Class ProcessedExpressionDataVectorDaoImpl

java.lang.Object

ubic.gemma.persistence.service.AbstractDao<ProcessedExpressionDataVector>

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

ubic.gemma.persistence.service.expression.bioAssayData.ProcessedExpressionDataVectorDaoImpl

All Implemented Interfaces:

BaseDao<ProcessedExpressionDataVector>, DesignElementDataVectorDao<ProcessedExpressionDataVector>, ProcessedExpressionDataVectorDao

@Repository
public class ProcessedExpressionDataVectorDaoImpl
extends AbstractDesignElementDataVectorDao<ProcessedExpressionDataVector>
implements ProcessedExpressionDataVectorDao

Author:

Paul

Nested Class Summary

Nested classes/interfaces inherited from interface ProcessedExpressionDataVectorDao

ProcessedExpressionDataVectorDao.RankMethod

Field Summary

Fields inherited from class AbstractDao

log

Constructor Summary

Constructors

Constructor	Description
ProcessedExpressionDataVectorDaoImpl(SessionFactory sessionFactory)

Method Summary

Modifier and Type	Method	Description
Collection<ProcessedExpressionDataVector>	find(Collection<CompositeSequence> designElements, QuantitationType quantitationType)	Retrieve the processed vectors for a set of design elements within a given quantitation type.
Map<ProcessedExpressionDataVector, Collection<Long>>	getGenes(Collection<ProcessedExpressionDataVector> vectors)	Obtain the genes associated to each vector.
Collection<ProcessedExpressionDataVector>	getProcessedVectors(ExpressionExperiment ee)
List<ProcessedExpressionDataVector>	getProcessedVectors(ExpressionExperiment ee, BioAssayDimension dimension, int offset, int limit)	Retrieve a slice of processed vectors.
Map<ProcessedExpressionDataVector, Collection<Long>>	getProcessedVectorsAndGenes(Collection<ExpressionExperiment> ees, Map<Long, Collection<Long>> cs2gene)	Obtain processed expression vectors with their associated genes.
List<CompositeSequence>	getProcessedVectorsDesignElements(ExpressionExperiment ee, BioAssayDimension dimension, int offset, int limit)	Only retrieve the design elements for a slice of vectors.
Collection<ProcessedExpressionDataVector>	getRandomProcessedVectors(ExpressionExperiment ee, int limit)	Obtain a random sample of processed vectors for the given experiment.
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)

Methods inherited from class AbstractDesignElementDataVectorDao

find, find, find, findByExpressionExperiment, thaw, thaw

Methods inherited from class AbstractDao

countAll, create, create, find, findByProperty, findByPropertyIn, findIdByProperty, findOneByProperty, findOrCreate, getBatchSize, getElementClass, getEntityName, getIdentifierPropertyName, getSessionFactory, load, load, loadAll, loadReference, loadReference, reload, reload, remove, remove, save, save, streamAll, streamAll, streamQuery, update, update

Methods inherited from class Object

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

Methods inherited from interface BaseDao

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

Methods inherited from interface DesignElementDataVectorDao

find, find, find, findByExpressionExperiment, thaw, thaw

Constructor Details

ProcessedExpressionDataVectorDaoImpl

@Autowired
public ProcessedExpressionDataVectorDaoImpl(SessionFactory sessionFactory)

Method Details

getProcessedVectors

public Collection<ProcessedExpressionDataVector> getProcessedVectors(ExpressionExperiment ee)

Specified by:

getProcessedVectors in interface ProcessedExpressionDataVectorDao

Parameters:

ee - ee

Returns:

Processed data for the given experiment. NOTE the vectors are thawed before returning.

getProcessedVectors

public List<ProcessedExpressionDataVector> getProcessedVectors(ExpressionExperiment ee,
 BioAssayDimension dimension,
 int offset,
 int limit)

Description copied from interface: ProcessedExpressionDataVectorDao

Retrieve a slice of processed vectors.

Specified by:

getProcessedVectors in interface ProcessedExpressionDataVectorDao

find

public Collection<ProcessedExpressionDataVector> find(Collection<CompositeSequence> designElements,
 QuantitationType quantitationType)

Description copied from interface: ProcessedExpressionDataVectorDao

Retrieve the processed vectors for a set of design elements within a given quantitation type. Symmetric with RawExpressionDataVectorDao.find(Collection, QuantitationType). Returns the stored entities, whose data has NOT had read-time outlier masking applied — used to recover un-masked values for a previously selected set of probes.

Specified by:

find in interface ProcessedExpressionDataVectorDao

Parameters:

designElements - probes to retrieve; empty collection yields an empty result.

quantitationType - the (processed) quantitation type; scopes the result to a single experiment.

Returns:

the matching processed vectors, thawed for the bioAssayDimension / quantitationType / designElement.

getProcessedVectorsAndGenes

public Map<ProcessedExpressionDataVector, Collection<Long>> getProcessedVectorsAndGenes(@Nullable
 Collection<ExpressionExperiment> ees,
 Map<Long, Collection<Long>> cs2gene)

Description copied from interface: ProcessedExpressionDataVectorDao

Obtain processed expression vectors with their associated genes.

Specified by:

getProcessedVectorsAndGenes in interface ProcessedExpressionDataVectorDao

Parameters:

ees - ees

cs2gene - Map of probe to genes.

Returns:

map of vectors to genes.

getRandomProcessedVectors

public Collection<ProcessedExpressionDataVector> getRandomProcessedVectors(ExpressionExperiment ee,
 int limit)

Obtain a random sample of processed vectors for the given experiment.

Specified by:

getRandomProcessedVectors in interface ProcessedExpressionDataVectorDao

Parameters:

ee - ee

limit - if >0, you will get a "random" set of vectors for the experiment

Returns:

processed data vectors

getProcessedVectorsDesignElements

public List<CompositeSequence> getProcessedVectorsDesignElements(ExpressionExperiment ee,
 BioAssayDimension dimension,
 int offset,
 int limit)

Description copied from interface: ProcessedExpressionDataVectorDao

Only retrieve the design elements for a slice of vectors.

Specified by:

getProcessedVectorsDesignElements in interface ProcessedExpressionDataVectorDao

getRanks

public Map<ExpressionExperiment, Map<Gene, Collection<Double>>> getRanks(Collection<ExpressionExperiment> expressionExperiments,
 Collection<Gene> genes,
 ProcessedExpressionDataVectorDao.RankMethod method)

Specified by:

getRanks in interface ProcessedExpressionDataVectorDao

getRanks

public Map<Gene, Collection<Double>> getRanks(ExpressionExperiment expressionExperiment,
 Collection<Gene> genes,
 ProcessedExpressionDataVectorDao.RankMethod method)

Specified by:

getRanks in interface ProcessedExpressionDataVectorDao

getGenes

public Map<ProcessedExpressionDataVector, Collection<Long>> getGenes(Collection<ProcessedExpressionDataVector> vectors)

Description copied from interface: ProcessedExpressionDataVectorDao

Obtain the genes associated to each vector.

Specified by:

getGenes in interface ProcessedExpressionDataVectorDao