Package ubic.gemma.persistence.service.genome

Class GeneDaoImpl

java.lang.Object

ubic.gemma.persistence.service.AbstractDao<Gene>

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

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

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

ubic.gemma.persistence.service.genome.GeneDaoImpl

All Implemented Interfaces:

org.springframework.beans.factory.InitializingBean, BaseDao<Gene>, BaseVoEnabledDao<Gene,GeneValueObject>, CachedFilteringDao<Gene>, CachedFilteringVoEnabledDao<Gene,GeneValueObject>, FilteringDao<Gene>, FilteringVoEnabledDao<Gene,GeneValueObject>, GeneDao

@Repository
public class GeneDaoImpl
extends AbstractQueryFilteringVoEnabledDao<Gene,GeneValueObject>
implements GeneDao, org.springframework.beans.factory.InitializingBean

Base Spring DAO Class: is able to create, update, remove, load, and find objects of type Gene.

See Also:

• Gene

Nested Class Summary

Nested classes/interfaces inherited from class ubic.gemma.persistence.service.AbstractFilteringVoEnabledDao

AbstractFilteringVoEnabledDao.FilterablePropertiesConfigurer, AbstractFilteringVoEnabledDao.FilterablePropertyMeta

Field Summary

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

REPORT_SLOW_QUERY_AFTER_MS

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

log

Fields inherited from interface ubic.gemma.persistence.service.genome.GeneDao

OBJECT_ALIAS

Constructor Summary

Constructors

Constructor	Description
GeneDaoImpl(SessionFactory sessionFactory)

Method Summary

Modifier and Type	Method	Description
protected GeneValueObject	doLoadValueObject(Gene entity)	Load a value object for a given entity.
Gene	find(Gene gene)	Does a look up for the given entity in the persistent storage, usually looking for a specific identifier ( either id or a string property).
Collection<Gene>	find(PhysicalLocation physicalLocation)	Find all genes at a physical location.
Gene	findByAccession(String accession, ExternalDatabase source)
Collection<Gene>	findByAlias(String search)	Gets all the genes referred to by the alias defined by the search string.
Gene	findByEnsemblId(String id)
Gene	findByNcbiId(Integer ncbiId)
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)
long	getCompositeSequenceCount(Gene gene, boolean includeDummyProducts)	Obtain the number of platform elements (e.g.
long	getCompositeSequenceCountById(long id, boolean includeDummyProducts)	Gets a count of the CompositeSequences related to the gene identified by the given id.
Collection<CompositeSequence>	getCompositeSequences(Gene gene, boolean includeDummyProducts)	Get the composite sequences (e.g.
Collection<CompositeSequence>	getCompositeSequences(Gene gene, ArrayDesign arrayDesign, boolean includeDummyProducts)	Get the composite sequences (e.g.
Collection<CompositeSequence>	getCompositeSequencesById(long id, boolean includeDummyProducts)	Gets all the CompositeSequences related to the gene identified by the given id.
protected Query	getFilteringCountQuery(Filters filters)	Produce a query that will be used to retrieve the size of AbstractQueryFilteringVoEnabledDao.getFilteringQuery(Filters, Sort).
protected Query	getFilteringQuery(Filters filters, Sort sort)	Produce a query for retrieving value objects after applying a set of filters and a given ordering.
Collection<Gene>	getMicroRnaByTaxon(Taxon taxon)
long	getPlatformCountById(Long id, boolean includeDummyProducts)
protected void	initializeCachedFilteringResult(Gene entity)	Initialize a result from AbstractQueryFilteringVoEnabledDao.getFilteringQuery(Filters, Sort) retrieved from the Hibernate StandardQueryCache.
Collection<Gene>	loadKnownGenes(Taxon taxon)
List<Gene>	loadThawed(Collection<Long> ids)
Collection<Gene>	loadThawedLiter(Collection<Long> ids)
protected void	postProcessValueObjects(List<GeneValueObject> geneValueObjects)	Post-process VOs in bulk.
void	remove(Gene gene)	Remove a persistent instance
int	removeAll()
Gene	thaw(Gene gene)
Gene	thawAliases(Gene gene)	Only thaw the Aliases, very light version
Collection<Gene>	thawLite(Collection<Gene> genes)
Gene	thawLite(Gene gene)
Gene	thawLiter(Gene gene)

Methods inherited from class ubic.gemma.persistence.service.AbstractQueryFilteringVoEnabledDao

count, countWithCache, getEntityTransformer, getFilteringIdQuery, getValueObjectTransformer, load, load, loadIds, loadIdsWithCache, loadValueObjects, loadValueObjects, loadValueObjectsWithCache, loadValueObjectsWithCache, loadWithCache, loadWithCache

Methods inherited from class ubic.gemma.persistence.service.AbstractFilteringVoEnabledDao

afterPropertiesSet, configureFilterableProperties, getFilter, getFilter, getFilter, getFilter, getFilter, getFilter, getFilterableProperties, getFilterablePropertyAllowedValues, getFilterablePropertyDescription, getFilterablePropertyMeta, getFilterablePropertyType, getSort, isFilterablePropertyDeprecated, isFilterablePropertyUsingSubquery, resolveFilterablePropertyMeta, resolveFilterablePropertyMeta

Methods inherited from class ubic.gemma.persistence.service.AbstractVoEnabledDao

doLoadValueObjects, loadAllValueObjects, loadValueObject, loadValueObjectById, loadValueObjects, loadValueObjectsByIds

Methods inherited from class ubic.gemma.persistence.service.AbstractDao

countAll, create, create, findByProperty, findByPropertyIn, findOneByProperty, findOrCreate, getBatchSize, getElementClass, getEntityName, getIdentifierPropertyName, getSessionFactory, load, load, loadAll, loadReference, loadReference, reload, reload, remove, remove, save, save, streamAll, streamAll, streamQuery, 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.BaseDao

countAll, create, create, findOrCreate, getElementClass, load, load, loadAll, loadReference, loadReference, reload, reload, remove, remove, save, save, streamAll, streamAll, 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, getFilter, getFilter, getFilterableProperties, getFilterablePropertyAllowedValues, getFilterablePropertyDescription, getFilterablePropertyType, getSort, isFilterablePropertyDeprecated, isFilterablePropertyUsingSubquery, load, load, loadIds

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

loadValueObjects, loadValueObjects

Methods inherited from interface org.springframework.beans.factory.InitializingBean

afterPropertiesSet

Constructor Details

GeneDaoImpl

@Autowired
public GeneDaoImpl(SessionFactory sessionFactory)

Method Details

find

public Collection<Gene> find(PhysicalLocation physicalLocation)

Description copied from interface: GeneDao

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 GeneDao

Parameters:

physicalLocation - physical location

Returns:

found genes

findByAccession

public Gene findByAccession(String accession,
 @Nullable
 ExternalDatabase source)

Specified by:

findByAccession in interface GeneDao

findByAlias

public Collection<Gene> findByAlias(String search)

Gets all the genes referred to by the alias defined by the search string.

Specified by:

findByAlias in interface GeneDao

Parameters:

search - search string

Returns:

Collection

findByEnsemblId

public Gene findByEnsemblId(String id)

Specified by:

findByEnsemblId in interface GeneDao

findByNcbiId

public Gene findByNcbiId(Integer ncbiId)

Specified by:

findByNcbiId in interface GeneDao

findByOfficialSymbol

public Collection<Gene> findByOfficialSymbol(String officialSymbol)

Specified by:

findByOfficialSymbol in interface GeneDao

findByOfficialName

public Collection<Gene> findByOfficialName(String officialName)

Specified by:

findByOfficialName in interface GeneDao

findByOfficialNameInexact

public Collection<Gene> findByOfficialNameInexact(String officialName)

Specified by:

findByOfficialNameInexact in interface GeneDao

findByOfficialSymbol

public Gene findByOfficialSymbol(String symbol,
 Taxon taxon)

Specified by:

findByOfficialSymbol in interface GeneDao

findByOfficialSymbolInexact

public Collection<Gene> findByOfficialSymbolInexact(String officialSymbol)

Specified by:

findByOfficialSymbolInexact in interface GeneDao

findByOfficialSymbols

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

Description copied from interface: GeneDao

Quickly load exact matches.

Specified by:

findByOfficialSymbols in interface GeneDao

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

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

Description copied from interface: GeneDao

Quickly load exact matches.

Specified by:

findByNcbiIds in interface GeneDao

Parameters:

ncbiIds - ncbi ids

Returns:

map of NCBI Id to the gene.

findByPhysicalLocation

public Collection<Gene> findByPhysicalLocation(PhysicalLocation location)

Specified by:

findByPhysicalLocation in interface GeneDao

getCompositeSequenceCount

public long getCompositeSequenceCount(Gene gene,
 boolean includeDummyProducts)

Description copied from interface: GeneDao

Obtain the number of platform elements (e.g. probes) associated to this gene, totalled up over all platforms.

Note that ACLs are applied to the platforms.

Specified by:

getCompositeSequenceCount in interface GeneDao

Parameters:

includeDummyProducts - if true, include platform elements related via dummy GeneProducts

getCompositeSequenceCountById

public long getCompositeSequenceCountById(long id,
 boolean includeDummyProducts)

Gets a count of the CompositeSequences related to the gene identified by the given id.

Specified by:

getCompositeSequenceCountById in interface GeneDao

Returns:

Collection

See Also:

• GeneDao.getCompositeSequences(Gene, boolean)

getCompositeSequences

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

Description copied from interface: GeneDao

Get the composite sequences (e.g. probes) associated with this gene via a particular platform.

Specified by:

getCompositeSequences in interface GeneDao

Parameters:

arrayDesign - platform to restrict composite sequences to

includeDummyProducts - if true, include platform elements related via dummy GeneProducts

getCompositeSequences

public Collection<CompositeSequence> getCompositeSequences(Gene gene,
 boolean includeDummyProducts)

Description copied from interface: GeneDao

Get the composite sequences (e.g. probes) associated with this gene, for any platform.

Specified by:

getCompositeSequences in interface GeneDao

Parameters:

includeDummyProducts - if true, include platform elements related via dummy GeneProducts

getCompositeSequencesById

public Collection<CompositeSequence> getCompositeSequencesById(long id,
 boolean includeDummyProducts)

Gets all the CompositeSequences related to the gene identified by the given id.

Specified by:

getCompositeSequencesById in interface GeneDao

Returns:

Collection

See Also:

• GeneDao.getCompositeSequences(Gene, boolean)

getMicroRnaByTaxon

public Collection<Gene> getMicroRnaByTaxon(Taxon taxon)

Specified by:

getMicroRnaByTaxon in interface GeneDao

Parameters:

taxon - taxon

Returns:

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

getPlatformCountById

public long getPlatformCountById(Long id,
 boolean includeDummyProducts)

Specified by:

getPlatformCountById in interface GeneDao

Parameters:

id - id

includeDummyProducts - include platforms related via dummy GeneProducts in the count

Returns:

how many platforms have a representation of this gene

loadKnownGenes

public Collection<Gene> loadKnownGenes(Taxon taxon)

Specified by:

loadKnownGenes in interface GeneDao

Parameters:

taxon - taxon

Returns:

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

loadThawed

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

Specified by:

loadThawed in interface GeneDao

loadThawedLiter

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

Specified by:

loadThawedLiter in interface GeneDao

thaw

public Gene thaw(Gene gene)

Specified by:

thaw in interface GeneDao

thawAliases

public Gene thawAliases(Gene gene)

Only thaw the Aliases, very light version

Specified by:

thawAliases in interface GeneDao

thawLite

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

Specified by:

thawLite in interface GeneDao

thawLite

public Gene thawLite(Gene gene)

Specified by:

thawLite in interface GeneDao

thawLiter

public Gene thawLiter(Gene gene)

Specified by:

thawLiter in interface GeneDao

removeAll

public int removeAll()

Specified by:

removeAll in interface GeneDao

remove

public void remove(Gene gene)

Description copied from interface: BaseDao

Remove a persistent instance

Specified by:

remove in interface BaseDao<Gene>

Overrides:

remove in class AbstractDao<Gene>

Parameters:

gene - the entity to be removed

find

public Gene find(Gene gene)

Description copied from interface: BaseDao

Does a look up for the given entity in the persistent storage, usually looking for a specific identifier ( either id or a string property).

Specified by:

find in interface BaseDao<Gene>

Overrides:

find in class AbstractDao<Gene>

Parameters:

gene - the entity to look for.

Returns:

an entity that was found in the persistent storage, or null if no such entity was found.

doLoadValueObject

protected GeneValueObject doLoadValueObject(Gene entity)

Description copied from class: AbstractVoEnabledDao

Load a value object for a given entity.

This should be fast and efficient, and avoid any database query or post-processing. If you need to perform additional queries, implement AbstractVoEnabledDao.postProcessValueObjects(List) instead.

Specified by:

doLoadValueObject in class AbstractVoEnabledDao<Gene,GeneValueObject>

getFilteringQuery

protected Query getFilteringQuery(@Nullable
 Filters filters,
 @Nullable
 Sort sort)

Description copied from class: AbstractQueryFilteringVoEnabledDao

Produce a query for retrieving value objects after applying a set of filters and a given ordering.

Note that if your implementation does not produce a List of AbstractQueryFilteringVoEnabledDao when Query.list() is invoked, you must override AbstractQueryFilteringVoEnabledDao.getValueObjectTransformer().

The make the cached query (i.e. AbstractQueryFilteringVoEnabledDao.loadWithCache(Filters, Sort) behave the same, you also have to explicitly initialize any lazy relations in AbstractVoEnabledDao.doLoadValueObject(Identifiable) because the VO constructor will not initialize them.

Specified by:

getFilteringQuery in class AbstractQueryFilteringVoEnabledDao<Gene,GeneValueObject>

Parameters:

filters - see FilterQueryUtils.formRestrictionClause(Filters) filters argument for description.

Returns:

a Hibernated Query object ready to be used for TaxonVO retrieval.

initializeCachedFilteringResult

protected void initializeCachedFilteringResult(Gene entity)

Description copied from class: AbstractQueryFilteringVoEnabledDao

Initialize a result from AbstractQueryFilteringVoEnabledDao.getFilteringQuery(Filters, Sort) retrieved from the Hibernate StandardQueryCache.

Lazy-loaded relations that are fetched in AbstractQueryFilteringVoEnabledDao.getFilteringQuery(Filters, Sort) must be initialized manually in this method to ensure that the entity has all the expected fields if they are retrieved from the second-level cache.

Specified by:

initializeCachedFilteringResult in class AbstractQueryFilteringVoEnabledDao<Gene,GeneValueObject>

getFilteringCountQuery

protected Query getFilteringCountQuery(@Nullable
 Filters filters)

Description copied from class: AbstractQueryFilteringVoEnabledDao

Produce a query that will be used to retrieve the size of AbstractQueryFilteringVoEnabledDao.getFilteringQuery(Filters, Sort).

Overrides:

getFilteringCountQuery in class AbstractQueryFilteringVoEnabledDao<Gene,GeneValueObject>

Returns:

a Query which must return a single Long value

postProcessValueObjects

protected void postProcessValueObjects(List<GeneValueObject> geneValueObjects)

Description copied from class: AbstractVoEnabledDao

Post-process VOs in bulk.

Use this as an opportunity to load extra informations that could not be populated in the initial AbstractVoEnabledDao.doLoadValueObject(Identifiable) or AbstractVoEnabledDao.doLoadValueObjects(Collection)

Overrides:

postProcessValueObjects in class AbstractVoEnabledDao<Gene,GeneValueObject>