Package ubic.gemma.persistence.service.genome.biosequence

Class BioSequenceDaoImpl

java.lang.Object

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

ubic.gemma.persistence.service.AbstractVoEnabledDao<BioSequence,BioSequenceValueObject>

ubic.gemma.persistence.service.genome.biosequence.BioSequenceDaoImpl

All Implemented Interfaces:

BaseDao<BioSequence>, BaseVoEnabledDao<BioSequence,BioSequenceValueObject>, BioSequenceDao

@Repository
public class BioSequenceDaoImpl
extends AbstractVoEnabledDao<BioSequence,BioSequenceValueObject>
implements BioSequenceDao

Author:

pavlidis

See Also:

• BioSequence

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
BioSequenceDaoImpl(SessionFactory sessionFactory)

Method Summary

Modifier and Type	Method	Description
protected BioSequenceValueObject	doLoadValueObject(BioSequence entity)	Load a value object for a given entity.
BioSequence	find(BioSequence bioSequence)	Does a look up for the given entity in the persistent storage, usually looking for a specific identifier ( either id or a string property).
BioSequence	findByAccession(DatabaseEntry databaseEntry)
BioSequence	findByCompositeSequence(CompositeSequence compositeSequence)
Map<Gene,Collection<BioSequence>>	findByGenes(Collection<Gene> genes)	Returns matching biosequences for the given genes in a Map (gene to biosequences).
Collection<BioSequence>	findByName(String name)
Collection<Gene>	getGenesByAccession(String search)
Collection<Gene>	getGenesByName(String search)	For a biosequence name, get the genes
Collection<BioSequence>	thaw(Collection<BioSequence> bioSequences)
BioSequence	thaw(BioSequence bioSequence)

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

BioSequenceDaoImpl

@Autowired
public BioSequenceDaoImpl(SessionFactory sessionFactory)

Method Details

findByAccession

public BioSequence findByAccession(DatabaseEntry databaseEntry)

Specified by:

findByAccession in interface BioSequenceDao

findByGenes

public Map<Gene,Collection<BioSequence>> findByGenes(Collection<Gene> genes)

Description copied from interface: BioSequenceDao

Returns matching biosequences for the given genes in a Map (gene to biosequences). Genes which had no associated sequences are not included in the result.

Specified by:

findByGenes in interface BioSequenceDao

Parameters:

genes - genes

Returns:

map to biosequences

findByName

public Collection<BioSequence> findByName(String name)

Specified by:

findByName in interface BioSequenceDao

getGenesByAccession

public Collection<Gene> getGenesByAccession(String search)

Specified by:

getGenesByAccession in interface BioSequenceDao

getGenesByName

public Collection<Gene> getGenesByName(String search)

Description copied from interface: BioSequenceDao

For a biosequence name, get the genes

Specified by:

getGenesByName in interface BioSequenceDao

Parameters:

search - name

Returns:

genes

thaw

public Collection<BioSequence> thaw(Collection<BioSequence> bioSequences)

Specified by:

thaw in interface BioSequenceDao

thaw

public BioSequence thaw(BioSequence bioSequence)

Specified by:

thaw in interface BioSequenceDao

findByCompositeSequence

public BioSequence findByCompositeSequence(CompositeSequence compositeSequence)

Specified by:

findByCompositeSequence in interface BioSequenceDao

doLoadValueObject

protected BioSequenceValueObject doLoadValueObject(BioSequence 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<BioSequence,BioSequenceValueObject>

find

public BioSequence find(BioSequence bioSequence)

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<BioSequence>

Overrides:

find in class AbstractDao<BioSequence>

Parameters:

bioSequence - the entity to look for.

Returns:

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