Class CompositeSequenceDaoImpl
- All Implemented Interfaces:
org.springframework.beans.factory.InitializingBean,BaseDao<CompositeSequence>,BaseVoEnabledDao<CompositeSequence,,CompositeSequenceValueObject> CachedFilteringDao<CompositeSequence>,CachedFilteringVoEnabledDao<CompositeSequence,,CompositeSequenceValueObject> CompositeSequenceDao,FilteringDao<CompositeSequence>,FilteringVoEnabledDao<CompositeSequence,CompositeSequenceValueObject>
- Author:
- pavlidis
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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_MSFields inherited from class ubic.gemma.persistence.service.AbstractDao
logFields inherited from interface ubic.gemma.persistence.service.expression.designElement.CompositeSequenceDao
OBJECT_ALIAS -
Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptionprotected CompositeSequenceValueObjectdoLoadValueObject(CompositeSequence entity) Load a value object for a given entity.find(CompositeSequence compositeSequence) Does a look up for the given entity in the persistent storage, usually looking for a specific identifier ( either id or a string property).findByBioSequence(BioSequence bioSequence) findByBioSequenceName(String name) findByGene(Gene gene) findByGene(Gene gene, int start, int limit) findByGene(Gene gene, ArrayDesign arrayDesign) findByName(String name) findByName(ArrayDesign arrayDesign, String name) protected QuerygetFilteringCountQuery(Filters filters) Produce a query that will be used to retrieve the size ofAbstractQueryFilteringVoEnabledDao.getFilteringQuery(Filters, Sort).protected QuerygetFilteringIdQuery(Filters filters, Sort sort) Produce a query that will be used to retrieve IDs ofAbstractQueryFilteringVoEnabledDao.getFilteringQuery(Filters, Sort).protected QuerygetFilteringQuery(Filters filters, Sort sort) Produce a query for retrieving value objects after applying a set of filters and a given ordering.getGenes(Collection<CompositeSequence> compositeSequences) Given a collection of composite sequences returns a map of the given composite sequences to a collection of genesgetGenes(CompositeSequence compositeSequence, int offset, int limit) given a composite sequence returns a collection of genesgetGenesWithSpecificity(Collection<CompositeSequence> compositeSequences) Collection<Object[]> getRawSummary(Collection<CompositeSequence> compositeSequences) Collection<Object[]> getRawSummary(ArrayDesign arrayDesign, int numResults) protected voidinitializeCachedFilteringResult(CompositeSequence cachedEntity) Initialize a result fromAbstractQueryFilteringVoEnabledDao.getFilteringQuery(Filters, Sort)retrieved from the HibernateStandardQueryCache.voidthaw(Collection<CompositeSequence> compositeSequences) voidMethods inherited from class ubic.gemma.persistence.service.AbstractQueryFilteringVoEnabledDao
count, countWithCache, getEntityTransformer, getValueObjectTransformer, load, load, loadIds, loadIdsWithCache, loadValueObjects, loadValueObjects, loadValueObjectsWithCache, loadValueObjectsWithCache, loadWithCache, loadWithCacheMethods 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, resolveFilterablePropertyMetaMethods inherited from class ubic.gemma.persistence.service.AbstractVoEnabledDao
doLoadValueObjects, loadAllValueObjects, loadValueObject, loadValueObjectById, loadValueObjects, loadValueObjectsByIds, postProcessValueObjectsMethods 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, remove, save, save, streamAll, streamAll, streamQuery, update, updateMethods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, waitMethods inherited from interface ubic.gemma.persistence.service.BaseDao
countAll, create, create, findOrCreate, getElementClass, load, load, loadAll, loadReference, loadReference, reload, reload, remove, remove, remove, save, save, streamAll, streamAll, update, updateMethods inherited from interface ubic.gemma.persistence.service.BaseVoEnabledDao
loadAllValueObjects, loadValueObject, loadValueObjectById, loadValueObjects, loadValueObjectsByIdsMethods inherited from interface ubic.gemma.persistence.service.FilteringDao
count, getFilter, getFilter, getFilter, getFilter, getFilter, getFilter, getFilterableProperties, getFilterablePropertyAllowedValues, getFilterablePropertyDescription, getFilterablePropertyType, getSort, isFilterablePropertyDeprecated, isFilterablePropertyUsingSubquery, load, load, loadIdsMethods inherited from interface ubic.gemma.persistence.service.FilteringVoEnabledDao
loadValueObjects, loadValueObjects
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Constructor Details
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CompositeSequenceDaoImpl
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Method Details
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doLoadValueObject
Description copied from class:AbstractVoEnabledDaoLoad 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:
doLoadValueObjectin classAbstractVoEnabledDao<CompositeSequence,CompositeSequenceValueObject>
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getFilteringQuery
Description copied from class:AbstractQueryFilteringVoEnabledDaoProduce 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
ListofAbstractQueryFilteringVoEnabledDaowhenQuery.list()is invoked, you must overrideAbstractQueryFilteringVoEnabledDao.getValueObjectTransformer().The make the cached query (i.e.
AbstractQueryFilteringVoEnabledDao.loadWithCache(Filters, Sort)behave the same, you also have to explicitly initialize any lazy relations inAbstractVoEnabledDao.doLoadValueObject(Identifiable)because the VO constructor will not initialize them.- Specified by:
getFilteringQueryin classAbstractQueryFilteringVoEnabledDao<CompositeSequence,CompositeSequenceValueObject> - Returns:
- a
Querythat produce a list ofAbstractQueryFilteringVoEnabledDao
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initializeCachedFilteringResult
Description copied from class:AbstractQueryFilteringVoEnabledDaoInitialize a result fromAbstractQueryFilteringVoEnabledDao.getFilteringQuery(Filters, Sort)retrieved from the HibernateStandardQueryCache.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. -
getFilteringIdQuery
Description copied from class:AbstractQueryFilteringVoEnabledDaoProduce a query that will be used to retrieve IDs ofAbstractQueryFilteringVoEnabledDao.getFilteringQuery(Filters, Sort). -
getFilteringCountQuery
Description copied from class:AbstractQueryFilteringVoEnabledDaoProduce a query that will be used to retrieve the size ofAbstractQueryFilteringVoEnabledDao.getFilteringQuery(Filters, Sort).- Overrides:
getFilteringCountQueryin classAbstractQueryFilteringVoEnabledDao<CompositeSequence,CompositeSequenceValueObject> - Returns:
- a
Querywhich must return a singleLongvalue
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findByBioSequence
- Specified by:
findByBioSequencein interfaceCompositeSequenceDao
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findByBioSequenceName
- Specified by:
findByBioSequenceNamein interfaceCompositeSequenceDao
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findByGene
- Specified by:
findByGenein interfaceCompositeSequenceDao
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findByGene
- Specified by:
findByGenein interfaceCompositeSequenceDao
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findByGene
- Specified by:
findByGenein interfaceCompositeSequenceDao
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findByName
- Specified by:
findByNamein interfaceCompositeSequenceDao
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findByName
- Specified by:
findByNamein interfaceCompositeSequenceDao
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getGenes
public Map<CompositeSequence,Collection<Gene>> getGenes(Collection<CompositeSequence> compositeSequences) Description copied from interface:CompositeSequenceDaoGiven a collection of composite sequences returns a map of the given composite sequences to a collection of genes- Specified by:
getGenesin interfaceCompositeSequenceDao- Parameters:
compositeSequences- composite sequences- Returns:
- map
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getGenes
Description copied from interface:CompositeSequenceDaogiven a composite sequence returns a collection of genes- Specified by:
getGenesin interfaceCompositeSequenceDao- Parameters:
compositeSequence- sequenceoffset- offsetlimit- limit- Returns:
- collection of genes
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getGenesWithSpecificity
public Map<CompositeSequence,Collection<BioSequence2GeneProduct>> getGenesWithSpecificity(Collection<CompositeSequence> compositeSequences) - Specified by:
getGenesWithSpecificityin interfaceCompositeSequenceDao- Parameters:
compositeSequences- sequences- Returns:
- a map of CompositeSequences to BlatAssociations.
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getRawSummary
public Collection<Object[]> getRawSummary(@Nullable Collection<CompositeSequence> compositeSequences) - Specified by:
getRawSummaryin interfaceCompositeSequenceDao
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getRawSummary
- Specified by:
getRawSummaryin interfaceCompositeSequenceDao
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thaw
- Specified by:
thawin interfaceCompositeSequenceDao
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thaw
- Specified by:
thawin interfaceCompositeSequenceDao
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find
Description copied from interface:BaseDaoDoes 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:
findin interfaceBaseDao<CompositeSequence>- Overrides:
findin classAbstractDao<CompositeSequence>- Parameters:
compositeSequence- the entity to look for.- Returns:
- an entity that was found in the persistent storage, or null if no such entity was found.
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