MzTabM Class Reference

Data model of MzTab-M files Please see the MzTab-M specification at https://github.com/HUPO-PSI/mzTab/blob/master/specification_document-releases/2_0-Metabolomics-Release/mzTab_format_specification_2_0-M_release.adoc#use-cases-for-mztab. More...

#include <OpenMS/FORMAT/MzTabM.h>

Inheritance diagram for MzTabM:

Collaboration diagram for MzTabM:

Public Member Functions
	MzTabM ()=default
	Default constructor. More...
	~MzTabM ()=default
	Destructor. More...
const MzTabMMetaData &	getMetaData () const
	Extract MzTabMMetaData. More...
void	setMetaData (const MzTabMMetaData &m_md)
	Set MzTabMMetaData. More...
const MzTabMSmallMoleculeSectionRows &	getMSmallMoleculeSectionRows () const
	Extract MzTabMSmallMoleculeSectionRows. More...
void	setMSmallMoleculeSectionRows (const MzTabMSmallMoleculeSectionRows &m_smsd)
	Set MzTabMSmallMoleculeSectionRows. More...
const MzTabMSmallMoleculeFeatureSectionRows &	getMSmallMoleculeFeatureSectionRows () const
	Extract MzTabMSmallMoleculeFeatureSectionRows. More...
void	setMSmallMoleculeFeatureSectionRows (const MzTabMSmallMoleculeFeatureSectionRows &m_smfsd)
	Set MzTabMSmallMoleculeFeatureSectionRows. More...
const MzTabMSmallMoleculeEvidenceSectionRows &	getMSmallMoleculeEvidenceSectionRows () const
	Extract MzTabMSmallMoleculeEvidenceSectionRows. More...
void	setMSmallMoleculeEvidenceSectionRows (const MzTabMSmallMoleculeEvidenceSectionRows &m_smesd)
	Set MzTabMSmallMoleculeEvidenceSectionRows. More...
void	setCommentRows (const std::map< Size, String > &com)
	Set comment rows. More...
void	setEmptyRows (const std::vector< Size > &empty)
	Set empty rows. More...
const std::vector< Size > &	getEmptyRows () const
	Get empty rows. More...
const std::map< Size, String > &	getCommentRows () const
	Get comment rows. More...
std::vector< String >	getMSmallMoleculeOptionalColumnNames () const
	Extract opt_ (custom, optional column names) More...
std::vector< String >	getMSmallMoleculeFeatureOptionalColumnNames () const
	Extract opt_ (custom, optional column names) More...
std::vector< String >	getMSmallMoleculeEvidenceOptionalColumnNames () const
	Extract opt_ (custom, optional column names) More...
Public Member Functions inherited from MzTabBase
	MzTabBase ()=default
virtual	~MzTabBase ()=default

Static Public Member Functions
static void	addMetaInfoToOptionalColumns (const std::set< String > &keys, std::vector< MzTabOptionalColumnEntry > &opt, const String &id, const MetaInfoInterface &meta)
static MzTabM	exportFeatureMapToMzTabM (const FeatureMap &feature_map)
	Export FeatureMap with Identifications to MzTabM. More...

Static Protected Member Functions
static String	getAdductString_ (const IdentificationDataInternal::ObservationMatchRef &match_ref)
static void	getFeatureMapMetaValues_ (const FeatureMap &feature_map, std::set< String > &feature_user_value_keys, std::set< String > &observationmatch_user_value_keys, std::set< String > &compound_user_value_keys)

Protected Attributes
MzTabMMetaData	m_meta_data_
MzTabMSmallMoleculeSectionRows	m_small_molecule_data_
MzTabMSmallMoleculeFeatureSectionRows	m_small_molecule_feature_data_
MzTabMSmallMoleculeEvidenceSectionRows	m_small_molecule_evidence_data_
std::vector< Size >	empty_rows_
	index of empty rows More...
std::map< Size, String >	comment_rows_
	comments More...
std::vector< String >	sml_optional_column_names_
std::vector< String >	smf_optional_column_names_
std::vector< String >	sme_optional_column_names_

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

Detailed Description

Data model of MzTab-M files Please see the MzTab-M specification at https://github.com/HUPO-PSI/mzTab/blob/master/specification_document-releases/2_0-Metabolomics-Release/mzTab_format_specification_2_0-M_release.adoc#use-cases-for-mztab.

Constructor & Destructor Documentation

MzTabM()

MzTabM ( )

default

Default constructor.

~MzTabM()

~MzTabM ( )

default

Destructor.

Member Function Documentation

addMetaInfoToOptionalColumns()

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

static

exportFeatureMapToMzTabM()

static MzTabM exportFeatureMapToMzTabM ( const FeatureMap &  feature_map )

static

Export FeatureMap with Identifications to MzTabM.

Returns

MzTabM object

getAdductString_()

static String getAdductString_ ( const IdentificationDataInternal::ObservationMatchRef &  match_ref )

staticprotected

getCommentRows()

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

(

)

const

Get comment rows.

getEmptyRows()

const std::vector<Size>& getEmptyRows

(

)

const

Get empty rows.

getFeatureMapMetaValues_()

static void getFeatureMapMetaValues_ ( const FeatureMap &  feature_map, std::set< String > &  feature_user_value_keys, std::set< String > &  observationmatch_user_value_keys, std::set< String > &  compound_user_value_keys  )

staticprotected

getMetaData()

const MzTabMMetaData& getMetaData

(

)

const

Extract MzTabMMetaData.

getMSmallMoleculeEvidenceOptionalColumnNames()

std::vector<String> getMSmallMoleculeEvidenceOptionalColumnNames

(

)

const

Extract opt_ (custom, optional column names)

getMSmallMoleculeEvidenceSectionRows()

const MzTabMSmallMoleculeEvidenceSectionRows& getMSmallMoleculeEvidenceSectionRows

(

)

const

Extract MzTabMSmallMoleculeEvidenceSectionRows.

getMSmallMoleculeFeatureOptionalColumnNames()

std::vector<String> getMSmallMoleculeFeatureOptionalColumnNames

(

)

const

Extract opt_ (custom, optional column names)

getMSmallMoleculeFeatureSectionRows()

const MzTabMSmallMoleculeFeatureSectionRows& getMSmallMoleculeFeatureSectionRows

(

)

const

Extract MzTabMSmallMoleculeFeatureSectionRows.

getMSmallMoleculeOptionalColumnNames()

std::vector<String> getMSmallMoleculeOptionalColumnNames

(

)

const

Extract opt_ (custom, optional column names)

getMSmallMoleculeSectionRows()

const MzTabMSmallMoleculeSectionRows& getMSmallMoleculeSectionRows

(

)

const

Extract MzTabMSmallMoleculeSectionRows.

setCommentRows()

void setCommentRows

(

const std::map< Size, String > &

com

)

Set comment rows.

setEmptyRows()

void setEmptyRows

(

const std::vector< Size > &

empty

)

Set empty rows.

setMetaData()

void setMetaData

(

const MzTabMMetaData &

m_md

)

Set MzTabMMetaData.

setMSmallMoleculeEvidenceSectionRows()

void setMSmallMoleculeEvidenceSectionRows

(

const MzTabMSmallMoleculeEvidenceSectionRows &

m_smesd

)

Set MzTabMSmallMoleculeEvidenceSectionRows.

setMSmallMoleculeFeatureSectionRows()

void setMSmallMoleculeFeatureSectionRows

(

const MzTabMSmallMoleculeFeatureSectionRows &

m_smfsd

)

Set MzTabMSmallMoleculeFeatureSectionRows.

setMSmallMoleculeSectionRows()

void setMSmallMoleculeSectionRows

(

const MzTabMSmallMoleculeSectionRows &

m_smsd

)

Set MzTabMSmallMoleculeSectionRows.

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

m_meta_data_

MzTabMMetaData m_meta_data_

protected

m_small_molecule_data_

MzTabMSmallMoleculeSectionRows m_small_molecule_data_

protected

m_small_molecule_evidence_data_

MzTabMSmallMoleculeEvidenceSectionRows m_small_molecule_evidence_data_

protected

m_small_molecule_feature_data_

MzTabMSmallMoleculeFeatureSectionRows m_small_molecule_feature_data_

protected

sme_optional_column_names_

std::vector<String> sme_optional_column_names_

protected

smf_optional_column_names_

std::vector<String> smf_optional_column_names_

protected

sml_optional_column_names_

std::vector<String> sml_optional_column_names_

protected