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

Class GeneProductDaoImpl

java.lang.Object

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

ubic.gemma.persistence.service.AbstractVoEnabledDao<GeneProduct,GeneProductValueObject>

ubic.gemma.persistence.service.genome.gene.GeneProductDaoImpl

All Implemented Interfaces:

BaseDao<GeneProduct>, BaseVoEnabledDao<GeneProduct,GeneProductValueObject>, GeneProductDao

@Repository
public class GeneProductDaoImpl
extends AbstractVoEnabledDao<GeneProduct,GeneProductValueObject>
implements GeneProductDao

Author:

pavlidis

See Also:

• GeneProduct

Field Summary

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

REPORT_SLOW_QUERY_AFTER_MS

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

log

Constructor Summary

Constructors

Constructor	Description
GeneProductDaoImpl(SessionFactory sessionFactory)

Method Summary

Modifier and Type	Method	Description
protected GeneProductValueObject	doLoadValueObject(GeneProduct entity)	Load a value object for a given entity.
GeneProduct	find(GeneProduct geneProduct)	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<GeneProduct>	findByName(String name, Taxon taxon)
GeneProduct	findByNcbiId(String ncbiId)
Collection<Gene>	getGenesByName(String search)
Collection<Gene>	getGenesByNcbiId(String search)
GeneProduct	thaw(GeneProduct existing)

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

doLoadValueObjects, loadAllValueObjects, loadValueObject, loadValueObjectById, loadValueObjects, loadValueObjectsByIds, postProcessValueObjects

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, remove, remove, save, save, streamAll, streamAll, streamQuery, update, update

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, remove, remove, save, save, streamAll, streamAll, update, update

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

loadAllValueObjects, loadValueObject, loadValueObjectById, loadValueObjects, loadValueObjectsByIds

Constructor Details

GeneProductDaoImpl

@Autowired
public GeneProductDaoImpl(SessionFactory sessionFactory)

Method Details

findByNcbiId

public GeneProduct findByNcbiId(String ncbiId)

Specified by:

findByNcbiId in interface GeneProductDao

getGenesByName

public Collection<Gene> getGenesByName(String search)

Specified by:

getGenesByName in interface GeneProductDao

getGenesByNcbiId

public Collection<Gene> getGenesByNcbiId(String search)

Specified by:

getGenesByNcbiId in interface GeneProductDao

findByName

public Collection<GeneProduct> findByName(String name,
 Taxon taxon)

Specified by:

findByName in interface GeneProductDao

thaw

public GeneProduct thaw(GeneProduct existing)

Specified by:

thaw in interface GeneProductDao

find

public GeneProduct find(GeneProduct geneProduct)

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<GeneProduct>

Overrides:

find in class AbstractDao<GeneProduct>

Parameters:

geneProduct - the entity to look for.

Returns:

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

doLoadValueObject

protected GeneProductValueObject doLoadValueObject(GeneProduct entity)

Description copied from class: AbstractVoEnabledDao

Load a value object for a given entity.

This should be fast and efficient, and avoid any database query or post-processing. If you need to perform additional queries, implement AbstractVoEnabledDao.postProcessValueObjects(List) instead.

Specified by:

doLoadValueObject in class AbstractVoEnabledDao<GeneProduct,GeneProductValueObject>