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

Class ProcessedExpressionDataVectorServiceImpl

java.lang.Object

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

ubic.gemma.persistence.service.expression.bioAssayData.AbstractDesignElementDataVectorService<ProcessedExpressionDataVector>

ubic.gemma.persistence.service.expression.bioAssayData.ProcessedExpressionDataVectorServiceImpl

All Implemented Interfaces:

BaseImmutableService<ProcessedExpressionDataVector>, BaseReadOnlyService<ProcessedExpressionDataVector>, BaseService<ProcessedExpressionDataVector>, ProcessedExpressionDataVectorService

@Service
public class ProcessedExpressionDataVectorServiceImpl
extends AbstractDesignElementDataVectorService<ProcessedExpressionDataVector>
implements ProcessedExpressionDataVectorService

Author:

Paul

Field Summary

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

log

Constructor Summary

Constructors

Modifier	Constructor	Description
protected	ProcessedExpressionDataVectorServiceImpl(ProcessedExpressionDataVectorDao mainDao)

Method Summary

Modifier and Type	Method	Description
int	createProcessedDataVectors(ExpressionExperiment expressionExperiment, boolean updateRanks)	Create processed vectors and optionally update ranks.
int	createProcessedDataVectors(ExpressionExperiment expressionExperiment, boolean updateRanks, boolean ignoreQuantitationMismatch)	Create processed vectors and optionally update ranks.
void	evictFromCache(ExpressionExperiment ee)
Collection<T>	find(Collection<QuantitationType> quantitationTypes)	Find specific type (DesignElementDataVectorService) of vectors that meet the given criteria.
Collection<T>	find(QuantitationType quantitationType)	Find specific type (DesignElementDataVectorService) of vectors that meet the given criteria.
Collection<T>	find(BioAssayDimension bioAssayDimension)	Find specific type (raw or processed, depending on the service) of vectors that meet the given criteria.
Collection<T>	findAndThaw(Collection<QuantitationType> quantitationTypes)
Collection<T>	findAndThaw(QuantitationType quantitationType)	Find and thaw specific type (DesignElementDataVectorService) of vectors that meet the given criteria.
Collection<T>	findAndThaw(BioAssayDimension bioAssayDimension)
List<DoubleVectorValueObject>	getDiffExVectors(Long resultSetId, double threshold, int maxNumberOfResults)
List<ExperimentExpressionLevelsValueObject>	getExpressionLevels(Collection<ExpressionExperiment> ees, Collection<Gene> genes, boolean keepGeneNonSpecific, String consolidateMode)
List<ExperimentExpressionLevelsValueObject>	getExpressionLevelsByIds(Collection<Long> eeIds, Collection<Gene> genes, boolean keepGeneNonSpecific, String consolidateMode)	Retrieve expression levels by dataset IDs.
List<ExperimentExpressionLevelsValueObject>	getExpressionLevelsDiffEx(Collection<ExpressionExperiment> ees, Long diffExResultSetId, double threshold, int max, boolean keepGeneNonSpecific, String consolidateMode)
List<ExperimentExpressionLevelsValueObject>	getExpressionLevelsPca(Collection<ExpressionExperiment> ees, int limit, int component, boolean keepGeneNonSpecific, String consolidateMode)
Collection<DoubleVectorValueObject>	getProcessedDataArrays(Collection<ExpressionExperiment> expressionExperiments, Collection<Long> genes)
Collection<DoubleVectorValueObject>	getProcessedDataArrays(BioAssaySet bioAssaySet, Collection<Long> genes)
Collection<DoubleVectorValueObject>	getProcessedDataArrays(ExpressionExperiment expressionExperiment)
Collection<DoubleVectorValueObject>	getProcessedDataArraysByProbe(Collection<ExpressionExperiment> expressionExperiments, Collection<CompositeSequence> compositeSequences)
Collection<DoubleVectorValueObject>	getProcessedDataArraysByProbe(ExpressionExperiment ee, Collection<CompositeSequence> compositeSequences)
Collection<ProcessedExpressionDataVector>	getProcessedDataVectors(ExpressionExperiment expressionExperiment)
Slice<ProcessedExpressionDataVector>	getProcessedDataVectors(ExpressionExperiment expressionExperiment, BioAssayDimension dimension, int offset, int limit)
Collection<ProcessedExpressionDataVector>	getProcessedDataVectorsAndThaw(ExpressionExperiment expressionExperiment)	Retrieve and thaw a collection of vectors for a given experiment.
Slice<CompositeSequence>	getProcessedDataVectorsDesignElements(ExpressionExperiment expressionExperiment, BioAssayDimension dimension, int offset, int limit)
Collection<DoubleVectorValueObject>	getRandomProcessedDataArrays(ExpressionExperiment ee, int limit)
Map<ExpressionExperiment,Map<Gene,Collection<Double>>>	getRanks(Collection<ExpressionExperiment> expressionExperiments, Collection<Gene> genes, ProcessedExpressionDataVectorDao.RankMethod method)
int	removeProcessedDataVectors(ExpressionExperiment ee)	Remove the processed vectors of an EE.
void	reorderByDesign(ExpressionExperiment ee)	Creates new bioAssayDimensions to match the experimental design, reorders the data to match, updates.
int	replaceProcessedDataVectors(ExpressionExperiment ee, Collection<ProcessedExpressionDataVector> vectors, boolean updateRanks)	Replace the processed vectors of a EE with the given vectors.
Collection<T>	thaw(Collection<T> vectors)	Deprecated. Use findAndThaw(QuantitationType), findAndThaw(Collection) or findAndThaw(BioAssayDimension) instead, it's much more efficient.
void	updateRanks(ExpressionExperiment ee)	Update the ranks of the processed vectors for the given experiment.

Methods inherited from class ubic.gemma.persistence.service.expression.bioAssayData.AbstractDesignElementDataVectorService

find, find, find, findAndThaw, findAndThaw, findAndThaw, thaw

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, remove, save, save, streamAll, streamAll, 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.BaseReadOnlyService

countAll, find, findOrFail, getElementClass, load, load, loadAll, loadOrFail, loadOrFail, loadOrFail, loadOrFail, streamAll, streamAll

Constructor Detail

ProcessedExpressionDataVectorServiceImpl

@Autowired
protected ProcessedExpressionDataVectorServiceImpl(ProcessedExpressionDataVectorDao mainDao)

Method Detail

createProcessedDataVectors

@Transactional(rollbackFor=QuantitationTypeConversionException.class)
public int createProcessedDataVectors(ExpressionExperiment expressionExperiment,
                                      boolean updateRanks)
                               throws QuantitationTypeConversionException

Description copied from interface: ProcessedExpressionDataVectorService

Create processed vectors and optionally update ranks.

Mismatch between quantitation type and data is ignored.

This also adds an audit event and evict the vectors from the cache.

Specified by:

createProcessedDataVectors in interface ProcessedExpressionDataVectorService

updateRanks - whether to update the rnaks of the vectors or not

Throws:

QuantitationTypeConversionException - if the data cannot be converted, generally to log2 scale

See Also:

ProcessedExpressionDataVectorService.updateRanks(ExpressionExperiment), ProcessedExpressionDataVectorDao.createProcessedDataVectors(ExpressionExperiment, boolean)

createProcessedDataVectors

@Transactional(rollbackFor={QuantitationTypeDetectionException.class,QuantitationTypeConversionException.class})
public int createProcessedDataVectors(ExpressionExperiment expressionExperiment,
                                      boolean updateRanks,
                                      boolean ignoreQuantitationMismatch)
                               throws QuantitationTypeDetectionException,
                                      QuantitationTypeConversionException

Description copied from interface: ProcessedExpressionDataVectorService

Create processed vectors and optionally update ranks.

This also adds an audit event and evict the vectors from the cache.

Specified by:

createProcessedDataVectors in interface ProcessedExpressionDataVectorService

Throws:

QuantitationTypeDetectionException - if the QT caanot be detected from data, never raised if ignoreQuantitationMismatch is set to true

QuantitationTypeConversionException - if the data cannot be converted, generally to log2 scale

See Also:

ProcessedExpressionDataVectorService.createProcessedDataVectors(ExpressionExperiment, boolean), ProcessedExpressionDataVectorService.updateRanks(ExpressionExperiment)

replaceProcessedDataVectors

@Transactional
public int replaceProcessedDataVectors(ExpressionExperiment ee,
                                       Collection<ProcessedExpressionDataVector> vectors,
                                       boolean updateRanks)

Description copied from interface: ProcessedExpressionDataVectorService

Replace the processed vectors of a EE with the given vectors.

Ranks are recomputed, no conversion of QT is done.

This also adds an audit event and evict the vectors from the cache.

Specified by:

replaceProcessedDataVectors in interface ProcessedExpressionDataVectorService

Parameters:

ee - ee

vectors - non-persistent, all of the same QuantitationType

updateRanks - whether to update ranks or not

See Also:

ProcessedExpressionDataVectorDao.createProcessedDataVectors(ExpressionExperiment, boolean)

removeProcessedDataVectors

@Transactional
public int removeProcessedDataVectors(ExpressionExperiment ee)

Description copied from interface: ProcessedExpressionDataVectorService

Remove the processed vectors of an EE.

This also adds an audit event and evict the vectors from the cache.

Specified by:

removeProcessedDataVectors in interface ProcessedExpressionDataVectorService

See Also:

ExpressionExperimentService.removeProcessedDataVectors(ExpressionExperiment)

reorderByDesign

@Transactional
public void reorderByDesign(ExpressionExperiment ee)

Description copied from interface: ProcessedExpressionDataVectorService

Creates new bioAssayDimensions to match the experimental design, reorders the data to match, updates.

This also adds an audit event and evict the vectors from the cache.

Specified by:

reorderByDesign in interface ProcessedExpressionDataVectorService

updateRanks

@Transactional
public void updateRanks(ExpressionExperiment ee)

Description copied from interface: ProcessedExpressionDataVectorService

Update the ranks of the processed vectors for the given experiment.

This also adds an audit event and evict the vectors from the cache.

Specified by:

updateRanks in interface ProcessedExpressionDataVectorService

getExpressionLevels

@Transactional(readOnly=true)
public List<ExperimentExpressionLevelsValueObject> getExpressionLevels(Collection<ExpressionExperiment> ees,
                                                                       Collection<Gene> genes,
                                                                       boolean keepGeneNonSpecific,
                                                                       @Nullable
                                                                       String consolidateMode)

Specified by:

getExpressionLevels in interface ProcessedExpressionDataVectorService

Parameters:

ees - expressionExperiments

genes - genes

keepGeneNonSpecific - whether to keep vectors that are not specific to the gene

consolidateMode - how to consolidate the vectors when there is more than one

Returns:

value objects containing structured information about the expression levels of given genes

getExpressionLevelsByIds

@Transactional(readOnly=true)
public List<ExperimentExpressionLevelsValueObject> getExpressionLevelsByIds(Collection<Long> eeIds,
                                                                            Collection<Gene> genes,
                                                                            boolean keepGeneNonSpecific,
                                                                            @Nullable
                                                                            String consolidateMode)

Description copied from interface: ProcessedExpressionDataVectorService

Retrieve expression levels by dataset IDs.

Specified by:

getExpressionLevelsByIds in interface ProcessedExpressionDataVectorService

See Also:

ProcessedExpressionDataVectorService.getExpressionLevels(Collection, Collection, boolean, String)

getExpressionLevelsPca

@Transactional(readOnly=true)
public List<ExperimentExpressionLevelsValueObject> getExpressionLevelsPca(Collection<ExpressionExperiment> ees,
                                                                          int limit,
                                                                          int component,
                                                                          boolean keepGeneNonSpecific,
                                                                          @Nullable
                                                                          String consolidateMode)

Specified by:

getExpressionLevelsPca in interface ProcessedExpressionDataVectorService

Parameters:

ees - expressionExperiments

limit - threshold

component - the principal component

keepGeneNonSpecific - whether to keep vectors that are not specific to the gene

consolidateMode - how to consolidate the vectors when there is more than one

Returns:

value objects containing structured information about the expression levels of genes highly loaded in the given principal component.

getExpressionLevelsDiffEx

@Transactional(readOnly=true)
public List<ExperimentExpressionLevelsValueObject> getExpressionLevelsDiffEx(Collection<ExpressionExperiment> ees,
                                                                             Long diffExResultSetId,
                                                                             double threshold,
                                                                             int max,
                                                                             boolean keepGeneNonSpecific,
                                                                             @Nullable
                                                                             String consolidateMode)

Specified by:

getExpressionLevelsDiffEx in interface ProcessedExpressionDataVectorService

Parameters:

ees - ees

diffExResultSetId - the differential expression result set to access

threshold - threshold

max - max level

keepGeneNonSpecific - whether to keep vectors that are not specific to the gene

consolidateMode - how to consolidate the vectors when there is more than one

Returns:

value objects containing structured information about the expression levels of genes highly loaded in the given principal component.

getProcessedDataArrays

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

Specified by:

getProcessedDataArrays in interface ProcessedExpressionDataVectorService

See Also:

CachedProcessedExpressionDataVectorService.getProcessedDataArrays(Collection, Collection)

getProcessedDataArrays

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

Specified by:

getProcessedDataArrays in interface ProcessedExpressionDataVectorService

See Also:

CachedProcessedExpressionDataVectorService.getProcessedDataArrays(BioAssaySet, Collection)

getProcessedDataArrays

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

Specified by:

getProcessedDataArrays in interface ProcessedExpressionDataVectorService

See Also:

CachedProcessedExpressionDataVectorService.getProcessedDataArrays(BioAssaySet)

getRandomProcessedDataArrays

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

Specified by:

getRandomProcessedDataArrays in interface ProcessedExpressionDataVectorService

See Also:

CachedProcessedExpressionDataVectorService.getRandomProcessedDataArrays(BioAssaySet, int)

getProcessedDataArraysByProbe

@Transactional(readOnly=true)
public Collection<DoubleVectorValueObject> getProcessedDataArraysByProbe(ExpressionExperiment ee,
                                                                         Collection<CompositeSequence> compositeSequences)

Specified by:

getProcessedDataArraysByProbe in interface ProcessedExpressionDataVectorService

getProcessedDataArraysByProbe

@Transactional(readOnly=true)
public Collection<DoubleVectorValueObject> getProcessedDataArraysByProbe(Collection<ExpressionExperiment> expressionExperiments,
                                                                         Collection<CompositeSequence> compositeSequences)

Specified by:

getProcessedDataArraysByProbe in interface ProcessedExpressionDataVectorService

See Also:

CachedProcessedExpressionDataVectorService.getProcessedDataArraysByProbe(Collection, Collection)

getProcessedDataVectors

@Transactional(readOnly=true)
public Collection<ProcessedExpressionDataVector> getProcessedDataVectors(ExpressionExperiment expressionExperiment)

Specified by:

getProcessedDataVectors in interface ProcessedExpressionDataVectorService

See Also:

ProcessedExpressionDataVectorDao.getProcessedVectors(ExpressionExperiment)

getProcessedDataVectors

@Transactional(readOnly=true)
public Slice<ProcessedExpressionDataVector> getProcessedDataVectors(ExpressionExperiment expressionExperiment,
                                                                    BioAssayDimension dimension,
                                                                    int offset,
                                                                    int limit)

Specified by:

getProcessedDataVectors in interface ProcessedExpressionDataVectorService

getProcessedDataVectorsDesignElements

@Transactional(readOnly=true)
public Slice<CompositeSequence> getProcessedDataVectorsDesignElements(ExpressionExperiment expressionExperiment,
                                                                      BioAssayDimension dimension,
                                                                      int offset,
                                                                      int limit)

Specified by:

getProcessedDataVectorsDesignElements in interface ProcessedExpressionDataVectorService

getProcessedDataVectorsAndThaw

@Transactional(readOnly=true)
public Collection<ProcessedExpressionDataVector> getProcessedDataVectorsAndThaw(ExpressionExperiment expressionExperiment)

Description copied from interface: ProcessedExpressionDataVectorService

Retrieve and thaw a collection of vectors for a given experiment.

Specified by:

getProcessedDataVectorsAndThaw in interface ProcessedExpressionDataVectorService

See Also:

ProcessedExpressionDataVectorDao.getProcessedVectors(ExpressionExperiment), DesignElementDataVectorDao.thaw(Collection)

getRanks

@Transactional(readOnly=true)
public Map<ExpressionExperiment,Map<Gene,Collection<Double>>> getRanks(Collection<ExpressionExperiment> expressionExperiments,
                                                                                   Collection<Gene> genes,
                                                                                   ProcessedExpressionDataVectorDao.RankMethod method)

Specified by:

getRanks in interface ProcessedExpressionDataVectorService

See Also:

ProcessedExpressionDataVectorDao.getRanks(ExpressionExperiment, Collection, ProcessedExpressionDataVectorDao.RankMethod)

getDiffExVectors

@Transactional(readOnly=true)
public List<DoubleVectorValueObject> getDiffExVectors(Long resultSetId,
                                                      double threshold,
                                                      int maxNumberOfResults)

Specified by:

getDiffExVectors in interface ProcessedExpressionDataVectorService

evictFromCache

public void evictFromCache(ExpressionExperiment ee)

Specified by:

evictFromCache in interface ProcessedExpressionDataVectorService

find

@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","AFTER_ACL_DATAVECTOR_COLLECTION_READ"})
public abstract Collection<T> find(BioAssayDimension bioAssayDimension)

Find specific type (raw or processed, depending on the service) of vectors that meet the given criteria.

Parameters:

bioAssayDimension - the BA dimension

Returns:

the found vectors of type DesignElementDataVectorService

findAndThaw

@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","AFTER_ACL_DATAVECTOR_COLLECTION_READ"})
public abstract Collection<T> findAndThaw(BioAssayDimension bioAssayDimension)

find

@Secured("GROUP_ADMIN")
public abstract Collection<T> find(Collection<QuantitationType> quantitationTypes)

Find specific type (DesignElementDataVectorService) of vectors that meet the given criteria.

Parameters:

quantitationTypes - the QTs

Returns:

the found vectors of type DesignElementDataVectorService

findAndThaw

@Secured("GROUP_ADMIN")
public abstract Collection<T> findAndThaw(Collection<QuantitationType> quantitationTypes)

find

@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","AFTER_ACL_DATAVECTOR_COLLECTION_READ"})
public abstract Collection<T> find(QuantitationType quantitationType)

Find specific type (DesignElementDataVectorService) of vectors that meet the given criteria.

Parameters:

quantitationType - the QT

Returns:

the found vectors of type DesignElementDataVectorService

findAndThaw

@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","AFTER_ACL_DATAVECTOR_COLLECTION_READ"})
public abstract Collection<T> findAndThaw(QuantitationType quantitationType)

Find and thaw specific type (DesignElementDataVectorService) of vectors that meet the given criteria.

thaw

@CheckReturnValue
@Deprecated
public abstract Collection<T> thaw(Collection<T> vectors)

Deprecated.

Use findAndThaw(QuantitationType), findAndThaw(Collection) or findAndThaw(BioAssayDimension) instead, it's much more efficient.

Thaw the given vectors.