Class BioSequenceServiceImpl
- java.lang.Object
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- ubic.gemma.persistence.service.AbstractService<O>
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- ubic.gemma.persistence.service.AbstractVoEnabledService<BioSequence,BioSequenceValueObject>
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- ubic.gemma.persistence.service.genome.biosequence.BioSequenceServiceImpl
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- 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 forBioSequenceService
, provides access to all services and entities referenced by this service.- Author:
- keshav, pavlidis
- See Also:
BioSequenceService
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Field Summary
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Fields inherited from class ubic.gemma.persistence.service.AbstractService
log
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Constructor Summary
Constructors Constructor Description BioSequenceServiceImpl(BioSequenceDao bioSequenceDao)
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Method Summary
All Methods Instance Methods Concrete Methods 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)
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Methods inherited from class ubic.gemma.persistence.service.AbstractVoEnabledService
loadAllValueObjects, loadValueObject, loadValueObjectById, loadValueObjects, loadValueObjectsByIds
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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, update, update
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Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
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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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Methods inherited from interface ubic.gemma.persistence.service.genome.biosequence.BioSequenceService
create, findOrCreate, remove, update
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Constructor Detail
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BioSequenceServiceImpl
@Autowired public BioSequenceServiceImpl(BioSequenceDao bioSequenceDao)
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Method Detail
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findByAccession
@Transactional(readOnly=true) public BioSequence findByAccession(DatabaseEntry accession)
- Specified by:
findByAccession
in interfaceBioSequenceService
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findByGenes
@Transactional(readOnly=true) public Map<Gene,Collection<BioSequence>> findByGenes(Collection<Gene> genes)
- Specified by:
findByGenes
in interfaceBioSequenceService
- 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
@Transactional(readOnly=true) public Collection<BioSequence> findByName(String name)
- Specified by:
findByName
in interfaceBioSequenceService
- 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
@Transactional(readOnly=true) public Collection<BioSequence> findOrCreate(Collection<BioSequence> bioSequences)
- Specified by:
findOrCreate
in interfaceBioSequenceService
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getGenesByAccession
@Transactional(readOnly=true) public Collection<Gene> getGenesByAccession(String search)
- Specified by:
getGenesByAccession
in interfaceBioSequenceService
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getGenesByName
@Transactional(readOnly=true) public Collection<Gene> getGenesByName(String search)
- Specified by:
getGenesByName
in interfaceBioSequenceService
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thaw
@Transactional(readOnly=true) public Collection<BioSequence> thaw(Collection<BioSequence> bioSequences)
- Specified by:
thaw
in interfaceBioSequenceService
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thaw
@Transactional(readOnly=true) public BioSequence thaw(BioSequence bioSequence)
- Specified by:
thaw
in interfaceBioSequenceService
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findByCompositeSequence
@Transactional(readOnly=true) public BioSequence findByCompositeSequence(CompositeSequence compositeSequence)
- Specified by:
findByCompositeSequence
in interfaceBioSequenceService
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