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OpenMS
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#include <OpenMS/FORMAT/MzTabBase.h>#include <OpenMS/KERNEL/FeatureMap.h>#include <OpenMS/METADATA/ID/IdentificationData.h>#include <OpenMS/METADATA/MetaInfoInterface.h>#include <set>Go to the source code of this file.
Namespaces | |
| OpenMS | |
| Main OpenMS namespace. | |
Typedefs | |
| typedef std::vector< MzTabMSmallMoleculeSectionRow > | MzTabMSmallMoleculeSectionRows |
| typedef std::vector< MzTabMSmallMoleculeFeatureSectionRow > | MzTabMSmallMoleculeFeatureSectionRows |
| typedef std::vector< MzTabMSmallMoleculeEvidenceSectionRow > | MzTabMSmallMoleculeEvidenceSectionRows |
| class OpenMS::MzTabMAssayMetaData |
MztabM Assay Metadata.
| Class Members | ||
|---|---|---|
| map< Size, MzTabParameter > | custom | Additional parameters or values for a given assay. |
| MzTabString | external_uri | A reference to further information about the assay. |
| MzTabInteger | ms_run_ref | An association from a given assay to the source MS run. |
| MzTabString | name | Name of the assay. |
| MzTabInteger | sample_ref | An association from a given assay to the sample analysed. |
| class OpenMS::MzTabMMSRunMetaData |
MztabM MSRun Metadata.
| Class Members | ||
|---|---|---|
| MzTabParameter | format | Parameter specifying the data format of the external MS data file. |
| map< Size, MzTabParameter > | fragmentation_method | The type of fragmentation used in a given ms run. |
| MzTabString | hash | Hash value of the corresponding external MS data file. |
| MzTabParameter | hash_method | Parameter specifying the hash methods. |
| MzTabParameter | id_format | Parameter specifying the id format used in the external data file. |
| MzTabInteger | instrument_ref | Link to a specific instrument. |
| MzTabString | location | Location of the external data file. |
| map< Size, MzTabParameter > | scan_polarity | The polarity mode of a given run. |
| class OpenMS::MzTabMStudyVariableMetaData |
MztabM StudyVariable Metadata.
| Class Members | ||
|---|---|---|
| vector< int > | assay_refs | References to the IDs of assays grouped in the study variable. |
| MzTabParameter | average_function | The function used to calculate the study variable quantification value. |
| MzTabString | description | A textual description of the study variable. |
| MzTabParameterList | factors | Additional parameters or factors. |
| MzTabString | name | Name of the study variable. |
| MzTabParameter | variation_function | The function used to calculate the study variable quantification variation value. |
| class OpenMS::MzTabMDatabaseMetaData |
MztabM Database Metadata.
| Class Members | ||
|---|---|---|
| MzTabParameter | database | The description of databases used. |
| MzTabString | prefix | The prefix used in the “identifier” column of data tables. |
| MzTabString | uri | The URI to the database. |
| MzTabString | version | The database version. |
| class OpenMS::MzTabMSmallMoleculeSectionRow |
SML Small molecule section (mztab-m)
| Class Members | ||
|---|---|---|
| MzTabStringList | adducts | Adducts. |
| MzTabParameter | best_id_confidence_measure | The identification approach with the highest confidence. |
| MzTabDouble | best_id_confidence_value | The best confidence measure. |
| MzTabStringList | chemical_formula | Potential chemical formula of the reported compound. |
| MzTabStringList | chemical_name | Possible chemical/common names or general description. |
| MzTabStringList | database_identifier | Names of the used databases. |
| MzTabStringList | inchi | InChi of the potential compound identifications. |
| vector< MzTabOptionalColumnEntry > | opt_ | Optional columns must start with “opt_”. |
| MzTabString | reliability | Reliability of the given small molecule identification. |
| map< Size, MzTabDouble > | small_molecule_abundance_assay | The small molecule’s abundance in every assay described in the metadata section. |
| map< Size, MzTabDouble > | small_molecule_abundance_study_variable | The small molecule’s abundance in all the study variables described in the metadata section. |
| map< Size, MzTabDouble > | small_molecule_abundance_variation_study_variable | A measure of the variability of the study variable abundance measurement. |
| MzTabStringList | smf_id_refs | References to all the features on which quantification has been based. |
| MzTabStringList | smiles | Molecular structure in SMILES format. |
| MzTabString | sml_identifier | The small molecule’s identifier. |
| MzTabDoubleList | theoretical_neutral_mass | Precursor theoretical neutral mass. |
| MzTabStringList | uri | The source entry’s location. |
| class OpenMS::MzTabMSmallMoleculeFeatureSectionRow |
SMF Small molecule feature section (mztab-m)
| Class Members | ||
|---|---|---|
| MzTabString | adduct | Adduct. |
| MzTabInteger | charge | Precursor ion’s charge. |
| MzTabDouble | exp_mass_to_charge | Precursor ion’s m/z. |
| MzTabParameter | isotopomer | If de-isotoping has not been performed, then the isotopomer quantified MUST be reported here. |
| vector< MzTabOptionalColumnEntry > | opt_ | Optional columns must start with “opt_”. |
| MzTabDouble | retention_time | Time point in seconds. |
| MzTabDouble | rt_end | The end time of the feature on the retention time axis. |
| MzTabDouble | rt_start | The start time of the feature on the retention time axis. |
| map< Size, MzTabDouble > | small_molecule_feature_abundance_assay | Feature abundance in every assay. |
| MzTabInteger | sme_id_ref_ambiguity_code | Ambiguity in identifications. |
| MzTabStringList | sme_id_refs | Reference to the identification evidence. |
| MzTabString | smf_identifier | Within file unique identifier for the small molecule feature. |
| class OpenMS::MzTabMSmallMoleculeEvidenceSectionRow |
SME Small molecule evidence section (mztab-m)
| Class Members | ||
|---|---|---|
| MzTabString | adduct | Adduct. |
| MzTabDouble | calc_mass_to_charge | Precursor ion’s m/z. |
| MzTabInteger | charge | Precursor ion’s charge. |
| MzTabString | chemical_formula | The putative molecular formula. |
| MzTabString | chemical_name | Possible chemical/common names or general description. |
| MzTabString | database_identifier | The putative identification for the small molecule sourced from an external database. |
| MzTabParameter | derivatized_form | derivatized form. |
| MzTabString | evidence_input_id | Within file unique identifier for the input data used to support this identification e.g. fragment spectrum, RT and m/z pair. |
| MzTabDouble | exp_mass_to_charge | Precursor ion’s m/z. |
| map< Size, MzTabDouble > | id_confidence_measure | Statistical value or score for the identification. |
| MzTabParameter | identification_method | Database search, search engine or process that was used to identify this small molecule. |
| MzTabString | inchi | InChi of the potential compound identifications. |
| MzTabParameter | ms_level | The highest MS level used to inform identification. |
| vector< MzTabOptionalColumnEntry > | opt_ | Optional columns must start with “opt_”. |
| MzTabInteger | rank | Rank of the identification (1 = best) |
| MzTabString | sme_identifier | Within file unique identifier for the small molecule evidence result. |
| MzTabString | smiles | Potential molecular structure as SMILES. |
| MzTabSpectraRef | spectra_ref | Reference to a spectrum. |
| MzTabString | uri | The source entry’s location. |
1.9.1