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

Packages that use MsRun

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.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.
uk.ac.ebi.pride.jmztab2.utils.parser	This package contains text file line parser implementations for the mzTab-M document sections.

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

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

Modifier and Type	Method	Description
void	MsRunSerializer.serialize(MsRun msRun, com.fasterxml.jackson.core.JsonGenerator jg, com.fasterxml.jackson.databind.SerializerProvider sp)
void	MsRunSerializer.serializeWithType(MsRun 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 MsRun

Constructor	Description
MsRunSerializer(Class<MsRun> t)	Constructor for MsRunSerializer.

Uses of MsRun in de.isas.mztab2.io.validators

Methods in de.isas.mztab2.io.validators with parameters of type MsRun

Modifier and Type	Method	Description
protected Optional<MZTabError>	SpectraRefValidator.validatePattern(Pattern pattern, String reference, int lineNumber, IMZTabColumn column, String field, MsRun run)

Uses of MsRun in de.isas.mztab2.model

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

Modifier and Type	Method	Description
MsRun	MsRun.addFragmentationMethodItem(Parameter fragmentationMethodItem)	Add a single fragmentationMethodItem to the fragmentationMethod collection.
MsRun	MsRun.addScanPolarityItem(Parameter scanPolarityItem)	Add a single scanPolarityItem to the scanPolarity collection.
MsRun	MsRun.format(Parameter format)	Builder method for format.
MsRun	MsRun.fragmentationMethod(List<Parameter> fragmentationMethod)	Builder method for fragmentationMethod.
@NotNull @Valid MsRun	SpectraRef.getMsRun()	The ms run object reference by this spectral reference.
MsRun	MsRun.hash(String hash)	Builder method for hash.
MsRun	MsRun.hashMethod(Parameter hashMethod)	Builder method for hashMethod.
MsRun	MsRun.id(Integer id)	Builder method for id.
MsRun	MsRun.idFormat(Parameter idFormat)	Builder method for idFormat.
MsRun	MsRun.instrumentRef(Instrument instrumentRef)	Builder method for instrumentRef.
MsRun	MsRun.location(String location)	Builder method for location.
MsRun	MsRun.name(String name)	Builder method for name.
MsRun	MsRun.scanPolarity(List<Parameter> scanPolarity)	Builder method for scanPolarity.

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

Modifier and Type	Method	Description
@NotNull @Valid List<MsRun>	Metadata.getMsRun()	Specification of ms_run.
Optional<MsRun>	MzTabAccess.getMsRunFor(Integer id, Metadata metadata)	Tries to locate the ms run referenced by id from the metadata section.
@NotNull @Valid @Size(min=1) List<MsRun>	Assay.getMsRunRef()	The ms run(s) referenced by this assay.

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

Modifier and Type	Method	Description
Metadata	Metadata.addMsRunItem(MsRun msRunItem)	Add a single msRunItem to the msRun collection.
Assay	Assay.addMsRunRefItem(MsRun msRunRefItem)	Add a single msRunRefItem to the msRunRef collection.
SpectraRef	SpectraRef.msRun(MsRun msRun)	Builder method for msRun.
void	SpectraRef.setMsRun(MsRun msRun)	Set msRun.

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

Modifier and Type	Method	Description
Metadata	Metadata.msRun(List<MsRun> msRun)	Builder method for msRun.
Assay	Assay.msRunRef(List<MsRun> msRunRef)	Builder method for msRunRef.
void	Metadata.setMsRun(List<MsRun> msRun)	Set msRun.
void	Assay.setMsRunRef(List<MsRun> msRunRef)	Set msRunRef.

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

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

Modifier and Type	Method	Description
MsRun	MZTabParserContext.addMsRun(Metadata metadata, MsRun msRun)	Add a ms_run[id] into metadata.
MsRun	MZTabParserContext.addMsRunFormat(Metadata metadata, Integer id, Parameter format)	Add ms_run[id]-format into metadata.
MsRun	MZTabParserContext.addMsRunFragmentationMethod(Metadata metadata, Integer id, Parameter fragmentationMethod)	Add ms_run[id]-fragmentation_method into metadata.
MsRun	MZTabParserContext.addMsRunHash(Metadata metadata, Integer id, String hash)	addMsRunHash.
MsRun	MZTabParserContext.addMsRunHashMethod(Metadata metadata, Integer id, Parameter hashMethod)	addMsRunHashMethod.
MsRun	MZTabParserContext.addMsRunIdFormat(Metadata metadata, Integer id, Parameter idFormat)	Add ms_run[id]-id_format into metadata.
MsRun	MZTabParserContext.addMsRunInstrumentRef(Metadata metadata, Integer id, Instrument instrument)	Add ms_run[id]-instrument_ref into metadata.
MsRun	MZTabParserContext.addMsRunLocation(Metadata metadata, Integer id, URI location)	Add ms_run[id]-location into metadata.
MsRun	MZTabParserContext.addMsRunScanPolarity(Metadata metadata, Integer id, Parameter scanPolarity)	addMsRunScanPolarity.

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

Modifier and Type	Method	Description
Assay	MZTabParserContext.addAssayMsRun(Metadata metadata, Integer id, MsRun msRun)	Add assay[id]-ms_run_ref into metadata.
MsRun	MZTabParserContext.addMsRun(Metadata metadata, MsRun msRun)	Add a ms_run[id] into metadata.