MzTabFile Class Reference [File IO]

File adapter for MzTab files. More...

#include <OpenMS/FORMAT/MzTabFile.h>

List of all members.

Public Types
typedef std::map< std::pair < String, String > , std::vector< PeptideHit > >	MapAccPepType
Public Member Functions
	MzTabFile ()
	Default constructor.
	~MzTabFile ()
	Destructor.
void	store (const String &filename, const std::vector< ProteinIdentification > &protein_ids, const std::vector< PeptideIdentification > &peptide_ids, String in, String document_id) const
void	store (const String &filename, const MzTab &mz_tab) const
Protected Member Functions
void	generateMzTabMetaDataSection_ (const MzTabMetaData &map, StringList &sl) const
void	generateProteinHeader_ (Int n_subsamples, const std::vector< String > &optional_protein_columns, StringList &sl) const
String	generateMzTabProteinSectionRow_ (const MzTabProteinSectionRow &row, const String &unit_id) const
void	generateMzTabProteinSection_ (const MzTabProteinSectionData &map, StringList &sl) const
void	generateMzTabPeptideSection_ (const MzTabPeptideSectionData &map, StringList &sl) const
void	generateMzTabSmallMoleculeSection_ (const MzTabSmallMoleculeSectionData &map, StringList &sl) const
String	generateMzTabPeptideHeader_ (Int n_subsamples, const std::vector< String > &optional_protein_columns) const
String	generateMzTabPeptideSectionRow_ (const MzTabPeptideSectionRow &row, const String &unit_id) const
String	generateMzTabSmallMoleculeHeader_ (Int n_subsamples, const std::vector< String > &optional_smallmolecule_columns) const
String	generateMzTabSmallMoleculeSectionRow_ (const MzTabSmallMoleculeSectionRow &row, const String &unit_id) const
Static Protected Member Functions
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.
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
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.
static String	extractPeptideModifications_ (const PeptideHit &peptide_hit)
	Extracts, modifications and positions of a peptide hit in mzTab format.
static String	mapSearchEngineToCvParam_ (const String &openms_search_engine_name)
	Map search engine identifier to CV, param etc.
static String	mapSearchEngineScoreToCvParam_ (const String &openms_search_engine_name, DoubleReal score, String score_type)
static String	extractNumPeptides (const String &common_identifier, const String &protein_accession, const MapAccPepType &map_run_accesion_to_peptides)
static String	extractNumPeptidesDistinct (String common_identifier, String protein_accession, const MapAccPepType &map_run_accesion_to_peptides)
static String	extractNumPeptidesUnambiguous (String common_identifier, String protein_accession, const MapAccPepType &map_run_accesion_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_accesion_to_peptides, const std::map< String, Size > &map_run_to_num_sub)

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Detailed Description

File adapter for MzTab files.

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Member Typedef Documentation

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

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Constructor & Destructor Documentation

MzTabFile

(

)

Default constructor.

~MzTabFile

(

)

Destructor.

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Member Function Documentation

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

static std::map<String, Size> extractNumberOfSubSamples_

(

const std::map< String, std::vector< ProteinIdentification > > &

map_run_to_proids

)

[static, protected]

static String extractNumPeptides	(	const String &	common_identifier,
		const String &	protein_accession,
		const MapAccPepType &	map_run_accesion_to_peptides
	)			[static, protected]

static String extractNumPeptidesDistinct	(	String	common_identifier,
		String	protein_accession,
		const MapAccPepType &	map_run_accesion_to_peptides
	)			[static, protected]

static String extractNumPeptidesUnambiguous	(	String	common_identifier,
		String	protein_accession,
		const MapAccPepType &	map_run_accesion_to_peptides
	)			[static, protected]

static String extractPeptideModifications_

(

const PeptideHit &

peptide_hit

)

[static, protected]

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

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.

void generateMzTabMetaDataSection_	(	const MzTabMetaData &	map,
		StringList &	sl
	)			const [protected]

String generateMzTabPeptideHeader_	(	Int	n_subsamples,
		const std::vector< String > &	optional_protein_columns
	)			const [protected]

void generateMzTabPeptideSection_	(	const MzTabPeptideSectionData &	map,
		StringList &	sl
	)			const [protected]

String generateMzTabPeptideSectionRow_	(	const MzTabPeptideSectionRow &	row,
		const String &	unit_id
	)			const [protected]

void generateMzTabProteinSection_	(	const MzTabProteinSectionData &	map,
		StringList &	sl
	)			const [protected]

String generateMzTabProteinSectionRow_	(	const MzTabProteinSectionRow &	row,
		const String &	unit_id
	)			const [protected]

String generateMzTabSmallMoleculeHeader_	(	Int	n_subsamples,
		const std::vector< String > &	optional_smallmolecule_columns
	)			const [protected]

void generateMzTabSmallMoleculeSection_	(	const MzTabSmallMoleculeSectionData &	map,
		StringList &	sl
	)			const [protected]

String generateMzTabSmallMoleculeSectionRow_	(	const MzTabSmallMoleculeSectionRow &	row,
		const String &	unit_id
	)			const [protected]

void generateProteinHeader_	(	Int	n_subsamples,
		const std::vector< String > &	optional_protein_columns,
		StringList &	sl
	)			const [protected]

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

static String mapSearchEngineScoreToCvParam_	(	const String &	openms_search_engine_name,
		DoubleReal	score,
		String	score_type
	)			[static, protected]

static String mapSearchEngineToCvParam_

(

const String &

openms_search_engine_name

)

[static, protected]

Map search engine identifier to CV, param etc.

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.

static void sortPSM_	(	std::vector< PeptideIdentification >::iterator	begin,
		std::vector< PeptideIdentification >::iterator	end
	)			[static, protected]

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

void store	(	const String &	filename,
		const std::vector< ProteinIdentification > &	protein_ids,
		const std::vector< PeptideIdentification > &	peptide_ids,
		String	in,
		String	document_id
	)			const

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

static void writeProteinData_	(	SVOutStream &	output,
		const ProteinIdentification &	prot_id,
		Size	run_count,
		String	input_filename,
		bool	has_coverage,
		const MapAccPepType &	map_run_accesion_to_peptides,
		const std::map< String, Size > &	map_run_to_num_sub
	)			[static, protected]

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