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

Packages that use IndexedElement

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.

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

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

Modifier and Type	Method	Description
static <T extends IndexedElement> void	Serializers.addIndexedLine(com.fasterxml.jackson.core.JsonGenerator jg, com.fasterxml.jackson.databind.SerializerProvider sp, String prefix, Object element, List<T> indexedElementList)	addIndexedLine for elements like assay[1] that have an id and a list of additional property elements
static <T extends IndexedElement> void	Serializers.addIndexedLine(com.fasterxml.jackson.core.JsonGenerator jg, com.fasterxml.jackson.databind.SerializerProvider sp, String prefix, Object element, T indexedElement)	addIndexedLine for elements like assay[1] that have an id and one additional property element
static <T extends IndexedElement> void	MetadataSerializer.serializeListWithMetadataElement(List<T> list, MetadataElement mtdElement, com.fasterxml.jackson.core.JsonGenerator jg, com.fasterxml.jackson.databind.SerializerProvider sp, Comparator<? super T> comparator)	Serialize a list of Parameters for the provided metadata element.

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

Modifier and Type	Method	Description
static void	Serializers.checkIndexedElement(IndexedElement element)

Uses of IndexedElement in de.isas.mztab2.model

Subclasses of IndexedElement in de.isas.mztab2.model

Modifier and Type	Class	Description
class	Assay	Specification of assay.
class	Contact	The contact’s name, affiliation and e-mail.
class	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.
class	Database	Specification of databases.
class	Instrument	The name, source, analyzer and detector of the instruments used in the experiment.
class	MsRun	Specification of ms_run.
class	Parameter	mzTab makes use of CV parameters.
class	Publication	A publication associated with this file.
class	Sample	Specification of sample.
class	SampleProcessing	A list of parameters describing a sample processing, preparation or handling step similar to a biological or analytical methods report.
class	Software	Software used to analyze the data and obtain the reported results.
class	StudyVariable	Specification of study_variable.
class	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.

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

Modifier and Type	Method	Description
IndexedElement	IndexedElement.elementType(String elementType)	Builder method for elementType.
IndexedElement	IndexedElement.id(Integer id)	Builder method for id.

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

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

Modifier and Type	Method	Description
<T extends IndexedElement> String	MZTabColumnFactory.addOptionalColumn(T columnEntity, Parameter param, Class columnType)	Add ParameterOptionColumn followed by an indexed element (study variable, assay, ms run) into MZTabColumnFactory.optionalColumnMapping and MZTabColumnFactory.columnMapping.
<T extends IndexedElement> String	MZTabColumnFactory.addOptionalColumn(T columnEntity, String name, Class columnType)	Add OptionColumn followed by an indexed element (study variable, assay, ms run) into MZTabColumnFactory.optionalColumnMapping and MZTabColumnFactory.columnMapping.

Methods in uk.ac.ebi.pride.jmztab2.model that return IndexedElement

Modifier and Type	Method	Description
IndexedElement	IMZTabColumn.getElement()	Indexed element used in optional column header and logical position definition.
IndexedElement	MZTabColumn.getElement()	Indexed element used in optional column header and logical position definition.
IndexedElement	SmallMoleculeColumn.getElement()	Indexed element used in optional column header and logical position definition.
IndexedElement	SmallMoleculeEvidenceColumn.getElement()	Indexed element used in optional column header and logical position definition.
IndexedElement	SmallMoleculeFeatureColumn.getElement()	Indexed element used in optional column header and logical position definition.
static IndexedElement	MZTabUtils.parseIndexedElement(String target, MetadataElement element)	parse the target into a IndexedElement object.

Methods in uk.ac.ebi.pride.jmztab2.model that return types with arguments of type IndexedElement

Modifier and Type	Method	Description
static List<IndexedElement>	MZTabUtils.parseRefList(String target, MetadataElement element)	Parse the target into a IndexedElement list.

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

Modifier and Type	Method	Description
static OptColumnMappingBuilder.IndexedElementOptColumnMappingBuilder	OptColumnMappingBuilder.forIndexedElement(IndexedElement indexedElement)	Configure the builder for an object reference (indexed element) type column.
static String	OptionColumn.getHeader(IndexedElement element, String name)	Get the optional column header, which start with the prefix "opt_". the format: opt_{indexedElement[id]}_{name}.
static String	ParameterOptionColumn.getHeader(IndexedElement element, Parameter param)	get column header like: opt_{OBJECT_ID}_cv_{accession}_{parameter name} Spaces within the parameter's name MUST be replaced by '_'.
void	IMZTabColumn.setElement(IndexedElement element)	Indexed element used in optional column header and logical position definition.
void	MZTabColumn.setElement(IndexedElement element)	Indexed element used in optional column header and logical position definition.
void	SmallMoleculeColumn.setElement(IndexedElement element)	Indexed element used in optional column header and logical position definition.
void	SmallMoleculeEvidenceColumn.setElement(IndexedElement element)	Indexed element used in optional column header and logical position definition.
void	SmallMoleculeFeatureColumn.setElement(IndexedElement element)	Indexed element used in optional column header and logical position definition.

Constructors in uk.ac.ebi.pride.jmztab2.model with parameters of type IndexedElement

Constructor	Description
IndexedElementOptColumnMappingBuilder(IndexedElement indexedElement)	Configure this builder to create optional column mapping for an indexed element, such as Assay, StudyVariable, or MsRun.
OptionColumn(IndexedElement element, String value, Class columnType, int offset)	Create a optional column.
ParameterOptionColumn(IndexedElement element, Parameter param, Class columnType, int offset)	Define a OptionColumn which use CV parameter accessions in following the format: opt_{OBJECT_ID}_cv_{accession}_{parameter name}.