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

Class BioSequenceServiceImpl

java.lang.Object

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

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

ubic.gemma.persistence.service.genome.biosequence.BioSequenceServiceImpl

All Implemented Interfaces:

BaseImmutableService<BioSequence>, BaseReadOnlyService<BioSequence>, BaseService<BioSequence>, BaseVoEnabledService<BioSequence,BioSequenceValueObject>, BioSequenceService

@Service
public class BioSequenceServiceImpl
extends AbstractVoEnabledService<BioSequence,BioSequenceValueObject>
implements BioSequenceService

Spring Service base class for BioSequenceService, provides access to all services and entities referenced by this service.

Author:

keshav, pavlidis

See Also:

• BioSequenceService

Field Summary

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

log

Constructor Summary

Constructors

Constructor	Description
BioSequenceServiceImpl(BioSequenceDao bioSequenceDao)

Method Summary

Modifier and Type	Method	Description
BioSequence	findByAccession(DatabaseEntry accession)
BioSequence	findByCompositeSequence(CompositeSequence compositeSequence)
Map<Gene,Collection<BioSequence>>	findByGenes(Collection<Gene> genes)
Collection<BioSequence>	findByName(String name)
Collection<BioSequence>	findOrCreate(Collection<BioSequence> bioSequences)
Collection<Gene>	getGenesByAccession(String search)
Collection<Gene>	getGenesByName(String search)
Collection<BioSequence>	thaw(Collection<BioSequence> bioSequences)
BioSequence	thaw(BioSequence bioSequence)

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

loadAllValueObjects, loadValueObject, loadValueObjectById, loadValueObjects, loadValueObjectsByIds

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

countAll, create, create, ensureInSession, ensureInSession, find, findOrCreate, findOrFail, getElementClass, load, load, loadAll, loadOrFail, loadOrFail, loadOrFail, loadOrFail, remove, remove, remove, save, save, streamAll, streamAll, 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.BaseImmutableService

create, remove, remove

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

countAll, find, findOrFail, getElementClass, load, load, loadAll, loadOrFail, loadOrFail, loadOrFail, loadOrFail, streamAll, streamAll

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

save, save, update

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

loadAllValueObjects, loadValueObject, loadValueObjectById, loadValueObjects, loadValueObjectsByIds

Methods inherited from interface ubic.gemma.persistence.service.genome.biosequence.BioSequenceService

create, findOrCreate, remove, update

Constructor Details

BioSequenceServiceImpl

@Autowired
public BioSequenceServiceImpl(BioSequenceDao bioSequenceDao)

Method Details

findByAccession

@Transactional(readOnly=true)
public BioSequence findByAccession(DatabaseEntry accession)

Specified by:

findByAccession in interface BioSequenceService

findByGenes

@Transactional(readOnly=true)
public Map<Gene,Collection<BioSequence>> findByGenes(Collection<Gene> genes)

Specified by:

findByGenes in interface BioSequenceService

Parameters:

genes - genes

Returns:

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

findByName

@Transactional(readOnly=true)
public Collection<BioSequence> findByName(String name)

Specified by:

findByName in interface BioSequenceService

Parameters:

name - name

Returns:

all biosequences with names matching the given string. This matches only the name field, not the accession.

findOrCreate

@Transactional(readOnly=true)
public Collection<BioSequence> findOrCreate(Collection<BioSequence> bioSequences)

Specified by:

findOrCreate in interface BioSequenceService

getGenesByAccession

@Transactional(readOnly=true)
public Collection<Gene> getGenesByAccession(String search)

Specified by:

getGenesByAccession in interface BioSequenceService

getGenesByName

@Transactional(readOnly=true)
public Collection<Gene> getGenesByName(String search)

Specified by:

getGenesByName in interface BioSequenceService

thaw

@Transactional(readOnly=true)
public Collection<BioSequence> thaw(Collection<BioSequence> bioSequences)

Specified by:

thaw in interface BioSequenceService

thaw

@Transactional(readOnly=true)
public BioSequence thaw(BioSequence bioSequence)

Specified by:

thaw in interface BioSequenceService

findByCompositeSequence

@Transactional(readOnly=true)
public BioSequence findByCompositeSequence(CompositeSequence compositeSequence)

Specified by:

findByCompositeSequence in interface BioSequenceService