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

Packages that use GeneProduct

Package	Description
ubic.gemma.core.analysis.sequence
ubic.gemma.core.goldenpath
ubic.gemma.core.loader.genome.gene.ncbi
ubic.gemma.model.association
ubic.gemma.model.genome
ubic.gemma.model.genome.gene
ubic.gemma.persistence.service.genome.gene
ubic.gemma.persistence.service.genome.sequenceAnalysis
ubic.gemma.persistence.util

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

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

Modifier and Type	Method	Description
Collection<GeneProduct>	CompositeSequenceMapSummary.getGeneProducts()

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

Modifier and Type	Method	Description
static int	SequenceManipulation.getGeneProductExonOverlap(String starts, String sizes, String strand, GeneProduct geneProduct)	Compute the overlap of a physical location with a transcript (gene product).

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

Modifier and Type	Method	Description
void	CompositeSequenceMapSummary.setGeneProducts(Collection<GeneProduct> geneProducts)

Uses of GeneProduct in ubic.gemma.core.goldenpath

Methods in ubic.gemma.core.goldenpath that return types with arguments of type GeneProduct

Modifier and Type	Method	Description
Collection<GeneProduct>	GoldenPathSequenceAnalysis.findKnownGenesByLocation(String chromosome, Long start, Long end, String strand)	Find "Known" genes contained in or overlapping a region.
Collection<GeneProduct>	GoldenPathSequenceAnalysis.findRefGenesByLocation(String chromosome, Long start, Long end, String strand)	Find RefSeq genes contained in or overlapping a region.

Uses of GeneProduct in ubic.gemma.core.loader.genome.gene.ncbi

Methods in ubic.gemma.core.loader.genome.gene.ncbi that return types with arguments of type GeneProduct

Modifier and Type	Method	Description
Collection<GeneProduct>	NcbiGeneConverter.convert(NCBIGene2Accession acc, Gene gene)

Uses of GeneProduct in ubic.gemma.model.association

Methods in ubic.gemma.model.association that return GeneProduct

Modifier and Type	Method	Description
GeneProduct	BioSequence2GeneProduct.getGeneProduct()

Methods in ubic.gemma.model.association with parameters of type GeneProduct

Modifier and Type	Method	Description
void	BioSequence2GeneProduct.setGeneProduct(GeneProduct geneProduct)

Uses of GeneProduct in ubic.gemma.model.genome

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

Modifier and Type	Method	Description
Set<GeneProduct>	Gene.getProducts()

Method parameters in ubic.gemma.model.genome with type arguments of type GeneProduct

Modifier and Type	Method	Description
void	Gene.setProducts(Set<GeneProduct> products)

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

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

Modifier and Type	Method	Description
static GeneProduct	GeneProduct.Factory.newInstance()

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

Modifier	Constructor	Description
	GeneProductValueObject(GeneProduct entity)	Populates the VO properties with values from the given entity.

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

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

Modifier and Type	Method	Description
GeneProduct	GeneProductService.create(GeneProduct entity)
GeneProduct	GeneProductDaoImpl.find(GeneProduct geneProduct)
GeneProduct	GeneProductDao.findByNcbiId(String ncbiGi)
GeneProduct	GeneProductDaoImpl.findByNcbiId(String ncbiId)
GeneProduct	GeneProductService.findOrCreate(GeneProduct geneProduct)
GeneProduct	GeneProductDao.thaw(GeneProduct existing)
GeneProduct	GeneProductDaoImpl.thaw(GeneProduct existing)
GeneProduct	GeneProductService.thaw(GeneProduct geneProduct)
GeneProduct	GeneProductServiceImpl.thaw(GeneProduct existing)

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

Modifier and Type	Method	Description
Collection<GeneProduct>	GeneProductDao.findByName(String name, Taxon taxon)
Collection<GeneProduct>	GeneProductDaoImpl.findByName(String name, Taxon taxon)
Collection<GeneProduct>	GeneProductService.findByName(String name, Taxon taxon)
Collection<GeneProduct>	GeneProductServiceImpl.findByName(String name, Taxon taxon)

Methods in ubic.gemma.persistence.service.genome.gene with parameters of type GeneProduct

Modifier and Type	Method	Description
GeneProduct	GeneProductService.create(GeneProduct entity)
protected GeneProductValueObject	GeneProductDaoImpl.doLoadValueObject(GeneProduct entity)
GeneProduct	GeneProductDaoImpl.find(GeneProduct geneProduct)
GeneProduct	GeneProductService.findOrCreate(GeneProduct geneProduct)
void	GeneProductService.remove(GeneProduct entity)
void	GeneProductServiceImpl.remove(GeneProduct entity)
GeneProduct	GeneProductDao.thaw(GeneProduct existing)
GeneProduct	GeneProductDaoImpl.thaw(GeneProduct existing)
GeneProduct	GeneProductService.thaw(GeneProduct geneProduct)
GeneProduct	GeneProductServiceImpl.thaw(GeneProduct existing)
void	GeneProductService.update(GeneProduct entity)

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

Modifier and Type	Method	Description
void	GeneProductService.remove(Collection<GeneProduct> toRemove)
void	GeneProductServiceImpl.remove(Collection<GeneProduct> toRemove)
void	GeneProductService.update(Collection<GeneProduct> entities)

Uses of GeneProduct in ubic.gemma.persistence.service.genome.sequenceAnalysis

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

Modifier and Type	Method	Description
Collection<AnnotationAssociation>	AnnotationAssociationDao.find(Collection<GeneProduct> gps)
Collection<AnnotationAssociation>	AnnotationAssociationDaoImpl.find(Collection<GeneProduct> gps)
Collection<BlatAssociation>	BlatAssociationDao.find(Collection<GeneProduct> toRemove)
Collection<BlatAssociation>	BlatAssociationDaoImpl.find(Collection<GeneProduct> gps)

Uses of GeneProduct in ubic.gemma.persistence.util

Methods in ubic.gemma.persistence.util with parameters of type GeneProduct

Modifier and Type	Method	Description
static void	BusinessKey.checkValidKey(GeneProduct geneProduct)
static void	BusinessKey.createQueryObject(Criteria queryObject, GeneProduct geneProduct)