Uses of Class
ubic.gemma.model.genome.PhysicalLocation

Packages that use PhysicalLocation

Package	Description
ubic.gemma.core.analysis.sequence
ubic.gemma.model.genome
ubic.gemma.model.genome.gene
ubic.gemma.model.genome.sequenceAnalysis
ubic.gemma.persistence.service.genome
ubic.gemma.persistence.service.genome.gene
ubic.gemma.persistence.util

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

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

Modifier and Type	Method	Description
static int	SequenceManipulation.computeOverlap(PhysicalLocation a, PhysicalLocation b)	Compute the overlap between two physical locations.

Uses of PhysicalLocation in ubic.gemma.model.genome

Methods in ubic.gemma.model.genome that return PhysicalLocation

Modifier and Type	Method	Description
PhysicalLocation	ChromosomeFeature.getPhysicalLocation()
static PhysicalLocation	PhysicalLocation.Factory.newInstance()
static PhysicalLocation	PhysicalLocation.Factory.newInstance(Chromosome chromosome)
static PhysicalLocation	PhysicalLocation.Factory.newInstance(Chromosome chromosome, Long nucleotide, Integer nucleotideLength, String strand, Integer bin)

Methods in ubic.gemma.model.genome with parameters of type PhysicalLocation

Modifier and Type	Method	Description
int	PhysicalLocation.computeOverlap(PhysicalLocation other)
void	ChromosomeFeature.setPhysicalLocation(PhysicalLocation physicalLocation)

Constructors in ubic.gemma.model.genome with parameters of type PhysicalLocation

Constructor	Description
PhysicalLocationValueObject(PhysicalLocation location)

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

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

Modifier and Type	Method	Description
Set<PhysicalLocation>	GeneProduct.getExons()	Only used for transient instances in sequence analysis, we do not store exon locations in the database.

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

Modifier and Type	Method	Description
void	GeneProduct.setExons(Set<PhysicalLocation> exons)	Only used for transient instances, we do not store exon locations in the database.

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

Methods in ubic.gemma.model.genome.sequenceAnalysis that return PhysicalLocation

Modifier and Type	Method	Description
PhysicalLocation	SequenceSimilaritySearchResult.getTargetAlignedRegion()

Methods in ubic.gemma.model.genome.sequenceAnalysis with parameters of type PhysicalLocation

Modifier and Type	Method	Description
void	SequenceSimilaritySearchResult.setTargetAlignedRegion(PhysicalLocation targetAlignedRegion)

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

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

Modifier and Type	Method	Description
Collection<Gene>	GeneDao.find(PhysicalLocation physicalLocation)	Find all genes at a physical location.
Collection<Gene>	GeneDaoImpl.find(PhysicalLocation physicalLocation)
Collection<Gene>	GeneDao.findByPhysicalLocation(PhysicalLocation location)	Deprecated.
Collection<Gene>	GeneDaoImpl.findByPhysicalLocation(PhysicalLocation location)

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

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

Modifier and Type	Method	Description
Collection<Gene>	GeneService.find(PhysicalLocation physicalLocation)	Find all genes at a physical location.
Collection<Gene>	GeneServiceImpl.find(PhysicalLocation physicalLocation)

Uses of PhysicalLocation in ubic.gemma.persistence.util

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

Modifier and Type	Method	Description
static void	BusinessKey.attachCriteria(Criteria queryObject, PhysicalLocation physicalLocation, String attributeName)