Interface BioSequenceService
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- 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
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Method Summary
All Methods Instance Methods Abstract Methods 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
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Methods inherited from interface ubic.gemma.persistence.service.BaseReadOnlyService
countAll, find, findOrFail, getElementClass, load, load, loadAll, loadOrFail, loadOrFail, loadOrFail, loadOrFail
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Methods inherited from interface ubic.gemma.persistence.service.BaseService
save, save, update
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Methods inherited from interface ubic.gemma.persistence.service.BaseVoEnabledService
loadAllValueObjects, loadValueObject, loadValueObjectById, loadValueObjects, loadValueObjectsByIds
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Method Detail
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findByAccession
BioSequence findByAccession(DatabaseEntry accession)
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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.
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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.
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findOrCreate
@Secured("GROUP_USER") Collection<BioSequence> findOrCreate(Collection<BioSequence> bioSequences)
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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 interfaceBaseImmutableService<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.
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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 interfaceBaseImmutableService<BioSequence>
- Parameters:
bioSequence
- the entity to be created.- Returns:
- object referencing the persistent instance of the given entity.
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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 interfaceBaseImmutableService<BioSequence>
- Parameters:
bioSequence
- the entity to be removed.
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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 interfaceBaseService<BioSequence>
- Parameters:
bioSequence
- the entity to be updated.
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getGenesByAccession
Collection<Gene> getGenesByAccession(String search)
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getGenesByName
Collection<Gene> getGenesByName(String search)
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thaw
Collection<BioSequence> thaw(Collection<BioSequence> bioSequences)
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thaw
BioSequence thaw(BioSequence bs)
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findByCompositeSequence
BioSequence findByCompositeSequence(CompositeSequence compositeSequence)
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