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

Class GeneServiceImpl

java.lang.Object

ubic.gemma.persistence.service.AbstractService<O>

ubic.gemma.persistence.service.AbstractFilteringVoEnabledService<Gene,GeneValueObject>

ubic.gemma.persistence.service.genome.gene.GeneServiceImpl

All Implemented Interfaces:

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

@Service
@ParametersAreNonnullByDefault
public class GeneServiceImpl
extends AbstractFilteringVoEnabledService<Gene,GeneValueObject>
implements GeneService

Author:

pavlidis, keshav

See Also:

GeneService

Field Summary

Fields inherited from class ubic.gemma.persistence.service.AbstractService

log

Constructor Summary

Constructors

Constructor	Description
GeneServiceImpl(GeneDao geneDao)

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)
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)
GeneValueObject	loadValueObjectById(Long id)
List<GeneValueObject>	loadValueObjectsByIds(Collection<Long> ids)	Load value objects by a given collection of IDs.
Collection<GeneValueObject>	loadValueObjectsByIdsLiter(Collection<Long> ids)
int	removeAll()
Collection<GeneValueObject>	searchGenes(String query, Long taxonId)	Search for genes (by name or symbol)
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 class ubic.gemma.persistence.service.AbstractFilteringVoEnabledService

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

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

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

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, loadValueObjects

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

count, 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

Methods inherited from interface ubic.gemma.persistence.service.genome.gene.GeneService

create, remove

Constructor Detail

GeneServiceImpl

@Autowired
public GeneServiceImpl(GeneDao geneDao)

Method Detail

find

@Transactional(readOnly=true)
public Collection<Gene> find(PhysicalLocation physicalLocation)

Description copied from interface: GeneService

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.

Specified by:

find in interface GeneService

Parameters:

physicalLocation - physical location of gene

Returns:

all genes at given location

findByAccession

@Transactional(readOnly=true)
public Gene findByAccession(String accession,
                            @Nullable
                            ExternalDatabase source)

Specified by:

findByAccession in interface GeneService

findByAlias

@Transactional(readOnly=true)
public Collection<Gene> findByAlias(String search)

Specified by:

findByAlias in interface GeneService

findByEnsemblId

@Transactional(readOnly=true)
public Gene findByEnsemblId(String exactString)

Description copied from interface: GeneService

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.

Specified by:

findByEnsemblId in interface GeneService

Parameters:

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

Returns:

a Gene with the given Ensembl ID.

findByNCBIId

@Transactional(readOnly=true)
public Gene findByNCBIId(Integer accession)

Specified by:

findByNCBIId in interface GeneService

findByNCBIIdValueObject

@Transactional(readOnly=true)
public GeneValueObject findByNCBIIdValueObject(Integer accession)

Specified by:

findByNCBIIdValueObject in interface GeneService

findByNcbiIds

@Transactional(readOnly=true)
public Map<Integer,GeneValueObject> findByNcbiIds(Collection<Integer> ncbiIds)

Description copied from interface: GeneService

Quickly load exact matches.

Specified by:

findByNcbiIds in interface GeneService

Parameters:

ncbiIds - ncbi IDs

Returns:

map of NCBI Id to the gene.

findByOfficialName

@Transactional(readOnly=true)
public Collection<Gene> findByOfficialName(String officialName)

Specified by:

findByOfficialName in interface GeneService

findByOfficialNameInexact

@Transactional(readOnly=true)
public Collection<Gene> findByOfficialNameInexact(String officialName)

Specified by:

findByOfficialNameInexact in interface GeneService

findByOfficialSymbol

@Transactional(readOnly=true)
public Collection<Gene> findByOfficialSymbol(String officialSymbol)

Specified by:

findByOfficialSymbol in interface GeneService

findByOfficialSymbol

@Transactional(readOnly=true)
public Gene findByOfficialSymbol(String symbol,
                                 Taxon taxon)

Specified by:

findByOfficialSymbol in interface GeneService

findByOfficialSymbolInexact

@Transactional(readOnly=true)
public Collection<Gene> findByOfficialSymbolInexact(String officialSymbol)

Specified by:

findByOfficialSymbolInexact in interface GeneService

findByOfficialSymbols

@Transactional(readOnly=true)
public Map<String,GeneValueObject> findByOfficialSymbols(Collection<String> query,
                                                               Long taxonId)

Description copied from interface: GeneService

Quickly load exact matches.

Specified by:

findByOfficialSymbols in interface GeneService

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

@Transactional(readOnly=true)
public Collection<AnnotationValueObject> findGOTerms(Long geneId)

Specified by:

findGOTerms in interface GeneService

getCompositeSequenceCountById

@Transactional(readOnly=true)
public long getCompositeSequenceCountById(Long id)

Specified by:

getCompositeSequenceCountById in interface GeneService

getCompositeSequences

@Transactional(readOnly=true)
public Collection<CompositeSequence> getCompositeSequences(Gene gene,
                                                           ArrayDesign arrayDesign)

Description copied from interface: GeneService

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

Specified by:

getCompositeSequences in interface GeneService

Parameters:

gene - gene

arrayDesign - platform

Returns:

composite sequences

getCompositeSequencesById

@Transactional(readOnly=true)
public Collection<CompositeSequence> getCompositeSequencesById(Long id)

Specified by:

getCompositeSequencesById in interface GeneService

Parameters:

id - Gemma gene id

Returns:

Return probes for a given gene id.

getPhysicalLocationsValueObjects

@Transactional(readOnly=true)
public List<PhysicalLocationValueObject> getPhysicalLocationsValueObjects(Gene gene)

Specified by:

getPhysicalLocationsValueObjects in interface GeneService

getProducts

@Transactional(readOnly=true)
public Collection<GeneProductValueObject> getProducts(Long geneId)

Specified by:

getProducts in interface GeneService

Parameters:

geneId - gene id

Returns:

empty collection if no products

loadAll

@Transactional(readOnly=true)
public Collection<Gene> loadAll(Taxon taxon)

Specified by:

loadAll in interface GeneService

Parameters:

taxon - taxon

Returns:

a collection of genes for the specified taxon

loadFullyPopulatedValueObject

@Transactional(readOnly=true)
public GeneValueObject loadFullyPopulatedValueObject(Long id)

Description copied from interface: GeneService

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

Specified by:

loadFullyPopulatedValueObject in interface GeneService

Parameters:

id - The gene id

Returns:

GeneDetailsValueObject a representation of that gene

loadGenePhenotypes

@Transactional(readOnly=true)
public GeneValueObject loadGenePhenotypes(Long geneId)

Specified by:

loadGenePhenotypes in interface GeneService

loadMicroRNAs

@Transactional(readOnly=true)
public Collection<Gene> loadMicroRNAs(Taxon taxon)

Specified by:

loadMicroRNAs in interface GeneService

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

@Transactional(readOnly=true)
public Collection<Gene> loadThawed(Collection<Long> ids)

Description copied from interface: GeneService

Load with objects already thawed.

Specified by:

loadThawed in interface GeneService

Parameters:

ids - ids

Returns:

pre-thawed genes

loadThawedLiter

@Transactional(readOnly=true)
public Collection<Gene> loadThawedLiter(Collection<Long> ids)

Specified by:

loadThawedLiter in interface GeneService

loadValueObjectById

@Transactional(readOnly=true)
public GeneValueObject loadValueObjectById(Long id)

Specified by:

loadValueObjectById in interface BaseVoEnabledService<Gene,GeneValueObject>

Overrides:

loadValueObjectById in class AbstractFilteringVoEnabledService<Gene,GeneValueObject>

See Also:

BaseVoEnabledDao.loadValueObjectById(Long)

loadValueObjectsByIds

@Transactional(readOnly=true)
public List<GeneValueObject> loadValueObjectsByIds(Collection<Long> ids)

Description copied from interface: BaseVoEnabledService

Load value objects by a given collection of IDs.

Specified by:

loadValueObjectsByIds in interface BaseVoEnabledService<Gene,GeneValueObject>

Overrides:

loadValueObjectsByIds in class AbstractFilteringVoEnabledService<Gene,GeneValueObject>

loadValueObjectsByIdsLiter

@Transactional(readOnly=true)
public Collection<GeneValueObject> loadValueObjectsByIdsLiter(Collection<Long> ids)

Specified by:

loadValueObjectsByIdsLiter in interface GeneService

thaw

@Transactional(readOnly=true)
public Gene thaw(Gene gene)

Specified by:

thaw in interface GeneService

thawAliases

@Transactional(readOnly=true)
public Gene thawAliases(Gene gene)

Specified by:

thawAliases in interface GeneService

Parameters:

gene - gene

Returns:

thaw the Aliases, very light version

thawLite

@Transactional(readOnly=true)
public Collection<Gene> thawLite(Collection<Gene> genes)

Specified by:

thawLite in interface GeneService

thawLite

@Transactional(readOnly=true)
public Gene thawLite(Gene gene)

Specified by:

thawLite in interface GeneService

thawLiter

@Transactional(readOnly=true)
public Gene thawLiter(Gene gene)

Specified by:

thawLiter in interface GeneService

searchGenes

@Transactional(readOnly=true)
public Collection<GeneValueObject> searchGenes(String query,
                                               Long taxonId)
                                        throws SearchException

Search for genes (by name or symbol)

Specified by:

searchGenes in interface GeneService

Parameters:

taxonId - , can be null to not constrain by taxon

Returns:

Collection of Gene entity objects

Throws:

SearchException

removeAll

@Transactional
public int removeAll()

Specified by:

removeAll in interface GeneService