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>

Collaboration diagram for MzTab:

Classes
class	CMMzTabStream
class	IDMzTabStream

Public Member Functions
	MzTab ()=default
	Default constructor. More...
	~MzTab ()=default
const MzTabMetaData &	getMetaData () const
void	setMetaData (const MzTabMetaData &md)
MzTabProteinSectionRows &	getProteinSectionRows ()
const MzTabProteinSectionRows &	getProteinSectionRows () const
void	setProteinSectionRows (const MzTabProteinSectionRows &psd)
MzTabPeptideSectionRows &	getPeptideSectionRows ()
const MzTabPeptideSectionRows &	getPeptideSectionRows () const
void	setPeptideSectionRows (const MzTabPeptideSectionRows &psd)
MzTabPSMSectionRows &	getPSMSectionRows ()
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)
	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, bool export_empty_pep_ids=false, const String &title="ID export from OpenMS")
	Export peptide and protein identifications to mzTab. More...
static MzTabModificationList	extractModificationList (const PeptideHit &pep_hit, const std::vector< String > &fixed_mods, const std::vector< String > &localization_mods)
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 std::map< String, Size >	mapIDRunIdentifier2IDRunIndex_ (const std::vector< const ProteinIdentification * > &prot_ids)
static boost::optional< MzTabPSMSectionRow >	PSMSectionRowFromPeptideID_ (const PeptideIdentification &pid, const std::vector< const ProteinIdentification * > &prot_id, std::map< String, size_t > &idrun_2_run_index, std::map< std::pair< size_t, size_t >, size_t > &map_run_fileidx_2_msfileidx, std::map< Size, std::vector< std::pair< String, String >>> &run_to_search_engines, const int psm_id, const MzTabString &db, const MzTabString &db_version, const bool export_empty_pep_ids)
static MzTabPeptideSectionRow	peptideSectionRowFromConsensusFeature_ (const ConsensusFeature &c, const ConsensusMap &consensus_map, const StringList &ms_runs, const Size n_study_variables, const std::set< String > &consensus_feature_user_value_keys, const std::set< String > &peptide_hit_user_value_keys, const std::map< String, size_t > &idrun_2_run_index, const std::map< std::pair< size_t, size_t >, size_t > &map_run_fileidx_2_msfileidx, const std::map< std::pair< String, unsigned >, unsigned > &path_label_to_assay, const std::vector< String > &fixed_mods, bool export_subfeatures)
static MzTabPeptideSectionRow	peptideSectionRowFromFeature_ (const Feature &c, const std::set< String > &feature_user_value_keys, const std::set< String > &peptide_hit_user_value_keys, const std::vector< String > &fixed_mods)
static MzTabProteinSectionRow	proteinSectionRowFromProteinHit_ (const ProteinHit &hit, const MzTabString &db, const MzTabString &db_version, const std::set< String > &protein_hit_user_value_keys)
static MzTabProteinSectionRow	nextProteinSectionRowFromProteinGroup_ (const ProteinIdentification::ProteinGroup &group, const MzTabString &db, const MzTabString &db_version)
static MzTabProteinSectionRow	nextProteinSectionRowFromIndistinguishableGroup_ (const std::vector< ProteinHit > &protein_hits, const ProteinIdentification::ProteinGroup &group, const size_t g, const std::map< Size, std::set< Size >> &ind2prot, const MzTabString &db, const MzTabString &db_version)
static void	addMSRunMetaData_ (const std::map< size_t, String > &msrunindex_2_msfilename, MzTabMetaData &meta_data)
static void	mapBetweenMSFileNameAndMSRunIndex_ (const std::vector< const ProteinIdentification * > &prot_ids, bool skip_first, std::map< String, size_t > &msfilename_2_msrunindex, std::map< size_t, String > &msrunindex_2_msfilename)
static size_t	getQuantStudyVariables_ (const ProteinIdentification &pid)
static MzTabParameter	getProteinScoreType_ (const ProteinIdentification &prot_id)
static void	getConsensusMapMetaValues_ (const ConsensusMap &consensus_map, std::set< String > &consensus_feature_user_value_keys, std::set< String > &peptide_hit_user_value_keys)
static void	getFeatureMapMetaValues_ (const FeatureMap &feature_map, std::set< String > &feature_user_value_keys, std::set< String > &peptide_hit_user_value_keys)
static void	getIdentificationMetaValues_ (const std::vector< const ProteinIdentification * > &prot_ids, std::vector< const PeptideIdentification * > &peptide_ids_, std::set< String > &protein_hit_user_value_keys, std::set< String > &peptide_id_user_value_keys, std::set< String > &peptide_hit_user_value_keys)
template<class ForwardIterator >
static void	replaceWhiteSpaces_ (ForwardIterator first, ForwardIterator last)
static void	replaceWhiteSpaces_ (std::set< String > &keys)
static MzTabParameter	getMSRunSpectrumIdentifierType_ (const std::vector< const PeptideIdentification * > &peptide_ids_)
static void	mapBetweenRunAndSearchEngines_ (const std::vector< const ProteinIdentification * > &prot_ids, const std::vector< const PeptideIdentification * > &pep_ids, bool skip_first_run, std::map< std::tuple< String, String, String >, std::set< Size >> &search_engine_to_runs, std::map< Size, std::vector< std::pair< String, String >>> &run_to_search_engines, std::map< Size, std::vector< std::vector< std::pair< String, String >>>> &run_to_search_engines_settings, std::map< String, std::vector< std::pair< String, String >>> &search_engine_to_settings)
static std::map< Size, std::set< Size > >	mapGroupsToProteins_ (const std::vector< ProteinIdentification::ProteinGroup > &groups, const std::vector< ProteinHit > &proteins)
static void	addSearchMetaData_ (const std::vector< const ProteinIdentification * > &prot_ids, const std::map< std::tuple< String, String, String >, std::set< Size >> &search_engine_to_runs, const std::map< String, std::vector< std::pair< String, String >>> &search_engine_to_settings, MzTabMetaData &meta_data, bool first_run_inference_only)
static void	mapIDRunFileIndex2MSFileIndex_ (const std::vector< const ProteinIdentification * > &prot_ids, const std::map< String, size_t > &msfilename_2_msrunindex, bool skip_first_run, std::map< std::pair< size_t, size_t >, size_t > &map_run_fileidx_2_msfileidx)
static void	getSearchModifications_ (const std::vector< const ProteinIdentification * > &prot_ids, StringList &var_mods, StringList &fixed_mods)
static MzTabString	getModificationIdentifier_ (const ResidueModification &r)
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

Default constructor.

~MzTab()

~MzTab ( )

default

Member Function Documentation

addMetaInfoToOptionalColumns()

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

static

addMSRunMetaData_()

static void addMSRunMetaData_ ( const std::map< size_t, String > &  msrunindex_2_msfilename, MzTabMetaData &  meta_data  )

staticprotected

addPepEvidenceToRows()

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

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.

addSearchMetaData_()

static void addSearchMetaData_ ( const std::vector< const ProteinIdentification * > &  prot_ids, const std::map< std::tuple< String, String, String >, std::set< Size >> &  search_engine_to_runs, const std::map< String, std::vector< std::pair< String, String >>> &  search_engine_to_settings, MzTabMetaData &  meta_data, bool  first_run_inference_only  )

staticprotected

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, bool  export_empty_pep_ids = false, const String &  title = "ID export from OpenMS"  )

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?

Returns

mzTab object

extractModificationList()

static MzTabModificationList extractModificationList ( const PeptideHit &  pep_hit, const std::vector< String > &  fixed_mods, const std::vector< String > &  localization_mods  )

static

Generate MzTab style list of PTMs from PeptideHit (PSM) 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). If meta values for modification localization are found, this information is added.

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

getConsensusMapMetaValues_()

static void getConsensusMapMetaValues_ ( const ConsensusMap &  consensus_map, std::set< String > &  consensus_feature_user_value_keys, std::set< String > &  peptide_hit_user_value_keys  )

staticprotected

getEmptyRows()

const std::vector<Size>& getEmptyRows

(

)

const

getFeatureMapMetaValues_()

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

staticprotected

getIdentificationMetaValues_()

static void getIdentificationMetaValues_ ( const std::vector< const ProteinIdentification * > &  prot_ids, std::vector< const PeptideIdentification * > &  peptide_ids_, std::set< String > &  protein_hit_user_value_keys, std::set< String > &  peptide_id_user_value_keys, std::set< String > &  peptide_hit_user_value_keys  )

staticprotected

getMetaData()

const MzTabMetaData& getMetaData

(

)

const

getModificationIdentifier_()

static MzTabString getModificationIdentifier_ ( const ResidueModification &  r )

staticprotected

getMSRunSpectrumIdentifierType_()

static MzTabParameter getMSRunSpectrumIdentifierType_ ( const std::vector< const PeptideIdentification * > &  peptide_ids_ )

staticprotected

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() [1/2]

MzTabPeptideSectionRows& getPeptideSectionRows

(

)

getPeptideSectionRows() [2/2]

const MzTabPeptideSectionRows& getPeptideSectionRows

(

)

const

getProteinOptionalColumnNames()

std::vector<String> getProteinOptionalColumnNames

(

)

const

Extract opt_ (custom, optional column names)

getProteinScoreType_()

static MzTabParameter getProteinScoreType_ ( const ProteinIdentification &  prot_id )

staticprotected

getProteinSectionRows() [1/2]

MzTabProteinSectionRows& getProteinSectionRows

(

)

getProteinSectionRows() [2/2]

const MzTabProteinSectionRows& getProteinSectionRows

(

)

const

getPSMOptionalColumnNames()

std::vector<String> getPSMOptionalColumnNames

(

)

const

Extract opt_ (custom, optional column names)

getPSMSectionRows() [1/2]

MzTabPSMSectionRows& getPSMSectionRows

(

)

getPSMSectionRows() [2/2]

const MzTabPSMSectionRows& getPSMSectionRows

(

)

const

getQuantStudyVariables_()

static size_t getQuantStudyVariables_ ( const ProteinIdentification &  pid )

staticprotected

getSearchModifications_()

static void getSearchModifications_ ( const std::vector< const ProteinIdentification * > &  prot_ids, StringList &  var_mods, StringList &  fixed_mods  )

staticprotected

getSmallMoleculeOptionalColumnNames()

std::vector<String> getSmallMoleculeOptionalColumnNames

(

)

const

Extract opt_ (custom, optional column names)

getSmallMoleculeSectionRows()

const MzTabSmallMoleculeSectionRows& getSmallMoleculeSectionRows

(

)

const

mapBetweenMSFileNameAndMSRunIndex_()

static void mapBetweenMSFileNameAndMSRunIndex_ ( const std::vector< const ProteinIdentification * > &  prot_ids, bool  skip_first, std::map< String, size_t > &  msfilename_2_msrunindex, std::map< size_t, String > &  msrunindex_2_msfilename  )

staticprotected

mapBetweenRunAndSearchEngines_()

static void mapBetweenRunAndSearchEngines_ ( const std::vector< const ProteinIdentification * > &  prot_ids, const std::vector< const PeptideIdentification * > &  pep_ids, bool  skip_first_run, std::map< std::tuple< String, String, String >, std::set< Size >> &  search_engine_to_runs, std::map< Size, std::vector< std::pair< String, String >>> &  run_to_search_engines, std::map< Size, std::vector< std::vector< std::pair< String, String >>>> &  run_to_search_engines_settings, std::map< String, std::vector< std::pair< String, String >>> &  search_engine_to_settings  )

staticprotected

mapGroupsToProteins_()

static std::map<Size, std::set<Size> > mapGroupsToProteins_ ( const std::vector< ProteinIdentification::ProteinGroup > &  groups, const std::vector< ProteinHit > &  proteins  )

staticprotected

mapIDRunFileIndex2MSFileIndex_()

static void mapIDRunFileIndex2MSFileIndex_ ( const std::vector< const ProteinIdentification * > &  prot_ids, const std::map< String, size_t > &  msfilename_2_msrunindex, bool  skip_first_run, std::map< std::pair< size_t, size_t >, size_t > &  map_run_fileidx_2_msfileidx  )

staticprotected

mapIDRunIdentifier2IDRunIndex_()

static std::map<String, Size> mapIDRunIdentifier2IDRunIndex_ ( const std::vector< const ProteinIdentification * > &  prot_ids )

staticprotected

nextProteinSectionRowFromIndistinguishableGroup_()

static MzTabProteinSectionRow nextProteinSectionRowFromIndistinguishableGroup_ ( const std::vector< ProteinHit > &  protein_hits, const ProteinIdentification::ProteinGroup &  group, const size_t  g, const std::map< Size, std::set< Size >> &  ind2prot, const MzTabString &  db, const MzTabString &  db_version  )

staticprotected

nextProteinSectionRowFromProteinGroup_()

static MzTabProteinSectionRow nextProteinSectionRowFromProteinGroup_ ( const ProteinIdentification::ProteinGroup &  group, const MzTabString &  db, const MzTabString &  db_version  )

staticprotected

peptideSectionRowFromConsensusFeature_()

static MzTabPeptideSectionRow peptideSectionRowFromConsensusFeature_ ( const ConsensusFeature &  c, const ConsensusMap &  consensus_map, const StringList &  ms_runs, const Size  n_study_variables, const std::set< String > &  consensus_feature_user_value_keys, const std::set< String > &  peptide_hit_user_value_keys, const std::map< String, size_t > &  idrun_2_run_index, const std::map< std::pair< size_t, size_t >, size_t > &  map_run_fileidx_2_msfileidx, const std::map< std::pair< String, unsigned >, unsigned > &  path_label_to_assay, const std::vector< String > &  fixed_mods, bool  export_subfeatures  )

staticprotected

peptideSectionRowFromFeature_()

static MzTabPeptideSectionRow peptideSectionRowFromFeature_ ( const Feature &  c, const std::set< String > &  feature_user_value_keys, const std::set< String > &  peptide_hit_user_value_keys, const std::vector< String > &  fixed_mods  )

staticprotected

proteinSectionRowFromProteinHit_()

static MzTabProteinSectionRow proteinSectionRowFromProteinHit_ ( const ProteinHit &  hit, const MzTabString &  db, const MzTabString &  db_version, const std::set< String > &  protein_hit_user_value_keys  )

staticprotected

PSMSectionRowFromPeptideID_()

static boost::optional<MzTabPSMSectionRow> PSMSectionRowFromPeptideID_ ( const PeptideIdentification &  pid, const std::vector< const ProteinIdentification * > &  prot_id, std::map< String, size_t > &  idrun_2_run_index, std::map< std::pair< size_t, size_t >, size_t > &  map_run_fileidx_2_msfileidx, std::map< Size, std::vector< std::pair< String, String >>> &  run_to_search_engines, const int  psm_id, const MzTabString &  db, const MzTabString &  db_version, const bool  export_empty_pep_ids  )

staticprotected

replaceWhiteSpaces_() [1/2]

static void replaceWhiteSpaces_ ( ForwardIterator  first, ForwardIterator  last  )

inlinestaticprotected

replaceWhiteSpaces_() [2/2]

static void replaceWhiteSpaces_ ( std::set< String > &  keys )

inlinestaticprotected

References String::substitute().

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