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

Interface CompositeSequenceService

All Superinterfaces:

BaseImmutableService<CompositeSequence>, BaseReadOnlyService<CompositeSequence>, BaseService<CompositeSequence>, BaseVoEnabledService<CompositeSequence,CompositeSequenceValueObject>, FilteringService<CompositeSequence>, FilteringVoEnabledService<CompositeSequence,CompositeSequenceValueObject>

All Known Implementing Classes:

CompositeSequenceServiceImpl

public interface CompositeSequenceService
extends BaseService<CompositeSequence>, FilteringVoEnabledService<CompositeSequence,CompositeSequenceValueObject>

Author:

paul

Method Summary

Modifier and Type	Method	Description
CompositeSequence	create(CompositeSequence compositeSequence)	Creates the given entity in the persistent storage.
CompositeSequence	find(CompositeSequence compositeSequence)	Does a search for the entity in the persistent storage
Collection<CompositeSequence>	findByBioSequence(BioSequence bioSequence)
Collection<CompositeSequence>	findByBioSequenceName(String name)
Collection<CompositeSequence>	findByGene(Gene gene)
Collection<CompositeSequence>	findByGene(Gene gene, ArrayDesign arrayDesign)
Collection<CompositeSequence>	findByName(String name)
CompositeSequence	findByName(ArrayDesign arrayDesign, String name)
Collection<CompositeSequence>	findByNamesInArrayDesigns(Collection<String> compositeSequenceNames, Collection<ArrayDesign> arrayDesigns)
CompositeSequence	findOrCreate(CompositeSequence compositeSequence)	Does a search for the entity in the persistent storage, and if not found, creates it.
Collection<GeneMappingSummary>	getGeneMappingSummary(BioSequence biologicalCharacteristic, CompositeSequenceValueObject cs)
Map<CompositeSequence,Collection<Gene>>	getGenes(Collection<CompositeSequence> sequences)	Given a Collection of composite sequences returns of map of a composite sequence to a collection of genes
Collection<Gene>	getGenes(CompositeSequence compositeSequence)
Slice<Gene>	getGenes(CompositeSequence compositeSequence, int offset, int limit)
Map<CompositeSequence,Collection<BioSequence2GeneProduct>>	getGenesWithSpecificity(Collection<CompositeSequence> compositeSequences)
Collection<Object[]>	getRawSummary(Collection<CompositeSequence> compositeSequences)
Collection<Object[]>	getRawSummary(ArrayDesign arrayDesign, int numResults)
Collection<CompositeSequence>	load(Collection<Long> ids)	Loads objects with given ids.
Slice<CompositeSequenceValueObject>	loadValueObjectsForGene(Gene gene, int start, int limit)
CompositeSequenceValueObject	loadValueObjectWithGeneMappingSummary(CompositeSequence cs)	Include gene mapping summary in the CompositeSequenceValueObject.
void	remove(CompositeSequence compositeSequence)	Removes the given entity from the persistent storage.
Collection<CompositeSequence>	thaw(Collection<CompositeSequence> compositeSequences)
CompositeSequence	thaw(CompositeSequence compositeSequence)
void	update(CompositeSequence compositeSequence)	Updates the given entity in the persistent storage.

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

create, remove, remove

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

countAll, findOrFail, getElementClass, load, loadAll, loadOrFail, loadOrFail, loadOrFail, loadOrFail

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

save, save, update

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

loadAllValueObjects, loadValueObject, loadValueObjectById, loadValueObjects, loadValueObjectsByIds

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

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

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

loadValueObjects, loadValueObjects

Method Detail

find

@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","AFTER_ACL_ARRAYDESIGN_COLLECTION_READ"})
CompositeSequence find(CompositeSequence compositeSequence)

Description copied from interface: BaseReadOnlyService

Does a search for the entity in the persistent storage

Specified by:

find in interface BaseReadOnlyService<CompositeSequence>

Parameters:

compositeSequence - the entity to be searched for

Returns:

the version of entity retrieved from the persistent storage, if found, otherwise null.

findOrCreate

@Secured("GROUP_USER")
CompositeSequence findOrCreate(CompositeSequence compositeSequence)

Description copied from interface: BaseImmutableService

Does a search for the entity in the persistent storage, and if not found, creates it.

Specified by:

findOrCreate in interface BaseImmutableService<CompositeSequence>

Parameters:

compositeSequence - the entity to look for, and create if not found.

Returns:

the entity retrieved from the persistent storage, either found or created.

create

@Secured("GROUP_USER")
CompositeSequence create(CompositeSequence compositeSequence)

Description copied from interface: BaseImmutableService

Creates the given entity in the persistent storage.

Specified by:

create in interface BaseImmutableService<CompositeSequence>

Parameters:

compositeSequence - the entity to be created.

Returns:

object referencing the persistent instance of the given entity.

load

@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","AFTER_ACL_ARRAYDESIGN_COLLECTION_READ"})
Collection<CompositeSequence> load(Collection<Long> ids)

Description copied from interface: BaseReadOnlyService

Loads objects with given ids.

Specified by:

load in interface BaseReadOnlyService<CompositeSequence>

Parameters:

ids - the ids of objects to be loaded.

Returns:

collection containing object with given IDs.

remove

@Secured("GROUP_USER")
void remove(CompositeSequence compositeSequence)

Description copied from interface: BaseImmutableService

Removes the given entity from the persistent storage.

Specified by:

remove in interface BaseImmutableService<CompositeSequence>

Parameters:

compositeSequence - the entity to be removed.

update

@Secured("GROUP_USER")
void update(CompositeSequence compositeSequence)

Description copied from interface: BaseService

Updates the given entity in the persistent storage.

Specified by:

update in interface BaseService<CompositeSequence>

Parameters:

compositeSequence - the entity to be updated.

findByBioSequence

@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","AFTER_ACL_ARRAYDESIGN_COLLECTION_READ"})
Collection<CompositeSequence> findByBioSequence(BioSequence bioSequence)

findByBioSequenceName

@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","AFTER_ACL_ARRAYDESIGN_COLLECTION_READ"})
Collection<CompositeSequence> findByBioSequenceName(String name)

findByGene

@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","AFTER_ACL_ARRAYDESIGN_COLLECTION_READ"})
Collection<CompositeSequence> findByGene(Gene gene)

loadValueObjectWithGeneMappingSummary

@Nullable
@Transactional(readOnly=true)
CompositeSequenceValueObject loadValueObjectWithGeneMappingSummary(CompositeSequence cs)

Include gene mapping summary in the CompositeSequenceValueObject.

loadValueObjectsForGene

Slice<CompositeSequenceValueObject> loadValueObjectsForGene(Gene gene,
                                                            int start,
                                                            int limit)

findByGene

@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","AFTER_ACL_ARRAYDESIGN_COLLECTION_READ"})
Collection<CompositeSequence> findByGene(Gene gene,
                                         ArrayDesign arrayDesign)

findByName

@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","AFTER_ACL_ARRAYDESIGN_COLLECTION_READ"})
Collection<CompositeSequence> findByName(String name)

findByName

@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","AFTER_ACL_ARRAYDESIGN_READ"})
CompositeSequence findByName(ArrayDesign arrayDesign,
                             String name)

findByNamesInArrayDesigns

@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","AFTER_ACL_ARRAYDESIGN_COLLECTION_READ"})
Collection<CompositeSequence> findByNamesInArrayDesigns(Collection<String> compositeSequenceNames,
                                                        Collection<ArrayDesign> arrayDesigns)

getGenes

Map<CompositeSequence,Collection<Gene>> getGenes(Collection<CompositeSequence> sequences)

Given a Collection of composite sequences returns of map of a composite sequence to a collection of genes

Parameters:

sequences - sequences

Returns:

map

getGenes

Collection<Gene> getGenes(CompositeSequence compositeSequence)

getGenes

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

getGenesWithSpecificity

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

Parameters:

compositeSequences - sequences

Returns:

a map of CompositeSequences to collection of BioSequence2GeneProducts at each location.

getRawSummary

Collection<Object[]> getRawSummary(Collection<CompositeSequence> compositeSequences)

getRawSummary

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

getGeneMappingSummary

Collection<GeneMappingSummary> getGeneMappingSummary(BioSequence biologicalCharacteristic,
                                                     @Nullable
                                                     CompositeSequenceValueObject cs)

thaw

@CheckReturnValue
Collection<CompositeSequence> thaw(Collection<CompositeSequence> compositeSequences)

thaw

@CheckReturnValue
CompositeSequence thaw(CompositeSequence compositeSequence)