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

Interface CompositeSequenceDao

All Superinterfaces:

BaseDao<CompositeSequence>, BaseVoEnabledDao<CompositeSequence,CompositeSequenceValueObject>, FilteringDao<CompositeSequence>, FilteringVoEnabledDao<CompositeSequence,CompositeSequenceValueObject>

All Known Implementing Classes:

CompositeSequenceDaoImpl

public interface CompositeSequenceDao
extends FilteringVoEnabledDao<CompositeSequence,CompositeSequenceValueObject>

See Also:

CompositeSequence

Field Summary

Fields

Modifier and Type	Field	Description
static String	OBJECT_ALIAS

Method Summary

Modifier and Type	Method	Description
Collection<CompositeSequence>	findByBioSequence(BioSequence bioSequence)
Collection<CompositeSequence>	findByBioSequenceName(String name)
Collection<CompositeSequence>	findByGene(Gene gene)
Slice<CompositeSequence>	findByGene(Gene gene, int start, int limit)
Collection<CompositeSequence>	findByGene(Gene gene, ArrayDesign arrayDesign)
Collection<CompositeSequence>	findByName(String name)
CompositeSequence	findByName(ArrayDesign arrayDesign, String name)
Map<CompositeSequence,Collection<Gene>>	getGenes(Collection<CompositeSequence> compositeSequences)	Given a collection of composite sequences returns a map of the given composite sequences to a collection of genes
Slice<Gene>	getGenes(CompositeSequence compositeSequence, int offset, int limit)	given a composite sequence returns a collection of genes
Map<CompositeSequence,Collection<BioSequence2GeneProduct>>	getGenesWithSpecificity(Collection<CompositeSequence> compositeSequences)
Collection<Object[]>	getRawSummary(Collection<CompositeSequence> compositeSequences)
Collection<Object[]>	getRawSummary(ArrayDesign arrayDesign, int numResults)
void	thaw(Collection<CompositeSequence> compositeSequences)
void	thaw(CompositeSequence compositeSequence)

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

countAll, create, create, find, findOrCreate, getElementClass, getIdentifierPropertyName, load, load, loadAll, loadReference, loadReference, remove, remove, remove, save, save, update, update

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

loadAllValueObjects, loadValueObject, loadValueObjectById, loadValueObjects, loadValueObjectsByIds

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

count, getFilter, getFilter, getFilter, getFilter, getFilterableProperties, getFilterablePropertyAllowedValues, getFilterablePropertyDescription, getFilterablePropertyIsUsingSubquery, getFilterablePropertyType, getSort, load, load, loadIds

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

loadValueObjects, loadValueObjects

Field Detail

OBJECT_ALIAS

static final String OBJECT_ALIAS

See Also:

Constant Field Values

Method Detail

findByBioSequence

Collection<CompositeSequence> findByBioSequence(BioSequence bioSequence)

findByBioSequenceName

Collection<CompositeSequence> findByBioSequenceName(String name)

findByGene

Collection<CompositeSequence> findByGene(Gene gene)

findByGene

Slice<CompositeSequence> findByGene(Gene gene,
                                    int start,
                                    int limit)

findByGene

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

findByName

Collection<CompositeSequence> findByName(String name)

findByName

CompositeSequence findByName(ArrayDesign arrayDesign,
                             String name)

getGenes

Map<CompositeSequence,Collection<Gene>> getGenes(Collection<CompositeSequence> compositeSequences)

Given a collection of composite sequences returns a map of the given composite sequences to a collection of genes

Parameters:

compositeSequences - composite sequences

Returns:

map

getGenes

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

given a composite sequence returns a collection of genes

Parameters:

compositeSequence - sequence

offset - offset

limit - limit

Returns:

collection of genes

getGenesWithSpecificity

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

Parameters:

compositeSequences - sequences

Returns:

a map of CompositeSequences to BlatAssociations.

getRawSummary

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

getRawSummary

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

thaw

void thaw(Collection<CompositeSequence> compositeSequences)

thaw

void thaw(CompositeSequence compositeSequence)