MzTab Class Reference

Data model of MzTab files. Please see the official MzTab specification at https://code.google.com/p/mztab/. More...

#include <OpenMS/FORMAT/MzTab.h>

Public Member Functions
	MzTab ()
	Default constructor. More...
virtual	~MzTab ()
	Destructor. More...
const MzTabMetaData &	getMetaData () const
void	setMetaData (const MzTabMetaData &md)
const MzTabProteinSectionRows &	getProteinSectionRows () const
void	setProteinSectionRows (const MzTabProteinSectionRows &psd)
const MzTabPeptideSectionRows &	getPeptideSectionRows () const
void	setPeptideSectionRows (const MzTabPeptideSectionRows &psd)
const MzTabPSMSectionRows &	getPSMSectionRows () const
void	setPSMSectionRows (const MzTabPSMSectionRows &psd)
const MzTabSmallMoleculeSectionRows &	getSmallMoleculeSectionRows () const
void	setSmallMoleculeSectionRows (const MzTabSmallMoleculeSectionRows &smsd)
const MzTabNucleicAcidSectionRows &	getNucleicAcidSectionRows () const
void	setNucleicAcidSectionRows (const MzTabNucleicAcidSectionRows &nasd)
const MzTabOligonucleotideSectionRows &	getOligonucleotideSectionRows () const
void	setOligonucleotideSectionRows (const MzTabOligonucleotideSectionRows &onsd)
const MzTabOSMSectionRows &	getOSMSectionRows () const
void	setOSMSectionRows (const MzTabOSMSectionRows &osd)
void	setCommentRows (const std::map< Size, String > &com)
void	setEmptyRows (const std::vector< Size > &empty)
const std::vector< Size > &	getEmptyRows () const
const std::map< Size, String > &	getCommentRows () const
std::vector< String >	getProteinOptionalColumnNames () const
	Extract opt_ (custom, optional column names) More...
std::vector< String >	getPeptideOptionalColumnNames () const
	Extract opt_ (custom, optional column names) More...
std::vector< String >	getPSMOptionalColumnNames () const
	Extract opt_ (custom, optional column names) More...
std::vector< String >	getSmallMoleculeOptionalColumnNames () const
	Extract opt_ (custom, optional column names) More...
std::vector< String >	getNucleicAcidOptionalColumnNames () const
	Extract opt_ (custom, optional column names) More...
std::vector< String >	getOligonucleotideOptionalColumnNames () const
	Extract opt_ (custom, optional column names) More...
std::vector< String >	getOSMOptionalColumnNames () const
	Extract opt_ (custom, optional column names) More...

Static Public Member Functions
static void	addPepEvidenceToRows (const std::vector< PeptideEvidence > &peptide_evidences, MzTabPSMSectionRow &row, MzTabPSMSectionRows &rows)
	Gets peptide_evidences with data from internal structures adds their info to an MzTabPSMSectionRow (pre- or unfilled) More...
static void	addMetaInfoToOptionalColumns (const std::set< String > &keys, std::vector< MzTabOptionalColumnEntry > &opt, const String &id, const MetaInfoInterface &meta)
static std::map< Size, MzTabModificationMetaData >	generateMzTabStringFromModifications (const std::vector< String > &mods)
static std::map< Size, MzTabModificationMetaData >	generateMzTabStringFromVariableModifications (const std::vector< String > &mods)
static std::map< Size, MzTabModificationMetaData >	generateMzTabStringFromFixedModifications (const std::vector< String > &mods)
static MzTab	exportFeatureMapToMzTab (const FeatureMap &feature_map, const String &filename)
static MzTab	exportIdentificationsToMzTab (const std::vector< ProteinIdentification > &prot_ids, const std::vector< PeptideIdentification > &peptide_ids, const String &filename, bool first_run_inference_only, std::map< std::pair< size_t, size_t >, size_t > &map_run_fileidx_2_msfileidx, std::map< String, size_t > &idrun_2_run_index, bool export_empty_pep_ids=false)
	Export peptide and protein identifications to mzTab. More...
static MzTabModificationList	extractModificationListFromAASequence (const AASequence &aas, const std::vector< String > &fixed_mods=std::vector< String >())
static MzTab	exportConsensusMapToMzTab (const ConsensusMap &consensus_map, const String &filename, 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 String &title="ConsensusMap export from OpenMS")
	export linked peptide features aka consensus map More...

Protected Member Functions
template<typename SectionRows >
std::vector< String >	getOptionalColumnNames_ (const SectionRows &rows) const
	Helper function for "get...OptionalColumnNames" functions. More...

Static Protected Member Functions
static void	checkSequenceUniqueness_ (const std::vector< PeptideIdentification > &curr_pep_ids)

Protected Attributes
MzTabMetaData	meta_data_
MzTabProteinSectionRows	protein_data_
MzTabPeptideSectionRows	peptide_data_
MzTabPSMSectionRows	psm_data_
MzTabSmallMoleculeSectionRows	small_molecule_data_
MzTabNucleicAcidSectionRows	nucleic_acid_data_
MzTabOligonucleotideSectionRows	oligonucleotide_data_
MzTabOSMSectionRows	osm_data_
	/ oligonucleotide-spectrum matches More...
std::vector< Size >	empty_rows_
	index of empty rows More...
std::map< Size, String >	comment_rows_
	comments More...

Detailed Description

Data model of MzTab files. Please see the official MzTab specification at https://code.google.com/p/mztab/.

Constructor & Destructor Documentation

MzTab()

MzTab

(

)

Default constructor.

~MzTab()

virtual ~MzTab ( )

virtual

Destructor.

Member Function Documentation

addMetaInfoToOptionalColumns()

static void addMetaInfoToOptionalColumns ( const std::set< String > &  keys, std::vector< MzTabOptionalColumnEntry > &  opt, const String &  id, const MetaInfoInterface &  meta  )

static

addPepEvidenceToRows()

static void addPepEvidenceToRows ( const std::vector< PeptideEvidence > &  peptide_evidences, MzTabPSMSectionRow &  row, MzTabPSMSectionRows &  rows  )

static

Gets peptide_evidences with data from internal structures adds their info to an MzTabPSMSectionRow (pre- or unfilled)

Parameters

peptide_evidences	Vector of PeptideEvidence holding internal data.
row	Pre- or unfilled MzTabPSMSectionRow to be filled with the data.
rows	Vector of MzTabPSMSectionRow to add the differently updated rows to.

checkSequenceUniqueness_()

static void checkSequenceUniqueness_ ( const std::vector< PeptideIdentification > &  curr_pep_ids )

staticprotected

exportConsensusMapToMzTab()

static MzTab exportConsensusMapToMzTab ( const ConsensusMap &  consensus_map, const String &  filename, 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 String &  title = "ConsensusMap export from OpenMS"  )

static

export linked peptide features aka consensus map

Parameters

consensus_map	data structure of the linked peptide features
filename	input consensusXML file name
export_unidentified_features	Should not identified peptide features be exported?
export_unassigned_ids	Should unassigned identifications be exported?
export_subfeatures	The position of the consensus feature will always be exported. Should the individual subfeatures be exported as well?

Returns

mzTab object

exportFeatureMapToMzTab()

static MzTab exportFeatureMapToMzTab ( const FeatureMap &  feature_map, const String &  filename  )

static

exportIdentificationsToMzTab()

static MzTab exportIdentificationsToMzTab ( const std::vector< ProteinIdentification > &  prot_ids, const std::vector< PeptideIdentification > &  peptide_ids, const String &  filename, bool  first_run_inference_only, std::map< std::pair< size_t, size_t >, size_t > &  map_run_fileidx_2_msfileidx, std::map< String, size_t > &  idrun_2_run_index, bool  export_empty_pep_ids = false  )

static

Export peptide and protein identifications to mzTab.

Additionally this function fills two std::maps with mappings for external usage.

Parameters

[IN]	prot_ids Data structure containing protein identifications
[IN]	peptide_ids Data structure containing peptide identifications
[IN]	filename Input idXML file name
[IN]	first_run_inference_only Is all protein inference information stored in the first run?
[OUT]	map_run_fileidx_2_msfileidx Mapping from (run index, input file index) to experimental design file index. The experimental design file index is either given, or a simplified version created from the input file index on the fly.
[OUT]	idrun_2_run_index Mapping from protein identification identifier (search engine + date) to run index, i.e. for storing file origins from different runs

Returns

mzTab object

extractModificationListFromAASequence()

static MzTabModificationList extractModificationListFromAASequence ( const AASequence &  aas, const std::vector< String > &  fixed_mods = std::vector< String >()  )

static

Generate MzTab style list of PTMs from AASequence object. All passed fixed modifications are not reported (as suggested by the standard for the PRT and PEP section). In contrast, all modifications are reported in the PSM section (see standard document for details).

generateMzTabStringFromFixedModifications()

static std::map<Size, MzTabModificationMetaData> generateMzTabStringFromFixedModifications ( const std::vector< String > &  mods )

static

generateMzTabStringFromModifications()

static std::map<Size, MzTabModificationMetaData> generateMzTabStringFromModifications ( const std::vector< String > &  mods )

static

generateMzTabStringFromVariableModifications()

static std::map<Size, MzTabModificationMetaData> generateMzTabStringFromVariableModifications ( const std::vector< String > &  mods )

static

getCommentRows()

const std::map<Size, String>& getCommentRows

(

)

const

getEmptyRows()

const std::vector<Size>& getEmptyRows

(

)

const

getMetaData()

const MzTabMetaData& getMetaData

(

)

const

getNucleicAcidOptionalColumnNames()

std::vector<String> getNucleicAcidOptionalColumnNames

(

)

const

Extract opt_ (custom, optional column names)

getNucleicAcidSectionRows()

const MzTabNucleicAcidSectionRows& getNucleicAcidSectionRows

(

)

const

Referenced by NucleicAcidSearchEngine::main_().

getOligonucleotideOptionalColumnNames()

std::vector<String> getOligonucleotideOptionalColumnNames

(

)

const

Extract opt_ (custom, optional column names)

getOligonucleotideSectionRows()

const MzTabOligonucleotideSectionRows& getOligonucleotideSectionRows

(

)

const

Referenced by NucleicAcidSearchEngine::main_().

getOptionalColumnNames_()

std::vector<String> getOptionalColumnNames_ ( const SectionRows &  rows ) const

inlineprotected

Helper function for "get...OptionalColumnNames" functions.

References seqan::find().

getOSMOptionalColumnNames()

std::vector<String> getOSMOptionalColumnNames

(

)

const

Extract opt_ (custom, optional column names)

getOSMSectionRows()

const MzTabOSMSectionRows& getOSMSectionRows

(

)

const

Referenced by NucleicAcidSearchEngine::main_().

getPeptideOptionalColumnNames()

std::vector<String> getPeptideOptionalColumnNames

(

)

const

Extract opt_ (custom, optional column names)

getPeptideSectionRows()

const MzTabPeptideSectionRows& getPeptideSectionRows

(

)

const

getProteinOptionalColumnNames()

std::vector<String> getProteinOptionalColumnNames

(

)

const

Extract opt_ (custom, optional column names)

getProteinSectionRows()

const MzTabProteinSectionRows& getProteinSectionRows

(

)

const

getPSMOptionalColumnNames()

std::vector<String> getPSMOptionalColumnNames

(

)

const

Extract opt_ (custom, optional column names)

getPSMSectionRows()

const MzTabPSMSectionRows& getPSMSectionRows

(

)

const

getSmallMoleculeOptionalColumnNames()

std::vector<String> getSmallMoleculeOptionalColumnNames

(

)

const

Extract opt_ (custom, optional column names)

getSmallMoleculeSectionRows()

const MzTabSmallMoleculeSectionRows& getSmallMoleculeSectionRows

(

)

const

setCommentRows()

void setCommentRows

(

const std::map< Size, String > &

com

)

setEmptyRows()

void setEmptyRows

(

const std::vector< Size > &

empty

)

setMetaData()

void setMetaData

(

const MzTabMetaData &

md

)

setNucleicAcidSectionRows()

void setNucleicAcidSectionRows

(

const MzTabNucleicAcidSectionRows &

nasd

)

setOligonucleotideSectionRows()

void setOligonucleotideSectionRows

(

const MzTabOligonucleotideSectionRows &

onsd

)

setOSMSectionRows()

void setOSMSectionRows

(

const MzTabOSMSectionRows &

osd

)

setPeptideSectionRows()

void setPeptideSectionRows

(

const MzTabPeptideSectionRows &

psd

)

setProteinSectionRows()

void setProteinSectionRows

(

const MzTabProteinSectionRows &

psd

)

setPSMSectionRows()

void setPSMSectionRows

(

const MzTabPSMSectionRows &

psd

)

setSmallMoleculeSectionRows()

void setSmallMoleculeSectionRows

(

const MzTabSmallMoleculeSectionRows &

smsd

)

Member Data Documentation

comment_rows_

std::map<Size, String> comment_rows_

protected

comments

empty_rows_

std::vector<Size> empty_rows_

protected

index of empty rows

meta_data_

MzTabMetaData meta_data_

protected

nucleic_acid_data_

MzTabNucleicAcidSectionRows nucleic_acid_data_

protected

oligonucleotide_data_

MzTabOligonucleotideSectionRows oligonucleotide_data_

protected

osm_data_

MzTabOSMSectionRows osm_data_

protected

/ oligonucleotide-spectrum matches

peptide_data_

MzTabPeptideSectionRows peptide_data_

protected

protein_data_

MzTabProteinSectionRows protein_data_

protected

psm_data_

MzTabPSMSectionRows psm_data_

protected

small_molecule_data_

MzTabSmallMoleculeSectionRows small_molecule_data_

protected