ubic.gemma.web.services.rest.util.args

Class GeneArg<T>

java.lang.Object

ubic.gemma.web.services.rest.util.args.AbstractArg<T>

ubic.gemma.web.services.rest.util.args.AbstractEntityArg<T,Gene,GeneService>

ubic.gemma.web.services.rest.util.args.GeneArg<T>

All Implemented Interfaces:

Arg<T>

Direct Known Subclasses:

GeneAnyIdArg, GeneSymbolArg

public abstract class GeneArg<T>
extends AbstractEntityArg<T,Gene,GeneService>

Mutable argument type base class for Gene API.

Author:

tesarst

Constructor Summary

Constructors

Modifier	Constructor and Description
protected	GeneArg(T value)

Method Summary

Modifier and Type	Method and Description
List<GeneEvidenceValueObject>	getGeneEvidence(GeneService geneService, PhenotypeAssociationManagerService phenotypeAssociationManagerService, Taxon taxon) Searches for gene evidence of the gene that this GeneArg represents, on the given taxon.
abstract List<PhysicalLocationValueObject>	getGeneLocation(GeneService geneService) Returns all known locations of the gene(s) that this GeneArg represents.
abstract List<PhysicalLocationValueObject>	getGeneLocation(GeneService geneService, Taxon taxon) Returns all known locations of the gene that this GeneArg represents.
List<GeneValueObject>	getGenesOnTaxon(GeneService geneService, TaxonService taxonService, TaxonArg<?> taxonArg)
List<GeneOntologyTermValueObject>	getGoTerms(GeneService geneService, GeneOntologyService geneOntologyService) Returns GO terms for the gene that this GeneArg represents.
abstract List<GeneValueObject>	getValueObjects(GeneService service)
static GeneArg<?>	valueOf(String s) Used by RS to parse value of request parameters.

Methods inherited from class ubic.gemma.web.services.rest.util.args.AbstractEntityArg

checkEntity, getEntity, getObjectFilters, getPropertyName

Methods inherited from class ubic.gemma.web.services.rest.util.args.AbstractArg

getValue, toString

Methods inherited from class java.lang.Object

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

Constructor Detail

GeneArg

protected GeneArg(T value)

Method Detail

valueOf

public static GeneArg<?> valueOf(String s)

Used by RS to parse value of request parameters.

Parameters:

s - the request Gene argument

Returns:

instance of appropriate implementation of GeneArg based on the actual property the argument represents.

getGenesOnTaxon

public List<GeneValueObject> getGenesOnTaxon(GeneService geneService,
                                             TaxonService taxonService,
                                             TaxonArg<?> taxonArg)

Parameters:

geneService - service that will be used to retrieve the persistent Gene object.

Returns:

a collection of Gene value objects..

getGeneEvidence

public List<GeneEvidenceValueObject> getGeneEvidence(GeneService geneService,
                                                     PhenotypeAssociationManagerService phenotypeAssociationManagerService,
                                                     Taxon taxon)
                                              throws SearchException

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

Parameters:

geneService - service that will be used to retrieve the persistent Gene object.

phenotypeAssociationManagerService - service used to execute the search.

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

getValueObjects

public abstract List<GeneValueObject> getValueObjects(GeneService service)

Parameters:

service - the service used to load the Gene value objects.

Returns:

all genes that match the value of the GeneArg.

getGeneLocation

public abstract List<PhysicalLocationValueObject> getGeneLocation(GeneService geneService)

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

Parameters:

geneService - service that will be used to retrieve the persistent Gene object.

Returns:

collection of physical location objects.

getGeneLocation

public abstract List<PhysicalLocationValueObject> getGeneLocation(GeneService geneService,
                                                                  Taxon taxon)

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

Parameters:

geneService - service that will be used to retrieve the persistent Gene object.

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

Returns:

collection of physical location objects.

getGoTerms

public List<GeneOntologyTermValueObject> getGoTerms(GeneService geneService,
                                                    GeneOntologyService geneOntologyService)

Returns GO terms for the gene that this GeneArg represents.

Parameters:

geneService - service that will be used to retrieve the persistent Gene object.

Returns:

collection of physical location objects.