Interface GeneSetDao
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- All Superinterfaces:
BaseDao<GeneSet>
,BaseVoEnabledDao<GeneSet,DatabaseBackedGeneSetValueObject>
- All Known Implementing Classes:
GeneSetDaoImpl
@ParametersAreNonnullByDefault public interface GeneSetDao extends BaseVoEnabledDao<GeneSet,DatabaseBackedGeneSetValueObject>
The interface for managing groupings of genes.- Author:
- kelsey
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Method Summary
All Methods Instance Methods Abstract Methods Modifier and Type Method Description Collection<GeneSet>
findByGene(Gene gene)
Collection<GeneSet>
findByName(String name)
Collection<GeneSet>
findByName(String name, Taxon taxon)
int
getGeneCount(Long id)
This method does not do any permissions filtering.List<Taxon>
getTaxa(GeneSet geneSet)
Return all the taxa of the gene set members.Taxon
getTaxon(GeneSet geneSet)
Returns the taxon of an arbitrary member of the set.Collection<GeneSet>
loadAll(Taxon tax)
DatabaseBackedGeneSetValueObject
loadValueObjectByIdLite(Long id)
List<DatabaseBackedGeneSetValueObject>
loadValueObjectsByIdsLite(Collection<Long> geneSetIds)
int
removeAll()
void
thaw(GeneSet geneSet)
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Methods inherited from interface ubic.gemma.persistence.service.BaseDao
countAll, create, create, find, findOrCreate, getElementClass, getIdentifierPropertyName, load, load, loadAll, loadReference, loadReference, remove, remove, remove, save, save, update, update
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Methods inherited from interface ubic.gemma.persistence.service.BaseVoEnabledDao
loadAllValueObjects, loadValueObject, loadValueObjectById, loadValueObjects, loadValueObjectsByIds
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Method Detail
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getGeneCount
int getGeneCount(Long id)
This method does not do any permissions filtering. It assumes that id the user can see the set, they can see all the members.- Parameters:
id
- gene set id- Returns:
- integer count of genes in set
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getTaxon
@Nullable Taxon getTaxon(GeneSet geneSet)
Returns the taxon of an arbitrary member of the set.- Returns:
- the taxon, or null if the gene set does not have any member
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loadValueObjectByIdLite
DatabaseBackedGeneSetValueObject loadValueObjectByIdLite(Long id)
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loadValueObjectsByIdsLite
List<DatabaseBackedGeneSetValueObject> loadValueObjectsByIdsLite(Collection<Long> geneSetIds)
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findByGene
Collection<GeneSet> findByGene(Gene gene)
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findByName
Collection<GeneSet> findByName(String name)
- Parameters:
name
- uses the given name to do a name* search in the db- Returns:
- a collection of geneSets that match the given search term.
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findByName
Collection<GeneSet> findByName(String name, @Nullable Taxon taxon)
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loadAll
Collection<GeneSet> loadAll(@Nullable Taxon tax)
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thaw
void thaw(GeneSet geneSet)
- Parameters:
geneSet
- gene set
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removeAll
int removeAll()
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