Package ubic.gemma.persistence.service.expression.arrayDesign

Interface ArrayDesignDao

All Superinterfaces:

BaseDao<ArrayDesign>, BaseVoEnabledDao<ArrayDesign,ArrayDesignValueObject>, CachedFilteringDao<ArrayDesign>, CachedFilteringVoEnabledDao<ArrayDesign,ArrayDesignValueObject>, CuratableDao<ArrayDesign>, FilteringDao<ArrayDesign>, FilteringVoEnabledDao<ArrayDesign,ArrayDesignValueObject>

All Known Implementing Classes:

ArrayDesignDaoImpl

@Repository
public interface ArrayDesignDao
extends CuratableDao<ArrayDesign>, CachedFilteringVoEnabledDao<ArrayDesign,ArrayDesignValueObject>

Created by tesarst on 13/03/17. ArrayDesignDao interface

Field Summary

Fields

Modifier and Type	Field	Description
static final String	OBJECT_ALIAS

Method Summary

Modifier and Type	Method	Description
void	addProbes(ArrayDesign arrayDesign, Collection<CompositeSequence> newProbes)
void	deleteAlignmentData(ArrayDesign arrayDesign)
void	deleteGeneProductAlignmentAssociations(ArrayDesign arrayDesign)
void	deleteGeneProductAnnotationAssociations(ArrayDesign arrayDesign)
void	deleteGeneProductAssociations(ArrayDesign arrayDesign)
Collection<ArrayDesign>	findByAlternateName(String queryString)
Collection<ArrayDesign>	findByManufacturer(String queryString)
Collection<ArrayDesign>	findByName(String name)
ArrayDesign	findByShortName(String shortName)
Collection<ArrayDesign>	findByTaxon(Taxon taxon)
ArrayDesign	findOneByAlternateName(String name)
ArrayDesign	findOneByName(String name)
Collection<BioAssay>	getAllAssociatedBioAssays(ArrayDesign arrayDesign)
Map<Long,Collection<AuditEvent>>	getAuditEvents(Collection<Long> ids)
Map<CompositeSequence,BioSequence>	getBioSequences(ArrayDesign arrayDesign)
Collection<ExpressionExperiment>	getExpressionExperiments(ArrayDesign arrayDesign)
long	getExpressionExperimentsCount(ArrayDesign arrayDesign)	Obtain the number of associated expression experiments.
Collection<Gene>	getGenes(ArrayDesign arrayDesign)	Obtain all the genes associated to the platform.
Map<CompositeSequence,Set<Gene>>	getGenesByCompositeSequence(Collection<ArrayDesign> arrayDesign)
Map<CompositeSequence,Set<Gene>>	getGenesByCompositeSequence(ArrayDesign arrayDesign)	Obtain all the genes associated to the platform organized by corresponding design elements.
Map<Taxon,Long>	getPerTaxonCount()
Collection<ExpressionExperiment>	getSwitchedExpressionExperiments(ArrayDesign arrayDesign)	Obtain a collection of ExpressionExperiment identifiers that have been switched from a given platform.
Long	getSwitchedExpressionExperimentsCount(ArrayDesign arrayDesign)	Count the number of switched ExpressionExperiment from a given platform.
Collection<Taxon>	getTaxa(ArrayDesign arrayDesign)
Map<Long,Boolean>	isMerged(Collection<Long> ids)
Map<Long,Boolean>	isMergee(Collection<Long> ids)
Map<Long,Boolean>	isSubsumed(Collection<Long> ids)
Map<Long,Boolean>	isSubsumer(Collection<Long> ids)
Map<CompositeSequence,Collection<BlatResult>>	loadAlignments(ArrayDesign arrayDesign)
Collection<ArrayDesign>	loadAllGenericGenePlatforms()
Slice<ArrayDesignValueObject>	loadBlacklistedValueObjects(Filters filters, Sort sort, int offset, int limit)
Collection<CompositeSequence>	loadCompositeSequences(ArrayDesign arrayDesign, int limit, int offset)
List<ArrayDesignValueObject>	loadValueObjectsForEE(Long eeId)
long	numAllCompositeSequenceWithBioSequences()
long	numAllCompositeSequenceWithBioSequences(Collection<Long> ids)
long	numAllCompositeSequenceWithBlatResults()
long	numAllCompositeSequenceWithBlatResults(Collection<Long> ids)
long	numAllCompositeSequenceWithGenes()
long	numAllCompositeSequenceWithGenes(Collection<Long> ids)
long	numAllGenes()
long	numAllGenes(Collection<Long> ids)
long	numBioSequences(ArrayDesign arrayDesign)
long	numBlatResults(ArrayDesign arrayDesign)
long	numCompositeSequences(ArrayDesign id)
long	numCompositeSequenceWithBioSequences(ArrayDesign arrayDesign)
long	numCompositeSequenceWithBlatResults(ArrayDesign arrayDesign)
long	numCompositeSequenceWithGenes(ArrayDesign arrayDesign)
long	numExperiments(ArrayDesign arrayDesign)
long	numGenes(ArrayDesign arrayDesign)
void	removeBiologicalCharacteristics(ArrayDesign arrayDesign)
void	thaw(ArrayDesign arrayDesign)	Thaw the given platform as per thawLite(ArrayDesign) with its probes and genes.
void	thawCompositeSequences(ArrayDesign arrayDesign)	Only thaw the design elements of a given platform.
void	thawLite(ArrayDesign arrayDesign)	Lightly thaw the given platform.
boolean	updateSubsumingStatus(ArrayDesign candidateSubsumer, ArrayDesign candidateSubsumee)

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

countAll, create, create, find, 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.CachedFilteringDao

countWithCache, loadIdsWithCache, loadWithCache, loadWithCache

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

loadValueObjectsWithCache, loadValueObjectsWithCache

Methods inherited from interface ubic.gemma.persistence.service.common.auditAndSecurity.curation.CuratableDao

loadTroubledIds, updateCurationDetailsFromAuditEvent

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

Field Details

OBJECT_ALIAS

static final String OBJECT_ALIAS

See Also:

• Constant Field Values

Method Details

loadAllGenericGenePlatforms

Collection<ArrayDesign> loadAllGenericGenePlatforms()

addProbes

void addProbes(ArrayDesign arrayDesign,
 Collection<CompositeSequence> newProbes)

deleteAlignmentData

void deleteAlignmentData(ArrayDesign arrayDesign)

deleteGeneProductAssociations

void deleteGeneProductAssociations(ArrayDesign arrayDesign)

findByShortName

@Nullable
ArrayDesign findByShortName(String shortName)

findByName

Collection<ArrayDesign> findByName(String name)

findOneByName

@Nullable
ArrayDesign findOneByName(String name)

findByAlternateName

Collection<ArrayDesign> findByAlternateName(String queryString)

findOneByAlternateName

@Nullable
ArrayDesign findOneByAlternateName(String name)

findByManufacturer

Collection<ArrayDesign> findByManufacturer(String queryString)

findByTaxon

Collection<ArrayDesign> findByTaxon(Taxon taxon)

getAllAssociatedBioAssays

Collection<BioAssay> getAllAssociatedBioAssays(ArrayDesign arrayDesign)

getAuditEvents

Map<Long,Collection<AuditEvent>> getAuditEvents(Collection<Long> ids)

getBioSequences

Map<CompositeSequence,BioSequence> getBioSequences(ArrayDesign arrayDesign)

getGenes

Collection<Gene> getGenes(ArrayDesign arrayDesign)

Obtain all the genes associated to the platform.

getGenesByCompositeSequence

Map<CompositeSequence,Set<Gene>> getGenesByCompositeSequence(ArrayDesign arrayDesign)

Obtain all the genes associated to the platform organized by corresponding design elements.

getGenesByCompositeSequence

Map<CompositeSequence,Set<Gene>> getGenesByCompositeSequence(Collection<ArrayDesign> arrayDesign)

getExpressionExperiments

Collection<ExpressionExperiment> getExpressionExperiments(ArrayDesign arrayDesign)

getExpressionExperimentsCount

long getExpressionExperimentsCount(ArrayDesign arrayDesign)

Obtain the number of associated expression experiments.

This is much faster than looking up the size of getExpressionExperiments(ArrayDesign).

getPerTaxonCount

Map<Taxon,Long> getPerTaxonCount()

getSwitchedExpressionExperiments

Collection<ExpressionExperiment> getSwitchedExpressionExperiments(ArrayDesign arrayDesign)

Obtain a collection of ExpressionExperiment identifiers that have been switched from a given platform.

If you only need to count them, consider using the more performant getSwitchedExpressionExperimentsCount(ArrayDesign) instead.

getSwitchedExpressionExperimentsCount

Long getSwitchedExpressionExperimentsCount(ArrayDesign arrayDesign)

Count the number of switched ExpressionExperiment from a given platform.

getTaxa

Collection<Taxon> getTaxa(ArrayDesign arrayDesign)

isMerged

Map<Long,Boolean> isMerged(Collection<Long> ids)

isMergee

Map<Long,Boolean> isMergee(Collection<Long> ids)

isSubsumed

Map<Long,Boolean> isSubsumed(Collection<Long> ids)

isSubsumer

Map<Long,Boolean> isSubsumer(Collection<Long> ids)

loadAlignments

Map<CompositeSequence,Collection<BlatResult>> loadAlignments(ArrayDesign arrayDesign)

loadCompositeSequences

Collection<CompositeSequence> loadCompositeSequences(ArrayDesign arrayDesign,
 int limit,
 int offset)

loadValueObjectsForEE

List<ArrayDesignValueObject> loadValueObjectsForEE(Long eeId)

numAllCompositeSequenceWithBioSequences

long numAllCompositeSequenceWithBioSequences()

numAllCompositeSequenceWithBioSequences

long numAllCompositeSequenceWithBioSequences(Collection<Long> ids)

numAllCompositeSequenceWithBlatResults

long numAllCompositeSequenceWithBlatResults()

numAllCompositeSequenceWithBlatResults

long numAllCompositeSequenceWithBlatResults(Collection<Long> ids)

numAllCompositeSequenceWithGenes

long numAllCompositeSequenceWithGenes()

numAllCompositeSequenceWithGenes

long numAllCompositeSequenceWithGenes(Collection<Long> ids)

numAllGenes

long numAllGenes()

numAllGenes

long numAllGenes(Collection<Long> ids)

numBioSequences

long numBioSequences(ArrayDesign arrayDesign)

numBlatResults

long numBlatResults(ArrayDesign arrayDesign)

numCompositeSequences

long numCompositeSequences(ArrayDesign id)

numCompositeSequenceWithBioSequences

long numCompositeSequenceWithBioSequences(ArrayDesign arrayDesign)

numCompositeSequenceWithBlatResults

long numCompositeSequenceWithBlatResults(ArrayDesign arrayDesign)

numCompositeSequenceWithGenes

long numCompositeSequenceWithGenes(ArrayDesign arrayDesign)

numExperiments

long numExperiments(ArrayDesign arrayDesign)

numGenes

long numGenes(ArrayDesign arrayDesign)

removeBiologicalCharacteristics

void removeBiologicalCharacteristics(ArrayDesign arrayDesign)

thawLite

void thawLite(ArrayDesign arrayDesign)

Lightly thaw the given platform.

This includes all the to-one relations, but not the design elements.

thaw

void thaw(ArrayDesign arrayDesign)

Thaw the given platform as per thawLite(ArrayDesign) with its probes and genes.

thawCompositeSequences

void thawCompositeSequences(ArrayDesign arrayDesign)

Only thaw the design elements of a given platform.

updateSubsumingStatus

boolean updateSubsumingStatus(ArrayDesign candidateSubsumer,
 ArrayDesign candidateSubsumee)

deleteGeneProductAlignmentAssociations

void deleteGeneProductAlignmentAssociations(ArrayDesign arrayDesign)

deleteGeneProductAnnotationAssociations

void deleteGeneProductAnnotationAssociations(ArrayDesign arrayDesign)

loadBlacklistedValueObjects

Slice<ArrayDesignValueObject> loadBlacklistedValueObjects(@Nullable
 Filters filters,
 @Nullable
 Sort sort,
 int offset,
 int limit)