Package ubic.gemma.persistence.service.genome.gene

Interface GeneService

All Superinterfaces:

BaseImmutableService<Gene>, BaseReadOnlyService<Gene>, BaseService<Gene>, BaseVoEnabledService<Gene,GeneValueObject>, FilteringService<Gene>, FilteringVoEnabledService<Gene,GeneValueObject>

All Known Implementing Classes:

GeneServiceImpl

@ParametersAreNonnullByDefault
public interface GeneService
extends BaseService<Gene>, FilteringVoEnabledService<Gene,GeneValueObject>

Author:

kelsey

Method Summary

Modifier and Type	Method	Description
Gene	create(Gene gene)	Creates the given entity in the persistent storage.
Collection<Gene>	find(PhysicalLocation physicalLocation)	Find all genes at a physical location.
Gene	findByAccession(String accession, ExternalDatabase source)
Collection<Gene>	findByAlias(String search)
Gene	findByEnsemblId(String exactString)	Searches for a gene based on its ensembl ID.
Gene	findByNCBIId(Integer accession)
Map<Integer,GeneValueObject>	findByNcbiIds(Collection<Integer> ncbiIds)	Quickly load exact matches.
GeneValueObject	findByNCBIIdValueObject(Integer accession)
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,GeneValueObject>	findByOfficialSymbols(Collection<String> query, Long taxonId)	Quickly load exact matches.
Collection<AnnotationValueObject>	findGOTerms(Long geneId)
long	getCompositeSequenceCountById(Long id)
Collection<CompositeSequence>	getCompositeSequences(Gene gene, ArrayDesign arrayDesign)	Returns a list of compositeSequences associated with the given gene and array design
Collection<CompositeSequence>	getCompositeSequencesById(Long id)
List<PhysicalLocationValueObject>	getPhysicalLocationsValueObjects(Gene gene)
Collection<GeneProductValueObject>	getProducts(Long geneId)
Collection<Gene>	loadAll(Taxon taxon)
GeneValueObject	loadFullyPopulatedValueObject(Long id)	Returns a detailVO for a geneDd This method may be unnecessary now that we have put all the logic into the GeneService
GeneValueObject	loadGenePhenotypes(Long geneId)
Collection<Gene>	loadMicroRNAs(Taxon taxon)
Collection<Gene>	loadThawed(Collection<Long> ids)	Load with objects already thawed.
Collection<Gene>	loadThawedLiter(Collection<Long> ids)
Collection<GeneValueObject>	loadValueObjectsByIdsLiter(Collection<Long> ids)
void	remove(Gene gene)	Removes the given entity from the persistent storage.
int	removeAll()
Collection<GeneValueObject>	searchGenes(String query, Long taxonId)
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.BaseImmutableService

create, findOrCreate, remove, remove

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

countAll, find, findOrFail, getElementClass, load, load, loadAll, loadOrFail, loadOrFail, loadOrFail, loadOrFail

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

save, save, update, update

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

loadAllValueObjects, loadValueObject, loadValueObjectById, loadValueObjects, loadValueObjectsByIds

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

count, getFilter, getFilter, getFilter, getFilter, getFilter, getFilter, getFilterableProperties, getFilterablePropertyAllowedValues, getFilterablePropertyConfigAttributes, getFilterablePropertyDescription, getFilterablePropertyIsUsingSubquery, getFilterablePropertyResolvableAllowedValuesLabels, getFilterablePropertyType, getIdentifierPropertyName, getSort, load, load, loadIds

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

loadValueObjects, loadValueObjects

Method Detail

create

@Secured("GROUP_ADMIN")
Gene create(Gene gene)

Description copied from interface: BaseImmutableService

Creates the given entity in the persistent storage.

Specified by:

create in interface BaseImmutableService<Gene>

Parameters:

gene - the entity to be created.

Returns:

object referencing the persistent instance of the given entity.

remove

@Secured("GROUP_ADMIN")
void remove(Gene gene)

Description copied from interface: BaseImmutableService

Removes the given entity from the persistent storage.

Specified by:

remove in interface BaseImmutableService<Gene>

Parameters:

gene - the entity to be removed.

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 of gene

Returns:

all genes at given location

findByAccession

Gene findByAccession(String accession,
                     @Nullable
                     ExternalDatabase source)

findByAlias

Collection<Gene> findByAlias(String search)

findByEnsemblId

Gene findByEnsemblId(String exactString)

Searches for a gene based on its ensembl ID. There is a small amount of genes in our database that have duplicate ensembl IDs. These genes are believed to be somehow unusable anyway, so we ignore those cases at the moment - Aug. 11th 2017.

Parameters:

exactString - the ensembl ID that the gene will be looked up by.

Returns:

a Gene with the given Ensembl ID.

findByNCBIId

Gene findByNCBIId(Integer accession)

findByNCBIIdValueObject

GeneValueObject findByNCBIIdValueObject(Integer accession)

findByNcbiIds

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

Quickly load exact matches.

Parameters:

ncbiIds - ncbi IDs

Returns:

map of NCBI Id to the gene.

findByOfficialName

Collection<Gene> findByOfficialName(String officialName)

findByOfficialNameInexact

Collection<Gene> findByOfficialNameInexact(String officialName)

findByOfficialSymbol

Collection<Gene> findByOfficialSymbol(String officialSymbol)

findByOfficialSymbol

Gene findByOfficialSymbol(String symbol,
                          Taxon taxon)

findByOfficialSymbolInexact

Collection<Gene> findByOfficialSymbolInexact(String officialSymbol)

findByOfficialSymbols

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

Quickly load exact matches.

Parameters:

query - query

taxonId - taxon id

Returns:

map of lower-cased gene symbol to the gene. The actual query that led to the gene is not retained.

findGOTerms

Collection<AnnotationValueObject> findGOTerms(Long geneId)

getCompositeSequenceCountById

long getCompositeSequenceCountById(Long id)

getCompositeSequences

@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","AFTER_ACL_ARRAYDESIGN_COLLECTION_READ"})
Collection<CompositeSequence> getCompositeSequences(Gene gene,
                                                    ArrayDesign arrayDesign)

Returns a list of compositeSequences associated with the given gene and array design

Parameters:

gene - gene

arrayDesign - platform

Returns:

composite sequences

getCompositeSequencesById

@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","AFTER_ACL_ARRAYDESIGN_COLLECTION_READ"})
Collection<CompositeSequence> getCompositeSequencesById(Long id)

Parameters:

id - Gemma gene id

Returns:

Return probes for a given gene id.

getPhysicalLocationsValueObjects

List<PhysicalLocationValueObject> getPhysicalLocationsValueObjects(Gene gene)

getProducts

Collection<GeneProductValueObject> getProducts(Long geneId)

Parameters:

geneId - gene id

Returns:

empty collection if no products

loadAll

Collection<Gene> loadAll(Taxon taxon)

Parameters:

taxon - taxon

Returns:

a collection of genes for the specified taxon

loadFullyPopulatedValueObject

GeneValueObject loadFullyPopulatedValueObject(Long id)

Returns a detailVO for a geneDd This method may be unnecessary now that we have put all the logic into the GeneService

Parameters:

id - The gene id

Returns:

GeneDetailsValueObject a representation of that gene

loadGenePhenotypes

GeneValueObject loadGenePhenotypes(Long geneId)

loadMicroRNAs

Collection<Gene> loadMicroRNAs(Taxon taxon)

Parameters:

taxon - taxon

Returns:

all the microRNAs for a given taxon. Note query could be slow or inexact due to use of wild card searching of the genes description

loadThawed

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

Load with objects already thawed.

Parameters:

ids - ids

Returns:

pre-thawed genes

loadThawedLiter

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

loadValueObjectsByIdsLiter

Collection<GeneValueObject> loadValueObjectsByIdsLiter(Collection<Long> ids)

thaw

Gene thaw(Gene gene)

thawAliases

Gene thawAliases(Gene gene)

Parameters:

gene - gene

Returns:

thaw the Aliases, very light version

thawLite

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

thawLite

Gene thawLite(Gene gene)

thawLiter

Gene thawLiter(Gene gene)

searchGenes

Collection<GeneValueObject> searchGenes(String query,
                                        Long taxonId)
                                 throws SearchException

Throws:

SearchException

removeAll

@Secured("GROUP_ADMIN")
int removeAll()