Interface BioSequenceDao
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- All Superinterfaces:
BaseDao<BioSequence>
,BaseVoEnabledDao<BioSequence,BioSequenceValueObject>
- All Known Implementing Classes:
BioSequenceDaoImpl
public interface BioSequenceDao extends BaseVoEnabledDao<BioSequence,BioSequenceValueObject>
- See Also:
BioSequence
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Method Summary
All Methods Instance Methods Abstract Methods Modifier and Type Method Description BioSequence
findByAccession(DatabaseEntry accession)
BioSequence
findByCompositeSequence(CompositeSequence compositeSequence)
Map<Gene,Collection<BioSequence>>
findByGenes(Collection<Gene> genes)
Returns matching biosequences for the given genes in a Map (gene to biosequences).Collection<BioSequence>
findByName(String name)
Collection<Gene>
getGenesByAccession(String search)
Collection<Gene>
getGenesByName(String search)
For a biosequence name, get the genesCollection<BioSequence>
thaw(Collection<BioSequence> bioSequences)
BioSequence
thaw(BioSequence bioSequence)
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Methods inherited from interface ubic.gemma.persistence.service.BaseDao
countAll, create, create, find, findOrCreate, getElementClass, getIdentifierPropertyName, load, load, loadAll, loadReference, loadReference, remove, remove, remove, save, save, update, update
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Methods inherited from interface ubic.gemma.persistence.service.BaseVoEnabledDao
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)
Returns matching biosequences for the given genes in a Map (gene to biosequences). Genes which had no associated sequences are not included in the result.
- Parameters:
genes
- genes- Returns:
- map to biosequences
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findByName
Collection<BioSequence> findByName(String name)
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getGenesByAccession
Collection<Gene> getGenesByAccession(String search)
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getGenesByName
Collection<Gene> getGenesByName(String search)
For a biosequence name, get the genes- Parameters:
search
- name- Returns:
- genes
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thaw
Collection<BioSequence> thaw(Collection<BioSequence> bioSequences)
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thaw
BioSequence thaw(BioSequence bioSequence)
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findByCompositeSequence
BioSequence findByCompositeSequence(CompositeSequence compositeSequence)
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