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 <map>
#include <vector>
#include <list>
#include <algorithm>

Go to the source code of this file.

Classes
class	MzTabNullAbleInterface
class	MzTabNullNaNAndInfAbleInterface
class	MzTabNullAbleBase
class	MzTabNullNaNAndInfAbleBase
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
struct	MzTabProteinSectionRow
struct	MzTabPeptideSectionRow
struct	MzTabPSMSectionRow
struct	MzTabSmallMoleculeSectionRow
class	MzTab
	Data model of MzTab files. Please see the official MzTab specification at https://code.google.com/p/mztab/. More...

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

Enumerations
enum	MzTabCellStateType {   MZTAB_CELLSTATE_DEFAULT, MZTAB_CELLSTATE_NULL, MZTAB_CELLSTATE_NAN, MZTAB_CELLSTATE_INF,   SIZE_OF_MZTAB_CELLTYPE }
	Data model of MzTab files. Please see the official MzTab specification at https://code.google.com/p/mztab/. More...

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Class Documentation

OpenMS::MzTabSampleMetaData

struct OpenMS::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

Class Members
map< Size, MzTabString >	setting
MzTabParameter	software

OpenMS::MzTabModificationMetaData

struct OpenMS::MzTabModificationMetaData

Class Members
MzTabParameter	modification
MzTabString	position
MzTabString	site

OpenMS::MzTabAssayMetaData

struct OpenMS::MzTabAssayMetaData

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

OpenMS::MzTabCVMetaData

struct OpenMS::MzTabCVMetaData

Class Members
MzTabString	full_name
MzTabString	label
MzTabString	url
MzTabString	version

OpenMS::MzTabInstrumentMetaData

struct OpenMS::MzTabInstrumentMetaData

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

OpenMS::MzTabContactMetaData

struct OpenMS::MzTabContactMetaData

Class Members
MzTabString	affiliation
MzTabString	email
MzTabString	name

OpenMS::MzTabMSRunMetaData

struct OpenMS::MzTabMSRunMetaData

Class Members
MzTabParameter	format
MzTabParameterList	fragmentation_method
MzTabParameter	id_format
MzTabString	location

OpenMS::MzTabStudyVariableMetaData

struct OpenMS::MzTabStudyVariableMetaData

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

OpenMS::MzTabPeptideSectionRow

struct OpenMS::MzTabPeptideSectionRow

Class Members
MzTabString	accession
map< Size, MzTabDouble >	best_search_engine_score
MzTabInteger	charge
MzTabString	database
MzTabString	database_version
MzTabDouble	mass_to_charge
MzTabModificationList	modifications
vector< MzTabOptionalColumnEntry >	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
MzTabDoubleList	retention_time
MzTabDoubleList	retention_time_window
MzTabParameterList	search_engine
map< Size, map< Size, MzTabDouble > >	search_engine_score_ms_run
MzTabString	sequence
MzTabSpectraRef	spectra_ref
MzTabBoolean	unique
MzTabString	uri

OpenMS::MzTabPSMSectionRow

struct OpenMS::MzTabPSMSectionRow

Class Members
MzTabString	accession
MzTabDouble	calc_mass_to_charge
MzTabInteger	charge
MzTabString	database
MzTabString	database_version
MzTabString	end
MzTabDouble	exp_mass_to_charge
MzTabModificationList	modifications
vector< MzTabOptionalColumnEntry >	opt_
MzTabString	post
MzTabString	pre
MzTabInteger	PSM_ID
MzTabInteger	reliability
MzTabDoubleList	retention_time
MzTabParameterList	search_engine
map< Size, MzTabDouble >	search_engine_score
MzTabString	sequence
MzTabSpectraRef	spectra_ref
MzTabString	start
MzTabBoolean	unique
MzTabString	uri

OpenMS::MzTabSmallMoleculeSectionRow

struct OpenMS::MzTabSmallMoleculeSectionRow

Class Members
map< Size, MzTabDouble >	best_search_engine_score
MzTabDouble	calc_mass_to_charge
MzTabDouble	charge
MzTabString	chemical_formula
MzTabString	database
MzTabString	database_version
MzTabString	description
MzTabDouble	exp_mass_to_charge
MzTabStringList	identifier
MzTabString	inchi_key
MzTabString	modifications
vector< MzTabOptionalColumnEntry >	opt_
MzTabInteger	reliability
MzTabDoubleList	retention_time
MzTabParameterList	search_engine
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
MzTabString	species
MzTabSpectraRef	spectra_ref
MzTabInteger	taxid
MzTabString	uri