Uses of Class
ubic.gemma.model.genome.gene.GeneValueObject

Packages that use GeneValueObject

Package	Description
ubic.gemma.core.analysis.expression.coexpression
ubic.gemma.core.analysis.expression.diff
ubic.gemma.core.analysis.sequence
ubic.gemma.core.association.phenotype
ubic.gemma.core.loader.genome.gene.ncbi.homology
ubic.gemma.core.tasks.visualization
ubic.gemma.model.analysis.expression.diff
ubic.gemma.model.genome.gene
ubic.gemma.model.genome.gene.phenotype.valueObject
ubic.gemma.persistence.service.association.phenotype
ubic.gemma.persistence.service.association.phenotype.service
ubic.gemma.persistence.service.genome
ubic.gemma.persistence.service.genome.gene
ubic.gemma.rest
ubic.gemma.rest.util.args
ubic.gemma.web.controller.genome.gene
ubic.gemma.web.controller.visualization
ubic.gemma.web.persistence

Uses of GeneValueObject in ubic.gemma.core.analysis.expression.coexpression

Methods in ubic.gemma.core.analysis.expression.coexpression that return GeneValueObject

Modifier and Type	Method	Description
GeneValueObject	CoexpressionValueObjectExt.getFoundGene()
GeneValueObject	CoexpressionValueObjectExt.getQueryGene()

Methods in ubic.gemma.core.analysis.expression.coexpression that return types with arguments of type GeneValueObject

Modifier and Type	Method	Description
Collection<GeneValueObject>	CoexpressionMetaValueObject.getQueryGenes()

Methods in ubic.gemma.core.analysis.expression.coexpression with parameters of type GeneValueObject

Modifier and Type	Method	Description
void	CoexpressionValueObjectExt.setFoundGene(GeneValueObject foundGene)
void	CoexpressionValueObjectExt.setQueryGene(GeneValueObject queryGene)

Method parameters in ubic.gemma.core.analysis.expression.coexpression with type arguments of type GeneValueObject

Modifier and Type	Method	Description
void	CoexpressionMetaValueObject.setQueryGenes(Collection<GeneValueObject> queryGenes)

Uses of GeneValueObject in ubic.gemma.core.analysis.expression.diff

Methods in ubic.gemma.core.analysis.expression.diff that return GeneValueObject

Modifier and Type	Method	Description
GeneValueObject	DifferentialExpressionMetaAnalysisValueObject.getGene()

Methods in ubic.gemma.core.analysis.expression.diff with parameters of type GeneValueObject

Modifier and Type	Method	Description
void	DifferentialExpressionMetaAnalysisValueObject.setGene(GeneValueObject gene)

Uses of GeneValueObject in ubic.gemma.core.analysis.sequence

Methods in ubic.gemma.core.analysis.sequence that return GeneValueObject

Modifier and Type	Method	Description
GeneValueObject	GeneMappingSummary.getGene(GeneProductValueObject geneProduct)

Methods in ubic.gemma.core.analysis.sequence that return types with arguments of type GeneValueObject

Modifier and Type	Method	Description
Map<String,GeneValueObject>	GeneMappingSummary.getGeneProductIdGeneMap()
Map<GeneProductValueObject,GeneValueObject>	GeneMappingSummary.getGeneProductMap()
Map<Long,GeneValueObject>	CompositeSequenceMapValueObject.getGenes()

Methods in ubic.gemma.core.analysis.sequence with parameters of type GeneValueObject

Modifier and Type	Method	Description
void	GeneMappingSummary.addGene(GeneProductValueObject geneProduct, GeneValueObject gene)

Method parameters in ubic.gemma.core.analysis.sequence with type arguments of type GeneValueObject

Modifier and Type	Method	Description
void	GeneMappingSummary.setGeneProductMap(Map<GeneProductValueObject,GeneValueObject> geneProductMap)
void	CompositeSequenceMapValueObject.setGenes(Map<Long,GeneValueObject> genes)

Uses of GeneValueObject in ubic.gemma.core.association.phenotype

Methods in ubic.gemma.core.association.phenotype that return types with arguments of type GeneValueObject

Modifier and Type	Method	Description
Map<String,Collection<? extends GeneValueObject>>	PhenotypeAssociationManagerService.findCandidateGenesForEach(Set<String> phenotypeUris, Taxon taxon)	Deprecated.
Map<String,Collection<? extends GeneValueObject>>	PhenotypeAssociationManagerServiceImpl.findCandidateGenesForEach(Set<String> phenotypeUris, Taxon taxon)	Deprecated.
Map<GeneValueObject,OntologyTerm>	PhenotypeAssociationManagerService.findGenesForPhenotype(String phenotype, Long taxonId, boolean includeIEA)	Deprecated.
Map<GeneValueObject,OntologyTerm>	PhenotypeAssociationManagerServiceImpl.findGenesForPhenotype(String phenotype, Long taxonId, boolean includeIEA)	Deprecated.

Uses of GeneValueObject in ubic.gemma.core.loader.genome.gene.ncbi.homology

Methods in ubic.gemma.core.loader.genome.gene.ncbi.homology that return GeneValueObject

Modifier and Type	Method	Description
GeneValueObject	HomologeneService.getHomologueValueObject(Long geneId, String taxonCommonName)
GeneValueObject	HomologeneServiceImpl.getHomologueValueObject(Long geneId, String taxonCommonName)

Uses of GeneValueObject in ubic.gemma.core.tasks.visualization

Methods in ubic.gemma.core.tasks.visualization that return types with arguments of type GeneValueObject

Modifier and Type	Method	Description
Collection<GeneValueObject>	DifferentialExpressionSearchTaskCommand.getGeneGroup()

Constructor parameters in ubic.gemma.core.tasks.visualization with type arguments of type GeneValueObject

Constructor	Description
DifferentialExpressionSearchTaskCommand(Collection<GeneValueObject> geneGroup, Collection<ExpressionExperimentDetailsValueObject> experimentGroup, String geneGroupName, String experimentGroupName)

Uses of GeneValueObject in ubic.gemma.model.analysis.expression.diff

Methods in ubic.gemma.model.analysis.expression.diff that return GeneValueObject

Modifier and Type	Method	Description
GeneValueObject	DifferentialExpressionValueObject.getGene()

Methods in ubic.gemma.model.analysis.expression.diff with parameters of type GeneValueObject

Modifier and Type	Method	Description
void	DifferentialExpressionValueObject.setGene(GeneValueObject gene)

Uses of GeneValueObject in ubic.gemma.model.genome.gene

Methods in ubic.gemma.model.genome.gene that return GeneValueObject

Modifier and Type	Method	Description
static GeneValueObject	GeneValueObject.convert2ValueObject(Gene gene)	Converts a Gene to a GeneValueObject

Methods in ubic.gemma.model.genome.gene that return types with arguments of type GeneValueObject

Modifier and Type	Method	Description
static Collection<GeneValueObject>	GeneValueObject.convertMembers2GeneValueObjects(Collection<GeneSetMember> setMembers)	A static method for easily converting GeneSetMembers into GeneValueObjects

Constructors in ubic.gemma.model.genome.gene with parameters of type GeneValueObject

Constructor	Description
GeneValueObject(GeneValueObject otherBean)	Copies constructor from other GeneValueObject

Uses of GeneValueObject in ubic.gemma.model.genome.gene.phenotype.valueObject

Subclasses of GeneValueObject in ubic.gemma.model.genome.gene.phenotype.valueObject

Modifier and Type	Class	Description
class	GeneEvidenceValueObject	Deprecated.

Uses of GeneValueObject in ubic.gemma.persistence.service.association.phenotype

Methods in ubic.gemma.persistence.service.association.phenotype that return types with arguments of type GeneValueObject

Modifier and Type	Method	Description
Map<GeneValueObject,OntologyTerm>	PhenotypeAssociationDao.findGenesForPhenotype(OntologyTerm term, Long taxon, boolean includeIEA)
Map<GeneValueObject,OntologyTerm>	PhenotypeAssociationDaoImpl.findGenesForPhenotype(OntologyTerm term, Long taxon, boolean includeIEA)

Uses of GeneValueObject in ubic.gemma.persistence.service.association.phenotype.service

Methods in ubic.gemma.persistence.service.association.phenotype.service that return types with arguments of type GeneValueObject

Modifier and Type	Method	Description
Map<GeneValueObject,OntologyTerm>	PhenotypeAssociationService.findGenesForPhenotype(OntologyTerm phenotype, Long taxonId, boolean includeIEA)
Map<GeneValueObject,OntologyTerm>	PhenotypeAssociationServiceImpl.findGenesForPhenotype(OntologyTerm phenotype, Long taxonId, boolean includeIEA)

Uses of GeneValueObject in ubic.gemma.persistence.service.genome

Methods in ubic.gemma.persistence.service.genome that return GeneValueObject

Modifier and Type	Method	Description
protected GeneValueObject	GeneDaoImpl.doLoadValueObject(Gene entity)

Method parameters in ubic.gemma.persistence.service.genome with type arguments of type GeneValueObject

Modifier and Type	Method	Description
protected void	GeneDaoImpl.postProcessValueObjects(List<GeneValueObject> geneValueObjects)

Uses of GeneValueObject in ubic.gemma.persistence.service.genome.gene

Methods in ubic.gemma.persistence.service.genome.gene that return GeneValueObject

Modifier and Type	Method	Description
GeneValueObject	GeneService.findByNCBIIdValueObject(Integer accession)
GeneValueObject	GeneServiceImpl.findByNCBIIdValueObject(Integer accession)
GeneValueObject	GeneService.loadFullyPopulatedValueObject(Long id)	Returns a detailVO for a geneDd This method may be unnecessary now that we have put all the logic into the GeneService
GeneValueObject	GeneServiceImpl.loadFullyPopulatedValueObject(Long id)
GeneValueObject	GeneService.loadGenePhenotypes(Long geneId)
GeneValueObject	GeneServiceImpl.loadGenePhenotypes(Long geneId)
GeneValueObject	GeneServiceImpl.loadValueObjectById(Long id)

Methods in ubic.gemma.persistence.service.genome.gene that return types with arguments of type GeneValueObject

Modifier and Type	Method	Description
Map<Integer,GeneValueObject>	GeneService.findByNcbiIds(Collection<Integer> ncbiIds)	Quickly load exact matches.
Map<Integer,GeneValueObject>	GeneServiceImpl.findByNcbiIds(Collection<Integer> ncbiIds)
Map<String,GeneValueObject>	GeneService.findByOfficialSymbols(Collection<String> query, Long taxonId)	Quickly load exact matches.
Map<String,GeneValueObject>	GeneServiceImpl.findByOfficialSymbols(Collection<String> query, Long taxonId)
Collection<GeneValueObject>	GeneSearchService.getGenesByGOId(String goId, Long taxonId)	get all genes in the given taxon that are annotated with the given go id, including its child terms in the hierarchy
Collection<GeneValueObject>	GeneSearchServiceImpl.getGenesByGOId(String goId, Long taxonId)
Collection<GeneValueObject>	GeneSetService.getGenesInGroup(GeneSetValueObject object)	Get the gene value objects for the members of the group param
Collection<GeneValueObject>	GeneSetServiceImpl.getGenesInGroup(GeneSetValueObject object)
List<GeneValueObject>	GeneServiceImpl.loadValueObjectsByIds(Collection<Long> ids)
Collection<GeneValueObject>	GeneService.loadValueObjectsByIdsLiter(Collection<Long> ids)
Collection<GeneValueObject>	GeneServiceImpl.loadValueObjectsByIdsLiter(Collection<Long> ids)
Collection<GeneValueObject>	GeneCoreService.searchGenes(String query, Long taxonId)	Search for genes (by name or symbol)
Collection<GeneValueObject>	GeneService.searchGenes(String query, Long taxonId)
Collection<GeneValueObject>	GeneServiceImpl.searchGenes(String query, Long taxonId)	Search for genes (by name or symbol)
Collection<GeneValueObject>	GeneSearchService.searchMultipleGenes(String query, Long taxonId)	Search for multiple genes at once.
Collection<GeneValueObject>	GeneSearchServiceImpl.searchMultipleGenes(String query, Long taxonId)
Map<String,GeneValueObject>	GeneSearchService.searchMultipleGenesGetMap(Collection<String> query, Long taxonId)	Search for multiple genes at once.
Map<String,GeneValueObject>	GeneSearchServiceImpl.searchMultipleGenesGetMap(Collection<String> query, Long taxonId)

Uses of GeneValueObject in ubic.gemma.rest

Methods in ubic.gemma.rest that return types with arguments of type GeneValueObject

Modifier and Type	Method	Description
ResponseDataObject<List<GeneValueObject>>	GeneWebService.getGenes(GeneArrayArg genes)	Retrieves all genes matching the identifier.
PaginatedResponseDataObject<GeneValueObject>	GeneWebService.getGenes(OffsetArg offsetArg, LimitArg limitArg)
FilteredAndPaginatedResponseDataObject<GeneValueObject>	PlatformsWebService.getPlatformElementGenes(PlatformArg<?> platformArg, CompositeSequenceArg<?> probeArg, OffsetArg offset, LimitArg limit)	Retrieves the genes on the given platform element.
PaginatedResponseDataObject<GeneValueObject>	TaxaWebService.getTaxonGenes(TaxonArg<?> taxonArg, OffsetArg offsetArg, LimitArg limitArg)
ResponseDataObject<List<GeneValueObject>>	TaxaWebService.getTaxonGenesByIds(TaxonArg<?> taxonArg, GeneArrayArg geneArg)	Retrieves genes matching the identifier on the given taxon.
ResponseDataObject<List<GeneValueObject>>	TaxaWebService.getTaxonGenesOverlappingChromosome(TaxonArg<?> taxonArg, String chromosomeName, String strand, Long start, Integer size)	Finds genes overlapping a given region.

Uses of GeneValueObject in ubic.gemma.rest.util.args

Methods in ubic.gemma.rest.util.args that return types with arguments of type GeneValueObject

Modifier and Type	Method	Description
Slice<GeneValueObject>	GeneArgService.getGenes(int offset, int limit)
Slice<GeneValueObject>	GeneArgService.getGenesInTaxon(Taxon taxon, int offset, int limit)
List<GeneValueObject>	GeneArgService.getGenesInTaxon(GeneArrayArg arg, Taxon taxon)
List<GeneValueObject>	TaxonArgService.getGenesOnChromosome(TaxonArg<?> arg, String chromosomeName, String strand, long start, int size)	Lists Genes overlapping a location on a specific chromosome on a taxon that this TaxonArg represents.

Uses of GeneValueObject in ubic.gemma.web.controller.genome.gene

Methods in ubic.gemma.web.controller.genome.gene that return GeneValueObject

Modifier and Type	Method	Description
GeneValueObject	GeneController.loadGeneDetails(Long geneId)
GeneValueObject	GeneController.loadGenePhenotypes(Long geneId)

Methods in ubic.gemma.web.controller.genome.gene that return types with arguments of type GeneValueObject

Modifier and Type	Method	Description
Collection<GeneValueObject>	GenePickerController.getGenes(Collection<Long> geneIds)	AJAX
Collection<GeneValueObject>	GenePickerController.getGenesByGOId(String goId, Long taxonId)	for AJAX get all genes in the given taxon that are annotated with the given go id, including its child terms in the hierarchy
Collection<GeneValueObject>	GeneSetController.getGenesInGroup(Long groupId, Integer limit)	AJAX If the current user has access to given gene group, will return the gene value objects in the gene group
Collection<GeneValueObject>	GenePickerController.searchGenes(String query, Long taxonId)	AJAX (used by GeneCombo.js)
Collection<GeneValueObject>	GenePickerController.searchGenesWithNCBIId(String query, Long taxonId)	AJAX (used by Phenocarta)
Collection<GeneValueObject>	GenePickerController.searchMultipleGenes(String query, Long taxonId)	AJAX Search for multiple genes at once.
Map<String,GeneValueObject>	GenePickerController.searchMultipleGenesGetMap(Collection<String> query, Long taxonId)	AJAX Search for multiple genes at once.

Uses of GeneValueObject in ubic.gemma.web.controller.visualization

Methods in ubic.gemma.web.controller.visualization that return types with arguments of type GeneValueObject

Modifier and Type	Method	Description
Collection<GeneValueObject>	GeneExpressionProfile.getGenes()

Method parameters in ubic.gemma.web.controller.visualization with type arguments of type GeneValueObject

Modifier and Type	Method	Description
void	GeneExpressionProfile.setGenes(Collection<GeneValueObject> genes)

Constructor parameters in ubic.gemma.web.controller.visualization with type arguments of type GeneValueObject

Constructor	Description
GeneExpressionProfile(DoubleVectorValueObject vector, Collection<GeneValueObject> genes)
GeneExpressionProfile(DoubleVectorValueObject vector, Collection<GeneValueObject> genes, String color, Integer factor, Double pValue)
GeneExpressionProfile(DoubleVectorValueObject vector, Collection<GeneValueObject> genes, String color, Integer factor, Double pValue, boolean standardize)
VisualizationValueObject(Collection<DoubleVectorValueObject> vectors, List<GeneValueObject> genes, Collection<Long> validatedProbeList)
VisualizationValueObject(Collection<DoubleVectorValueObject> vectors, List<GeneValueObject> genes, Collection<Long> validatedProbeIdList, Double minPvalue)

Uses of GeneValueObject in ubic.gemma.web.persistence

Methods in ubic.gemma.web.persistence that return types with arguments of type GeneValueObject

Modifier and Type	Method	Description
Collection<GeneValueObject>	SessionListManager.getGenesInGroup(Long groupId)	AJAX If the current user has access to given gene group will return the gene ids in the gene group
Collection<GeneValueObject>	SessionListManagerImpl.getGenesInGroup(Long groupId)