OpenMS  2.8.0
Public Member Functions | Static Public Member Functions | Static Protected Member Functions | Protected Attributes | List of all members
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:
[legend]
Collaboration diagram for MzTabM:
[legend]

Public Member Functions

 MzTabM ()=default
 Default constructor. More...
 
 ~MzTabM ()=default
 Destructor. More...
 
const MzTabMMetaDatagetMetaData () const
 Extract MzTabMMetaData. More...
 
void setMetaData (const MzTabMMetaData &m_md)
 Set MzTabMMetaData. More...
 
const MzTabMSmallMoleculeSectionRowsgetMSmallMoleculeSectionRows () const
 Extract MzTabMSmallMoleculeSectionRows. More...
 
void setMSmallMoleculeSectionRows (const MzTabMSmallMoleculeSectionRows &m_smsd)
 Set MzTabMSmallMoleculeSectionRows. More...
 
const MzTabMSmallMoleculeFeatureSectionRowsgetMSmallMoleculeFeatureSectionRows () const
 Extract MzTabMSmallMoleculeFeatureSectionRows. More...
 
void setMSmallMoleculeFeatureSectionRows (const MzTabMSmallMoleculeFeatureSectionRows &m_smfsd)
 Set MzTabMSmallMoleculeFeatureSectionRows. More...
 
const MzTabMSmallMoleculeEvidenceSectionRowsgetMSmallMoleculeEvidenceSectionRows () 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< StringgetMSmallMoleculeOptionalColumnNames () const
 Extract opt_ (custom, optional column names) More...
 
std::vector< StringgetMSmallMoleculeFeatureOptionalColumnNames () const
 Extract opt_ (custom, optional column names) More...
 
std::vector< StringgetMSmallMoleculeEvidenceOptionalColumnNames () 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< Sizeempty_rows_
 index of empty rows More...
 
std::map< Size, Stringcomment_rows_
 comments More...
 
std::vector< Stringsml_optional_column_names_
 
std::vector< Stringsmf_optional_column_names_
 
std::vector< Stringsme_optional_column_names_
 

Additional Inherited Members

- Protected Member Functions inherited from MzTabBase
template<typename SectionRows >
std::vector< StringgetOptionalColumnNames_ (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)

◆ 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