| OpenMS 2.5.0

Public Types | Public Member Functions | Protected Member Functions | Static Protected Member Functions | Protected Attributes | List of all members
MzTabFile Class Reference
Format » File IO

File adapter for MzTab files. More...

`#include <OpenMS/FORMAT/MzTabFile.h>`

## Public Types

typedef std::map< std::pair< String, String >, std::vector< PeptideHit > > | MapAccPepType

## Public Member Functions

| MzTabFile ()
| Default constructor. More...
| ~MzTabFile ()
| Destructor. More...
void | store (const String &filename, const MzTab &mz_tab) const
void | storeProteinReliabilityColumn (bool store)
void | storePeptideReliabilityColumn (bool store)
void | storePSMReliabilityColumn (bool store)
void | storeSmallMoleculeReliabilityColumn (bool store)
void | storeProteinUriColumn (bool store)
void | storePeptideUriColumn (bool store)
void | storePSMUriColumn (bool store)
void | storeSmallMoleculeUriColumn (bool store)
void | storeProteinGoTerms (bool store)
void | load (const String &filename, MzTab &mz_tab)

## Protected Member Functions

void | generateMzTabMetaDataSection_ (const MzTabMetaData &map, StringList &sl) const
String | generateMzTabProteinHeader_ (const MzTabProteinSectionRow &reference_row, const Size n_best_search_engine_scores, const std::vector< String > &optional_columns) const
String | generateMzTabSectionRow_ (const MzTabProteinSectionRow &row, const std::vector< String > &optional_columns) const
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
String | generateMzTabSectionRow_ (const MzTabPeptideSectionRow &row, const std::vector< String > &optional_columns) const
String | generateMzTabPSMHeader_ (Size n_search_engine_scores, const std::vector< String > &optional_columns) const
String | generateMzTabSectionRow_ (const MzTabPSMSectionRow &row, const std::vector< String > &optional_columns) const
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
String | generateMzTabSectionRow_ (const MzTabSmallMoleculeSectionRow &row, const std::vector< String > &optional_columns) const
String | generateMzTabNucleicAcidHeader_ (Size search_ms_runs, Size n_best_search_engine_scores, Size n_search_engine_scores, const std::vector< String > &optional_columns) const
String | generateMzTabSectionRow_ (const MzTabNucleicAcidSectionRow &row, const std::vector< String > &optional_columns) const
String | generateMzTabOligonucleotideHeader_ (Size search_ms_runs, Size n_best_search_engine_scores, Size n_search_engine_score, const std::vector< String > &optional_columns) const
String | generateMzTabSectionRow_ (const MzTabOligonucleotideSectionRow &row, const std::vector< String > &optional_columns) const
String | generateMzTabOSMHeader_ (Size n_search_engine_scores, const std::vector< String > &optional_columns) const
String | generateMzTabSectionRow_ (const MzTabOSMSectionRow &row, const std::vector< String > &optional_columns) const
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...

## Static Protected Member Functions

static void | addOptionalColumnsToSectionRow_ (const std::vector< String > &column_names, const std::vector< MzTabOptionalColumnEntry > &column_entries, StringList &output)
| Helper function for "generateMzTabSectionRow_" functions. More...
static std::pair< int, int > | extractIndexPairsFromBrackets_ (const String &s)
static void | sortPSM_ (std::vector< PeptideIdentification >::iterator begin, std::vector< PeptideIdentification >::iterator end)
static void | keepFirstPSM_ (std::vector< PeptideIdentification >::iterator begin, std::vector< PeptideIdentification >::iterator end)
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...
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...
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...
static String | extractPeptideModifications_ (const PeptideHit &peptide_hit)
| Extracts, modifications and positions of a peptide hit in mzTab format. More...
static String | mapSearchEngineToCvParam_ (const String &openms_search_engine_name)
| Map search engine identifier to CV, param etc. More...
static String | mapSearchEngineScoreToCvParam_ (const String &openms_search_engine_name, double score, String score_type)
static String | extractNumPeptides_ (const String &common_identifier, const String &protein_accession, const MapAccPepType &map_run_accession_to_peptides)
static String | extractNumPeptidesDistinct_ (String common_identifier, String protein_accession, const MapAccPepType &map_run_accession_to_peptides)
static String | extractNumPeptidesUnambiguous_ (String common_identifier, String protein_accession, const MapAccPepType &map_run_accession_to_peptides)
static std::map< String, Size > | extractNumberOfSubSamples_ (const std::map< String, std::vector< ProteinIdentification > > &map_run_to_proids)
static void | writePeptideHeader_ (SVOutStream &output, std::map< String, Size > n_sub_samples)
static void | writeProteinHeader_ (SVOutStream &output, std::map< String, Size > n_sub_samples)
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)

## Protected Attributes

bool | store_protein_reliability_
bool | store_peptide_reliability_
bool | store_psm_reliability_
bool | store_smallmolecule_reliability_
bool | store_protein_uri_
bool | store_peptide_uri_
bool | store_psm_uri_
bool | store_smallmolecule_uri_
bool | store_protein_goterms_
bool | store_nucleic_acid_reliability_
bool | store_oligonucleotide_reliability_
bool | store_osm_reliability_
bool | store_nucleic_acid_uri_
bool | store_oligonucleotide_uri_
bool | store_osm_uri_
bool | store_nucleic_acid_goterms_

## Detailed Description

File adapter for MzTab files.

## Member Typedef Documentation

## ◆ MapAccPepType

typedef std::map<std::pair<String, String>, std::vector<PeptideHit> > MapAccPepType

## Constructor & Destructor Documentation

## ◆ MzTabFile()

MzTabFile | ( |  | ) |

Default constructor.

## ◆ ~MzTabFile()

~MzTabFile | ( |  | ) |

Destructor.

## Member Function Documentation

## ◆ addOptionalColumnsToSectionRow_()

static void addOptionalColumnsToSectionRow_ | ( | const std::vector< String > & | column_names,
|  | const std::vector< MzTabOptionalColumnEntry > & | column_entries,
|  | StringList & | output
| ) |  |

static protected

Helper function for "generateMzTabSectionRow_" functions.

## ◆ createProteinToPeptideLinks_()

static void createProteinToPeptideLinks_ | ( | const std::map< String, std::vector< PeptideIdentification > > & | map_run_to_pepids,
|  | MapAccPepType & | map_run_accession_to_pephits
| ) |  |

static protected

create links from protein to peptides

## ◆ extractIndexPairsFromBrackets_()

static std::pair<int, int> extractIndexPairsFromBrackets_ | ( | const String & | s | ) |

static protected

## ◆ extractNumberOfSubSamples_()

static std::map<String, Size> extractNumberOfSubSamples_ | ( | const std::map< String, std::vector< ProteinIdentification > > & | map_run_to_proids | ) |

static protected

## ◆ extractNumPeptides_()

static String extractNumPeptides_ | ( | const String & | common_identifier,
|  | const String & | protein_accession,
|  | const MapAccPepType & | map_run_accession_to_peptides
| ) |  |

static protected

## ◆ extractNumPeptidesDistinct_()

static String extractNumPeptidesDistinct_ | ( | String | common_identifier,
|  | String | protein_accession,
|  | const MapAccPepType & | map_run_accession_to_peptides
| ) |  |

static protected

## ◆ extractNumPeptidesUnambiguous_()

static String extractNumPeptidesUnambiguous_ | ( | String | common_identifier,
|  | String | protein_accession,
|  | const MapAccPepType & | map_run_accession_to_peptides
| ) |  |

static protected

## ◆ extractPeptideModifications_()

static String extractPeptideModifications_ | ( | const PeptideHit & | peptide_hit | ) |

static protected

Extracts, modifications and positions of a peptide hit in mzTab format.

## ◆ extractProteinAccession_()

static String extractProteinAccession_ | ( | const PeptideHit & | peptide_hit | ) |

static protected

Extracts, if possible a unique protein accession for a peptide hit in mzTab format. Otherwise NA is returned.

## ◆ generateMzTabMetaDataSection_()

void generateMzTabMetaDataSection_ | ( | const MzTabMetaData & | map,
|  | StringList & | sl
| ) |  | const

protected

## ◆ generateMzTabNucleicAcidHeader_()

String generateMzTabNucleicAcidHeader_ | ( | Size | search_ms_runs,
|  | Size | n_best_search_engine_scores,
|  | Size | n_search_engine_scores,
|  | const std::vector< String > & | optional_columns
| ) |  | const

protected

## ◆ generateMzTabOligonucleotideHeader_()

String generateMzTabOligonucleotideHeader_ | ( | Size | search_ms_runs,
|  | Size | n_best_search_engine_scores,
|  | Size | n_search_engine_score,
|  | const std::vector< String > & | optional_columns
| ) |  | const

protected

## ◆ generateMzTabOSMHeader_()

String generateMzTabOSMHeader_ | ( | Size | n_search_engine_scores,
|  | const std::vector< String > & | optional_columns
| ) |  | const

protected

## ◆ generateMzTabPeptideHeader_()

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

protected

## ◆ generateMzTabProteinHeader_()

String generateMzTabProteinHeader_ | ( | const MzTabProteinSectionRow & | reference_row,
|  | const Size | n_best_search_engine_scores,
|  | const std::vector< String > & | optional_columns
| ) |  | const

protected

## ◆ generateMzTabPSMHeader_()

String generateMzTabPSMHeader_ | ( | Size | n_search_engine_scores,
|  | const std::vector< String > & | optional_columns
| ) |  | const

protected

## ◆ generateMzTabSection_()

void generateMzTabSection_ | ( | const std::vector< SectionRow > & | rows,
|  | const std::vector< String > & | optional_columns,
|  | StringList & | output
| ) |  | const

inline protected

Generate an mzTab section comprising multiple rows of the same type.

## ◆ generateMzTabSectionRow_() [1/7]

String generateMzTabSectionRow_ | ( | const MzTabProteinSectionRow & | row,
|  | const std::vector< String > & | optional_columns
| ) |  | const

protected

## ◆ generateMzTabSectionRow_() [2/7]

String generateMzTabSectionRow_ | ( | const MzTabPeptideSectionRow & | row,
|  | const std::vector< String > & | optional_columns
| ) |  | const

protected

## ◆ generateMzTabSectionRow_() [3/7]

String generateMzTabSectionRow_ | ( | const MzTabPSMSectionRow & | row,
|  | const std::vector< String > & | optional_columns
| ) |  | const

protected

## ◆ generateMzTabSectionRow_() [4/7]

String generateMzTabSectionRow_ | ( | const MzTabSmallMoleculeSectionRow & | row,
|  | const std::vector< String > & | optional_columns
| ) |  | const

protected

## ◆ generateMzTabSectionRow_() [5/7]

String generateMzTabSectionRow_ | ( | const MzTabNucleicAcidSectionRow & | row,
|  | const std::vector< String > & | optional_columns
| ) |  | const

protected

## ◆ generateMzTabSectionRow_() [6/7]

String generateMzTabSectionRow_ | ( | const MzTabOligonucleotideSectionRow & | row,
|  | const std::vector< String > & | optional_columns
| ) |  | const

protected

## ◆ generateMzTabSectionRow_() [7/7]

String generateMzTabSectionRow_ | ( | const MzTabOSMSectionRow & | row,
|  | const std::vector< String > & | optional_columns
| ) |  | const

protected

## ◆ generateMzTabSmallMoleculeHeader_()

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

protected

## ◆ keepFirstPSM_()

static void keepFirstPSM_ | ( | std::vector< PeptideIdentification >::iterator | begin,
|  | std::vector< PeptideIdentification >::iterator | end
| ) |  |

static protected

## ◆ load()

void load | ( | const String & | filename,
|  | MzTab & | mz_tab
| ) |  |

## ◆ mapSearchEngineScoreToCvParam_()

static String mapSearchEngineScoreToCvParam_ | ( | const String & | openms_search_engine_name,
|  | double | score,
|  | String | score_type
| ) |  |

static protected

## ◆ mapSearchEngineToCvParam_()

static String mapSearchEngineToCvParam_ | ( | const String & | openms_search_engine_name | ) |

static protected

Map search engine identifier to CV, param etc.

## ◆ partitionIntoRuns_()

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
| ) |  |

static protected

Extract protein and peptide identifications for each run. maps are assumed empty.

## ◆ sortPSM_()

static void sortPSM_ | ( | std::vector< PeptideIdentification >::iterator | begin,
|  | std::vector< PeptideIdentification >::iterator | end
| ) |  |

static protected

## ◆ store()

void store | ( | const String & | filename,
|  | const MzTab & | mz_tab
| ) |  | const

Referenced by NucleicAcidSearchEngine::main_(), and UTILProteomicsLFQ::main_().

## ◆ storePeptideReliabilityColumn()

void storePeptideReliabilityColumn | ( | bool | store | ) |

## ◆ storePeptideUriColumn()

void storePeptideUriColumn | ( | bool | store | ) |

## ◆ storeProteinGoTerms()

void storeProteinGoTerms | ( | bool | store | ) |

## ◆ storeProteinReliabilityColumn()

void storeProteinReliabilityColumn | ( | bool | store | ) |

## ◆ storeProteinUriColumn()

void storeProteinUriColumn | ( | bool | store | ) |

## ◆ storePSMReliabilityColumn()

void storePSMReliabilityColumn | ( | bool | store | ) |

## ◆ storePSMUriColumn()

void storePSMUriColumn | ( | bool | store | ) |

## ◆ storeSmallMoleculeReliabilityColumn()

void storeSmallMoleculeReliabilityColumn | ( | bool | store | ) |

## ◆ storeSmallMoleculeUriColumn()

void storeSmallMoleculeUriColumn | ( | bool | store | ) |

## ◆ writePeptideHeader_()

static void writePeptideHeader_ | ( | SVOutStream & | output,
|  | std::map< String, Size > | n_sub_samples
| ) |  |

static protected

## ◆ writeProteinData_()

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
| ) |  |

static protected

## ◆ writeProteinHeader_()

static void writeProteinHeader_ | ( | SVOutStream & | output,
|  | std::map< String, Size > | n_sub_samples
| ) |  |

static protected

## Member Data Documentation

## ◆ store_nucleic_acid_goterms_

bool store_nucleic_acid_goterms_

protected

## ◆ store_nucleic_acid_reliability_

bool store_nucleic_acid_reliability_

protected

## ◆ store_nucleic_acid_uri_

bool store_nucleic_acid_uri_

protected

## ◆ store_oligonucleotide_reliability_

bool store_oligonucleotide_reliability_

protected

## ◆ store_oligonucleotide_uri_

bool store_oligonucleotide_uri_

protected

## ◆ store_osm_reliability_

bool store_osm_reliability_

protected

## ◆ store_osm_uri_

bool store_osm_uri_

protected

## ◆ store_peptide_reliability_

bool store_peptide_reliability_

protected

## ◆ store_peptide_uri_

bool store_peptide_uri_

protected

## ◆ store_protein_goterms_

bool store_protein_goterms_

protected

## ◆ store_protein_reliability_

bool store_protein_reliability_

protected

## ◆ store_protein_uri_

bool store_protein_uri_

protected

## ◆ store_psm_reliability_

bool store_psm_reliability_

protected

## ◆ store_psm_uri_

bool store_psm_uri_

protected

## ◆ store_smallmolecule_reliability_

bool store_smallmolecule_reliability_

protected

## ◆ store_smallmolecule_uri_

bool store_smallmolecule_uri_

protected