Uses of Class
ubic.gemma.model.association.BioSequence2GeneProduct

Packages that use BioSequence2GeneProduct

Package	Description
ubic.gemma.core.goldenpath
ubic.gemma.model.association
ubic.gemma.model.genome.biosequence
ubic.gemma.model.genome.sequenceAnalysis
ubic.gemma.persistence.service.expression.designElement

Uses of BioSequence2GeneProduct in ubic.gemma.core.goldenpath

Methods in ubic.gemma.core.goldenpath that return types with arguments of type BioSequence2GeneProduct

Modifier and Type	Method	Description
Collection<BioSequence2GeneProduct>	GoldenPathSequenceAnalysis.getThreePrimeDistances(String identifier, ThreePrimeDistanceMethod method)	Uses default mapping settings
Collection<? extends BioSequence2GeneProduct>	GoldenPathSequenceAnalysis.getThreePrimeDistances(BlatResult br, ThreePrimeDistanceMethod method)	Given a physical location, find how close it is to the 3' end of a gene it is in, using default mapping settings.

Uses of BioSequence2GeneProduct in ubic.gemma.model.association

Subclasses of BioSequence2GeneProduct in ubic.gemma.model.association

Modifier and Type	Class	Description
class	ReferenceAssociation	An association between a BioSequence and a GeneProduct based on external database identifiers.

Uses of BioSequence2GeneProduct in ubic.gemma.model.genome.biosequence

Methods in ubic.gemma.model.genome.biosequence that return types with arguments of type BioSequence2GeneProduct

Modifier and Type	Method	Description
Set<BioSequence2GeneProduct>	BioSequence.getBioSequence2GeneProduct()

Method parameters in ubic.gemma.model.genome.biosequence with type arguments of type BioSequence2GeneProduct

Modifier and Type	Method	Description
void	BioSequence.setBioSequence2GeneProduct(Set<BioSequence2GeneProduct> bioSequence2GeneProduct)

Uses of BioSequence2GeneProduct in ubic.gemma.model.genome.sequenceAnalysis

Subclasses of BioSequence2GeneProduct in ubic.gemma.model.genome.sequenceAnalysis

Modifier and Type	Class	Description
class	AnnotationAssociation	An association between BioSequence and GeneProduct that is provided through an external annotation source, rather than our own sequence analysis.
class	BlatAssociation

Uses of BioSequence2GeneProduct in ubic.gemma.persistence.service.expression.designElement

Methods in ubic.gemma.persistence.service.expression.designElement that return types with arguments of type BioSequence2GeneProduct

Modifier and Type	Method	Description
Map<CompositeSequence,Collection<BioSequence2GeneProduct>>	CompositeSequenceDao.getGenesWithSpecificity(Collection<CompositeSequence> compositeSequences)
Map<CompositeSequence,Collection<BioSequence2GeneProduct>>	CompositeSequenceDaoImpl.getGenesWithSpecificity(Collection<CompositeSequence> compositeSequences)
Map<CompositeSequence,Collection<BioSequence2GeneProduct>>	CompositeSequenceService.getGenesWithSpecificity(Collection<CompositeSequence> compositeSequences)
Map<CompositeSequence,Collection<BioSequence2GeneProduct>>	CompositeSequenceServiceImpl.getGenesWithSpecificity(Collection<CompositeSequence> compositeSequences)