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, CompositeSequenceService compositeSequenceService)

Method Summary

Modifier and Type	Method	Description
List<Gene>	getEntitiesWithTaxon(GeneArg<?> genes, Taxon taxon)	Obtain genes from a specific taxon.
List<Gene>	getEntitiesWithTaxon(GeneArrayArg genes, Taxon taxon)	Obtain genes from a specific taxon.
Gene	getEntity(AbstractEntityArg<?,Gene,GeneService> entityArg)	Retrieve the entity represented by this argument.
Gene	getEntityWithTaxon(GeneArg<?> entityArg, Taxon taxon)	Obtain a gene from a specific taxon.
List<GeneEvidenceValueObject>	getGeneEvidence(GeneArg<?> arg, Taxon taxon)	Deprecated.
List<GeneOntologyTermValueObject>	getGeneGoTerms(GeneArg<?> arg)	Returns GO terms for the gene that this GeneArg represents.
List<GeneOntologyTermValueObject>	getGeneGoTermsInTaxon(GeneArg<?> geneArg, Taxon taxon)	Obtain GO terms for the gene in the given taxon.
List<PhysicalLocationValueObject>	getGeneLocation(GeneArg<?> geneArg)	Returns all known locations of the gene(s) that this GeneArg represents.
List<PhysicalLocationValueObject>	getGeneLocationInTaxon(GeneArg<?> arg, Taxon taxon)	Returns all known locations of the gene that this GeneArg represents.
Slice<CompositeSequenceValueObject>	getGeneProbes(GeneArg<?> geneArg, int offset, int limit)	Obtain probes for the gene across all platforms.
Slice<CompositeSequenceValueObject>	getGeneProbesInTaxon(GeneArg<?> geneArg, Taxon taxon, int offset, int limit)	Obtain probes for the gene in the given taxon across all platforms.
Slice<GeneValueObject>	getGenes(int offset, int limit)
Slice<GeneValueObject>	getGenesInTaxon(Taxon taxon, int offset, int limit)
List<GeneValueObject>	getGenesInTaxon(GeneArrayArg arg, Taxon taxon)

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

checkEntity, entityArgValueOf, getArgsByPropertyName, getElementClass, getEntities, getEntities, 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,
                      CompositeSequenceService compositeSequenceService)

Method Detail

getEntity

@Nonnull
public Gene getEntity(AbstractEntityArg<?,Gene,GeneService> entityArg)
               throws javax.ws.rs.NotFoundException,
                      javax.ws.rs.BadRequestException

Retrieve the entity represented by this argument.

Specified by:

getEntity in interface EntityArgService<Gene,GeneService>

Overrides:

getEntity in class AbstractEntityArgService<Gene,GeneService>

Throws:

javax.ws.rs.BadRequestException - if more than one gene match the supplied gene argument

javax.ws.rs.NotFoundException - if the entity does not exist

getEntityWithTaxon

@Nonnull
public Gene getEntityWithTaxon(GeneArg<?> entityArg,
                               Taxon taxon)

Obtain a gene from a specific taxon.

Throws:

javax.ws.rs.BadRequestException - if more than one gene match the supplied gene argumen in the given taxon

getEntitiesWithTaxon

public List<Gene> getEntitiesWithTaxon(GeneArg<?> genes,
                                       Taxon taxon)

Obtain genes from a specific taxon.

getEntitiesWithTaxon

public List<Gene> getEntitiesWithTaxon(GeneArrayArg genes,
                                       Taxon taxon)

Obtain genes from a specific taxon.

getGenes

public Slice<GeneValueObject> getGenes(int offset,
                                       int limit)

getGenesInTaxon

public Slice<GeneValueObject> getGenesInTaxon(Taxon taxon,
                                              int offset,
                                              int limit)

getGenesInTaxon

public List<GeneValueObject> getGenesInTaxon(GeneArrayArg arg,
                                             Taxon taxon)

Returns:

a collection of Gene value objects..

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.

getGeneLocationInTaxon

public List<PhysicalLocationValueObject> getGeneLocationInTaxon(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.

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

getGeneGoTerms

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

Returns GO terms for the gene that this GeneArg represents.

getGeneGoTermsInTaxon

public List<GeneOntologyTermValueObject> getGeneGoTermsInTaxon(GeneArg<?> geneArg,
                                                               Taxon taxon)

Obtain GO terms for the gene in the given taxon.

getGeneProbes

public Slice<CompositeSequenceValueObject> getGeneProbes(GeneArg<?> geneArg,
                                                         int offset,
                                                         int limit)

Obtain probes for the gene across all platforms.

getGeneProbesInTaxon

public Slice<CompositeSequenceValueObject> getGeneProbesInTaxon(GeneArg<?> geneArg,
                                                                Taxon taxon,
                                                                int offset,
                                                                int limit)

Obtain probes for the gene in the given taxon across all platforms.