Package ubic.gemma.persistence.service.expression.bioAssayData

Class CachedProcessedExpressionDataVectorServiceImpl

java.lang.Object

ubic.gemma.persistence.service.expression.bioAssayData.CachedProcessedExpressionDataVectorServiceImpl

All Implemented Interfaces:

CachedProcessedExpressionDataVectorService

@Service
public class CachedProcessedExpressionDataVectorServiceImpl
extends Object
implements CachedProcessedExpressionDataVectorService

Constructor Summary

Constructors

Constructor	Description
CachedProcessedExpressionDataVectorServiceImpl(ProcessedExpressionDataVectorDao processedExpressionDataVectorDao, SessionFactory sessionFactory)

Method Summary

Modifier and Type	Method	Description
Collection<DoubleVectorValueObject>	getProcessedDataArrays(Collection<? extends BioAssaySet> expressionExperiments, Collection<Long> genes)	Retrieve processed vectors by genes and experiments.
Collection<DoubleVectorValueObject>	getProcessedDataArrays(BioAssaySet expressionExperiment)	Retrieve processed vectors for a given experiment or subset.
Collection<DoubleVectorValueObject>	getProcessedDataArrays(BioAssaySet expressionExperiment, Collection<Long> genes)	Retrieve processed vectors by genes for a given experiment or subset.
Collection<DoubleVectorValueObject>	getProcessedDataArraysByProbe(Collection<? extends BioAssaySet> ees, Collection<CompositeSequence> probes)	Retrieves processed vectors by probes and experiments
Collection<DoubleVectorValueObject>	getProcessedDataArraysByProbeIds(BioAssaySet ee, Collection<Long> probes)
Collection<DoubleVectorValueObject>	getRandomProcessedDataArrays(BioAssaySet ee, int limit)	Retrieve random processed vectors for a given experiment or subset.

Methods inherited from class java.lang.Object

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

Constructor Detail

CachedProcessedExpressionDataVectorServiceImpl

@Autowired
public CachedProcessedExpressionDataVectorServiceImpl(ProcessedExpressionDataVectorDao processedExpressionDataVectorDao,
                                                      SessionFactory sessionFactory)

Method Detail

getProcessedDataArrays

@Transactional(readOnly=true)
public Collection<DoubleVectorValueObject> getProcessedDataArrays(BioAssaySet expressionExperiment)

Description copied from interface: CachedProcessedExpressionDataVectorService

Retrieve processed vectors for a given experiment or subset.

Specified by:

getProcessedDataArrays in interface CachedProcessedExpressionDataVectorService

getProcessedDataArrays

@Transactional(readOnly=true)
public Collection<DoubleVectorValueObject> getProcessedDataArrays(BioAssaySet expressionExperiment,
                                                                  Collection<Long> genes)

Description copied from interface: CachedProcessedExpressionDataVectorService

Retrieve processed vectors by genes for a given experiment or subset.

Specified by:

getProcessedDataArrays in interface CachedProcessedExpressionDataVectorService

getRandomProcessedDataArrays

@Transactional(readOnly=true)
public Collection<DoubleVectorValueObject> getRandomProcessedDataArrays(BioAssaySet ee,
                                                                        int limit)

Description copied from interface: CachedProcessedExpressionDataVectorService

Retrieve random processed vectors for a given experiment or subset.

Specified by:

getRandomProcessedDataArrays in interface CachedProcessedExpressionDataVectorService

getProcessedDataArrays

@Transactional(readOnly=true)
public Collection<DoubleVectorValueObject> getProcessedDataArrays(Collection<? extends BioAssaySet> expressionExperiments,
                                                                  Collection<Long> genes)

Description copied from interface: CachedProcessedExpressionDataVectorService

Retrieve processed vectors by genes and experiments.

Specified by:

getProcessedDataArrays in interface CachedProcessedExpressionDataVectorService

getProcessedDataArraysByProbe

@Transactional(readOnly=true)
public Collection<DoubleVectorValueObject> getProcessedDataArraysByProbe(Collection<? extends BioAssaySet> ees,
                                                                         Collection<CompositeSequence> probes)

Description copied from interface: CachedProcessedExpressionDataVectorService

Retrieves processed vectors by probes and experiments

Specified by:

getProcessedDataArraysByProbe in interface CachedProcessedExpressionDataVectorService

Parameters:

ees - EEs

probes - composite sequences

Returns:

double vector vos

getProcessedDataArraysByProbeIds

@Transactional(readOnly=true)
public Collection<DoubleVectorValueObject> getProcessedDataArraysByProbeIds(BioAssaySet ee,
                                                                            Collection<Long> probes)

Specified by:

getProcessedDataArraysByProbeIds in interface CachedProcessedExpressionDataVectorService