Package ubic.gemma.persistence.service.genome.gene

Interface GeneSetDao

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

Method Summary

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)

Methods inherited from interface ubic.gemma.persistence.service.BaseDao

countAll, create, create, find, findOrCreate, getElementClass, load, load, loadAll, loadReference, loadReference, reload, reload, remove, remove, remove, save, save, streamAll, streamAll, update, update

Methods inherited from interface ubic.gemma.persistence.service.BaseVoEnabledDao

loadAllValueObjects, loadValueObject, loadValueObjectById, loadValueObjects, loadValueObjectsByIds

Method Details

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

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

getTaxa

List<Taxon> getTaxa(GeneSet geneSet)

Return all the taxa of the gene set members.

loadValueObjectByIdLite

DatabaseBackedGeneSetValueObject loadValueObjectByIdLite(Long id)

loadValueObjectsByIdsLite

List<DatabaseBackedGeneSetValueObject> loadValueObjectsByIdsLite(Collection<Long> geneSetIds)

findByGene

Collection<GeneSet> findByGene(Gene gene)

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.

findByName

Collection<GeneSet> findByName(String name,
 @Nullable
 Taxon taxon)

loadAll

Collection<GeneSet> loadAll(@Nullable
 Taxon tax)

thaw

void thaw(GeneSet geneSet)

Parameters:

geneSet - gene set

removeAll

int removeAll()