MzTab.h File Reference

#include <OpenMS/FORMAT/SVOutStream.h>
#include <OpenMS/CONCEPT/Exception.h>
#include <OpenMS/KERNEL/StandardTypes.h>
#include <OpenMS/KERNEL/FeatureMap.h>
#include <OpenMS/KERNEL/ConsensusMap.h>
#include <OpenMS/CHEMISTRY/AASequence.h>
#include <OpenMS/METADATA/PeptideEvidence.h>
#include <boost/optional.hpp>
#include <map>
#include <vector>
#include <list>
#include <algorithm>

Include dependency graph for MzTab.h:

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Go to the source code of this file.

Classes
class	MzTabDouble
class	MzTabDoubleList
class	MzTabInteger
class	MzTabIntegerList
class	MzTabBoolean
class	MzTabString
class	MzTabParameter
class	MzTabParameterList
class	MzTabStringList
class	MzTabModification
class	MzTabModificationList
class	MzTabSpectraRef
struct	MzTabSampleMetaData
struct	MzTabSoftwareMetaData
struct	MzTabModificationMetaData
struct	MzTabAssayMetaData
struct	MzTabCVMetaData
struct	MzTabInstrumentMetaData
struct	MzTabContactMetaData
struct	MzTabMSRunMetaData
struct	MzTabStudyVariableMetaData
class	MzTabMetaData
	all meta data of a mzTab file. Please refer to specification for documentation. More...
struct	MzTabProteinSectionRow
	PRT - Protein section (Table based) More...
struct	MzTabProteinSectionRow::RowCompare
	Comparison operator for sorting rows. More...
struct	MzTabPeptideSectionRow
	PEP - Peptide section (Table based) More...
struct	MzTabPeptideSectionRow::RowCompare
	Comparison operator for sorting rows. More...
struct	MzTabPSMSectionRow
	PSM - PSM section (Table based) More...
struct	MzTabPSMSectionRow::RowCompare
	Comparison operator for sorting rows. More...
struct	MzTabSmallMoleculeSectionRow
	SML Small molecule section (table based) More...
struct	MzTabNucleicAcidSectionRow
	NUC - Nucleic acid section (table-based) More...
struct	MzTabNucleicAcidSectionRow::RowCompare
	Comparison operator for sorting rows. More...
struct	MzTabOligonucleotideSectionRow
	OLI - Oligonucleotide section (table-based) More...
struct	MzTabOligonucleotideSectionRow::RowCompare
	Comparison operator for sorting rows. More...
struct	MzTabOSMSectionRow
	OSM - OSM (oligonucleotide-spectrum match) section (table-based) More...
struct	MzTabOSMSectionRow::RowCompare
	Comparison operator for sorting rows. More...
class	MzTab
	Data model of MzTab files. Please see the official MzTab specification at https://code.google.com/p/mztab/. More...
class	MzTab::IDMzTabStream
class	MzTab::CMMzTabStream

Namespaces
	OpenMS
	Main OpenMS namespace.

Typedefs
typedef std::pair< String, MzTabString >	MzTabOptionalColumnEntry
typedef std::vector< MzTabProteinSectionRow >	MzTabProteinSectionRows
typedef std::vector< MzTabPeptideSectionRow >	MzTabPeptideSectionRows
typedef std::vector< MzTabPSMSectionRow >	MzTabPSMSectionRows
typedef std::vector< MzTabSmallMoleculeSectionRow >	MzTabSmallMoleculeSectionRows
typedef std::vector< MzTabNucleicAcidSectionRow >	MzTabNucleicAcidSectionRows
typedef std::vector< MzTabOligonucleotideSectionRow >	MzTabOligonucleotideSectionRows
typedef std::vector< MzTabOSMSectionRow >	MzTabOSMSectionRows

Enumerations
enum	MzTabCellStateType {   MZTAB_CELLSTATE_DEFAULT, MZTAB_CELLSTATE_NULL, MZTAB_CELLSTATE_NAN, MZTAB_CELLSTATE_INF,   SIZE_OF_MZTAB_CELLTYPE }
	Data model of MzTab files. More...

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Class Documentation

OpenMS::MzTabSampleMetaData

struct OpenMS::MzTabSampleMetaData

Collaboration diagram for MzTabSampleMetaData:

Class Members
map< Size, MzTabParameter >	cell_type
map< Size, MzTabParameter >	custom
MzTabString	description
map< Size, MzTabParameter >	disease
map< Size, MzTabParameter >	species
map< Size, MzTabParameter >	tissue

OpenMS::MzTabSoftwareMetaData

struct OpenMS::MzTabSoftwareMetaData

Collaboration diagram for MzTabSoftwareMetaData:

Class Members
map< Size, MzTabString >	setting
MzTabParameter	software

OpenMS::MzTabModificationMetaData

struct OpenMS::MzTabModificationMetaData

Collaboration diagram for MzTabModificationMetaData:

Class Members
MzTabParameter	modification
MzTabString	position
MzTabString	site

OpenMS::MzTabAssayMetaData

struct OpenMS::MzTabAssayMetaData

Collaboration diagram for MzTabAssayMetaData:

Class Members
vector< int >	ms_run_ref
map< Size, MzTabModificationMetaData >	quantification_mod
MzTabParameter	quantification_reagent
MzTabString	sample_ref

OpenMS::MzTabCVMetaData

struct OpenMS::MzTabCVMetaData

Collaboration diagram for MzTabCVMetaData:

Class Members
MzTabString	full_name
MzTabString	label
MzTabString	url
MzTabString	version

OpenMS::MzTabInstrumentMetaData

struct OpenMS::MzTabInstrumentMetaData

Collaboration diagram for MzTabInstrumentMetaData:

Class Members
map< Size, MzTabParameter >	analyzer
MzTabParameter	detector
MzTabParameter	name
MzTabParameter	source

OpenMS::MzTabContactMetaData

struct OpenMS::MzTabContactMetaData

Collaboration diagram for MzTabContactMetaData:

Class Members
MzTabString	affiliation
MzTabString	email
MzTabString	name

OpenMS::MzTabMSRunMetaData

struct OpenMS::MzTabMSRunMetaData

Collaboration diagram for MzTabMSRunMetaData:

Class Members
MzTabParameter	format
MzTabParameterList	fragmentation_method
MzTabParameter	id_format
MzTabString	location

OpenMS::MzTabStudyVariableMetaData

struct OpenMS::MzTabStudyVariableMetaData

Collaboration diagram for MzTabStudyVariableMetaData:

Class Members
vector< int >	assay_refs
MzTabString	description
vector< int >	sample_refs

OpenMS::MzTabPeptideSectionRow

struct OpenMS::MzTabPeptideSectionRow

PEP - Peptide section (Table based)

Collaboration diagram for MzTabPeptideSectionRow:

Class Members
MzTabString	accession	The protein’s accession.
map< Size, MzTabDouble >	best_search_engine_score	Search engine(s) score(s) for the peptide.
MzTabInteger	charge	Precursor ion’s charge.
MzTabString	database	Name of the sequence database.
MzTabString	database_version	Version (and optionally # of entries).
MzTabDouble	mass_to_charge	Precursor ion’s m/z.
MzTabModificationList	modifications	Modifications identified in the peptide.
vector< MzTabOptionalColumnEntry >	opt_	Optional columns must start with “opt_”.
map< Size, MzTabDouble >	peptide_abundance_assay
map< Size, MzTabDouble >	peptide_abundance_std_error_study_variable
map< Size, MzTabDouble >	peptide_abundance_stdev_study_variable
map< Size, MzTabDouble >	peptide_abundance_study_variable
MzTabInteger	reliability	(1-3) 0=null Identification reliability for the peptide.
MzTabDoubleList	retention_time	Time points in seconds. Semantics may vary.
MzTabDoubleList	retention_time_window
MzTabParameterList	search_engine	Search engine(s) that identified the peptide.
map< Size, map< Size, MzTabDouble > >	search_engine_score_ms_run
MzTabString	sequence	The peptide’s sequence.
MzTabSpectraRef	spectra_ref	Spectra identifying the peptide.
MzTabBoolean	unique	0=false, 1=true, null else: Peptide is unique for the protein.
MzTabString	uri	Location of the PSMs source entry.

OpenMS::MzTabPSMSectionRow

struct OpenMS::MzTabPSMSectionRow

PSM - PSM section (Table based)

Collaboration diagram for MzTabPSMSectionRow:

Class Members
MzTabString	accession	The protein’s accession.
MzTabDouble	calc_mass_to_charge
MzTabInteger	charge	The charge of the experimental precursor ion.
MzTabString	database	Name of the sequence database.
MzTabString	database_version	Version (and optionally # of entries).
MzTabString	end
MzTabDouble	exp_mass_to_charge	The m/z ratio of the experimental precursor ion.
MzTabModificationList	modifications	Modifications identified in the peptide.
vector< MzTabOptionalColumnEntry >	opt_	Optional columns must start with “opt_”.
MzTabString	post
MzTabString	pre
MzTabInteger	PSM_ID
MzTabInteger	reliability	(1-3) 0=null Identification reliability for the peptide.
MzTabDoubleList	retention_time	Time points in seconds. Semantics may vary.
MzTabParameterList	search_engine	Search engine(s) that identified the peptide.
map< Size, MzTabDouble >	search_engine_score	Search engine(s) score(s) for the peptide.
MzTabString	sequence	The peptide’s sequence.
MzTabSpectraRef	spectra_ref	Spectra identifying the peptide.
MzTabString	start
MzTabBoolean	unique	0=false, 1=true, null else: Peptide is unique for the protein.
MzTabString	uri	Location of the PSM’s source entry.

OpenMS::MzTabSmallMoleculeSectionRow

struct OpenMS::MzTabSmallMoleculeSectionRow

SML Small molecule section (table based)

Collaboration diagram for MzTabSmallMoleculeSectionRow:

Class Members
map< Size, MzTabDouble >	best_search_engine_score	Search engine(s) identifications score(s).
MzTabDouble	calc_mass_to_charge	Precursor ion’s m/z.
MzTabInteger	charge	Precursor ion’s charge.
MzTabString	chemical_formula	Chemical formula of the identified compound.
MzTabString	database	Name of the used database.
MzTabString	database_version	String Version of the database (and optionally # of compounds).
MzTabString	description	Human readable description (i.e. the name)
MzTabDouble	exp_mass_to_charge	Precursor ion’s m/z.
MzTabStringList	identifier	The small molecule’s identifier.
MzTabString	inchi_key	InChi Key of the identified compound.
MzTabString	modifications	Modifications identified on the small molecule.
vector< MzTabOptionalColumnEntry >	opt_	Optional columns must start with “opt_”.
MzTabInteger	reliability	(1-3) The identification reliability.
MzTabDoubleList	retention_time	Time points in seconds. Semantics may vary.
MzTabParameterList	search_engine	Search engine(s) identifying the small molecule.
map< Size, map< Size, MzTabDouble > >	search_engine_score_ms_run
map< Size, MzTabDouble >	smallmolecule_abundance_assay
map< Size, MzTabDouble >	smallmolecule_abundance_std_error_study_variable
map< Size, MzTabDouble >	smallmolecule_abundance_stdev_study_variable
map< Size, MzTabDouble >	smallmolecule_abundance_study_variable
MzTabString	smiles	Molecular structure in SMILES format.
MzTabString	species	Human readable name of the species.
MzTabSpectraRef	spectra_ref	Spectra identifying the small molecule.
MzTabInteger	taxid	NEWT taxonomy for the species.
MzTabString	uri	The source entry’s location.

OpenMS::MzTabNucleicAcidSectionRow

struct OpenMS::MzTabNucleicAcidSectionRow

NUC - Nucleic acid section (table-based)

Collaboration diagram for MzTabNucleicAcidSectionRow:

Class Members
MzTabString	accession	The nucleic acid’s accession.
MzTabStringList	ambiguity_members	Alternative nucleic acid identifications.
map< Size, MzTabDouble >	best_search_engine_score	Best search engine(s) score(s) (over all MS runs)
MzTabDouble	coverage	(0-1) Fraction of nucleic acid sequence identified.
MzTabString	database	Name of the sequence database.
MzTabString	database_version	Version of the sequence database.
MzTabString	description	Human readable description (i.e. the name)
MzTabStringList	go_terms	List of GO terms for the nucleic acid.
MzTabModificationList	modifications	Modifications identified in the nucleic acid.
map< Size, MzTabInteger >	num_oligos_distinct_ms_run
map< Size, MzTabInteger >	num_oligos_unique_ms_run
map< Size, MzTabInteger >	num_osms_ms_run
vector< MzTabOptionalColumnEntry >	opt_	Optional Columns must start with “opt_”
MzTabInteger	reliability
MzTabParameterList	search_engine	Search engine(s) that identified the nucleic acid.
map< Size, map< Size, MzTabDouble > >	search_engine_score_ms_run
MzTabString	species	Human readable name of the species.
MzTabInteger	taxid	NEWT taxonomy for the species.
MzTabString	uri	Location of the nucleic acid’s source entry.

OpenMS::MzTabOligonucleotideSectionRow

struct OpenMS::MzTabOligonucleotideSectionRow

OLI - Oligonucleotide section (table-based)

Collaboration diagram for MzTabOligonucleotideSectionRow:

Class Members
MzTabString	accession	The nucleic acid’s accession.
map< Size, MzTabDouble >	best_search_engine_score	Search engine(s) score(s) for the match.
MzTabInteger	end
MzTabModificationList	modifications	Modifications identified in the oligonucleotide.
vector< MzTabOptionalColumnEntry >	opt_	Optional columns must start with “opt_”.
MzTabString	post
MzTabString	pre
MzTabInteger	reliability	(1-3) 0=null Identification reliability for the match.
MzTabDoubleList	retention_time	Time points in seconds. Semantics may vary.
MzTabDoubleList	retention_time_window
MzTabParameterList	search_engine	Search engine(s) that identified the match.
map< Size, map< Size, MzTabDouble > >	search_engine_score_ms_run	Search engine(s) score(s) per individual MS run.
MzTabString	sequence	The oligonucleotide’s sequence.
MzTabInteger	start
MzTabBoolean	unique	0=false, 1=true, null else: Oligonucleotide maps uniquely to the nucleic acid sequence.
MzTabString	uri	Location of the oligonucleotide's source entry.

OpenMS::MzTabOSMSectionRow

struct OpenMS::MzTabOSMSectionRow

OSM - OSM (oligonucleotide-spectrum match) section (table-based)

Collaboration diagram for MzTabOSMSectionRow:

Class Members
MzTabDouble	calc_mass_to_charge	The theoretical m/z ratio of the oligonucleotide.
MzTabInteger	charge	The charge of the experimental precursor ion.
MzTabDouble	exp_mass_to_charge	The m/z ratio of the experimental precursor ion.
MzTabModificationList	modifications	Modifications identified in the oligonucleotide.
vector< MzTabOptionalColumnEntry >	opt_	Optional columns must start with “opt_”.
MzTabInteger	reliability	(1-3) 0=null Identification reliability for the match.
MzTabDoubleList	retention_time	Time points in seconds. Semantics may vary.
MzTabParameterList	search_engine	Search engine(s) that identified the match.
map< Size, MzTabDouble >	search_engine_score	Search engine(s) score(s) for the match.
MzTabString	sequence	The oligonucleotide’s sequence.
MzTabSpectraRef	spectra_ref	Reference to the spectrum underlying the match.
MzTabString	uri	Location of the OSM’s source entry.