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

Interface BioSequenceService

All Superinterfaces:

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

All Known Implementing Classes:

BioSequenceServiceImpl

public interface BioSequenceService
extends BaseService<BioSequence>, BaseVoEnabledService<BioSequence,BioSequenceValueObject>

Author:

kelsey

Method Summary

Modifier and Type	Method	Description
BioSequence	create(BioSequence bioSequence)	Creates the given entity in the persistent storage.
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)
BioSequence	findOrCreate(BioSequence bioSequence)	Does a search for the entity in the persistent storage, and if not found, creates it.
Collection<Gene>	getGenesByAccession(String search)
Collection<Gene>	getGenesByName(String search)
void	remove(BioSequence bioSequence)	Removes the given entity from the persistent storage.
Collection<BioSequence>	thaw(Collection<BioSequence> bioSequences)
BioSequence	thaw(BioSequence bs)
void	update(BioSequence bioSequence)	Updates the given entity in the persistent storage.

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, 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

Method Details

findByAccession

BioSequence findByAccession(DatabaseEntry accession)

findByGenes

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

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

Collection<BioSequence> findByName(String name)

Parameters:

name - name

Returns:

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

findOrCreate

@Secured("GROUP_USER")
Collection<BioSequence> findOrCreate(Collection<BioSequence> bioSequences)

findOrCreate

@Secured("GROUP_USER")
BioSequence findOrCreate(BioSequence bioSequence)

Description copied from interface: BaseImmutableService

Does a search for the entity in the persistent storage, and if not found, creates it.

Specified by:

findOrCreate in interface BaseImmutableService<BioSequence>

Parameters:

bioSequence - the entity to look for, and create if not found.

Returns:

the entity retrieved from the persistent storage, either found or created.

create

@Secured("GROUP_USER")
BioSequence create(BioSequence bioSequence)

Description copied from interface: BaseImmutableService

Creates the given entity in the persistent storage.

Specified by:

create in interface BaseImmutableService<BioSequence>

Parameters:

bioSequence - the entity to be created.

Returns:

object referencing the persistent instance of the given entity.

remove

@Secured("GROUP_USER")
void remove(BioSequence bioSequence)

Description copied from interface: BaseImmutableService

Removes the given entity from the persistent storage.

Specified by:

remove in interface BaseImmutableService<BioSequence>

Parameters:

bioSequence - the entity to be removed.

update

@Secured("GROUP_USER")
void update(BioSequence bioSequence)

Description copied from interface: BaseService

Updates the given entity in the persistent storage.

Specified by:

update in interface BaseService<BioSequence>

Parameters:

bioSequence - the entity to be updated.

getGenesByAccession

Collection<Gene> getGenesByAccession(String search)

getGenesByName

Collection<Gene> getGenesByName(String search)

thaw

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

thaw

BioSequence thaw(BioSequence bs)

findByCompositeSequence

BioSequence findByCompositeSequence(CompositeSequence compositeSequence)