mapSearchEngineToCvParam_ (const String &openms_search_engine_name) |
| Map search engine identifier to CV, param etc. More...
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static String | mapSearchEngineScoreToCvParam_ (const String &openms_search_engine_name, double score, String score_type) |
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static String | extractNumPeptides_ (const String &common_identifier, const String &protein_accession, const MapAccPepType &map_run_accession_to_peptides) |
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static String | extractNumPeptidesDistinct_ (String common_identifier, String protein_accession, const MapAccPepType &map_run_accession_to_peptides) |
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static String | extractNumPeptidesUnambiguous_ (String common_identifier, String protein_accession, const MapAccPepType &map_run_accession_to_peptides) |
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static std::map< String, Size > | extractNumberOfSubSamples_ (const std::map< String, std::vector< ProteinIdentification > > &map_run_to_proids) |
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static void | writePeptideHeader_ (SVOutStream &output, std::map< String, Size > n_sub_samples) |
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static void | writeProteinHeader_ (SVOutStream &output, std::map< String, Size > n_sub_samples) |
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static void | 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) |
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File adapter for MzTab files.