Uses of Package
de.isas.mztab2.model

Packages that use de.isas.mztab2.model

Package	Description
de.isas.lipidomics.mztab2.validation	This package contains classes that provide the basic validator infrastructure used in the jmztabm-validation module.
de.isas.lipidomics.mztab2.validation.validators	This package contains custom validators that implement the
de.isas.mztab2.cvmapping	This package contains classes for controlled vocabulary term access, comparison, results and external cv parameter resolution.
de.isas.mztab2.io	This package contains implementations for reading and writing of mzTab-M files.
de.isas.mztab2.io.serialization	This package contains classes that implement custom Jackson serializers for the mzTab-M model objects.
de.isas.mztab2.io.validators	This package contains implementations for validation of mzTab-M parts during parsing.
de.isas.mztab2.model	Base package for the jmztab-m data model, generated from the mzTab_m_swagger.yml specification.
de.isas.mztab2.validation	This package contains interfaces and implementations for the semantic validation via CvTerms.
de.isas.mztab2.validation.handlers	This package contains implementations for the semantic validation controlled vocabulary term rules.
uk.ac.ebi.pride.jmztab2.model	This package contains model classes for mzTab-M structural features like mandatory and optional columns.
uk.ac.ebi.pride.jmztab2.utils.errors	This package contains error type definitions and related classes used during mzTab validation.
uk.ac.ebi.pride.jmztab2.utils.parser	This package contains text file line parser implementations for the mzTab-M document sections.

Classes in de.isas.mztab2.model used by de.isas.lipidomics.mztab2.validation

Class	Description
MzTab	mzTab-M is intended as a reporting standard for quantitative results from metabolomics/lipodomics approaches.
ValidationMessage	ValidationMessage
ValidationMessage.MessageTypeEnum	Gets or Sets messageType

Classes in de.isas.mztab2.model used by de.isas.lipidomics.mztab2.validation.validators

Class	Description
Parameter	mzTab makes use of CV parameters.

Classes in de.isas.mztab2.model used by de.isas.mztab2.cvmapping

Class	Description
Parameter	mzTab makes use of CV parameters.

Classes in de.isas.mztab2.model used by de.isas.mztab2.io

Class	Description
ColumnParameterMapping	Defines the used unit for a column in the mzTab-M file.
Metadata.Properties	Property enumeration for Metadata.
MzTab	mzTab-M is intended as a reporting standard for quantitative results from metabolomics/lipodomics approaches.
MzTab.Properties	Property enumeration for MzTab.
ValidationMessage	ValidationMessage
ValidationMessage.MessageTypeEnum	Gets or Sets messageType

Classes in de.isas.mztab2.model used by de.isas.mztab2.io.serialization

Class	Description
Assay	Specification of assay.
Contact	The contact’s name, affiliation and e-mail.
CV	Specification of controlled vocabularies. label: A string describing the labels of the controlled vocabularies/ontologies used in the mzTab file as a short-hand e.g.
Database	Specification of databases.
IndexedElement	Indexed elements (IDs) define a unique ID for a collection of multiple metadata elements of the same type within the mzTab-M document, e.g. for sample, assay, study variable etc.
Instrument	The name, source, analyzer and detector of the instruments used in the experiment.
Metadata	The metadata section provides additional information about the dataset(s) reported in the mzTab file.
MsRun	Specification of ms_run.
OptColumnMapping	Additional columns can be added to the end of the small molecule table.
Parameter	mzTab makes use of CV parameters.
Publication	A publication associated with this file.
Sample	Specification of sample.
SampleProcessing	A list of parameters describing a sample processing, preparation or handling step similar to a biological or analytical methods report.
SmallMoleculeEvidence	The small molecule evidence section is table-based, representing evidence for identifications of small molecules/features, from database search or any other process used to give putative identifications to molecules.
SmallMoleculeFeature	The small molecule feature section is table-based, representing individual MS regions (generally considered to be the elution profile for all isotopomers formed from a single charge state of a molecule), that have been measured/quantified.
SmallMoleculeSummary	The small molecule summary section is table-based, represented summarized quantitative information across assays and study variables, grouped by identification in rows.
Software	Software used to analyze the data and obtain the reported results.
StudyVariable	Specification of study_variable.
Uri	A URI pointing to the file’s source data (e.g., a MetaboLights records) or an external file with more details about the study design.

Classes in de.isas.mztab2.model used by de.isas.mztab2.io.validators

Class	Description
Metadata	The metadata section provides additional information about the dataset(s) reported in the mzTab file.

Classes in de.isas.mztab2.model used by de.isas.mztab2.model

Class	Description
Assay	Specification of assay.
Assay.Properties	Property enumeration for Assay.
ColumnParameterMapping	Defines the used unit for a column in the mzTab-M file.
ColumnParameterMapping.Properties	Property enumeration for ColumnParameterMapping.
Comment	Comment lines can be placed anywhere in an mzTab file.
Comment.PrefixEnum	Gets or Sets prefix
Comment.Properties	Property enumeration for Comment.
Contact	The contact’s name, affiliation and e-mail.
Contact.Properties	Property enumeration for Contact.
CV	Specification of controlled vocabularies. label: A string describing the labels of the controlled vocabularies/ontologies used in the mzTab file as a short-hand e.g.
CV.Properties	Property enumeration for CV.
Database	Specification of databases.
Database.Properties	Property enumeration for Database.
Error	Error
Error.Properties	Property enumeration for Error.
IndexedElement	Indexed elements (IDs) define a unique ID for a collection of multiple metadata elements of the same type within the mzTab-M document, e.g. for sample, assay, study variable etc.
IndexedElement.Properties	Property enumeration for IndexedElement.
Instrument	The name, source, analyzer and detector of the instruments used in the experiment.
Instrument.Properties	Property enumeration for Instrument.
Metadata	The metadata section provides additional information about the dataset(s) reported in the mzTab file.
Metadata.PrefixEnum	The metadata section prefix.
Metadata.Properties	Property enumeration for Metadata.
MsRun	Specification of ms_run.
MsRun.Properties	Property enumeration for MsRun.
MzTab	mzTab-M is intended as a reporting standard for quantitative results from metabolomics/lipodomics approaches.
MzTab.Properties	Property enumeration for MzTab.
OptColumnMapping	Additional columns can be added to the end of the small molecule table.
OptColumnMapping.Properties	Property enumeration for OptColumnMapping.
Parameter	mzTab makes use of CV parameters.
Parameter.Properties	Property enumeration for Parameter.
Publication	A publication associated with this file.
Publication.Properties	Property enumeration for Publication.
PublicationItem	A publication item, defined by a qualifier and a native accession, e.g. pubmed id.
PublicationItem.Properties	Property enumeration for PublicationItem.
PublicationItem.TypeEnum	The type qualifier of this publication item.
Sample	Specification of sample.
Sample.Properties	Property enumeration for Sample.
SampleProcessing	A list of parameters describing a sample processing, preparation or handling step similar to a biological or analytical methods report.
SampleProcessing.Properties	Property enumeration for SampleProcessing.
SmallMoleculeEvidence	The small molecule evidence section is table-based, representing evidence for identifications of small molecules/features, from database search or any other process used to give putative identifications to molecules.
SmallMoleculeEvidence.HeaderPrefixEnum	The small molecule evidence table header prefix.
SmallMoleculeEvidence.PrefixEnum	The small molecule evidence table row prefix.
SmallMoleculeEvidence.Properties	Property enumeration for SmallMoleculeEvidence.
SmallMoleculeFeature	The small molecule feature section is table-based, representing individual MS regions (generally considered to be the elution profile for all isotopomers formed from a single charge state of a molecule), that have been measured/quantified.
SmallMoleculeFeature.HeaderPrefixEnum	The small molecule feature table header prefix.
SmallMoleculeFeature.PrefixEnum	The small molecule feature table row prefix.
SmallMoleculeFeature.Properties	Property enumeration for SmallMoleculeFeature.
SmallMoleculeSummary	The small molecule summary section is table-based, represented summarized quantitative information across assays and study variables, grouped by identification in rows.
SmallMoleculeSummary.HeaderPrefixEnum	The small molecule table header prefix.
SmallMoleculeSummary.PrefixEnum	The small molecule table row prefix.
SmallMoleculeSummary.Properties	Property enumeration for SmallMoleculeSummary.
Software	Software used to analyze the data and obtain the reported results.
Software.Properties	Property enumeration for Software.
SpectraRef	Reference to a spectrum in a spectrum file, for example a fragmentation spectrum has been used to support the identification.
SpectraRef.Properties	Property enumeration for SpectraRef.
StudyVariable	Specification of study_variable.
StudyVariable.Properties	Property enumeration for StudyVariable.
Uri	A URI pointing to the file’s source data (e.g., a MetaboLights records) or an external file with more details about the study design.
Uri.Properties	Property enumeration for Uri.
ValidationMessage	ValidationMessage
ValidationMessage.CategoryEnum	Gets or Sets category
ValidationMessage.MessageTypeEnum	Gets or Sets messageType
ValidationMessage.Properties	Property enumeration for ValidationMessage.

Classes in de.isas.mztab2.model used by de.isas.mztab2.validation

Class	Description
MzTab	mzTab-M is intended as a reporting standard for quantitative results from metabolomics/lipodomics approaches.
Parameter	mzTab makes use of CV parameters.
ValidationMessage	ValidationMessage

Classes in de.isas.mztab2.model used by de.isas.mztab2.validation.handlers

Class	Description
Parameter	mzTab makes use of CV parameters.
ValidationMessage	ValidationMessage

Classes in de.isas.mztab2.model used by uk.ac.ebi.pride.jmztab2.model

Class	Description
Assay	Specification of assay.
IndexedElement	Indexed elements (IDs) define a unique ID for a collection of multiple metadata elements of the same type within the mzTab-M document, e.g. for sample, assay, study variable etc.
Metadata	The metadata section provides additional information about the dataset(s) reported in the mzTab file.
OptColumnMapping	Additional columns can be added to the end of the small molecule table.
Parameter	mzTab makes use of CV parameters.
Publication	A publication associated with this file.
SpectraRef	Reference to a spectrum in a spectrum file, for example a fragmentation spectrum has been used to support the identification.
StudyVariable	Specification of study_variable.

Classes in de.isas.mztab2.model used by uk.ac.ebi.pride.jmztab2.utils.errors

Class	Description
ValidationMessage	ValidationMessage

Classes in de.isas.mztab2.model used by uk.ac.ebi.pride.jmztab2.utils.parser

Class	Description
Assay	Specification of assay.
Comment	Comment lines can be placed anywhere in an mzTab file.
Contact	The contact’s name, affiliation and e-mail.
CV	Specification of controlled vocabularies. label: A string describing the labels of the controlled vocabularies/ontologies used in the mzTab file as a short-hand e.g.
Database	Specification of databases.
Instrument	The name, source, analyzer and detector of the instruments used in the experiment.
Metadata	The metadata section provides additional information about the dataset(s) reported in the mzTab file.
MsRun	Specification of ms_run.
Parameter	mzTab makes use of CV parameters.
Publication	A publication associated with this file.
PublicationItem	A publication item, defined by a qualifier and a native accession, e.g. pubmed id.
PublicationItem.TypeEnum	The type qualifier of this publication item.
Sample	Specification of sample.
SampleProcessing	A list of parameters describing a sample processing, preparation or handling step similar to a biological or analytical methods report.
SmallMoleculeEvidence	The small molecule evidence section is table-based, representing evidence for identifications of small molecules/features, from database search or any other process used to give putative identifications to molecules.
SmallMoleculeFeature	The small molecule feature section is table-based, representing individual MS regions (generally considered to be the elution profile for all isotopomers formed from a single charge state of a molecule), that have been measured/quantified.
SmallMoleculeFeature.Properties	Property enumeration for SmallMoleculeFeature.
SmallMoleculeSummary	The small molecule summary section is table-based, represented summarized quantitative information across assays and study variables, grouped by identification in rows.
SmallMoleculeSummary.Properties	Property enumeration for SmallMoleculeSummary.
Software	Software used to analyze the data and obtain the reported results.
SpectraRef	Reference to a spectrum in a spectrum file, for example a fragmentation spectrum has been used to support the identification.
StudyVariable	Specification of study_variable.