Uses of Class
ubic.gemma.persistence.service.association.coexpression.CoexpressionValueObject

Packages that use CoexpressionValueObject

Package	Description
ubic.gemma.core.analysis.service
ubic.gemma.persistence.service.association.coexpression

Uses of CoexpressionValueObject in ubic.gemma.core.analysis.service

Method parameters in ubic.gemma.core.analysis.service with type arguments of type CoexpressionValueObject

Modifier and Type	Method	Description
void	CoexpressionWriter.write(ExpressionExperiment ee, Collection<CoexpressionValueObject> geneLinks, Writer writer)

Uses of CoexpressionValueObject in ubic.gemma.persistence.service.association.coexpression

Methods in ubic.gemma.persistence.service.association.coexpression that return CoexpressionValueObject

Modifier and Type	Method	Description
CoexpressionValueObject	CoexpressionCacheValueObject.toModifiable()

Methods in ubic.gemma.persistence.service.association.coexpression that return types with arguments of type CoexpressionValueObject

Modifier and Type	Method	Description
List<CoexpressionValueObject>	CoexpressionDao.findCoexpressionRelationships(Gene gene, Collection<Long> bas, int maxResults, boolean quick)	Find coexpression links for a gene that are common to all the given datasets.
Map<Long,List<CoexpressionValueObject>>	CoexpressionDao.findCoexpressionRelationships(Taxon taxon, Collection<Long> genes, Collection<Long> bas, int maxResults, boolean quick)	Find coexpression links for the genes that are common to all the given datasets, so stringency = bas.size().
Map<Long,List<CoexpressionValueObject>>	CoexpressionDao.findCoexpressionRelationships(Taxon t, Collection<Long> genes, Collection<Long> bas, int stringency, int maxResults, boolean quick)
List<CoexpressionValueObject>	CoexpressionDaoImpl.findCoexpressionRelationships(Gene gene, Collection<Long> bas, int maxResults, boolean quick)
Map<Long,List<CoexpressionValueObject>>	CoexpressionDaoImpl.findCoexpressionRelationships(Taxon taxon, Collection<Long> genes, Collection<Long> bas, int maxResults, boolean quick)
Map<Long,List<CoexpressionValueObject>>	CoexpressionDaoImpl.findCoexpressionRelationships(Taxon t, Collection<Long> genes, Collection<Long> bas, int stringency, int maxResults, boolean quick)
List<CoexpressionValueObject>	CoexpressionService.findCoexpressionRelationships(Gene gene, Collection<Long> bas, int maxResults, boolean quick)	Find links which are common to all of the given data sets.
List<CoexpressionValueObject>	CoexpressionService.findCoexpressionRelationships(Gene gene, Collection<Long> bas, int stringency, int maxResults, boolean quick)	Search for coexpression across all available data sets, for the given genes considered individually, subject to a stringency constraint.
Map<Long,List<CoexpressionValueObject>>	CoexpressionService.findCoexpressionRelationships(Taxon t, Collection<Long> genes, Collection<Long> bas, int maxResults, boolean quick)	Find coexpression links for the genes that are common to all the given datasets (that is, the stringency is equal to the size of the set of datasets)
Map<Long,List<CoexpressionValueObject>>	CoexpressionService.findCoexpressionRelationships(Taxon t, Collection<Long> genes, Collection<Long> bas, int stringency, int maxResults, boolean quick)	Find coexpression links for the genes that are common to at least stringency of the given datasets.
List<CoexpressionValueObject>	CoexpressionServiceImpl.findCoexpressionRelationships(Gene gene, Collection<Long> bas, int maxResults, boolean quick)
List<CoexpressionValueObject>	CoexpressionServiceImpl.findCoexpressionRelationships(Gene gene, Collection<Long> bas, int stringency, int maxResults, boolean quick)
Map<Long,List<CoexpressionValueObject>>	CoexpressionServiceImpl.findCoexpressionRelationships(Taxon t, Collection<Long> genes, Collection<Long> bas, int maxResults, boolean quick)
Map<Long,List<CoexpressionValueObject>>	CoexpressionServiceImpl.findCoexpressionRelationships(Taxon t, Collection<Long> genes, Collection<Long> bas, int stringency, int maxResults, boolean quick)
Map<Long,List<CoexpressionValueObject>>	CoexpressionDao.findInterCoexpressionRelationships(Taxon taxon, Collection<Long> genes, Collection<Long> bas, int stringency, boolean quick)	Return coexpression relationships among the given genes, limited to the given data sets.
Map<Long,List<CoexpressionValueObject>>	CoexpressionDaoImpl.findInterCoexpressionRelationships(Taxon taxon, Collection<Long> genes, Collection<Long> bas, int stringency, boolean quick)
Map<Long,List<CoexpressionValueObject>>	CoexpressionService.findInterCoexpressionRelationships(Taxon t, Collection<Long> genes, Collection<Long> bas, int stringency, boolean quick)	Return coexpression relationships among the given genes in the given data sets, in a map of query gene to coexpression objects.
Map<Long,List<CoexpressionValueObject>>	CoexpressionServiceImpl.findInterCoexpressionRelationships(Taxon t, Collection<Long> genes, Collection<Long> bas, int stringency, boolean quick)
List<CoexpressionValueObject>	CoexpressionCache.get(Long g)
List<CoexpressionValueObject>	CoexpressionCacheImpl.get(Long geneId)
Collection<CoexpressionValueObject>	CoexpressionDao.getCoexpression(Taxon taxon, ExpressionExperiment experiment, boolean quick)
Collection<CoexpressionValueObject>	CoexpressionDaoImpl.getCoexpression(Taxon taxon, ExpressionExperiment experiment, boolean quick)
Collection<CoexpressionValueObject>	CoexpressionService.getCoexpression(ExpressionExperiment experiment, boolean quick)
Collection<CoexpressionValueObject>	CoexpressionServiceImpl.getCoexpression(ExpressionExperiment experiment, boolean quick)

Methods in ubic.gemma.persistence.service.association.coexpression with parameters of type CoexpressionValueObject

Modifier and Type	Method	Description
int	CoexpressionValueObject.compareTo(CoexpressionValueObject o)

Method parameters in ubic.gemma.persistence.service.association.coexpression with type arguments of type CoexpressionValueObject

Modifier and Type	Method	Description
void	CoexpressionCache.cacheCoexpression(Long geneId, Collection<CoexpressionValueObject> r)
void	CoexpressionCache.cacheCoexpression(Map<Long,List<CoexpressionValueObject>> r)
void	CoexpressionCacheImpl.cacheCoexpression(Long geneId, Collection<CoexpressionValueObject> r)
void	CoexpressionCacheImpl.cacheCoexpression(Map<Long,List<CoexpressionValueObject>> r)

Constructors in ubic.gemma.persistence.service.association.coexpression with parameters of type CoexpressionValueObject

Modifier	Constructor	Description
	CoexpressionCacheValueObject(CoexpressionValueObject vo)