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)
CompositeSequence	find(CompositeSequence compositeSequence)
Collection<CompositeSequence>	findByBioSequence(BioSequence bioSequence)
Collection<CompositeSequence>	findByBioSequenceName(String name)
Collection<CompositeSequence>	findByGene(Gene gene, boolean useGene2Cs)
Collection<CompositeSequence>	findByGene(Gene gene, ArrayDesign arrayDesign, boolean useGene2Cs)
Map<Gene, Collection<CompositeSequence>>	findByGenes(Collection<Gene> genes, boolean useGene3Cs)
Map<Gene, Collection<CompositeSequence>>	findByGenes(Collection<Gene> genes, ArrayDesign arrayDesign, boolean useGene2Cs)
Collection<CompositeSequence>	findByName(String name)
CompositeSequence	findByName(ArrayDesign arrayDesign, String name)
Collection<CompositeSequence>	findByNamesInArrayDesigns(Collection<String> compositeSequenceNames, Collection<ArrayDesign> arrayDesigns)
Set<Long>	findIdsByGeneIds(Collection<Long> geneIds, Long arrayDesignId)
CompositeSequence	findOrCreate(CompositeSequence compositeSequence)
Map<Long, List<GeneReferenceValueObject>>	getGeneData(Collection<Long> compositeSequenceIds)
Collection<GeneMappingSummary>	getGeneMappingSummary(BioSequence biologicalCharacteristic, CompositeSequenceValueObject cs)
Map<CompositeSequence, Collection<Gene>>	getGenes(Collection<CompositeSequence> sequences, boolean useGene2Cs)
Collection<Gene>	getGenes(CompositeSequence compositeSequence, boolean useGene2Cs)
Slice<Gene>	getGenes(CompositeSequence compositeSequence, int offset, int limit, boolean useGene2Cs)
CursorPage<Gene>	getGenesByCursor(CompositeSequence compositeSequence, Cursor cursor, int limit, boolean useGene2Cs)	Cursor-mode counterpart to getGenes(CompositeSequence, int, int, boolean) — see CURSOR_PAGINATION_STEP1_PLAN.md step 1l.
Map<CompositeSequence, Collection<BioSequence2GeneProduct>>	getGenesWithSpecificity(Collection<CompositeSequence> compositeSequences)
Collection<Object[]>	getRawSummary(Collection<CompositeSequence> compositeSequences)
Collection<Object[]>	getRawSummary(ArrayDesign arrayDesign, int numResults)
Map<Long, CompositeSequenceDao.BioSequenceLite>	getSequenceData(Collection<Long> compositeSequenceIds)
Collection<CompositeSequence>	load(Collection<Long> ids)
Slice<CompositeSequenceValueObject>	loadValueObjectsForGene(Gene gene, int start, int limit, boolean useGene2Cs)
CursorPage<CompositeSequenceValueObject>	loadValueObjectsForGeneByCursor(Gene gene, Cursor cursor, int limit, boolean useGene2Cs)	Cursor-mode counterpart to loadValueObjectsForGene(Gene, int, int, boolean) — see CURSOR_PAGINATION_STEP1_PLAN.md step 1m.
CompositeSequenceValueObject	loadValueObjectWithGeneMappingSummary(CompositeSequence cs)	Include gene mapping summary in the CompositeSequenceValueObject.
void	remove(CompositeSequence compositeSequence)
Collection<CompositeSequence>	thaw(Collection<CompositeSequence> compositeSequences)
CompositeSequence	thaw(CompositeSequence compositeSequence)
void	update(CompositeSequence compositeSequence)

Methods inherited from interface BaseImmutableService

create, remove

Methods inherited from interface BaseReadOnlyService

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

Methods inherited from interface BaseService

save, save, update

Methods inherited from interface BaseVoEnabledService

loadAllValueObjects, loadValueObject, loadValueObjectById, loadValueObjects, loadValueObjectsByIds

Methods inherited from interface FilteringService

count, getFilter, getFilter, getFilter, getFilter, getFilter, getFilter, getFilter, getFilterableProperties, getFilterablePropertyAllowedValues, getFilterablePropertyConfigAttributes, getFilterablePropertyDescription, getFilterablePropertyResolvableAllowedValuesLabels, getFilterablePropertyType, getSort, isFilterablePropertyDeprecated, isFilterablePropertyUsingSubquery, load, load, loadIds

Methods inherited from interface FilteringVoEnabledService

loadValueObjects, loadValueObjects, loadValueObjectsByCursor

Method Details

find

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

Specified by:

find in interface BaseReadOnlyService<CompositeSequence>

See Also:

• BaseDao.find(Identifiable)

findOrCreate

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

Specified by:

findOrCreate in interface BaseImmutableService<CompositeSequence>

See Also:

• BaseDao.findOrCreate(Identifiable)

create

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

Specified by:

create in interface BaseImmutableService<CompositeSequence>

See Also:

• BaseDao.create(Identifiable)

load

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

Specified by:

load in interface BaseReadOnlyService<CompositeSequence>

See Also:

• BaseDao.load(Collection)

remove

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

Specified by:

remove in interface BaseImmutableService<CompositeSequence>

See Also:

• BaseDao.remove(Identifiable)

update

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

Specified by:

update in interface BaseService<CompositeSequence>

See Also:

• BaseDao.update(Identifiable)

findByBioSequence

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

findByBioSequenceName

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

findByGene

@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","AFTER_ACL_COMPOSITE_SEQUENCE_COLLECTION_READ"})
Collection<CompositeSequence> findByGene(Gene gene,
 boolean useGene2Cs)

findByGene

@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","AFTER_ACL_COMPOSITE_SEQUENCE_COLLECTION_READ"})
Collection<CompositeSequence> findByGene(Gene gene,
 ArrayDesign arrayDesign,
 boolean useGene2Cs)

findByGenes

@Secured("IS_AUTHENTICATED_ANONYMOUSLY")
Map<Gene, Collection<CompositeSequence>> findByGenes(Collection<Gene> genes,
 boolean useGene3Cs)

findByGenes

@Secured("IS_AUTHENTICATED_ANONYMOUSLY")
Map<Gene, Collection<CompositeSequence>> findByGenes(Collection<Gene> genes,
 ArrayDesign arrayDesign,
 boolean useGene2Cs)

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,
 boolean useGene2Cs)

loadValueObjectsForGeneByCursor

CursorPage<CompositeSequenceValueObject> loadValueObjectsForGeneByCursor(Gene gene,
 @Nullable
 Cursor cursor,
 int limit,
 boolean useGene2Cs)

Cursor-mode counterpart to loadValueObjectsForGene(Gene, int, int, boolean) — see CURSOR_PAGINATION_STEP1_PLAN.md step 1m. Always sorts by ascending cs.id (the primary key, indexed and unique); the cursor DAO restricts cursors to single-component id sorts until the index audit lands.

Same value-object shape as the offset variant: the per-row CompositeSequenceValueObject carries the ArrayDesign VO populated via a single loadValueObjects call over the platforms touched by the page (matching the offset implementation).

See Also:

• CompositeSequenceDao.findByGeneByCursor(Gene, Cursor, int, boolean)

findByName

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

findByName

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

findByNamesInArrayDesigns

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

getGenes

Map<CompositeSequence, Collection<Gene>> getGenes(Collection<CompositeSequence> sequences,
 boolean useGene2Cs)

getGenes

Collection<Gene> getGenes(CompositeSequence compositeSequence,
 boolean useGene2Cs)

getGenes

Slice<Gene> getGenes(CompositeSequence compositeSequence,
 int offset,
 int limit,
 boolean useGene2Cs)

getGenesByCursor

@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","AFTER_ACL_COMPOSITE_SEQUENCE_READ"})
CursorPage<Gene> getGenesByCursor(CompositeSequence compositeSequence,
 @Nullable
 Cursor cursor,
 int limit,
 boolean useGene2Cs)

Cursor-mode counterpart to getGenes(CompositeSequence, int, int, boolean) — see CURSOR_PAGINATION_STEP1_PLAN.md step 1l. Always sorts by ascending gene.id (the primary key, indexed and unique); the cursor DAO restricts cursors to single-component id sorts until the index audit lands.

See Also:

• CompositeSequenceDao.getGenesByCursor(CompositeSequence, Cursor, int, boolean)

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)

getSequenceData

Map<Long, CompositeSequenceDao.BioSequenceLite> getSequenceData(Collection<Long> compositeSequenceIds)

See Also:

• CompositeSequenceDao.getSequenceData(Collection)

getGeneData

Map<Long, List<GeneReferenceValueObject>> getGeneData(Collection<Long> compositeSequenceIds)

See Also:

• CompositeSequenceDao.getGeneData(Collection)

findIdsByGeneIds

Set<Long> findIdsByGeneIds(Collection<Long> geneIds,
 Long arrayDesignId)

See Also:

• CompositeSequenceDao.findIdsByGeneIds(Collection, Long)