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:

[legend]

Collaboration diagram for MzTabM:

[legend]

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

Public Member Functions

Static Public Member Functions

Static Protected Member Functions

Protected Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ MzTabM()

◆ ~MzTabM()

Member Function Documentation

◆ addMetaInfoToOptionalColumns()

◆ exportFeatureMapToMzTabM()

◆ getAdductString_()

◆ getCommentRows()

◆ getEmptyRows()

◆ getFeatureMapMetaValues_()

◆ getMetaData()

◆ getMSmallMoleculeEvidenceOptionalColumnNames()

◆ getMSmallMoleculeEvidenceSectionRows()

◆ getMSmallMoleculeFeatureOptionalColumnNames()

◆ getMSmallMoleculeFeatureSectionRows()

◆ getMSmallMoleculeOptionalColumnNames()

◆ getMSmallMoleculeSectionRows()

◆ setCommentRows()

◆ setEmptyRows()

◆ setMetaData()

◆ setMSmallMoleculeEvidenceSectionRows()

◆ setMSmallMoleculeFeatureSectionRows()

◆ setMSmallMoleculeSectionRows()

Member Data Documentation

◆ comment_rows_

◆ empty_rows_

◆ m_meta_data_

◆ m_small_molecule_data_

◆ m_small_molecule_evidence_data_

◆ m_small_molecule_feature_data_

◆ sme_optional_column_names_

◆ smf_optional_column_names_

◆ sml_optional_column_names_