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

Class GeneSetDaoImpl

java.lang.Object

ubic.gemma.persistence.service.AbstractDao<GeneSet>

ubic.gemma.persistence.service.genome.gene.GeneSetDaoImpl

All Implemented Interfaces:

BaseDao<GeneSet>, BaseVoEnabledDao<GeneSet,DatabaseBackedGeneSetValueObject>, GeneSetDao

@Repository
@ParametersAreNonnullByDefault
public class GeneSetDaoImpl
extends AbstractDao<GeneSet>
implements GeneSetDao

Base Spring DAO Class: is able to create, update, remove, load, and find objects of type ubic.gemma.model.genome.gene.GeneSet.

Author:

kelsey

See Also:

• GeneSet

Field Summary

Fields inherited from class ubic.gemma.persistence.service.AbstractDao

log

Constructor Summary

Constructors

Constructor	Description
GeneSetDaoImpl(SessionFactory sessionFactory)

Method Summary

Modifier and Type	Method	Description
GeneSet	find(GeneSet entity)	Does a look up for the given entity in the persistent storage, usually looking for a specific identifier ( either id or a string property).
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)
List<DatabaseBackedGeneSetValueObject>	loadAllValueObjects()
DatabaseBackedGeneSetValueObject	loadValueObject(GeneSet geneSet)	Load a value object corresponding to an entity
DatabaseBackedGeneSetValueObject	loadValueObjectById(Long id)
DatabaseBackedGeneSetValueObject	loadValueObjectByIdLite(Long id)
List<DatabaseBackedGeneSetValueObject>	loadValueObjects(Collection<GeneSet> entities)	Load value objects corresponding to entities
List<DatabaseBackedGeneSetValueObject>	loadValueObjectsByIds(Collection<Long> ids)
List<DatabaseBackedGeneSetValueObject>	loadValueObjectsByIdsLite(Collection<Long> ids)
final void	remove(Collection<GeneSet> entities)
final void	remove(GeneSet entity)	Remove a persistent instance
int	removeAll()
void	thaw(GeneSet geneSet)
final void	update(Collection<GeneSet> entities)
final void	update(GeneSet entity)

Methods inherited from class ubic.gemma.persistence.service.AbstractDao

countAll, create, create, findByProperty, findByPropertyIn, findOneByProperty, findOrCreate, getBatchSize, getElementClass, getEntityName, getIdentifierPropertyName, getSessionFactory, load, load, loadAll, loadReference, loadReference, reload, reload, remove, save, save, streamAll, streamAll, streamQuery

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

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

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

Constructor Details

GeneSetDaoImpl

@Autowired
public GeneSetDaoImpl(SessionFactory sessionFactory)

Method Details

getGeneCount

public int getGeneCount(Long id)

Description copied from interface: GeneSetDao

This method does not do any permissions filtering. It assumes that id the user can see the set, they can see all the members.

Specified by:

getGeneCount in interface GeneSetDao

Parameters:

id - gene set id

Returns:

integer count of genes in set

getTaxon

public Taxon getTaxon(GeneSet geneSet)

Description copied from interface: GeneSetDao

Returns the taxon of an arbitrary member of the set.

Specified by:

getTaxon in interface GeneSetDao

Returns:

the taxon, or null if the gene set does not have any member

getTaxa

public List<Taxon> getTaxa(GeneSet geneSet)

Description copied from interface: GeneSetDao

Return all the taxa of the gene set members.

Specified by:

getTaxa in interface GeneSetDao

loadValueObject

public DatabaseBackedGeneSetValueObject loadValueObject(GeneSet geneSet)

Description copied from interface: BaseVoEnabledDao

Load a value object corresponding to an entity

Specified by:

loadValueObject in interface BaseVoEnabledDao<GeneSet,DatabaseBackedGeneSetValueObject>

Parameters:

geneSet - the entity to turn into a value object

Returns:

a value object

loadValueObjectById

public DatabaseBackedGeneSetValueObject loadValueObjectById(Long id)

Specified by:

loadValueObjectById in interface BaseVoEnabledDao<GeneSet,DatabaseBackedGeneSetValueObject>

Returns:

a value object, or null if it could not be constructed

loadValueObjectByIdLite

public DatabaseBackedGeneSetValueObject loadValueObjectByIdLite(Long id)

Specified by:

loadValueObjectByIdLite in interface GeneSetDao

loadValueObjects

public List<DatabaseBackedGeneSetValueObject> loadValueObjects(Collection<GeneSet> entities)

Description copied from interface: BaseVoEnabledDao

Load value objects corresponding to entities

Specified by:

loadValueObjects in interface BaseVoEnabledDao<GeneSet,DatabaseBackedGeneSetValueObject>

Parameters:

entities - the entities to turn into value objects

Returns:

a collection of value objects

loadValueObjectsByIds

public List<DatabaseBackedGeneSetValueObject> loadValueObjectsByIds(Collection<Long> ids)

Specified by:

loadValueObjectsByIds in interface BaseVoEnabledDao<GeneSet,DatabaseBackedGeneSetValueObject>

loadValueObjectsByIdsLite

public List<DatabaseBackedGeneSetValueObject> loadValueObjectsByIdsLite(Collection<Long> ids)

Specified by:

loadValueObjectsByIdsLite in interface GeneSetDao

loadAllValueObjects

public List<DatabaseBackedGeneSetValueObject> loadAllValueObjects()

Specified by:

loadAllValueObjects in interface BaseVoEnabledDao<GeneSet,DatabaseBackedGeneSetValueObject>

findByGene

public Collection<GeneSet> findByGene(Gene gene)

Specified by:

findByGene in interface GeneSetDao

findByName

public Collection<GeneSet> findByName(String name)

Specified by:

findByName in interface GeneSetDao

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

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

Specified by:

findByName in interface GeneSetDao

loadAll

public Collection<GeneSet> loadAll(@Nullable
 Taxon tax)

Specified by:

loadAll in interface GeneSetDao

find

public GeneSet find(GeneSet entity)

Description copied from interface: BaseDao

Does a look up for the given entity in the persistent storage, usually looking for a specific identifier ( either id or a string property).

Specified by:

find in interface BaseDao<GeneSet>

Overrides:

find in class AbstractDao<GeneSet>

Parameters:

entity - the entity to look for.

Returns:

an entity that was found in the persistent storage, or null if no such entity was found.

thaw

public void thaw(GeneSet geneSet)

Specified by:

thaw in interface GeneSetDao

Parameters:

geneSet - gene set

removeAll

public int removeAll()

Specified by:

removeAll in interface GeneSetDao

update

public final void update(Collection<GeneSet> entities)

Specified by:

update in interface BaseDao<GeneSet>

Overrides:

update in class AbstractDao<GeneSet>

Parameters:

entities - Update the entities. Not supported if the entities are immutable.

update

public final void update(GeneSet entity)

Specified by:

update in interface BaseDao<GeneSet>

Overrides:

update in class AbstractDao<GeneSet>

Parameters:

entity - Update the entity. Not supported if the entity is immutable.

remove

public final void remove(Collection<GeneSet> entities)

Specified by:

remove in interface BaseDao<GeneSet>

Overrides:

remove in class AbstractDao<GeneSet>

remove

public final void remove(GeneSet entity)

Description copied from interface: BaseDao

Remove a persistent instance

Specified by:

remove in interface BaseDao<GeneSet>

Overrides:

remove in class AbstractDao<GeneSet>

Parameters:

entity - the entity to be removed