Package ubic.gemma.persistence.service.genome.sequenceAnalysis

Class AnnotationAssociationServiceImpl

java.lang.Object

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

ubic.gemma.persistence.service.genome.sequenceAnalysis.AnnotationAssociationServiceImpl

All Implemented Interfaces:

BaseImmutableService<AnnotationAssociation>, BaseReadOnlyService<AnnotationAssociation>, BaseService<AnnotationAssociation>, AnnotationAssociationService

@Service
public class AnnotationAssociationServiceImpl
extends AbstractService<AnnotationAssociation>
implements AnnotationAssociationService

Field Summary

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

log

Constructor Summary

Constructors

Constructor	Description
AnnotationAssociationServiceImpl(AnnotationAssociationDao annotationAssociationDao)

Method Summary

Modifier and Type	Method	Description
Collection<AnnotationAssociation>	find(BioSequence bioSequence)
Collection<AnnotationAssociation>	find(Gene gene)
Collection<AnnotationValueObject>	removeRootTerms(Collection<AnnotationValueObject> associations)	Remove root terms, like "molecular_function", "biological_process" and "cellular_component" Also removes any null objects.

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, 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.genome.sequenceAnalysis.AnnotationAssociationService

create, remove, remove

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

create, findOrCreate, remove

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

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

Constructor Details

AnnotationAssociationServiceImpl

@Autowired
public AnnotationAssociationServiceImpl(AnnotationAssociationDao annotationAssociationDao)

Method Details

find

@Transactional(readOnly=true)
public Collection<AnnotationAssociation> find(BioSequence bioSequence)

Specified by:

find in interface AnnotationAssociationService

find

@Transactional(readOnly=true)
public Collection<AnnotationAssociation> find(Gene gene)

Specified by:

find in interface AnnotationAssociationService

removeRootTerms

@Transactional
public Collection<AnnotationValueObject> removeRootTerms(Collection<AnnotationValueObject> associations)

Remove root terms, like "molecular_function", "biological_process" and "cellular_component" Also removes any null objects.

Specified by:

removeRootTerms in interface AnnotationAssociationService

Returns:

cleaned up associations