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

Class ArrayDesignServiceImpl

java.lang.Object

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

ubic.gemma.persistence.service.AbstractFilteringVoEnabledService<ArrayDesign,ArrayDesignValueObject>

ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignServiceImpl

All Implemented Interfaces:

BaseImmutableService<ArrayDesign>, BaseReadOnlyService<ArrayDesign>, BaseService<ArrayDesign>, BaseVoEnabledService<ArrayDesign,ArrayDesignValueObject>, SecurableBaseImmutableService<ArrayDesign>, SecurableBaseReadOnlyService<ArrayDesign>, SecurableBaseService<ArrayDesign>, SecurableBaseVoEnabledService<ArrayDesign,ArrayDesignValueObject>, SecurableFilteringVoEnabledService<ArrayDesign,ArrayDesignValueObject>, ArrayDesignService, FilteringService<ArrayDesign>, FilteringVoEnabledService<ArrayDesign,ArrayDesignValueObject>

@Service
public class ArrayDesignServiceImpl
extends AbstractFilteringVoEnabledService<ArrayDesign,ArrayDesignValueObject>
implements ArrayDesignService

Author:

klc

See Also:

• ArrayDesignService

Field Summary

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

log

Constructor Summary

Constructors

Constructor	Description
ArrayDesignServiceImpl(ArrayDesignDao arrayDesignDao, AuditEventDao auditEventDao)

Method Summary

Modifier and Type	Method	Description
void	addProbes(ArrayDesign arrayDesign, Collection<CompositeSequence> newProbes)
long	countWithCache(Filters filters)
void	deleteAlignmentData(ArrayDesign arrayDesign)	remove sequence alignment results associated with the bioSequences for this array design.
void	deleteGeneProductAlignmentAssociations(ArrayDesign arrayDesign)
void	deleteGeneProductAnnotationAssociations(ArrayDesign arrayDesign)
void	deleteGeneProductAssociations(ArrayDesign arrayDesign)	deletes the gene product associations on the specified array design.
Collection<ArrayDesign>	findByAlternateName(String queryString)
Collection<ArrayDesign>	findByManufacturer(String searchString)
Collection<ArrayDesign>	findByName(String name)
ArrayDesign	findByShortName(String shortName)
Collection<ArrayDesign>	findByTaxon(Taxon taxon)	Find by the primary taxon.
ArrayDesign	findOneByAlternateName(String name)
ArrayDesign	findOneByName(String name)
Map<CompositeSequence,Collection<BlatResult>>	getAlignments(ArrayDesign arrayDesign)	Retrieves alignments for the platform elements, limited to those which map to a gene product (so not all blat results)
Collection<BioAssay>	getAllAssociatedBioAssays(ArrayDesign arrayDesign)
Map<CompositeSequence,BioSequence>	getBioSequences(ArrayDesign arrayDesign)	Return all the (unique) biosequences associated with the array design.
Long	getCompositeSequenceCount(ArrayDesign arrayDesign)
Collection<CompositeSequence>	getCompositeSequences(ArrayDesign arrayDesign)
Collection<CompositeSequence>	getCompositeSequences(ArrayDesign arrayDesign, int limit, int offset)
Collection<ExpressionExperiment>	getExpressionExperiments(ArrayDesign arrayDesign)
long	getExpressionExperimentsCount(ArrayDesign arrayDesign)
Collection<Gene>	getGenes(ArrayDesign arrayDesign)
Map<CompositeSequence,Set<Gene>>	getGenesByCompositeSequence(Collection<ArrayDesign> arrayDesign)
Map<CompositeSequence,Set<Gene>>	getGenesByCompositeSequence(ArrayDesign arrayDesign)
Map<Long,AuditEvent>	getLastGeneMapping(Collection<Long> ids)	Gets the AuditEvents of the latest gene mapping for the specified array design ids.
Map<Long,AuditEvent>	getLastRepeatAnalysis(Collection<Long> ids)
Map<Long,AuditEvent>	getLastSequenceAnalysis(Collection<Long> ids)	Gets the AuditEvents of the latest sequence analyses for the specified array design ids.
Map<Long,AuditEvent>	getLastSequenceUpdate(Collection<Long> ids)	Gets the AuditEvents of the latest sequence update for the specified array design ids.
Map<Taxon,Long>	getPerTaxonCount()
Collection<ExpressionExperiment>	getSwitchedExperiments(ArrayDesign arrayDesign)	Get the ids of experiments that "originally" used this platform, but which don't any more due to a platform switch.
long	getSwitchedExpressionExperimentCount(ArrayDesign id)
Collection<Taxon>	getTaxa(ArrayDesign arrayDesign)	Return the taxa for the array design.
Taxon	getTaxon(Long id)
boolean	isBlackListed(String geoAccession)
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)
Collection<ArrayDesign>	loadAllGenericGenePlatforms()	Load *generic* gene-based platforms.
ArrayDesign	loadAndThaw(Long id)
<T extends Exception> ArrayDesign	loadAndThawLiteOrFail(Long id, Function<String,T> exceptionSupplier, String message)	Load a platform by ID and thaw it with ArrayDesignService.thawLite(ArrayDesign)
Slice<ArrayDesignValueObject>	loadBlacklistedValueObjects(Filters filters, Sort sort, int offset, int limit)	No need for ACL_VALUE_OBJECT_COLLECTION_READ because the filtering is done in the query.
List<ArrayDesignValueObject>	loadValueObjectsForEE(Long eeId)	Loads the Value Objects for array designs used by expression experiment with the given ID
Collection<ArrayDesignValueObject>	loadValueObjectsWithCache(Filters filters, Sort sort)
long	numAllCompositeSequenceWithBioSequences()	Function to return a count of all compositeSequences with bioSequence associations
long	numAllCompositeSequenceWithBioSequences(Collection<Long> ids)	Function to return the count of all composite sequences with biosequences, given a list of array design Ids
long	numAllCompositeSequenceWithBlatResults()	Function to return all composite sequences with blat results
long	numAllCompositeSequenceWithBlatResults(Collection<Long> ids)	Function to return the count of all composite sequences with blat results, given a list of array design Ids
long	numAllCompositeSequenceWithGenes()	Function to return a count of all composite sequences with associated genes.
long	numAllCompositeSequenceWithGenes(Collection<Long> ids)	Function to return the count of all composite sequences with genes, given a list of array design Ids
long	numAllGenes()	Returns a count of the number of genes associated with all arrayDesigns
long	numAllGenes(Collection<Long> ids)	Returns the number of unique Genes associated with the collection of ArrayDesign ids.
long	numBioSequences(ArrayDesign arrayDesign)	returns the number of bioSequences associated with this ArrayDesign id
long	numBlatResults(ArrayDesign arrayDesign)	returns the number of BlatResults (BioSequence2GeneProduct) entries associated with this ArrayDesign id.
long	numCompositeSequenceWithBioSequences(ArrayDesign arrayDesign)
long	numCompositeSequenceWithBlatResults(ArrayDesign arrayDesign)
long	numCompositeSequenceWithGenes(ArrayDesign arrayDesign)
long	numExperiments(ArrayDesign arrayDesign)
long	numGenes(ArrayDesign arrayDesign)	Returns the number of unique Genes associated with this ArrayDesign id
void	removeBiologicalCharacteristics(ArrayDesign arrayDesign)	Remove all associations that this array design has with BioSequences.
Collection<ArrayDesign>	thaw(Collection<ArrayDesign> aas)	Thaw a collection of platforms.
ArrayDesign	thaw(ArrayDesign arrayDesign)	Thaw a given platform.
Collection<ArrayDesign>	thawCompositeSequences(Collection<ArrayDesign> ads)
ArrayDesign	thawCompositeSequences(ArrayDesign arrayDesign)	Thaw the composite sequences of a given platform
Collection<ArrayDesign>	thawLite(Collection<ArrayDesign> arrayDesigns)
ArrayDesign	thawLite(ArrayDesign arrayDesign)	Perform a less intensive thaw of an array design: not the composite sequences.
boolean	updateSubsumingStatus(ArrayDesign candidateSubsumer, ArrayDesign candidateSubsumee)	Test whether the candidateSubsumer subsumes the candidateSubsumee.

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

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

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, streamAll, streamAll, 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.BaseReadOnlyService

countAll, getElementClass

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

count, getFilter, getFilter, getFilter, getFilter, getFilter, getFilter, getFilterableProperties, getFilterablePropertyAllowedValues, getFilterablePropertyConfigAttributes, getFilterablePropertyDescription, getFilterablePropertyIsUsingSubquery, getFilterablePropertyResolvableAllowedValuesLabels, getFilterablePropertyType, getIdentifierPropertyName, getSort

Methods inherited from interface ubic.gemma.persistence.service.common.auditAndSecurity.SecurableBaseImmutableService

create, create, findOrCreate, remove, remove, remove

Methods inherited from interface ubic.gemma.persistence.service.common.auditAndSecurity.SecurableBaseReadOnlyService

find, findOrFail, load, load, loadAll, loadOrFail, loadOrFail, loadOrFail, loadOrFail, streamAll, streamAll

Methods inherited from interface ubic.gemma.persistence.service.common.auditAndSecurity.SecurableBaseService

save, save, update, update

Methods inherited from interface ubic.gemma.persistence.service.common.auditAndSecurity.SecurableBaseVoEnabledService

loadAllValueObjects, loadValueObject, loadValueObjectById, loadValueObjects, loadValueObjectsByIds

Methods inherited from interface ubic.gemma.persistence.service.common.auditAndSecurity.SecurableFilteringVoEnabledService

load, load, loadIds, loadValueObjects, loadValueObjects

Constructor Details

ArrayDesignServiceImpl

@Autowired
public ArrayDesignServiceImpl(ArrayDesignDao arrayDesignDao,
 AuditEventDao auditEventDao)

Method Details

loadAllGenericGenePlatforms

@Transactional(readOnly=true)
public Collection<ArrayDesign> loadAllGenericGenePlatforms()

Description copied from interface: ArrayDesignService

Load *generic* gene-based platforms.

Specified by:

loadAllGenericGenePlatforms in interface ArrayDesignService

loadAndThaw

@Transactional(readOnly=true)
public ArrayDesign loadAndThaw(Long id)

Specified by:

loadAndThaw in interface ArrayDesignService

loadAndThawLiteOrFail

@Transactional(readOnly=true)
public <T extends Exception> ArrayDesign loadAndThawLiteOrFail(Long id,
 Function<String,T> exceptionSupplier,
 String message)
                                                        throws T

Description copied from interface: ArrayDesignService

Load a platform by ID and thaw it with ArrayDesignService.thawLite(ArrayDesign)

Specified by:

loadAndThawLiteOrFail in interface ArrayDesignService

Throws:

T

addProbes

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

Specified by:

addProbes in interface ArrayDesignService

deleteAlignmentData

@Transactional
public void deleteAlignmentData(ArrayDesign arrayDesign)

Description copied from interface: ArrayDesignService

remove sequence alignment results associated with the bioSequences for this array design. This can indirectly * affect other platforms that use the same sequences.

Specified by:

deleteAlignmentData in interface ArrayDesignService

Parameters:

arrayDesign - AD

deleteGeneProductAssociations

@Transactional
public void deleteGeneProductAssociations(ArrayDesign arrayDesign)

Description copied from interface: ArrayDesignService

deletes the gene product associations on the specified array design. If you only want to delete alignment-based or annotation-based associations, use deleteGeneProductAlignmentAssociation deleteGeneProductAnnotationAssociations.

Specified by:

deleteGeneProductAssociations in interface ArrayDesignService

Parameters:

arrayDesign - AD

findByAlternateName

@Transactional(readOnly=true)
public Collection<ArrayDesign> findByAlternateName(String queryString)

Specified by:

findByAlternateName in interface ArrayDesignService

findOneByAlternateName

@Transactional(readOnly=true)
public ArrayDesign findOneByAlternateName(String name)

Specified by:

findOneByAlternateName in interface ArrayDesignService

findByManufacturer

@Transactional(readOnly=true)
public Collection<ArrayDesign> findByManufacturer(String searchString)

Specified by:

findByManufacturer in interface ArrayDesignService

findByName

@Transactional(readOnly=true)
public Collection<ArrayDesign> findByName(String name)

Specified by:

findByName in interface ArrayDesignService

See Also:

• ArrayDesignService.findByName(java.lang.String)

findOneByName

@Transactional(readOnly=true)
public ArrayDesign findOneByName(String name)

Specified by:

findOneByName in interface ArrayDesignService

findByShortName

@Transactional(readOnly=true)
public ArrayDesign findByShortName(String shortName)

Specified by:

findByShortName in interface ArrayDesignService

findByTaxon

@Transactional(readOnly=true)
public Collection<ArrayDesign> findByTaxon(Taxon taxon)

Description copied from interface: ArrayDesignService

Find by the primary taxon.

Specified by:

findByTaxon in interface ArrayDesignService

Parameters:

taxon - taxon

Returns:

ADs

getAlignments

@Transactional(readOnly=true)
public Map<CompositeSequence,Collection<BlatResult>> getAlignments(ArrayDesign arrayDesign)

Description copied from interface: ArrayDesignService

Retrieves alignments for the platform elements, limited to those which map to a gene product (so not all blat results)

Specified by:

getAlignments in interface ArrayDesignService

Parameters:

arrayDesign - AD

Returns:

map of composite sequences to alignments, if available.

getAllAssociatedBioAssays

@Transactional(readOnly=true)
public Collection<BioAssay> getAllAssociatedBioAssays(ArrayDesign arrayDesign)

Specified by:

getAllAssociatedBioAssays in interface ArrayDesignService

getBioSequences

@Transactional(readOnly=true)
public Map<CompositeSequence,BioSequence> getBioSequences(ArrayDesign arrayDesign)

Description copied from interface: ArrayDesignService

Return all the (unique) biosequences associated with the array design. Composite sequences that don't have sequences are also returned, so this can be used to do a thawRawAndProcessed, in effect.

Specified by:

getBioSequences in interface ArrayDesignService

Parameters:

arrayDesign - AD

Returns:

map of composite seqs. to bio seqs.

getGenes

@Transactional(readOnly=true)
public Collection<Gene> getGenes(ArrayDesign arrayDesign)

Specified by:

getGenes in interface ArrayDesignService

See Also:

• ArrayDesignDao.getGenes(ArrayDesign)

getGenesByCompositeSequence

@Transactional(readOnly=true)
public Map<CompositeSequence,Set<Gene>> getGenesByCompositeSequence(ArrayDesign arrayDesign)

Specified by:

getGenesByCompositeSequence in interface ArrayDesignService

See Also:

• ArrayDesignDao.getGenesByCompositeSequence(ArrayDesign)

getGenesByCompositeSequence

@Transactional(readOnly=true)
public Map<CompositeSequence,Set<Gene>> getGenesByCompositeSequence(Collection<ArrayDesign> arrayDesign)

Specified by:

getGenesByCompositeSequence in interface ArrayDesignService

getCompositeSequenceCount

@Transactional(readOnly=true)
public Long getCompositeSequenceCount(ArrayDesign arrayDesign)

Specified by:

getCompositeSequenceCount in interface ArrayDesignService

getCompositeSequences

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

Specified by:

getCompositeSequences in interface ArrayDesignService

getCompositeSequences

@Transactional(readOnly=true)
public Collection<CompositeSequence> getCompositeSequences(ArrayDesign arrayDesign,
 int limit,
 int offset)

Specified by:

getCompositeSequences in interface ArrayDesignService

getExpressionExperiments

@Transactional(readOnly=true)
public Collection<ExpressionExperiment> getExpressionExperiments(ArrayDesign arrayDesign)

Specified by:

getExpressionExperiments in interface ArrayDesignService

getExpressionExperimentsCount

@Transactional(readOnly=true)
public long getExpressionExperimentsCount(ArrayDesign arrayDesign)

Specified by:

getExpressionExperimentsCount in interface ArrayDesignService

getLastGeneMapping

@Transactional(readOnly=true)
public Map<Long,AuditEvent> getLastGeneMapping(Collection<Long> ids)

Description copied from interface: ArrayDesignService

Gets the AuditEvents of the latest gene mapping for the specified array design ids. This returns a map of id -> AuditEvent. If the events do not exist, the map entry will point to null.

Specified by:

getLastGeneMapping in interface ArrayDesignService

Parameters:

ids - ids

Returns:

map of IDs to events

getLastRepeatAnalysis

@Transactional(readOnly=true)
public Map<Long,AuditEvent> getLastRepeatAnalysis(Collection<Long> ids)

Specified by:

getLastRepeatAnalysis in interface ArrayDesignService

getLastSequenceAnalysis

@Transactional(readOnly=true)
public Map<Long,AuditEvent> getLastSequenceAnalysis(Collection<Long> ids)

Description copied from interface: ArrayDesignService

Gets the AuditEvents of the latest sequence analyses for the specified array design ids. This returns a map of id -> AuditEvent. If the events do not exist, the map entry will point to null.

Specified by:

getLastSequenceAnalysis in interface ArrayDesignService

Parameters:

ids - ids

Returns:

map of IDs to events

getLastSequenceUpdate

@Transactional(readOnly=true)
public Map<Long,AuditEvent> getLastSequenceUpdate(Collection<Long> ids)

Description copied from interface: ArrayDesignService

Gets the AuditEvents of the latest sequence update for the specified array design ids. This returns a map of id -> AuditEvent. If the events do not exist, the map entry will point to null.

Specified by:

getLastSequenceUpdate in interface ArrayDesignService

Parameters:

ids - ids

Returns:

map of IDs to events

getPerTaxonCount

@Transactional(readOnly=true)
public Map<Taxon,Long> getPerTaxonCount()

Specified by:

getPerTaxonCount in interface ArrayDesignService

Returns:

a map of taxon -> count of how many array designs there are for that taxon. Taxa with no arrays are excluded.

getSwitchedExperiments

@Transactional(readOnly=true)
public Collection<ExpressionExperiment> getSwitchedExperiments(ArrayDesign arrayDesign)

Description copied from interface: ArrayDesignService

Get the ids of experiments that "originally" used this platform, but which don't any more due to a platform switch. Note that for some old platforms we may not have recorded this information.

Specified by:

getSwitchedExperiments in interface ArrayDesignService

Parameters:

arrayDesign - id of the platform

Returns:

collection of EE ids

getSwitchedExpressionExperimentCount

@Transactional(readOnly=true)
public long getSwitchedExpressionExperimentCount(ArrayDesign id)

Specified by:

getSwitchedExpressionExperimentCount in interface ArrayDesignService

getTaxa

@Transactional(readOnly=true)
public Collection<Taxon> getTaxa(ArrayDesign arrayDesign)

Description copied from interface: ArrayDesignService

Return the taxa for the array design. This can be multiple, or zero if the array is not processed.

Specified by:

getTaxa in interface ArrayDesignService

Parameters:

arrayDesign - The id of the array design

Returns:

The Set of Taxons for array design.

getTaxon

@Transactional(readOnly=true)
public Taxon getTaxon(Long id)

Specified by:

getTaxon in interface ArrayDesignService

isBlackListed

@Transactional(readOnly=true)
public boolean isBlackListed(String geoAccession)

Specified by:

isBlackListed in interface ArrayDesignService

Parameters:

geoAccession - for a GEO series or platform

deleteGeneProductAnnotationAssociations

@Transactional
public void deleteGeneProductAnnotationAssociations(ArrayDesign arrayDesign)

Specified by:

deleteGeneProductAnnotationAssociations in interface ArrayDesignService

deleteGeneProductAlignmentAssociations

@Transactional
public void deleteGeneProductAlignmentAssociations(ArrayDesign arrayDesign)

Specified by:

deleteGeneProductAlignmentAssociations in interface ArrayDesignService

loadBlacklistedValueObjects

@Transactional(readOnly=true)
public Slice<ArrayDesignValueObject> loadBlacklistedValueObjects(@Nullable
 Filters filters,
 @Nullable
 Sort sort,
 int offset,
 int limit)

Description copied from interface: ArrayDesignService

No need for ACL_VALUE_OBJECT_COLLECTION_READ because the filtering is done in the query.

Specified by:

loadBlacklistedValueObjects in interface ArrayDesignService

See Also:

• ArrayDesignDao.loadBlacklistedValueObjects(Filters, Sort, int, int)

loadValueObjectsWithCache

@Transactional(readOnly=true)
public Collection<ArrayDesignValueObject> loadValueObjectsWithCache(@Nullable
 Filters filters,
 @Nullable
 Sort sort)

Specified by:

loadValueObjectsWithCache in interface ArrayDesignService

countWithCache

@Transactional(readOnly=true)
public long countWithCache(@Nullable
 Filters filters)

Specified by:

countWithCache in interface ArrayDesignService

isMerged

@Transactional(readOnly=true)
public Map<Long,Boolean> isMerged(Collection<Long> ids)

Specified by:

isMerged in interface ArrayDesignService

isMergee

@Transactional(readOnly=true)
public Map<Long,Boolean> isMergee(Collection<Long> ids)

Specified by:

isMergee in interface ArrayDesignService

isSubsumed

@Transactional(readOnly=true)
public Map<Long,Boolean> isSubsumed(Collection<Long> ids)

Specified by:

isSubsumed in interface ArrayDesignService

isSubsumer

@Transactional(readOnly=true)
public Map<Long,Boolean> isSubsumer(Collection<Long> ids)

Specified by:

isSubsumer in interface ArrayDesignService

loadValueObjectsForEE

@Transactional(readOnly=true)
public List<ArrayDesignValueObject> loadValueObjectsForEE(Long eeId)

Description copied from interface: ArrayDesignService

Loads the Value Objects for array designs used by expression experiment with the given ID

Specified by:

loadValueObjectsForEE in interface ArrayDesignService

Parameters:

eeId - the id of an expression experiment

Returns:

AD VOs

numAllCompositeSequenceWithBioSequences

@Transactional(readOnly=true)
public long numAllCompositeSequenceWithBioSequences()

Description copied from interface: ArrayDesignService

Function to return a count of all compositeSequences with bioSequence associations

Specified by:

numAllCompositeSequenceWithBioSequences in interface ArrayDesignService

Returns:

count

numAllCompositeSequenceWithBioSequences

@Transactional(readOnly=true)
public long numAllCompositeSequenceWithBioSequences(Collection<Long> ids)

Description copied from interface: ArrayDesignService

Function to return the count of all composite sequences with biosequences, given a list of array design Ids

Specified by:

numAllCompositeSequenceWithBioSequences in interface ArrayDesignService

Parameters:

ids - ids

Returns:

count

numAllCompositeSequenceWithBlatResults

@Transactional(readOnly=true)
public long numAllCompositeSequenceWithBlatResults()

Description copied from interface: ArrayDesignService

Function to return all composite sequences with blat results

Specified by:

numAllCompositeSequenceWithBlatResults in interface ArrayDesignService

Returns:

count

numAllCompositeSequenceWithBlatResults

@Transactional(readOnly=true)
public long numAllCompositeSequenceWithBlatResults(Collection<Long> ids)

Description copied from interface: ArrayDesignService

Function to return the count of all composite sequences with blat results, given a list of array design Ids

Specified by:

numAllCompositeSequenceWithBlatResults in interface ArrayDesignService

Parameters:

ids - ids

Returns:

count

numAllCompositeSequenceWithGenes

@Transactional(readOnly=true)
public long numAllCompositeSequenceWithGenes()

Description copied from interface: ArrayDesignService

Function to return a count of all composite sequences with associated genes.

Specified by:

numAllCompositeSequenceWithGenes in interface ArrayDesignService

Returns:

count

numAllCompositeSequenceWithGenes

@Transactional(readOnly=true)
public long numAllCompositeSequenceWithGenes(Collection<Long> ids)

Description copied from interface: ArrayDesignService

Function to return the count of all composite sequences with genes, given a list of array design Ids

Specified by:

numAllCompositeSequenceWithGenes in interface ArrayDesignService

Parameters:

ids - ids

Returns:

count

numAllGenes

@Transactional(readOnly=true)
public long numAllGenes()

Description copied from interface: ArrayDesignService

Returns a count of the number of genes associated with all arrayDesigns

Specified by:

numAllGenes in interface ArrayDesignService

Returns:

count

numAllGenes

@Transactional(readOnly=true)
public long numAllGenes(Collection<Long> ids)

Description copied from interface: ArrayDesignService

Returns the number of unique Genes associated with the collection of ArrayDesign ids.

Specified by:

numAllGenes in interface ArrayDesignService

Parameters:

ids - ids

Returns:

count

numBioSequences

@Transactional(readOnly=true)
public long numBioSequences(ArrayDesign arrayDesign)

Description copied from interface: ArrayDesignService

returns the number of bioSequences associated with this ArrayDesign id

Specified by:

numBioSequences in interface ArrayDesignService

Parameters:

arrayDesign - AD

Returns:

count

numBlatResults

@Transactional(readOnly=true)
public long numBlatResults(ArrayDesign arrayDesign)

Description copied from interface: ArrayDesignService

returns the number of BlatResults (BioSequence2GeneProduct) entries associated with this ArrayDesign id.

Specified by:

numBlatResults in interface ArrayDesignService

Parameters:

arrayDesign - AD

Returns:

count

numCompositeSequenceWithBioSequences

@Transactional(readOnly=true)
public long numCompositeSequenceWithBioSequences(ArrayDesign arrayDesign)

Specified by:

numCompositeSequenceWithBioSequences in interface ArrayDesignService

numCompositeSequenceWithBlatResults

@Transactional(readOnly=true)
public long numCompositeSequenceWithBlatResults(ArrayDesign arrayDesign)

Specified by:

numCompositeSequenceWithBlatResults in interface ArrayDesignService

numCompositeSequenceWithGenes

@Transactional(readOnly=true)
public long numCompositeSequenceWithGenes(ArrayDesign arrayDesign)

Specified by:

numCompositeSequenceWithGenes in interface ArrayDesignService

numExperiments

@Transactional(readOnly=true)
public long numExperiments(ArrayDesign arrayDesign)

Specified by:

numExperiments in interface ArrayDesignService

Parameters:

arrayDesign - AD

Returns:

how many experiments use this platform (not including experiment subsets) security filtered

numGenes

@Transactional(readOnly=true)
public long numGenes(ArrayDesign arrayDesign)

Description copied from interface: ArrayDesignService

Returns the number of unique Genes associated with this ArrayDesign id

Specified by:

numGenes in interface ArrayDesignService

Parameters:

arrayDesign - AD

Returns:

count

removeBiologicalCharacteristics

@Transactional
public void removeBiologicalCharacteristics(ArrayDesign arrayDesign)

Description copied from interface: ArrayDesignService

Remove all associations that this array design has with BioSequences. This is needed for cases where the original import has associated the probes with the wrong sequences. A common case is for GEO data sets where the actual oligonucleotide is not given. Instead the submitter provides Genbank accessions, which are misleading. This method can be used to clear those until the "right" sequences can be identified and filled in. Note that this does not remove the BioSequences, it just nulls the BiologicalCharacteristics of the CompositeSequences.

Specified by:

removeBiologicalCharacteristics in interface ArrayDesignService

Parameters:

arrayDesign - AD

thaw

@Transactional(readOnly=true)
public ArrayDesign thaw(ArrayDesign arrayDesign)

Description copied from interface: ArrayDesignService

Thaw a given platform.

Specified by:

thaw in interface ArrayDesignService

See Also:

• ArrayDesignDao.thaw(ArrayDesign)

thaw

@Transactional(readOnly=true)
public Collection<ArrayDesign> thaw(Collection<ArrayDesign> aas)

Description copied from interface: ArrayDesignService

Thaw a collection of platforms.

Specified by:

thaw in interface ArrayDesignService

See Also:

• ArrayDesignDao.thaw(ArrayDesign)

thawCompositeSequences

@Transactional(readOnly=true)
public ArrayDesign thawCompositeSequences(ArrayDesign arrayDesign)

Description copied from interface: ArrayDesignService

Thaw the composite sequences of a given platform

Specified by:

thawCompositeSequences in interface ArrayDesignService

See Also:

• ArrayDesignDao.thawCompositeSequences(ArrayDesign)

thawCompositeSequences

@Transactional(readOnly=true)
public Collection<ArrayDesign> thawCompositeSequences(Collection<ArrayDesign> ads)

Specified by:

thawCompositeSequences in interface ArrayDesignService

thawLite

@Transactional(readOnly=true)
public ArrayDesign thawLite(ArrayDesign arrayDesign)

Description copied from interface: ArrayDesignService

Perform a less intensive thaw of an array design: not the composite sequences.

Specified by:

thawLite in interface ArrayDesignService

Parameters:

arrayDesign - AD

Returns:

AD

thawLite

@Transactional(readOnly=true)
public Collection<ArrayDesign> thawLite(Collection<ArrayDesign> arrayDesigns)

Specified by:

thawLite in interface ArrayDesignService

updateSubsumingStatus

@Transactional
public boolean updateSubsumingStatus(ArrayDesign candidateSubsumer,
 ArrayDesign candidateSubsumee)

Description copied from interface: ArrayDesignService

Test whether the candidateSubsumer subsumes the candidateSubsumee. If so, the array designs are updated to reflect this fact. The boolean value returned indicates whether there was indeed a subsuming relationship found.

Specified by:

updateSubsumingStatus in interface ArrayDesignService

Parameters:

candidateSubsumer - candidate subsumer

candidateSubsumee - candidate subsumee

Returns:

success