Package ubic.gemma.rest.util.args

Class GeneArgService

java.lang.Object

ubic.gemma.rest.util.args.AbstractEntityArgService<ubic.gemma.model.genome.Gene,ubic.gemma.core.genome.gene.service.GeneService>

ubic.gemma.rest.util.args.GeneArgService

All Implemented Interfaces:

EntityArgService<ubic.gemma.model.genome.Gene,ubic.gemma.core.genome.gene.service.GeneService>

@Service
public class GeneArgService
extends AbstractEntityArgService<ubic.gemma.model.genome.Gene,ubic.gemma.core.genome.gene.service.GeneService>

Field Summary

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

service

Constructor Summary

Constructors

Constructor	Description
GeneArgService(ubic.gemma.core.genome.gene.service.GeneService service, ubic.gemma.core.association.phenotype.PhenotypeAssociationManagerService phenotypeAssociationManagerService, ubic.gemma.core.ontology.providers.GeneOntologyService geneOntologyService)

Method Summary

Modifier and Type	Method	Description
ubic.gemma.model.genome.Gene	getEntityWithTaxon(GeneArg<?> arg, ubic.gemma.model.genome.Taxon taxon)
List<ubic.gemma.model.genome.gene.phenotype.valueObject.GeneEvidenceValueObject>	getGeneEvidence(GeneArg<?> arg, ubic.gemma.model.genome.Taxon taxon)	Deprecated.
List<ubic.gemma.model.genome.PhysicalLocationValueObject>	getGeneLocation(GeneArg<?> geneArg)	Returns all known locations of the gene(s) that this GeneArg represents.
List<ubic.gemma.model.genome.PhysicalLocationValueObject>	getGeneLocation(GeneArg<?> arg, ubic.gemma.model.genome.Taxon taxon)	Returns all known locations of the gene that this GeneArg represents.
List<ubic.gemma.model.genome.gene.GeneValueObject>	getGenesOnTaxon(GeneArg<?> arg, ubic.gemma.model.genome.Taxon taxon)
List<ubic.gemma.model.genome.GeneOntologyTermValueObject>	getGoTerms(GeneArg<?> arg)	Returns GO terms for the gene that this GeneArg represents.
List<ubic.gemma.model.genome.gene.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(ubic.gemma.core.genome.gene.service.GeneService service,
                      ubic.gemma.core.association.phenotype.PhenotypeAssociationManagerService phenotypeAssociationManagerService,
                      ubic.gemma.core.ontology.providers.GeneOntologyService geneOntologyService)

Method Detail

getEntityWithTaxon

public ubic.gemma.model.genome.Gene getEntityWithTaxon(GeneArg<?> arg,
                                                       ubic.gemma.model.genome.Taxon taxon)

getValueObjects

public List<ubic.gemma.model.genome.gene.GeneValueObject> getValueObjects(GeneArg<?> arg)

Returns:

all genes that match the value of the GeneArg.

getGeneLocation

public List<ubic.gemma.model.genome.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<ubic.gemma.model.genome.PhysicalLocationValueObject> getGeneLocation(GeneArg<?> arg,
                                                                                 ubic.gemma.model.genome.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<ubic.gemma.model.genome.gene.GeneValueObject> getGenesOnTaxon(GeneArg<?> arg,
                                                                          ubic.gemma.model.genome.Taxon taxon)

Returns:

a collection of Gene value objects..

getGeneEvidence

@Deprecated
public List<ubic.gemma.model.genome.gene.phenotype.valueObject.GeneEvidenceValueObject> getGeneEvidence(GeneArg<?> arg,
                                                                                                        @Nullable
                                                                                                        ubic.gemma.model.genome.Taxon taxon)
                                                                                                 throws ubic.gemma.core.search.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:

ubic.gemma.core.search.SearchException

getGoTerms

public List<ubic.gemma.model.genome.GeneOntologyTermValueObject> getGoTerms(GeneArg<?> arg)

Returns GO terms for the gene that this GeneArg represents.

Returns:

collection of physical location objects.