Class CompositeSequenceReadServiceImpl

java.lang.Object

ubic.gemma.persistence.service.expression.designElement.CompositeSequenceReadServiceImpl

All Implemented Interfaces:

CompositeSequenceReadService

@Service("compositeSequenceReadService")
public class CompositeSequenceReadServiceImpl
extends Object
implements CompositeSequenceReadService

Implementation of CompositeSequenceReadService.

All public methods are @Transactional(readOnly = true). ACL enforcement is the responsibility of the facade CompositeSequenceService interface — this class is unsecured at the AOP boundary on purpose, so intra-gemma-core callers can bypass duplicate ACL checks once authenticated.

See Also:

• CompositeSequenceService

Constructor Summary

Constructors

Constructor	Description
CompositeSequenceReadServiceImpl(CompositeSequenceDao compositeSequenceDao)

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.

Methods inherited from class Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Details

CompositeSequenceReadServiceImpl

@Autowired
public CompositeSequenceReadServiceImpl(CompositeSequenceDao compositeSequenceDao)

Method Details

findByBioSequence

@Transactional(readOnly=true)
public Collection<CompositeSequence> findByBioSequence(BioSequence bioSequence)

Specified by:

findByBioSequence in interface CompositeSequenceReadService

See Also:

• CompositeSequenceDao.findByBioSequence(BioSequence)

findByBioSequenceName

@Transactional(readOnly=true)
public Collection<CompositeSequence> findByBioSequenceName(String name)

Specified by:

findByBioSequenceName in interface CompositeSequenceReadService

See Also:

• CompositeSequenceDao.findByBioSequenceName(String)

findByGene

@Transactional(readOnly=true)
public Collection<CompositeSequence> findByGene(Gene gene,
 boolean useGene2Cs)

Specified by:

findByGene in interface CompositeSequenceReadService

See Also:

• CompositeSequenceDao.findByGene(Gene, boolean)

findByGene

@Transactional(readOnly=true)
public Collection<CompositeSequence> findByGene(Gene gene,
 ArrayDesign arrayDesign,
 boolean useGene2Cs)

Specified by:

findByGene in interface CompositeSequenceReadService

See Also:

• CompositeSequenceDao.findByGene(Gene, ArrayDesign, boolean)

findByGenes

@Transactional(readOnly=true)
public Map<Gene, Collection<CompositeSequence>> findByGenes(Collection<Gene> genes,
 boolean useGene2Cs)

Specified by:

findByGenes in interface CompositeSequenceReadService

See Also:

• CompositeSequenceDao.findByGenes(Collection, boolean)

findByGenes

@Transactional(readOnly=true)
public Map<Gene, Collection<CompositeSequence>> findByGenes(Collection<Gene> genes,
 ArrayDesign arrayDesign,
 boolean useGene2Cs)

Specified by:

findByGenes in interface CompositeSequenceReadService

See Also:

• CompositeSequenceDao.findByGenes(Collection, ArrayDesign, boolean)

findByName

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

Specified by:

findByName in interface CompositeSequenceReadService

See Also:

• CompositeSequenceDao.findByName(String)

findByName

@Transactional(readOnly=true)
public CompositeSequence findByName(ArrayDesign arrayDesign,
 String name)

Specified by:

findByName in interface CompositeSequenceReadService

See Also:

• CompositeSequenceDao.findByName(ArrayDesign, String)

findByNamesInArrayDesigns

@Transactional(readOnly=true)
@Nullable
public Collection<CompositeSequence> findByNamesInArrayDesigns(Collection<String> compositeSequenceNames,
 Collection<ArrayDesign> arrayDesigns)

Description copied from interface: CompositeSequenceReadService

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.

Specified by:

findByNamesInArrayDesigns in interface CompositeSequenceReadService

getGenes

@Transactional(readOnly=true)
public Map<CompositeSequence, Collection<Gene>> getGenes(Collection<CompositeSequence> sequences,
 boolean useGene2Cs)

Specified by:

getGenes in interface CompositeSequenceReadService

See Also:

• CompositeSequenceDao.getGenes(Collection, boolean)

getGenes

@Transactional(readOnly=true)
public Collection<Gene> getGenes(CompositeSequence compositeSequence,
 boolean useGene2Cs)

Description copied from interface: CompositeSequenceReadService

Return all genes mapped to the given composite sequence.

Specified by:

getGenes in interface CompositeSequenceReadService

getGenes

@Transactional(readOnly=true)
public Slice<Gene> getGenes(CompositeSequence compositeSequence,
 int offset,
 int limit,
 boolean useGene2Cs)

Specified by:

getGenes in interface CompositeSequenceReadService

See Also:

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

getGenesByCursor

@Transactional(readOnly=true)
public CursorPage<Gene> getGenesByCursor(CompositeSequence compositeSequence,
 @Nullable
 Cursor cursor,
 int limit,
 boolean useGene2Cs)

Specified by:

getGenesByCursor in interface CompositeSequenceReadService

See Also:

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

getGenesWithSpecificity

@Transactional(readOnly=true)
public Map<CompositeSequence, Collection<BioSequence2GeneProduct>> getGenesWithSpecificity(Collection<CompositeSequence> compositeSequences)

Specified by:

getGenesWithSpecificity in interface CompositeSequenceReadService

See Also:

• CompositeSequenceDao.getGenesWithSpecificity(Collection)

getRawSummary

@Transactional(readOnly=true)
public Collection<Object[]> getRawSummary(Collection<CompositeSequence> compositeSequences)

Specified by:

getRawSummary in interface CompositeSequenceReadService

See Also:

• CompositeSequenceDao.getRawSummary(Collection)

getRawSummary

@Transactional(readOnly=true)
public Collection<Object[]> getRawSummary(ArrayDesign arrayDesign,
 int numResults)

Specified by:

getRawSummary in interface CompositeSequenceReadService

See Also:

• CompositeSequenceDao.getRawSummary(ArrayDesign, int)

thaw

@Transactional(readOnly=true)
public Collection<CompositeSequence> thaw(Collection<CompositeSequence> compositeSequences)

Description copied from interface: CompositeSequenceReadService

Thaw a collection of CompositeSequence for full traversal.

Specified by:

thaw in interface CompositeSequenceReadService

thaw

@Transactional(readOnly=true)
public CompositeSequence thaw(CompositeSequence compositeSequence)

Description copied from interface: CompositeSequenceReadService

Thaw a single CompositeSequence for full traversal.

Specified by:

thaw in interface CompositeSequenceReadService

getSequenceData

@Transactional(readOnly=true)
public Map<Long, CompositeSequenceDao.BioSequenceLite> getSequenceData(Collection<Long> compositeSequenceIds)

Specified by:

getSequenceData in interface CompositeSequenceReadService

See Also:

• CompositeSequenceDao.getSequenceData(Collection)

getGeneData

@Transactional(readOnly=true)
public Map<Long, List<GeneReferenceValueObject>> getGeneData(Collection<Long> compositeSequenceIds)

Specified by:

getGeneData in interface CompositeSequenceReadService

See Also:

• CompositeSequenceDao.getGeneData(Collection)

findIdsByGeneIds

@Transactional(readOnly=true)
public Set<Long> findIdsByGeneIds(Collection<Long> geneIds,
 Long arrayDesignId)

Specified by:

findIdsByGeneIds in interface CompositeSequenceReadService

See Also:

• CompositeSequenceDao.findIdsByGeneIds(Collection, Long)