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)
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
const MzTabSmallMoleculeSectionRows &	getSmallMoleculeSectionRows () const
void	setSmallMoleculeSectionRows (const MzTabSmallMoleculeSectionRows &smsd)
std::vector< String >	getProteinOptionalColumnNames () const
std::vector< String >	getPeptideOptionalColumnNames () const
std::vector< String >	getPSMOptionalColumnNames () const
std::vector< String >	getSmallMoleculeOptionalColumnNames () const

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)
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 export_unidentified_features, const bool export_unassigned_ids, String title="ConsensusMap export from OpenMS")

Protected Attributes
MzTabMetaData	meta_data_
MzTabProteinSectionRows	protein_data_
MzTabPeptideSectionRows	peptide_data_
MzTabPSMSectionRows	psm_data_
MzTabSmallMoleculeSectionRows	small_molecule_data_
std::vector< Size >	empty_rows_
std::map< Size, String >	comment_rows_

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.

exportConsensusMapToMzTab()

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

static

Referenced by UTILProteomicsLFQ::main_().

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  )

static

extractModificationListFromAASequence()

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

static

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

getPeptideOptionalColumnNames()

std::vector<String> getPeptideOptionalColumnNames

(

)

const

getPeptideSectionRows()

const MzTabPeptideSectionRows& getPeptideSectionRows

(

)

const

getProteinOptionalColumnNames()

std::vector<String> getProteinOptionalColumnNames

(

)

const

getProteinSectionRows()

const MzTabProteinSectionRows& getProteinSectionRows

(

)

const

getPSMOptionalColumnNames()

std::vector<String> getPSMOptionalColumnNames

(

)

const

getPSMSectionRows()

const MzTabPSMSectionRows& getPSMSectionRows

(

)

const

getSmallMoleculeOptionalColumnNames()

std::vector<String> getSmallMoleculeOptionalColumnNames

(

)

const

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

)

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

empty_rows_

std::vector<Size> empty_rows_

protected

meta_data_

MzTabMetaData meta_data_

protected

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