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

Packages that use StudyVariable

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 StudyVariable in de.isas.mztab2.io.serialization

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

Modifier and Type	Method	Description
static String	Serializers.printAbundanceCoeffVarStudyVar(StudyVariable sv)	printAbundanceCoeffVarStudyVar.
static String	Serializers.printAbundanceStudyVar(StudyVariable sv)	printAbundanceStudyVar.
void	StudyVariableSerializer.serialize(StudyVariable studyVariable, com.fasterxml.jackson.core.JsonGenerator jg, com.fasterxml.jackson.databind.SerializerProvider sp)
void	StudyVariableSerializer.serializeWithType(StudyVariable 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 StudyVariable

Constructor	Description
StudyVariableSerializer(Class<StudyVariable> t)	Constructor for StudyVariableSerializer.

Uses of StudyVariable in de.isas.mztab2.model

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

Modifier and Type	Method	Description
StudyVariable	StudyVariable.addAssayRefsItem(Assay assayRefsItem)	Add a single assayRefsItem to the assayRefs collection.
StudyVariable	StudyVariable.addFactorsItem(Parameter factorsItem)	Add a single factorsItem to the factors collection.
StudyVariable	StudyVariable.assayRefs(List<Assay> assayRefs)	Builder method for assayRefs.
StudyVariable	StudyVariable.averageFunction(Parameter averageFunction)	Builder method for averageFunction.
StudyVariable	StudyVariable.description(String description)	Builder method for description.
StudyVariable	StudyVariable.factors(List<Parameter> factors)	Builder method for factors.
StudyVariable	StudyVariable.id(Integer id)	Builder method for id.
StudyVariable	StudyVariable.name(String name)	Builder method for name.
StudyVariable	StudyVariable.variationFunction(Parameter variationFunction)	Builder method for variationFunction.

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

Modifier and Type	Method	Description
@NotNull @Valid List<StudyVariable>	Metadata.getStudyVariable()	Specification of study_variable.
Optional<StudyVariable>	MzTabAccess.getStudyVariableFor(Integer id, Metadata metadata)	Tries to locate the study variable referenced by id from the metadata section.

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

Modifier and Type	Method	Description
Metadata	Metadata.addStudyVariableItem(StudyVariable studyVariableItem)	Add a single studyVariableItem to the studyVariable collection.
Double	MzTabAccess.getAbundanceFor(StudyVariable studyVariable, SmallMoleculeSummary sms)	Retrieves the abundance value for the provided study variable and small molecule summary object.
Double	MzTabAccess.getAbundanceVariationFor(StudyVariable studyVariable, SmallMoleculeSummary sms)	Retrieves the abundance variation value for the provided study variable and small molecule summary object.

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

Modifier and Type	Method	Description
void	Metadata.setStudyVariable(List<StudyVariable> studyVariable)	Set studyVariable.
Metadata	Metadata.studyVariable(List<StudyVariable> studyVariable)	Builder method for studyVariable.

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

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

Modifier and Type	Method	Description
String	MZTabColumnFactory.addAbundanceOptionalColumn(StudyVariable studyVariable, String columnHeader, String order)	Add an AbundanceColumn into AbundanceColumn, MZTabColumnFactory.optionalColumnMapping and MZTabColumnFactory.columnMapping.
static SortedMap<String,MZTabColumn>	AbundanceColumn.createOptionalColumns(Section section, StudyVariable studyVariable, Integer lastOrder)	createOptionalColumns.
static SortedMap<String,MZTabColumn>	AbundanceColumn.createOptionalColumns(Section section, StudyVariable studyVariable, String columnHeader, String order)	Generate an abundance optional column as measured in the given study variable.

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

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

Modifier and Type	Method	Description
StudyVariable	MZTabParserContext.addStudyVariable(Metadata metadata, StudyVariable studyVariable)	Add a study variable into metadata.
StudyVariable	MZTabParserContext.addStudyVariableAssay(Metadata metadata, Integer id, Assay assay)	Add a study_variable[id]-assay_refs.
StudyVariable	MZTabParserContext.addStudyVariableAverageFunction(Metadata metadata, Integer id, Parameter checkParameter)	Add a study_variable[id]-average_function.
StudyVariable	MZTabParserContext.addStudyVariableDescription(Metadata metadata, Integer id, String description)	Add a study_variable[id]-description.
StudyVariable	MZTabParserContext.addStudyVariableFactors(Metadata metadata, Integer id, Parameter checkParameter)	Add a study_variable[id]-factor.
StudyVariable	MZTabParserContext.addStudyVariableVariationFunction(Metadata metadata, Integer id, Parameter checkParameter)	Add a study_variable[id]-variation_function.

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

Modifier and Type	Method	Description
StudyVariable	MZTabParserContext.addStudyVariable(Metadata metadata, StudyVariable studyVariable)	Add a study variable into metadata.