Interface CompositeSequenceReadService

All Known Implementing Classes:

CompositeSequenceReadServiceImpl

public interface CompositeSequenceReadService

Read-only retrieval service for CompositeSequence.

Phase 3 of the CompositeSequenceService decomposition (strangler fig). This service houses the pure DAO-delegate read cluster previously implemented directly on the CompositeSequenceServiceImpl facade: the findByBioSequence* / findByGene* / findByGenes* / findByName* lookups, findByNamesInArrayDesigns, the getGenes* variants, getGenesWithSpecificity, the getRawSummary variants, and thaw. All methods delegate to CompositeSequenceDao with no orchestration of other collaborator services.

Methods that compose multiple read collaborators (gene-mapping summaries, VO-enrichment with platform VOs) remain on the facade for now; they may be split into their own slice later.

Callers should generally keep using CompositeSequenceService as the facade — the facade delegates to this service. Direct injection is appropriate where a class would otherwise create a Spring construction cycle through the heavier facade.

ACL / @Secured annotations live on CompositeSequenceService (the caller-facing facade interface); enforcement happens at the facade proxy boundary, so this interface is intentionally unsecured.

See Also:

• CompositeSequenceService

Method Summary

Modifier and Type	Method	Description
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 useGene2Cs)
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)	Resolve composite sequence names against a collection of array designs, preserving insertion order and discarding names that don't match any sequence on any of the supplied platforms.
Set<Long>	findIdsByGeneIds(Collection<Long> geneIds, Long arrayDesignId)
Map<Long, List<GeneReferenceValueObject>>	getGeneData(Collection<Long> compositeSequenceIds)
Map<CompositeSequence, Collection<Gene>>	getGenes(Collection<CompositeSequence> sequences, boolean useGene2Cs)
Collection<Gene>	getGenes(CompositeSequence compositeSequence, boolean useGene2Cs)	Return all genes mapped to the given composite sequence.
Slice<Gene>	getGenes(CompositeSequence compositeSequence, int offset, int limit, boolean useGene2Cs)
CursorPage<Gene>	getGenesByCursor(CompositeSequence compositeSequence, Cursor cursor, int limit, boolean useGene2Cs)
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>	thaw(Collection<CompositeSequence> compositeSequences)	Thaw a collection of CompositeSequence for full traversal.
CompositeSequence	thaw(CompositeSequence compositeSequence)	Thaw a single CompositeSequence for full traversal.

Method Details

findByBioSequence

Collection<CompositeSequence> findByBioSequence(BioSequence bioSequence)

See Also:

• CompositeSequenceDao.findByBioSequence(BioSequence)

findByBioSequenceName

Collection<CompositeSequence> findByBioSequenceName(String name)

See Also:

• CompositeSequenceDao.findByBioSequenceName(String)

findByGene

Collection<CompositeSequence> findByGene(Gene gene,
 boolean useGene2Cs)

See Also:

• CompositeSequenceDao.findByGene(Gene, boolean)

findByGene

Collection<CompositeSequence> findByGene(Gene gene,
 ArrayDesign arrayDesign,
 boolean useGene2Cs)

See Also:

• CompositeSequenceDao.findByGene(Gene, ArrayDesign, boolean)

findByGenes

Map<Gene, Collection<CompositeSequence>> findByGenes(Collection<Gene> genes,
 boolean useGene2Cs)

See Also:

• CompositeSequenceDao.findByGenes(Collection, boolean)

findByGenes

Map<Gene, Collection<CompositeSequence>> findByGenes(Collection<Gene> genes,
 ArrayDesign arrayDesign,
 boolean useGene2Cs)

See Also:

• CompositeSequenceDao.findByGenes(Collection, ArrayDesign, boolean)

findByName

Collection<CompositeSequence> findByName(String name)

See Also:

• CompositeSequenceDao.findByName(String)

findByName

CompositeSequence findByName(ArrayDesign arrayDesign,
 String name)

See Also:

• CompositeSequenceDao.findByName(ArrayDesign, String)

findByNamesInArrayDesigns

@Nullable
Collection<CompositeSequence> findByNamesInArrayDesigns(Collection<String> compositeSequenceNames,
 Collection<ArrayDesign> arrayDesigns)

Resolve composite sequence names against a collection of array designs, preserving insertion order and discarding names that don't match any sequence on any of the supplied platforms.

getGenes

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

See Also:

• CompositeSequenceDao.getGenes(Collection, boolean)

getGenes

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

Return all genes mapped to the given composite sequence.

getGenes

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

See Also:

• CompositeSequenceDao.getGenes(CompositeSequence, int, int, boolean)

getGenesByCursor

CursorPage<Gene> getGenesByCursor(CompositeSequence compositeSequence,
 @Nullable
 Cursor cursor,
 int limit,
 boolean useGene2Cs)

See Also:

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

getGenesWithSpecificity

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

See Also:

• CompositeSequenceDao.getGenesWithSpecificity(Collection)

getRawSummary

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

See Also:

• CompositeSequenceDao.getRawSummary(Collection)

getRawSummary

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

See Also:

• CompositeSequenceDao.getRawSummary(ArrayDesign, int)

thaw

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

Thaw a collection of CompositeSequence for full traversal.

thaw

@CheckReturnValue
CompositeSequence thaw(CompositeSequence compositeSequence)

Thaw a single CompositeSequence for full traversal.

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)