| OpenMS 2.5.0

Classes | Namespaces | Typedefs | Enumerations
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
| basic interface for all MzTab datatypes (can be null; are converted from and to cell string) More...
class | MzTabNullNaNAndInfAbleInterface
| interface for NaN- and Inf- able datatypes (Double and Integer in MzTab). These are as well null-able More...
class | MzTabNullAbleBase
| base class for atomic, non-container types (Double, Int) More...
class | MzTabNullNaNAndInfAbleBase
| base class for the atomic non-container like MzTab data types (Double, Int) More...
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...

## 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...

## 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

PEP - Peptide section (Table based)

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)

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)

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)

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)

Class Members
MzTabString | accession | The nucleic acid’s accession.
map< Size, MzTabDouble > | best_search_engine_score | Search engine(s) score(s) for the match.
MzTabString | 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.
MzTabString | 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)

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.