#include <OpenMS/FORMAT/MzTabFile.h>

Collaboration diagram for MzTabFile:

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	store (const String &filename, const std::vector< ProteinIdentification > &protein_identifications, const std::vector< PeptideIdentification > &peptide_identifications, bool first_run_inference_only, bool export_empty_pep_ids=false, bool export_all_psms=false, const String &title="ID export from OpenMS")

void	store (const String &filename, const ConsensusMap &cmap, const bool first_run_inference_only, const bool export_unidentified_features, const bool export_unassigned_ids, const bool export_subfeatures, const bool export_empty_pep_ids=false, const bool export_all_psms=false) 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 MzTabMetaData &meta, size_t &n_columns) const

String	generateMzTabSectionRow_ (const MzTabProteinSectionRow &row, const std::vector< String > &optional_columns, const MzTabMetaData &meta, size_t &n_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, size_t &n_columns) const

String	generateMzTabSectionRow_ (const MzTabPeptideSectionRow &row, const std::vector< String > &optional_columns, const MzTabMetaData &meta, size_t &n_columns) const

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

String	generateMzTabSectionRow_ (const MzTabPSMSectionRow &row, const std::vector< String > &optional_columns, const MzTabMetaData &meta, size_t &n_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, size_t &n_columns) const

String	generateMzTabSectionRow_ (const MzTabSmallMoleculeSectionRow &row, const std::vector< String > &optional_columns, const MzTabMetaData &meta, size_t &n_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, size_t &n_columns) const

String	generateMzTabSectionRow_ (const MzTabNucleicAcidSectionRow &row, const std::vector< String > &optional_columns, const MzTabMetaData &meta, size_t &n_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, size_t &n_columns) const

String	generateMzTabSectionRow_ (const MzTabOligonucleotideSectionRow &row, const std::vector< String > &optional_columns, const MzTabMetaData &meta, size_t &n_columns) const

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

String	generateMzTabSectionRow_ (const MzTabOSMSectionRow &row, const std::vector< String > &optional_columns, const MzTabMetaData &meta, size_t &n_columns) const

template<typename SectionRow >
void	generateMzTabSection_ (const std::vector< SectionRow > &rows, const std::vector< String > &optional_columns, const MzTabMetaData &meta, StringList &output, size_t n_header_columns) const
	Generate an mzTab section comprising multiple rows of the same type and perform sanity check. 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_

Friends
class	MzTabMFile

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
	)

staticprotected

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
	)

staticprotected

create links from protein to peptides

◆ extractIndexPairsFromBrackets_()

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

staticprotected

◆ extractNumberOfSubSamples_()

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

staticprotected

◆ extractNumPeptides_()

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

staticprotected

◆ extractNumPeptidesDistinct_()

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

staticprotected

◆ extractNumPeptidesUnambiguous_()

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

staticprotected

◆ extractPeptideModifications_()

static String extractPeptideModifications_ ( const PeptideHit & peptide_hit )

staticprotected

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

◆ extractProteinAccession_()

static String extractProteinAccession_ ( const PeptideHit & peptide_hit )

staticprotected

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,
		size_t &	n_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,
		size_t &	n_columns
	)		const

protected

◆ generateMzTabOSMHeader_()

String generateMzTabOSMHeader_	(	Size	n_search_engine_scores,
		const std::vector< String > &	optional_columns,
		size_t &	n_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,
		size_t &	n_columns
	)		const

protected

◆ generateMzTabProteinHeader_()

String generateMzTabProteinHeader_	(	const MzTabProteinSectionRow &	reference_row,
		const Size	n_best_search_engine_scores,
		const std::vector< String > &	optional_columns,
		const MzTabMetaData &	meta,
		size_t &	n_columns
	)		const

protected

Needs a reference row to get the collected optional columns from the MetaValues TODO refactor this behaviour by e.g. storing it in the MzTab object

◆ generateMzTabPSMHeader_()

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

protected

◆ generateMzTabSection_()

void generateMzTabSection_	(	const std::vector< SectionRow > &	rows,
		const std::vector< String > &	optional_columns,
		const MzTabMetaData &	meta,
		StringList &	output,
		size_t	n_header_columns
	)		const

inlineprotected

Generate an mzTab section comprising multiple rows of the same type and perform sanity check.

◆ generateMzTabSectionRow_() [1/7]

String generateMzTabSectionRow_	(	const MzTabNucleicAcidSectionRow &	row,
		const std::vector< String > &	optional_columns,
		const MzTabMetaData &	meta,
		size_t &	n_columns
	)		const

protected

◆ generateMzTabSectionRow_() [2/7]

String generateMzTabSectionRow_	(	const MzTabOligonucleotideSectionRow &	row,
		const std::vector< String > &	optional_columns,
		const MzTabMetaData &	meta,
		size_t &	n_columns
	)		const

protected

◆ generateMzTabSectionRow_() [3/7]

String generateMzTabSectionRow_	(	const MzTabOSMSectionRow &	row,
		const std::vector< String > &	optional_columns,
		const MzTabMetaData &	meta,
		size_t &	n_columns
	)		const

protected

◆ generateMzTabSectionRow_() [4/7]

String generateMzTabSectionRow_	(	const MzTabPeptideSectionRow &	row,
		const std::vector< String > &	optional_columns,
		const MzTabMetaData &	meta,
		size_t &	n_columns
	)		const

protected

◆ generateMzTabSectionRow_() [5/7]

String generateMzTabSectionRow_	(	const MzTabProteinSectionRow &	row,
		const std::vector< String > &	optional_columns,
		const MzTabMetaData &	meta,
		size_t &	n_columns
	)		const

protected

◆ generateMzTabSectionRow_() [6/7]

String generateMzTabSectionRow_	(	const MzTabPSMSectionRow &	row,
		const std::vector< String > &	optional_columns,
		const MzTabMetaData &	meta,
		size_t &	n_columns
	)		const

protected

◆ generateMzTabSectionRow_() [7/7]

String generateMzTabSectionRow_	(	const MzTabSmallMoleculeSectionRow &	row,
		const std::vector< String > &	optional_columns,
		const MzTabMetaData &	meta,
		size_t &	n_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,
		size_t &	n_columns
	)		const

protected

◆ keepFirstPSM_()

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

staticprotected

◆ load()

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

◆ mapSearchEngineScoreToCvParam_()

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

staticprotected

◆ mapSearchEngineToCvParam_()

static String mapSearchEngineToCvParam_ ( const String & openms_search_engine_name )

staticprotected

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
	)

staticprotected

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
	)

staticprotected

◆ store() [1/3]

void store	(	const String &	filename,
		const ConsensusMap &	cmap,
		const bool	first_run_inference_only,
		const bool	export_unidentified_features,
		const bool	export_unassigned_ids,
		const bool	export_subfeatures,
		const bool	export_empty_pep_ids = `false`,
		const bool	export_all_psms = `false`
	)		const

◆ store() [2/3]

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

Referenced by NucleicAcidSearchEngine::main_().

◆ store() [3/3]

void store	(	const String &	filename,
		const std::vector< ProteinIdentification > &	protein_identifications,
		const std::vector< PeptideIdentification > &	peptide_identifications,
		bool	first_run_inference_only,
		bool	export_empty_pep_ids = `false`,
		bool	export_all_psms = `false`,
		const String &	title = `"ID export from OpenMS"`
	)

◆ 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
	)

staticprotected

◆ 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
	)

staticprotected

◆ writeProteinHeader_()

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

staticprotected

Friends And Related Function Documentation

◆ MzTabMFile

friend class MzTabMFile

friend

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

Public Types

Public Member Functions

Protected Member Functions

Static Protected Member Functions

Protected Attributes

Friends

Detailed Description

Member Typedef Documentation

◆ MapAccPepType

Constructor & Destructor Documentation

◆ MzTabFile()

◆ ~MzTabFile()

Member Function Documentation

◆ addOptionalColumnsToSectionRow_()

◆ createProteinToPeptideLinks_()

◆ extractIndexPairsFromBrackets_()

◆ extractNumberOfSubSamples_()

◆ extractNumPeptides_()

◆ extractNumPeptidesDistinct_()

◆ extractNumPeptidesUnambiguous_()

◆ extractPeptideModifications_()

◆ extractProteinAccession_()

◆ generateMzTabMetaDataSection_()

◆ generateMzTabNucleicAcidHeader_()

◆ generateMzTabOligonucleotideHeader_()

◆ generateMzTabOSMHeader_()

◆ generateMzTabPeptideHeader_()

◆ generateMzTabProteinHeader_()

◆ generateMzTabPSMHeader_()

◆ generateMzTabSection_()

◆ generateMzTabSectionRow_() [1/7]

◆ generateMzTabSectionRow_() [2/7]

◆ generateMzTabSectionRow_() [3/7]

◆ generateMzTabSectionRow_() [4/7]

◆ generateMzTabSectionRow_() [5/7]

◆ generateMzTabSectionRow_() [6/7]

◆ generateMzTabSectionRow_() [7/7]

◆ generateMzTabSmallMoleculeHeader_()

◆ keepFirstPSM_()

◆ load()

◆ mapSearchEngineScoreToCvParam_()

◆ mapSearchEngineToCvParam_()

◆ partitionIntoRuns_()

◆ sortPSM_()

◆ store() [1/3]

◆ store() [2/3]

◆ store() [3/3]

◆ storePeptideReliabilityColumn()

◆ storePeptideUriColumn()

◆ storeProteinGoTerms()

◆ storeProteinReliabilityColumn()

◆ storeProteinUriColumn()

◆ storePSMReliabilityColumn()

◆ storePSMUriColumn()

◆ storeSmallMoleculeReliabilityColumn()

◆ storeSmallMoleculeUriColumn()

◆ writePeptideHeader_()

◆ writeProteinData_()

◆ writeProteinHeader_()

Friends And Related Function Documentation

◆ MzTabMFile

Member Data Documentation

◆ store_nucleic_acid_goterms_

◆ store_nucleic_acid_reliability_

◆ store_nucleic_acid_uri_

◆ store_oligonucleotide_reliability_

◆ store_oligonucleotide_uri_

◆ store_osm_reliability_

◆ store_osm_uri_

◆ store_peptide_reliability_

◆ store_peptide_uri_

◆ store_protein_goterms_

◆ store_protein_reliability_

◆ store_protein_uri_

◆ store_psm_reliability_

◆ store_psm_uri_

◆ store_smallmolecule_reliability_

◆ store_smallmolecule_uri_