Class CompositeSequenceServiceImpl

java.lang.Object

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

ubic.gemma.persistence.service.AbstractFilteringVoEnabledService<CompositeSequence, CompositeSequenceValueObject>

ubic.gemma.persistence.service.expression.designElement.CompositeSequenceServiceImpl

All Implemented Interfaces:

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

@Service
public class CompositeSequenceServiceImpl
extends AbstractFilteringVoEnabledService<CompositeSequence, CompositeSequenceValueObject>
implements CompositeSequenceService

Author:

keshav, pavlidis

See Also:

• CompositeSequenceService

Field Summary

Fields inherited from class AbstractService

log

Constructor Summary

Constructors

Constructor	Description
CompositeSequenceServiceImpl(CompositeSequenceDao compositeSequenceDao, BioSequenceService bioSequenceService, GeneProductService geneProductService, BlatResultService blatResultService, ArrayDesignService arrayDesignService, CompositeSequenceReadService compositeSequenceReadService)

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)	Checks to see if the CompositeSequence exists in any of the array designs.
Set<Long>	findIdsByGeneIds(Collection<Long> geneIds, Long arrayDesignId)
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 CompositeSequenceService.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)
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 CompositeSequenceService.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(Collection<CompositeSequence> sequencesToDelete)
Collection<CompositeSequence>	thaw(Collection<CompositeSequence> compositeSequences)
CompositeSequence	thaw(CompositeSequence compositeSequence)

Methods inherited from class AbstractFilteringVoEnabledService

count, getFilter, getFilter, getFilter, getFilter, getFilter, getFilter, getFilter, getFilterableProperties, getFilterablePropertyAllowedValues, getFilterablePropertyConfigAttributes, getFilterablePropertyDescription, getFilterablePropertyResolvableAllowedValuesLabels, getFilterablePropertyType, getSort, isFilterablePropertyDeprecated, isFilterablePropertyUsingSubquery, load, load, loadAllValueObjects, loadIds, loadValueObject, loadValueObjectById, loadValueObjects, loadValueObjects, loadValueObjects, loadValueObjectsByCursor, loadValueObjectsByIds

Methods inherited from class AbstractService

countAll, create, create, ensureInSession, ensureInSession, find, findOrCreate, findOrFail, getElementClass, load, load, loadAll, loadOrFail, loadOrFail, loadOrFail, loadOrFail, loadOrFail, loadOrFail, remove, save, save, streamAll, streamAll, update, update

Methods inherited from class Object

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

Methods inherited from interface BaseImmutableService

create

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 CompositeSequenceService

create, find, findOrCreate, load, remove, update

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

Constructor Details

CompositeSequenceServiceImpl

@Autowired
public CompositeSequenceServiceImpl(CompositeSequenceDao compositeSequenceDao,
 BioSequenceService bioSequenceService,
 GeneProductService geneProductService,
 BlatResultService blatResultService,
 ArrayDesignService arrayDesignService,
 CompositeSequenceReadService compositeSequenceReadService)

Method Details

findByBioSequence

public Collection<CompositeSequence> findByBioSequence(BioSequence bioSequence)

Specified by:

findByBioSequence in interface CompositeSequenceService

findByBioSequenceName

public Collection<CompositeSequence> findByBioSequenceName(String name)

Specified by:

findByBioSequenceName in interface CompositeSequenceService

findByGene

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

Specified by:

findByGene in interface CompositeSequenceService

loadValueObjectWithGeneMappingSummary

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

Description copied from interface: CompositeSequenceService

Include gene mapping summary in the CompositeSequenceValueObject.

Specified by:

loadValueObjectWithGeneMappingSummary in interface CompositeSequenceService

loadValueObjectsForGene

@Transactional(readOnly=true)
public Slice<CompositeSequenceValueObject> loadValueObjectsForGene(Gene gene,
 int start,
 int limit,
 boolean useGene2Cs)

Specified by:

loadValueObjectsForGene in interface CompositeSequenceService

loadValueObjectsForGeneByCursor

@Transactional(readOnly=true)
public CursorPage<CompositeSequenceValueObject> loadValueObjectsForGeneByCursor(Gene gene,
 @Nullable
 Cursor cursor,
 int limit,
 boolean useGene2Cs)

Description copied from interface: CompositeSequenceService

Cursor-mode counterpart to CompositeSequenceService.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).

Specified by:

loadValueObjectsForGeneByCursor in interface CompositeSequenceService

See Also:

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

findByGene

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

Specified by:

findByGene in interface CompositeSequenceService

findByGenes

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

Specified by:

findByGenes in interface CompositeSequenceService

findByGenes

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

Specified by:

findByGenes in interface CompositeSequenceService

findByName

public Collection<CompositeSequence> findByName(String name)

Specified by:

findByName in interface CompositeSequenceService

findByName

public CompositeSequence findByName(ArrayDesign arrayDesign,
 String name)

Specified by:

findByName in interface CompositeSequenceService

findByNamesInArrayDesigns

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

Checks to see if the CompositeSequence exists in any of the array designs. If so, it is internally stored in the collection of composite sequences as a HashSet, preserving order based on insertion.

Specified by:

findByNamesInArrayDesigns in interface CompositeSequenceService

getGenes

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

Specified by:

getGenes in interface CompositeSequenceService

getGenes

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

Specified by:

getGenes in interface CompositeSequenceService

getGenes

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

Specified by:

getGenes in interface CompositeSequenceService

getGenesByCursor

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

Description copied from interface: CompositeSequenceService

Cursor-mode counterpart to CompositeSequenceService.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.

Specified by:

getGenesByCursor in interface CompositeSequenceService

See Also:

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

getGenesWithSpecificity

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

Specified by:

getGenesWithSpecificity in interface CompositeSequenceService

Parameters:

compositeSequences - sequences

Returns:

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

getRawSummary

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

Specified by:

getRawSummary in interface CompositeSequenceService

getRawSummary

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

Specified by:

getRawSummary in interface CompositeSequenceService

getGeneMappingSummary

@Transactional(readOnly=true)
public Collection<GeneMappingSummary> getGeneMappingSummary(BioSequence biologicalCharacteristic,
 @Nullable
 CompositeSequenceValueObject cs)

Specified by:

getGeneMappingSummary in interface CompositeSequenceService

thaw

public Collection<CompositeSequence> thaw(Collection<CompositeSequence> compositeSequences)

Specified by:

thaw in interface CompositeSequenceService

thaw

public CompositeSequence thaw(CompositeSequence compositeSequence)

Specified by:

thaw in interface CompositeSequenceService

getSequenceData

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

Specified by:

getSequenceData in interface CompositeSequenceService

See Also:

• CompositeSequenceDao.getSequenceData(Collection)

getGeneData

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

Specified by:

getGeneData in interface CompositeSequenceService

See Also:

• CompositeSequenceDao.getGeneData(Collection)

findIdsByGeneIds

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

Specified by:

findIdsByGeneIds in interface CompositeSequenceService

See Also:

• CompositeSequenceDao.findIdsByGeneIds(Collection, Long)

remove

@Transactional
public void remove(Collection<CompositeSequence> sequencesToDelete)

Specified by:

remove in interface BaseImmutableService<CompositeSequence>

Overrides:

remove in class AbstractService<CompositeSequence>

See Also:

• BaseDao.remove(Collection)