Uses of Package
de.isas.mztab2.model
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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 thede.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 ValidationMessageValidationMessage.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 ValidationMessageValidationMessage.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.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.MsRun Specification of ms_run.SpectraRef Reference to a spectrum in a spectrum file, for example a fragmentation spectrum has been used to support the identification. -
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 prefixComment.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 ErrorError.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.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 ValidationMessageValidationMessage.CategoryEnum Gets or Sets categoryValidationMessage.MessageTypeEnum Gets or Sets messageTypeValidationMessage.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.