Uses of Class
de.isas.mztab2.model.MzTab

Packages that use MzTab

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.mztab2.io	This package contains implementations for reading and writing of mzTab-M files.
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.

Uses of MzTab in de.isas.lipidomics.mztab2.validation

Methods in de.isas.lipidomics.mztab2.validation with parameters of type MzTab

Modifier and Type	Method	Description
List<ValidationMessage>	MzTabValidator.validate(MzTab mzTab)
static List<ValidationMessage>	MzTabValidator.validate(MzTab mzTab, ValidationMessage.MessageTypeEnum validationLevel, Validator<MzTab>... validators)	Validate the given mzTab object, filtering messages that are of a lower level than the given one.

Uses of MzTab in de.isas.mztab2.io

Methods in de.isas.mztab2.io that return MzTab

Modifier and Type	Method	Description
MzTab	MzTabFileParser.getMZTabFile()	getMZTabFile.

Methods in de.isas.mztab2.io with parameters of type MzTab

Modifier and Type	Method	Description
com.fasterxml.jackson.dataformat.csv.CsvSchema	MzTabWriterDefaults.smallMoleculeEvidenceSchema(com.fasterxml.jackson.dataformat.csv.CsvMapper mapper, MzTab mzTabFile)	Creates the csv schema (column names and types) for the small molecule feature section.
com.fasterxml.jackson.dataformat.csv.CsvSchema	MzTabWriterDefaults.smallMoleculeFeatureSchema(com.fasterxml.jackson.dataformat.csv.CsvMapper mapper, MzTab mzTabFile)	Creates the csv schema (column names and types) for the small molecule feature section.
com.fasterxml.jackson.dataformat.csv.CsvSchema	MzTabWriterDefaults.smallMoleculeSummarySchema(com.fasterxml.jackson.dataformat.csv.CsvMapper mapper, MzTab mzTabFile)	Creates the csv schema (column names and types) for the small molecule summary section.
List<ValidationMessage>	MzTabValidatingWriter.WriteAndParseValidator.validate(MzTab mzTab)
Optional<Void>	MzTabNonValidatingWriter.write(OutputStreamWriter writer, MzTab mzTab)	Write the mzTab object to the provided output stream writer.
Optional<Void>	MzTabNonValidatingWriter.write(Path path, MzTab mzTab)	Write the mzTab object to the provided path.
Optional<List<ValidationMessage>>	MzTabValidatingWriter.write(OutputStreamWriter writer, MzTab mzTab)
Optional<List<ValidationMessage>>	MzTabValidatingWriter.write(Path path, MzTab mzTab)
Optional<T>	MzTabWriter.write(OutputStreamWriter writer, MzTab mzTab)	Write the mzTab object to the provided output stream writer.
Optional<T>	MzTabWriter.write(Path path, MzTab mzTab)	Write the mzTab object to the provided path file.

Constructor parameters in de.isas.mztab2.io with type arguments of type MzTab

Constructor	Description
MzTabValidatingWriter(Validator<MzTab> validator, boolean skipWriteOnValidationFailure)	Uses the provided validator and default writer configuration.
MzTabValidatingWriter(Validator<MzTab> validator, MzTabWriterDefaults writerDefaults, boolean skipWriteOnValidationFailure)	Uses the provided validator and writerDefaults.

Uses of MzTab in de.isas.mztab2.model

Methods in de.isas.mztab2.model that return MzTab

Modifier and Type	Method	Description
MzTab	MzTab.addCommentItem(Comment commentItem)	Add a single commentItem to the comment collection.
MzTab	MzTab.addSmallMoleculeEvidenceItem(SmallMoleculeEvidence smallMoleculeEvidenceItem)	Add a single smallMoleculeEvidenceItem to the smallMoleculeEvidence collection.
MzTab	MzTab.addSmallMoleculeFeatureItem(SmallMoleculeFeature smallMoleculeFeatureItem)	Add a single smallMoleculeFeatureItem to the smallMoleculeFeature collection.
MzTab	MzTab.addSmallMoleculeSummaryItem(SmallMoleculeSummary smallMoleculeSummaryItem)	Add a single smallMoleculeSummaryItem to the smallMoleculeSummary collection.
MzTab	MzTab.comment(List<Comment> comment)	Builder method for comment.
MzTab	MzTab.metadata(Metadata metadata)	Builder method for metadata.
MzTab	MzTab.smallMoleculeEvidence(List<SmallMoleculeEvidence> smallMoleculeEvidence)	Builder method for smallMoleculeEvidence.
MzTab	MzTab.smallMoleculeFeature(List<SmallMoleculeFeature> smallMoleculeFeature)	Builder method for smallMoleculeFeature.
MzTab	MzTab.smallMoleculeSummary(List<SmallMoleculeSummary> smallMoleculeSummary)	Builder method for smallMoleculeSummary.

Uses of MzTab in de.isas.mztab2.validation

Methods in de.isas.mztab2.validation with parameters of type MzTab

Modifier and Type	Method	Description
List<ValidationMessage>	CvDefinitionValidationHandler.validate(MzTab mzTab)
List<ValidationMessage>	CvMappingValidator.validate(MzTab mzTab)
List<ValidationMessage>	MzTabBeanValidator.validate(MzTab mzTab)	validate.

Method parameters in de.isas.mztab2.validation with type arguments of type MzTab

Modifier and Type	Method	Description
CvMappingValidator	CvMappingValidator.withPostValidator(Validator<MzTab> postValidator)	Add the provided validator implementation to the list of validators that run last.
CvMappingValidator	CvMappingValidator.withPreValidator(Validator<MzTab> preValidator)	Add the provided validator implementation to the list of validators that run first.