Package ubic.gemma.rest.util.args

Class GeneArgService

java.lang.Object

ubic.gemma.rest.util.args.AbstractEntityArgService<Gene,GeneService>

ubic.gemma.rest.util.args.GeneArgService

All Implemented Interfaces:

EntityArgService<Gene,GeneService>

@Service
public class GeneArgService
extends AbstractEntityArgService<Gene,GeneService>

Field Summary

Fields inherited from class ubic.gemma.rest.util.args.AbstractEntityArgService

service

Constructor Summary

Constructors

Constructor	Description
GeneArgService(GeneService service, PhenotypeAssociationManagerService phenotypeAssociationManagerService, GeneOntologyService geneOntologyService)

Method Summary

Modifier and Type	Method	Description
Gene	getEntityWithTaxon(GeneArg<?> arg, Taxon taxon)
List<GeneEvidenceValueObject>	getGeneEvidence(GeneArg<?> arg, Taxon taxon)	Deprecated.
List<PhysicalLocationValueObject>	getGeneLocation(GeneArg<?> geneArg)	Returns all known locations of the gene(s) that this GeneArg represents.
List<PhysicalLocationValueObject>	getGeneLocation(GeneArg<?> arg, Taxon taxon)	Returns all known locations of the gene that this GeneArg represents.
List<GeneValueObject>	getGenesOnTaxon(GeneArg<?> arg, Taxon taxon)
List<GeneOntologyTermValueObject>	getGoTerms(GeneArg<?> arg)	Returns GO terms for the gene that this GeneArg represents.
List<GeneValueObject>	getValueObjects(GeneArg<?> arg)

Methods inherited from class ubic.gemma.rest.util.args.AbstractEntityArgService

checkEntity, entityArgValueOf, getArgsByPropertyName, getElementClass, getEntities, getEntities, getEntity, getFilterableProperties, getFilterablePropertyAllowedValues, getFilterablePropertyConfigAttributes, getFilterablePropertyDescription, getFilterablePropertyIsUsingSubquery, getFilterablePropertyResolvableAllowedValuesLabels, getFilterablePropertyType, getFilters, getFilters, getFilters, getSort

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

GeneArgService

@Autowired
public GeneArgService(GeneService service,
                      PhenotypeAssociationManagerService phenotypeAssociationManagerService,
                      GeneOntologyService geneOntologyService)

Method Detail

getEntityWithTaxon

public Gene getEntityWithTaxon(GeneArg<?> arg,
                               Taxon taxon)

getValueObjects

public List<GeneValueObject> getValueObjects(GeneArg<?> arg)

Returns:

all genes that match the value of the GeneArg.

getGeneLocation

public List<PhysicalLocationValueObject> getGeneLocation(GeneArg<?> geneArg)

Returns all known locations of the gene(s) that this GeneArg represents.

Returns:

collection of physical location objects.

getGeneLocation

public List<PhysicalLocationValueObject> getGeneLocation(GeneArg<?> arg,
                                                         Taxon taxon)

Returns all known locations of the gene that this GeneArg represents.

Parameters:

taxon - the taxon to limit the search to. Can be null.

Returns:

collection of physical location objects.

getGenesOnTaxon

public List<GeneValueObject> getGenesOnTaxon(GeneArg<?> arg,
                                             Taxon taxon)

Returns:

a collection of Gene value objects..

getGeneEvidence

@Deprecated
public List<GeneEvidenceValueObject> getGeneEvidence(GeneArg<?> arg,
                                                     @Nullable
                                                     Taxon taxon)
                                              throws SearchException

Deprecated.

Searches for gene evidence of the gene that this GeneArg represents, on the given taxon.

Parameters:

taxon - the taxon to limit the search to. Can be null.

Returns:

collection of gene evidence VOs matching the criteria, or an error response, if there is an error.

Throws:

SearchException

getGoTerms

public List<GeneOntologyTermValueObject> getGoTerms(GeneArg<?> arg)

Returns GO terms for the gene that this GeneArg represents.

Returns:

collection of physical location objects.