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

Interface BioSequenceDao

All Superinterfaces:

BaseDao<BioSequence>, BaseVoEnabledDao<BioSequence,BioSequenceValueObject>

All Known Implementing Classes:

BioSequenceDaoImpl

public interface BioSequenceDao
extends BaseVoEnabledDao<BioSequence,BioSequenceValueObject>

See Also:

• BioSequence

Method Summary

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

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

countAll, create, create, find, findOrCreate, getElementClass, getIdentifierPropertyName, load, load, loadAll, loadReference, loadReference, reload, reload, remove, remove, remove, save, save, streamAll, streamAll, update, update

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

loadAllValueObjects, loadValueObject, loadValueObjectById, loadValueObjects, loadValueObjectsByIds

Method Details

findByAccession

BioSequence findByAccession(DatabaseEntry accession)

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

findByName

Collection<BioSequence> findByName(String name)

getGenesByAccession

Collection<Gene> getGenesByAccession(String search)

getGenesByName

Collection<Gene> getGenesByName(String search)

For a biosequence name, get the genes

Parameters:

search - name

Returns:

genes

thaw

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

thaw

BioSequence thaw(BioSequence bioSequence)

findByCompositeSequence

BioSequence findByCompositeSequence(CompositeSequence compositeSequence)