OpenMS  2.6.0
Classes | Public Member Functions | Static Public Member Functions | Protected Member Functions | Static Protected Member Functions | Protected Attributes | List of all members
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:
[legend]

Classes

class  CMMzTabStream
 
class  IDMzTabStream
 

Public Member Functions

 MzTab ()=default
 Default constructor. More...
 
 ~MzTab ()=default
 
const MzTabMetaDatagetMetaData () const
 
void setMetaData (const MzTabMetaData &md)
 
MzTabProteinSectionRowsgetProteinSectionRows ()
 
const MzTabProteinSectionRowsgetProteinSectionRows () const
 
void setProteinSectionRows (const MzTabProteinSectionRows &psd)
 
MzTabPeptideSectionRowsgetPeptideSectionRows ()
 
const MzTabPeptideSectionRowsgetPeptideSectionRows () const
 
void setPeptideSectionRows (const MzTabPeptideSectionRows &psd)
 
MzTabPSMSectionRowsgetPSMSectionRows ()
 
const MzTabPSMSectionRowsgetPSMSectionRows () const
 
void setPSMSectionRows (const MzTabPSMSectionRows &psd)
 
const MzTabSmallMoleculeSectionRowsgetSmallMoleculeSectionRows () const
 
void setSmallMoleculeSectionRows (const MzTabSmallMoleculeSectionRows &smsd)
 
const MzTabNucleicAcidSectionRowsgetNucleicAcidSectionRows () const
 
void setNucleicAcidSectionRows (const MzTabNucleicAcidSectionRows &nasd)
 
const MzTabOligonucleotideSectionRowsgetOligonucleotideSectionRows () const
 
void setOligonucleotideSectionRows (const MzTabOligonucleotideSectionRows &onsd)
 
const MzTabOSMSectionRowsgetOSMSectionRows () 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< StringgetProteinOptionalColumnNames () const
 Extract opt_ (custom, optional column names) More...
 
std::vector< StringgetPeptideOptionalColumnNames () const
 Extract opt_ (custom, optional column names) More...
 
std::vector< StringgetPSMOptionalColumnNames () const
 Extract opt_ (custom, optional column names) More...
 
std::vector< StringgetSmallMoleculeOptionalColumnNames () const
 Extract opt_ (custom, optional column names) More...
 
std::vector< StringgetNucleicAcidOptionalColumnNames () const
 Extract opt_ (custom, optional column names) More...
 
std::vector< StringgetOligonucleotideOptionalColumnNames () const
 Extract opt_ (custom, optional column names) More...
 
std::vector< StringgetOSMOptionalColumnNames () 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, MzTabModificationMetaDatagenerateMzTabStringFromModifications (const std::vector< String > &mods)
 
static std::map< Size, MzTabModificationMetaDatagenerateMzTabStringFromVariableModifications (const std::vector< String > &mods)
 
static std::map< Size, MzTabModificationMetaDatagenerateMzTabStringFromFixedModifications (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< StringgetOptionalColumnNames_ (const SectionRows &rows) const
 Helper function for "get...OptionalColumnNames" functions. More...
 

Static Protected Member Functions

static std::map< String, SizemapIDRunIdentifier2IDRunIndex_ (const std::vector< const ProteinIdentification * > &prot_ids)
 
static boost::optional< MzTabPSMSectionRowPSMSectionRowFromPeptideID_ (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< Sizeempty_rows_
 index of empty rows More...
 
std::map< Size, Stringcomment_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_evidencesVector of PeptideEvidence holding internal data.
rowPre- 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_mapdata structure of the linked peptide features
filenameinput consensusXML file name
export_unidentified_featuresShould not identified peptide features be exported?
export_unassigned_idsShould unassigned identifications be exported?
export_subfeaturesThe 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_idsData structure containing protein identifications
[in]peptide_idsData structure containing peptide identifications
[in]filenameInput idXML file name
[in]first_run_inference_onlyIs 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

◆ getOligonucleotideOptionalColumnNames()

std::vector<String> getOligonucleotideOptionalColumnNames ( ) const

Extract opt_ (custom, optional column names)

◆ getOligonucleotideSectionRows()

const MzTabOligonucleotideSectionRows& getOligonucleotideSectionRows ( ) const

◆ 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

◆ 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