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:

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

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

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
void	afterPropertiesSet()
void	clearCache()
void	computeProcessedExpressionData(ExpressionExperiment ee)	Compute processed expression data, ignoring mismatched with the inferred scale.
void	computeProcessedExpressionData(ExpressionExperiment ee, boolean ignoreQuantitationMismatch)	This method should not be called on its own, if possible.
Set<ProcessedExpressionDataVector>	createProcessedDataVectors(ExpressionExperiment expressionExperiment)
Set<ProcessedExpressionDataVector>	createProcessedDataVectors(ExpressionExperiment expressionExperiment, boolean ignoreQuantitationMismatch)	Populate the processed data for the given experiment.
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>	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 ee, Collection<Long> genes)
Collection<DoubleVectorValueObject>	getProcessedDataArrays(ExpressionExperiment expressionExperiment)
Collection<DoubleVectorValueObject>	getProcessedDataArrays(ExpressionExperiment ee, int limit)
Collection<DoubleVectorValueObject>	getProcessedDataArraysByProbe(Collection<ExpressionExperiment> expressionExperiments, Collection<CompositeSequence> compositeSequences)	Retrieves DEDV's by probes and experiments
Collection<DoubleVectorValueObject>	getProcessedDataArraysByProbeIds(BioAssaySet ee, Collection<Long> probes)
Collection<ProcessedExpressionDataVector>	getProcessedDataVectors(ExpressionExperiment expressionExperiment)
Collection<ProcessedExpressionDataVector>	getProcessedDataVectorsAndThaw(ExpressionExperiment expressionExperiment)
Map<ExpressionExperiment,Map<Gene,Collection<Double>>>	getRanks(Collection<ExpressionExperiment> expressionExperiments, Collection<Gene> genes, ProcessedExpressionDataVectorDao.RankMethod method)
Map<Gene,Collection<Double>>	getRanks(ExpressionExperiment expressionExperiment, Collection<Gene> genes, ProcessedExpressionDataVectorDao.RankMethod method)
Map<CompositeSequence,Double>	getRanks(ExpressionExperiment expressionExperiment, ProcessedExpressionDataVectorDao.RankMethod method)
Map<ExpressionExperiment,Map<Gene,Map<CompositeSequence,Double[]>>>	getRanksByProbe(Collection<ExpressionExperiment> eeCol, Collection<Gene> genes)	Retrieve expression level information for genes in experiments.
void	removeProcessedDataVectors(ExpressionExperiment expressionExperiment)
void	reorderByDesign(ExpressionExperiment ee)	Creates new bioAssayDimensions to match the experimental design, reorders the data to match, updates.
void	replaceProcessedDataVectors(ExpressionExperiment ee, Collection<ProcessedExpressionDataVector> vectors)	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)

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, 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

Methods inherited from interface ubic.gemma.persistence.service.expression.bioAssayData.ProcessedExpressionDataVectorService

update

Constructor Detail

ProcessedExpressionDataVectorServiceImpl

@Autowired
protected ProcessedExpressionDataVectorServiceImpl(ProcessedExpressionDataVectorDao mainDao)

Method Detail

afterPropertiesSet

public void afterPropertiesSet()
                        throws Exception

Specified by:

afterPropertiesSet in interface InitializingBean

Throws:

Exception

replaceProcessedDataVectors

@Transactional(propagation=NEVER)
public void replaceProcessedDataVectors(ExpressionExperiment ee,
                                        Collection<ProcessedExpressionDataVector> vectors)

Description copied from interface: ProcessedExpressionDataVectorService

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

Ranks are recomputed.

Specified by:

replaceProcessedDataVectors in interface ProcessedExpressionDataVectorService

Parameters:

ee - ee

vectors - non-persistent, all of the same quantitationtype

updateRanks

@Transactional
public void updateRanks(ExpressionExperiment ee)

Specified by:

updateRanks in interface ProcessedExpressionDataVectorService

clearCache

public void clearCache()

Specified by:

clearCache in interface ProcessedExpressionDataVectorService

createProcessedDataVectors

@Transactional
public Set<ProcessedExpressionDataVector> createProcessedDataVectors(ExpressionExperiment expressionExperiment)

Specified by:

createProcessedDataVectors in interface ProcessedExpressionDataVectorService

createProcessedDataVectors

@Transactional
public Set<ProcessedExpressionDataVector> createProcessedDataVectors(ExpressionExperiment expressionExperiment,
                                                                     boolean ignoreQuantitationMismatch)
                                                              throws QuantitationMismatchException

Description copied from interface: ProcessedExpressionDataVectorService

Populate the processed data for the given experiment. For two-channel studies, the missing value information should already have been computed.

Specified by:

createProcessedDataVectors in interface ProcessedExpressionDataVectorService

Parameters:

expressionExperiment - ee

Returns:

updated expressionExperiment

Throws:

QuantitationMismatchException

getProcessedDataArrays

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

Specified by:

getProcessedDataArrays in interface ProcessedExpressionDataVectorService

Parameters:

expressionExperiments - - expressionExperiments or expressionExperimentSubSets

genes - genes

Returns:

vectors, which will be subsetted if the bioassayset is a subset.

getProcessedDataArrays

public Collection<DoubleVectorValueObject> getProcessedDataArrays(BioAssaySet ee,
                                                                  Collection<Long> genes)

Specified by:

getProcessedDataArrays 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

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(ExpressionExperiment expressionExperiment)

Specified by:

getProcessedDataArrays in interface ProcessedExpressionDataVectorService

Parameters:

expressionExperiment - ee

Returns:

double vector vos

getProcessedDataArrays

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

Specified by:

getProcessedDataArrays in interface ProcessedExpressionDataVectorService

Parameters:

ee - ee

limit - (null limit = default hibernate limit).

Returns:

double vector vos

getProcessedDataArraysByProbe

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

Description copied from interface: ProcessedExpressionDataVectorService

Retrieves DEDV's by probes and experiments

Specified by:

getProcessedDataArraysByProbe in interface ProcessedExpressionDataVectorService

Parameters:

expressionExperiments - EEs

compositeSequences - composite sequences

Returns:

double vector vos

getProcessedDataArraysByProbeIds

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

Specified by:

getProcessedDataArraysByProbeIds in interface ProcessedExpressionDataVectorService

getProcessedDataVectors

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

Specified by:

getProcessedDataVectors in interface ProcessedExpressionDataVectorService

getProcessedDataVectorsAndThaw

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

Specified by:

getProcessedDataVectorsAndThaw in interface ProcessedExpressionDataVectorService

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

getRanks

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

Specified by:

getRanks in interface ProcessedExpressionDataVectorService

getRanks

@Transactional(readOnly=true)
public Map<CompositeSequence,Double> getRanks(ExpressionExperiment expressionExperiment,
                                                    ProcessedExpressionDataVectorDao.RankMethod method)

Specified by:

getRanks in interface ProcessedExpressionDataVectorService

getRanksByProbe

@Transactional(readOnly=true)
public Map<ExpressionExperiment,Map<Gene,Map<CompositeSequence,Double[]>>> getRanksByProbe(Collection<ExpressionExperiment> eeCol,
                                                                                                             Collection<Gene> genes)

Description copied from interface: ProcessedExpressionDataVectorService

Retrieve expression level information for genes in experiments.

Specified by:

getRanksByProbe in interface ProcessedExpressionDataVectorService

Parameters:

eeCol - ees

genes - genes

Returns:

A map of experiment -> gene -> probe -> array of doubles holding the 1) mean and 2) max expression rank.

removeProcessedDataVectors

@Transactional
public void removeProcessedDataVectors(ExpressionExperiment expressionExperiment)

Specified by:

removeProcessedDataVectors in interface ProcessedExpressionDataVectorService

getDiffExVectors

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

Specified by:

getDiffExVectors in interface ProcessedExpressionDataVectorService

computeProcessedExpressionData

@Transactional(propagation=NEVER)
public void computeProcessedExpressionData(ExpressionExperiment ee)

Description copied from interface: ProcessedExpressionDataVectorService

Compute processed expression data, ignoring mismatched with the inferred scale.

Specified by:

computeProcessedExpressionData in interface ProcessedExpressionDataVectorService

computeProcessedExpressionData

@Transactional(propagation=NEVER)
public void computeProcessedExpressionData(ExpressionExperiment ee,
                                           boolean ignoreQuantitationMismatch)
                                    throws QuantitationMismatchException

Description copied from interface: ProcessedExpressionDataVectorService

This method should not be called on its own, if possible. Use the PreprocessorService to do all necessary refreshing.

Specified by:

computeProcessedExpressionData in interface ProcessedExpressionDataVectorService

Throws:

QuantitationMismatchException

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.

Specified by:

reorderByDesign 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.