Package ubic.gemma.persistence.service.expression.designElement

Class CompositeSequenceDaoImpl

java.lang.Object

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

ubic.gemma.persistence.service.AbstractVoEnabledDao<O,VO>

ubic.gemma.persistence.service.AbstractFilteringVoEnabledDao<O,VO>

ubic.gemma.persistence.service.AbstractQueryFilteringVoEnabledDao<CompositeSequence,CompositeSequenceValueObject>

ubic.gemma.persistence.service.expression.designElement.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>

@Repository
public class CompositeSequenceDaoImpl
extends AbstractQueryFilteringVoEnabledDao<CompositeSequence,CompositeSequenceValueObject>
implements CompositeSequenceDao

Author:

pavlidis

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.expression.designElement.CompositeSequenceDao

OBJECT_ALIAS

Constructor Summary

Constructors

Constructor	Description
CompositeSequenceDaoImpl(SessionFactory sessionFactory)

Method Summary

Modifier and Type	Method	Description
protected CompositeSequenceValueObject	doLoadValueObject(CompositeSequence entity)	Load a value object for a given entity.
CompositeSequence	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).
Collection<CompositeSequence>	findByBioSequence(BioSequence bioSequence)
Collection<CompositeSequence>	findByBioSequenceName(String name)
Collection<CompositeSequence>	findByGene(Gene gene)
Slice<CompositeSequence>	findByGene(Gene gene, int start, int limit)
Collection<CompositeSequence>	findByGene(Gene gene, ArrayDesign arrayDesign)
Collection<CompositeSequence>	findByName(String name)
CompositeSequence	findByName(ArrayDesign arrayDesign, String name)
protected Query	getFilteringCountQuery(Filters filters)	Produce a query that will be used to retrieve the size of AbstractQueryFilteringVoEnabledDao.getFilteringQuery(Filters, Sort).
protected Query	getFilteringIdQuery(Filters filters, Sort sort)	Produce a query that will be used to retrieve IDs 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.
Map<CompositeSequence,Collection<Gene>>	getGenes(Collection<CompositeSequence> compositeSequences)	Given a collection of composite sequences returns a map of the given composite sequences to a collection of genes
Slice<Gene>	getGenes(CompositeSequence compositeSequence, int offset, int limit)	given a composite sequence returns a collection of genes
Map<CompositeSequence,Collection<BioSequence2GeneProduct>>	getGenesWithSpecificity(Collection<CompositeSequence> compositeSequences)
Collection<Object[]>	getRawSummary(Collection<CompositeSequence> compositeSequences)
Collection<Object[]>	getRawSummary(ArrayDesign arrayDesign, int numResults)
protected void	initializeCachedFilteringResult(CompositeSequence cachedEntity)	Initialize a result from AbstractQueryFilteringVoEnabledDao.getFilteringQuery(Filters, Sort) retrieved from the Hibernate StandardQueryCache.
void	thaw(Collection<CompositeSequence> compositeSequences)
void	thaw(CompositeSequence cs)

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

count, countWithCache, getEntityTransformer, 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, getFilterablePropertyIsUsingSubquery, getFilterablePropertyMeta, getFilterablePropertyMeta, getFilterablePropertyType, getSort

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

doLoadValueObjects, loadAllValueObjects, loadValueObject, loadValueObjectById, loadValueObjects, loadValueObjectsByIds, postProcessValueObjects

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

countAll, create, create, findByProperty, findByPropertyIn, findOneByProperty, findOrCreate, getBatchSize, getElementClass, getIdentifierPropertyName, getSessionFactory, load, load, loadAll, loadReference, loadReference, reload, reload, remove, 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, getIdentifierPropertyName, load, load, loadAll, loadReference, loadReference, reload, reload, remove, 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, getFilterablePropertyIsUsingSubquery, getFilterablePropertyType, getSort, load, load, loadIds

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

loadValueObjects, loadValueObjects

Constructor Detail

CompositeSequenceDaoImpl

@Autowired
public CompositeSequenceDaoImpl(SessionFactory sessionFactory)

Method Detail

doLoadValueObject

protected CompositeSequenceValueObject doLoadValueObject(CompositeSequence 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<CompositeSequence,CompositeSequenceValueObject>

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<CompositeSequence,CompositeSequenceValueObject>

Returns:

a Query that produce a list of AbstractQueryFilteringVoEnabledDao

initializeCachedFilteringResult

protected void initializeCachedFilteringResult(CompositeSequence cachedEntity)

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<CompositeSequence,CompositeSequenceValueObject>

getFilteringIdQuery

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

Description copied from class: AbstractQueryFilteringVoEnabledDao

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

Overrides:

getFilteringIdQuery in class AbstractQueryFilteringVoEnabledDao<CompositeSequence,CompositeSequenceValueObject>

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<CompositeSequence,CompositeSequenceValueObject>

Returns:

a Query which must return a single Long value

findByBioSequence

public Collection<CompositeSequence> findByBioSequence(BioSequence bioSequence)

Specified by:

findByBioSequence in interface CompositeSequenceDao

findByBioSequenceName

public Collection<CompositeSequence> findByBioSequenceName(String name)

Specified by:

findByBioSequenceName in interface CompositeSequenceDao

findByGene

public Collection<CompositeSequence> findByGene(Gene gene)

Specified by:

findByGene in interface CompositeSequenceDao

findByGene

public Slice<CompositeSequence> findByGene(Gene gene,
                                           int start,
                                           int limit)

Specified by:

findByGene in interface CompositeSequenceDao

findByGene

public Collection<CompositeSequence> findByGene(Gene gene,
                                                ArrayDesign arrayDesign)

Specified by:

findByGene in interface CompositeSequenceDao

findByName

public Collection<CompositeSequence> findByName(String name)

Specified by:

findByName in interface CompositeSequenceDao

findByName

public CompositeSequence findByName(ArrayDesign arrayDesign,
                                    String name)

Specified by:

findByName in interface CompositeSequenceDao

getGenes

public Map<CompositeSequence,Collection<Gene>> getGenes(Collection<CompositeSequence> compositeSequences)

Description copied from interface: CompositeSequenceDao

Given a collection of composite sequences returns a map of the given composite sequences to a collection of genes

Specified by:

getGenes in interface CompositeSequenceDao

Parameters:

compositeSequences - composite sequences

Returns:

map

getGenes

public Slice<Gene> getGenes(CompositeSequence compositeSequence,
                            int offset,
                            int limit)

Description copied from interface: CompositeSequenceDao

given a composite sequence returns a collection of genes

Specified by:

getGenes in interface CompositeSequenceDao

Parameters:

compositeSequence - sequence

offset - offset

limit - limit

Returns:

collection of genes

getGenesWithSpecificity

public Map<CompositeSequence,Collection<BioSequence2GeneProduct>> getGenesWithSpecificity(Collection<CompositeSequence> compositeSequences)

Specified by:

getGenesWithSpecificity in interface CompositeSequenceDao

Parameters:

compositeSequences - sequences

Returns:

a map of CompositeSequences to BlatAssociations.

getRawSummary

public Collection<Object[]> getRawSummary(@Nullable
                                          Collection<CompositeSequence> compositeSequences)

Specified by:

getRawSummary in interface CompositeSequenceDao

getRawSummary

public Collection<Object[]> getRawSummary(ArrayDesign arrayDesign,
                                          int numResults)

Specified by:

getRawSummary in interface CompositeSequenceDao

thaw

public void thaw(Collection<CompositeSequence> compositeSequences)

Specified by:

thaw in interface CompositeSequenceDao

thaw

public void thaw(CompositeSequence cs)

Specified by:

thaw in interface CompositeSequenceDao

find

public CompositeSequence find(CompositeSequence compositeSequence)

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<CompositeSequence>

Overrides:

find in class AbstractDao<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.