Package ubic.gemma.persistence.service.genome

Interface GeneDao

All Superinterfaces:

BaseDao<Gene>, BaseVoEnabledDao<Gene,GeneValueObject>, FilteringDao<Gene>, FilteringVoEnabledDao<Gene,GeneValueObject>

All Known Implementing Classes:

GeneDaoImpl

public interface GeneDao
extends FilteringVoEnabledDao<Gene,GeneValueObject>

See Also:

Gene

Field Summary

Fields

Modifier and Type	Field	Description
static String	OBJECT_ALIAS

Method Summary

Modifier and Type	Method	Description
Collection<Gene>	find(PhysicalLocation physicalLocation)	Find all genes at a physical location.
Gene	findByAccession(String accession, ExternalDatabase source)
Collection<Gene>	findByAlias(String search)	Locate genes that match the given alias string
Gene	findByEnsemblId(String exactString)
Gene	findByNcbiId(Integer accession)
Map<Integer,Gene>	findByNcbiIds(Collection<Integer> ncbiIds)	Quickly load exact matches.
Collection<Gene>	findByOfficialName(String officialName)
Collection<Gene>	findByOfficialNameInexact(String officialName)
Collection<Gene>	findByOfficialSymbol(String officialSymbol)
Gene	findByOfficialSymbol(String symbol, Taxon taxon)
Collection<Gene>	findByOfficialSymbolInexact(String officialSymbol)
Map<String,Gene>	findByOfficialSymbols(Collection<String> query, Long taxonId)	Quickly load exact matches.
Collection<Gene>	findByPhysicalLocation(PhysicalLocation location)	Deprecated.
long	getCompositeSequenceCountById(long id)
Collection<CompositeSequence>	getCompositeSequences(Gene gene, ArrayDesign arrayDesign)
Collection<CompositeSequence>	getCompositeSequencesById(long id)
Collection<Gene>	getGenesByTaxon(Taxon taxon)
Collection<Gene>	getMicroRnaByTaxon(Taxon taxon)
int	getPlatformCountById(Long id)
Collection<Gene>	loadKnownGenes(Taxon taxon)
List<Gene>	loadThawed(Collection<Long> ids)
Collection<Gene>	loadThawedLiter(Collection<Long> ids)
int	removeAll()
Gene	thaw(Gene gene)
Gene	thawAliases(Gene gene)
Collection<Gene>	thawLite(Collection<Gene> genes)
Gene	thawLite(Gene gene)
Gene	thawLiter(Gene gene)

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

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

loadAllValueObjects, loadValueObject, loadValueObjectById, loadValueObjects, loadValueObjectsByIds

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

count, getFilter, getFilter, getFilter, getFilter, getFilterableProperties, getFilterablePropertyAllowedValues, getFilterablePropertyDescription, getFilterablePropertyIsUsingSubquery, getFilterablePropertyType, getSort, load, load, loadIds

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

loadValueObjects, loadValueObjects

Field Detail

OBJECT_ALIAS

static final String OBJECT_ALIAS

See Also:

Constant Field Values

Method Detail

find

Collection<Gene> find(PhysicalLocation physicalLocation)

Find all genes at a physical location. All overlapping genes are returned. The location can be a point or a region. If strand is non-null, only genes on the same strand are returned.

Parameters:

physicalLocation - physical location

Returns:

found genes

findByAccession

Gene findByAccession(String accession,
                     @Nullable
                     ExternalDatabase source)

findByAlias

Collection<Gene> findByAlias(String search)

Locate genes that match the given alias string

Parameters:

search - search string

Returns:

found genes

findByEnsemblId

Gene findByEnsemblId(String exactString)

findByNcbiId

Gene findByNcbiId(Integer accession)

findByOfficialSymbol

Collection<Gene> findByOfficialSymbol(String officialSymbol)

findByOfficialName

Collection<Gene> findByOfficialName(String officialName)

findByOfficialNameInexact

Collection<Gene> findByOfficialNameInexact(String officialName)

findByOfficialSymbol

Gene findByOfficialSymbol(String symbol,
                          Taxon taxon)

findByOfficialSymbolInexact

Collection<Gene> findByOfficialSymbolInexact(String officialSymbol)

findByOfficialSymbols

Map<String,Gene> findByOfficialSymbols(Collection<String> query,
                                             Long taxonId)

Quickly load exact matches.

Parameters:

query - query

taxonId - taxon id

Returns:

map of gene symbol (toLowerCase()) to the gene. The actual query that led to the gene is not retained.

findByNcbiIds

Map<Integer,Gene> findByNcbiIds(Collection<Integer> ncbiIds)

Quickly load exact matches.

Parameters:

ncbiIds - ncbi ids

Returns:

map of NCBI Id to the gene.

findByPhysicalLocation

@Deprecated
Collection<Gene> findByPhysicalLocation(PhysicalLocation location)

Deprecated.

getCompositeSequenceCountById

long getCompositeSequenceCountById(long id)

Parameters:

id - id

Returns:

how many platform elements (e.g. probes) represent this gene, totalled up over all platforms.

getCompositeSequences

Collection<CompositeSequence> getCompositeSequences(Gene gene,
                                                    ArrayDesign arrayDesign)

getCompositeSequencesById

Collection<CompositeSequence> getCompositeSequencesById(long id)

getGenesByTaxon

Collection<Gene> getGenesByTaxon(Taxon taxon)

Parameters:

taxon - taxon

Returns:

a collections of genes that match the given taxon

getMicroRnaByTaxon

Collection<Gene> getMicroRnaByTaxon(Taxon taxon)

Parameters:

taxon - taxon

Returns:

a collection of genes that are actually MicroRNA for a given taxon

getPlatformCountById

int getPlatformCountById(Long id)

Parameters:

id - id

Returns:

how many platforms have a representation of this gene

loadKnownGenes

Collection<Gene> loadKnownGenes(Taxon taxon)

Parameters:

taxon - taxon

Returns:

a collection of genes for the specified taxon (not all genes, ie not probe aligned regions and predicted genes)

loadThawed

List<Gene> loadThawed(Collection<Long> ids)

loadThawedLiter

Collection<Gene> loadThawedLiter(Collection<Long> ids)

thaw

Gene thaw(Gene gene)

thawAliases

Gene thawAliases(Gene gene)

thawLite

Collection<Gene> thawLite(Collection<Gene> genes)

thawLite

Gene thawLite(Gene gene)

thawLiter

Gene thawLiter(Gene gene)

removeAll

int removeAll()