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

Packages that use Assay

Package	Description
de.isas.mztab2.io.serialization	This package contains classes that implement custom Jackson serializers for the mzTab-M model objects.
de.isas.mztab2.model	Base package for the jmztab-m data model, generated from the mzTab_m_swagger.yml specification.
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.parser	This package contains text file line parser implementations for the mzTab-M document sections.

Uses of Assay in de.isas.mztab2.io.serialization

Methods in de.isas.mztab2.io.serialization with parameters of type Assay

Modifier and Type	Method	Description
static String	Serializers.printAbundanceAssay(Assay a)	printAbundanceAssay.
void	AssaySerializer.serialize(Assay assay, com.fasterxml.jackson.core.JsonGenerator jg, com.fasterxml.jackson.databind.SerializerProvider sp)
void	AssaySerializer.serializeWithType(Assay value, com.fasterxml.jackson.core.JsonGenerator gen, com.fasterxml.jackson.databind.SerializerProvider serializers, com.fasterxml.jackson.databind.jsontype.TypeSerializer typeSer)

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

Constructor	Description
AssaySerializer(Class<Assay> t)	Constructor for AssaySerializer.

Uses of Assay in de.isas.mztab2.model

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

Modifier and Type	Method	Description
Assay	Assay.addCustomItem(Parameter customItem)	Add a single customItem to the custom collection.
Assay	Assay.addMsRunRefItem(MsRun msRunRefItem)	Add a single msRunRefItem to the msRunRef collection.
Assay	Assay.custom(List<Parameter> custom)	Builder method for custom.
Assay	Assay.externalUri(String externalUri)	Builder method for externalUri.
Assay	Assay.id(Integer id)	Builder method for id.
Assay	Assay.msRunRef(List<MsRun> msRunRef)	Builder method for msRunRef.
Assay	Assay.name(String name)	Builder method for name.
Assay	Assay.sampleRef(Sample sampleRef)	Builder method for sampleRef.

Methods in de.isas.mztab2.model that return types with arguments of type Assay

Modifier and Type	Method	Description
@NotNull @Valid List<Assay>	Metadata.getAssay()	Specification of assay.
Optional<Assay>	MzTabAccess.getAssayFor(OptColumnMapping columnMapping, Metadata metadata)	Tries to locate the assay referenced by id from the columnMapping identifier.
Optional<Assay>	MzTabAccess.getAssayFor(Integer id, Metadata metadata)	Tries to locate the assay referenced by id from the metadata section.
@Valid List<Assay>	StudyVariable.getAssayRefs()	The assays referenced by this study variable.

Methods in de.isas.mztab2.model with parameters of type Assay

Modifier and Type	Method	Description
Metadata	Metadata.addAssayItem(Assay assayItem)	Add a single assayItem to the assay collection.
StudyVariable	StudyVariable.addAssayRefsItem(Assay assayRefsItem)	Add a single assayRefsItem to the assayRefs collection.
Double	MzTabAccess.getAbundanceFor(Assay assay, SmallMoleculeFeature smf)	Retrieves the abundance value for the provided assay and small molecule feature object.
Double	MzTabAccess.getAbundanceFor(Assay assay, SmallMoleculeSummary sms)	Retrieves the abundance value for the provided assay and small molecule summary object.

Method parameters in de.isas.mztab2.model with type arguments of type Assay

Modifier and Type	Method	Description
Metadata	Metadata.assay(List<Assay> assay)	Builder method for assay.
StudyVariable	StudyVariable.assayRefs(List<Assay> assayRefs)	Builder method for assayRefs.
void	Metadata.setAssay(List<Assay> assay)	Set assay.
void	StudyVariable.setAssayRefs(List<Assay> assayRefs)	Set assayRefs.

Uses of Assay in uk.ac.ebi.pride.jmztab2.model

Methods in uk.ac.ebi.pride.jmztab2.model with parameters of type Assay

Modifier and Type	Method	Description
String	MZTabColumnFactory.addAbundanceOptionalColumn(Assay assay, String order)	addAbundanceOptionalColumn.
static MZTabColumn	AbundanceColumn.createOptionalColumn(Section section, Assay assay, int offset)	Generate a abundance optional column as measured in the given assay.The column header like protein_abundance_assay[1-n], the position always stay the most right of the tabled section, and the data type is Double.

Uses of Assay in uk.ac.ebi.pride.jmztab2.utils.parser

Methods in uk.ac.ebi.pride.jmztab2.utils.parser that return Assay

Modifier and Type	Method	Description
Assay	MZTabParserContext.addAssay(Metadata metadata, Assay assay)	Add a assay into metadata.
Assay	MZTabParserContext.addAssayCustom(Metadata metadata, Integer id, Parameter param)	Add a assay[id]-custom[i] into metadata.
Assay	MZTabParserContext.addAssayExternalUri(Metadata metadata, Integer id, URI location)	Add a assay[id]-external_uri into metadata.
Assay	MZTabParserContext.addAssayMsRun(Metadata metadata, Integer id, MsRun msRun)	Add assay[id]-ms_run_ref into metadata.
Assay	MZTabParserContext.addAssaySample(Metadata metadata, Integer id, Sample sample)	Add assay[id]-sample_ref into metadata.

Methods in uk.ac.ebi.pride.jmztab2.utils.parser with parameters of type Assay

Modifier and Type	Method	Description
Assay	MZTabParserContext.addAssay(Metadata metadata, Assay assay)	Add a assay into metadata.
StudyVariable	MZTabParserContext.addStudyVariableAssay(Metadata metadata, Integer id, Assay assay)	Add a study_variable[id]-assay_refs.