Package ubic.gemma.rest.util.args

Class GeneArgService

java.lang.Object

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

ubic.gemma.rest.util.args.GeneArgService

All Implemented Interfaces:

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

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

Field Summary

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

service

Constructor Summary

Constructors

Constructor	Description
GeneArgService(ubic.gemma.persistence.service.genome.gene.GeneService service, ubic.gemma.core.ontology.providers.GeneOntologyService geneOntologyService, ubic.gemma.persistence.service.expression.designElement.CompositeSequenceService compositeSequenceService)

Method Summary

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

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

checkEntity, entityArgValueOf, getArgsByPropertyName, getElementClass, getEntities, getEntities, getFilterableProperties, getFilterablePropertyAllowedValues, getFilterablePropertyConfigAttributes, getFilterablePropertyDescription, getFilterablePropertyResolvableAllowedValuesLabels, getFilterablePropertyType, getFilters, getFilters, getFilters, getSort, isFilterablePropertyDeprecated, isFilterablePropertyUsingSubquery

Methods inherited from class java.lang.Object

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

Constructor Details

GeneArgService

@Autowired
public GeneArgService(ubic.gemma.persistence.service.genome.gene.GeneService service,
 ubic.gemma.core.ontology.providers.GeneOntologyService geneOntologyService,
 ubic.gemma.persistence.service.expression.designElement.CompositeSequenceService compositeSequenceService)

Method Details

getEntity

@Nonnull
public ubic.gemma.model.genome.Gene getEntity(AbstractEntityArg<?,ubic.gemma.model.genome.Gene,ubic.gemma.persistence.service.genome.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<ubic.gemma.model.genome.Gene,ubic.gemma.persistence.service.genome.gene.GeneService>

Overrides:

getEntity in class AbstractEntityArgService<ubic.gemma.model.genome.Gene,ubic.gemma.persistence.service.genome.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 ubic.gemma.model.genome.Gene getEntityWithTaxon(GeneArg<?> entityArg,
 ubic.gemma.model.genome.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<ubic.gemma.model.genome.Gene> getEntitiesWithTaxon(GeneArg<?> genes,
 ubic.gemma.model.genome.Taxon taxon)

Obtain genes from a specific taxon.

getEntitiesWithTaxon

public List<ubic.gemma.model.genome.Gene> getEntitiesWithTaxon(GeneArrayArg genes,
 ubic.gemma.model.genome.Taxon taxon)

Obtain genes from a specific taxon.

getGenes

public ubic.gemma.persistence.util.Slice<ubic.gemma.model.genome.gene.GeneValueObject> getGenes(int offset,
 int limit)

getGenesInTaxon

public ubic.gemma.persistence.util.Slice<ubic.gemma.model.genome.gene.GeneValueObject> getGenesInTaxon(ubic.gemma.model.genome.Taxon taxon,
 int offset,
 int limit)

getGenesInTaxon

public List<ubic.gemma.model.genome.gene.GeneValueObject> getGenesInTaxon(GeneArrayArg arg,
 ubic.gemma.model.genome.Taxon taxon)

Returns:

a collection of Gene value objects..

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.

getGeneLocationInTaxon

public List<ubic.gemma.model.genome.PhysicalLocationValueObject> getGeneLocationInTaxon(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.

getGeneGoTerms

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

Returns GO terms for the gene that this GeneArg represents.

getGeneGoTermsInTaxon

public List<ubic.gemma.model.genome.GeneOntologyTermValueObject> getGeneGoTermsInTaxon(GeneArg<?> geneArg,
 ubic.gemma.model.genome.Taxon taxon)

Obtain GO terms for the gene in the given taxon.

getGeneProbes

public ubic.gemma.persistence.util.Slice<ubic.gemma.model.expression.designElement.CompositeSequenceValueObject> getGeneProbes(GeneArg<?> geneArg,
 int offset,
 int limit)

Obtain probes for the gene across all platforms.

getGeneProbesInTaxon

public ubic.gemma.persistence.util.Slice<ubic.gemma.model.expression.designElement.CompositeSequenceValueObject> getGeneProbesInTaxon(GeneArg<?> geneArg,
 ubic.gemma.model.genome.Taxon taxon,
 int offset,
 int limit)

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