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

Class CompositeSequenceServiceImpl

java.lang.Object

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

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 ubic.gemma.persistence.service.AbstractService

log

Constructor Summary

Constructors

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

Method Summary

Modifier and Type	Method	Description
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)	Checks to see if the CompositeSequence exists in any of the array designs.
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)
Slice<CompositeSequenceValueObject>	loadValueObjectsForGene(Gene gene, int start, int limit)
CompositeSequenceValueObject	loadValueObjectWithGeneMappingSummary(CompositeSequence cs)	Include gene mapping summary in the CompositeSequenceValueObject.
void	remove(Collection<CompositeSequence> sequencesToDelete)	Removes all the given entities from persistent storage.
Collection<CompositeSequence>	thaw(Collection<CompositeSequence> compositeSequences)
CompositeSequence	thaw(CompositeSequence compositeSequence)

Methods inherited from class ubic.gemma.persistence.service.AbstractFilteringVoEnabledService

count, getFilter, getFilter, getFilter, getFilter, getFilter, getFilter, getFilterableProperties, getFilterablePropertyAllowedValues, getFilterablePropertyConfigAttributes, getFilterablePropertyDescription, getFilterablePropertyIsUsingSubquery, getFilterablePropertyResolvableAllowedValuesLabels, getFilterablePropertyType, getIdentifierPropertyName, getSort, load, load, loadAllValueObjects, loadIds, loadValueObject, loadValueObjectById, loadValueObjects, loadValueObjects, loadValueObjects, loadValueObjectsByIds

Methods inherited from class ubic.gemma.persistence.service.AbstractService

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

Methods inherited from class java.lang.Object

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

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

create, 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.expression.designElement.CompositeSequenceService

create, find, findOrCreate, load, remove, update

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

count, getFilter, getFilter, 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

Constructor Detail

CompositeSequenceServiceImpl

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

Method Detail

findByBioSequence

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

Specified by:

findByBioSequence in interface CompositeSequenceService

findByBioSequenceName

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

Specified by:

findByBioSequenceName in interface CompositeSequenceService

findByGene

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

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)

Specified by:

loadValueObjectsForGene in interface CompositeSequenceService

findByGene

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

Specified by:

findByGene in interface CompositeSequenceService

findByName

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

Specified by:

findByName in interface CompositeSequenceService

findByName

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

Specified by:

findByName in interface CompositeSequenceService

findByNamesInArrayDesigns

@Transactional(readOnly=true)
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

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

Description copied from interface: CompositeSequenceService

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

Specified by:

getGenes in interface CompositeSequenceService

Parameters:

sequences - sequences

Returns:

map

getGenes

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

Specified by:

getGenes in interface CompositeSequenceService

getGenes

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

Specified by:

getGenes in interface CompositeSequenceService

getGenesWithSpecificity

@Transactional(readOnly=true)
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

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

Specified by:

getRawSummary in interface CompositeSequenceService

getRawSummary

@Transactional(readOnly=true)
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

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

Specified by:

thaw in interface CompositeSequenceService

thaw

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

Specified by:

thaw in interface CompositeSequenceService

remove

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

Description copied from interface: BaseImmutableService

Removes all the given entities from persistent storage.

Specified by:

remove in interface BaseImmutableService<CompositeSequence>

Overrides:

remove in class AbstractService<CompositeSequence>

Parameters:

sequencesToDelete - the entities to be removed.