Class CommonQueries

java.lang.Object

ubic.gemma.persistence.util.CommonQueries

public class CommonQueries
extends Object

Contains methods to perform 'common' queries that are needed across DAOs.

Author:

paul

Constructor Summary

Constructors

Constructor	Description
CommonQueries()

Method Summary

Modifier and Type	Method	Description
static Collection<Long>	filterProbesByPlatform(Collection<Long> probes, Collection<Long> arrayDesignIds, Session session)
static Collection<ArrayDesign>	getArrayDesignsUsed(Collection<? extends @MayBeUninitialized BioAssaySet> ees, Session session)	Retrieve a list of array designs used by the given experiments.
static Collection<ArrayDesign>	getArrayDesignsUsed(BioAssaySet bas, Session session)	Retrieve a list of array designs used in given expression experiment
static Map<ExpressionExperiment, Collection<ArrayDesign>>	getArrayDesignsUsedByExperiment(Collection<? extends @MayBeUninitialized BioAssaySet> ees, Session session)	Retrieve, in one query, a per-experiment map of array designs used.
static Collection<CompositeSequence>	getCompositeSequences(Gene gene, Session session)	Given a gene, get all the composite sequences that map to it.
static Map<Long, Collection<Long>>	getCs2GeneIdMapForGenes(Collection<Long> genes, Collection<Long> arrayDesigns, Session session)	Obtain a mapping of probe to gene IDs for the given gene IDs and platforms IDs.
static Map<CompositeSequence, Collection<Gene>>	getCs2GeneMap(Collection<Gene> genes, Collection<ArrayDesign> arrayDesigns, Session session)
static Map<CompositeSequence, Collection<Gene>>	getCs2GeneMap(Collection<Gene> genes, Session session)
static Map<Long, Collection<Long>>	getCs2GeneMapForProbes(Collection<Long> probes, Session session)
static ExpressionExperiment	getExperiment(@MayBeUninitialized BioAssaySet bas)	Resolve a BioAssaySet to the ExpressionExperiment that owns its data: itself if it is one, its source experiment if it is a subset.

Methods inherited from class Object

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

Constructor Details

CommonQueries

public CommonQueries()

Method Details

getArrayDesignsUsed

public static Collection<ArrayDesign> getArrayDesignsUsed(BioAssaySet bas,
 Session session)

Retrieve a list of array designs used in given expression experiment

getArrayDesignsUsed

public static Collection<ArrayDesign> getArrayDesignsUsed(Collection<? extends @MayBeUninitialized BioAssaySet> ees,
 Session session)

Retrieve a list of array designs used by the given experiments.

getArrayDesignsUsedByExperiment

public static Map<ExpressionExperiment, Collection<ArrayDesign>> getArrayDesignsUsedByExperiment(Collection<? extends @MayBeUninitialized BioAssaySet> ees,
 Session session)

Retrieve, in one query, a per-experiment map of array designs used.

Use this when you need to know which platform belongs to which EE (e.g. bulk pipeline-status assembly): the flat getArrayDesignsUsed(Collection, Session) loses that mapping. EEs with no resolved bio-assays are absent from the map.

getExperiment

public static ExpressionExperiment getExperiment(@MayBeUninitialized BioAssaySet bas)

Resolve a BioAssaySet to the ExpressionExperiment that owns its data: itself if it is one, its source experiment if it is a subset.

The argument is unproxied first. An association mapped against the abstract BioAssaySet -- SingleExperimentAnalysis.experimentAnalyzed is the common one -- hands back a BioAssaySet$HibernateProxy, which is an instance of neither concrete subclass and used to fall through to the throw below. Same remedy as ExpressionDataFileUtils .formatExperimentAnalyzedFilename and DifferentialExpressionAnalysisDaoImpl .getSourceExperiment.

Public because CachedProcessedExpressionDataVectorServiceImpl carried a byte-identical copy of this method; it now delegates here so the unproxy cannot be forgotten in one of the two.

Throws:

UnsupportedOperationException - if bas is neither an experiment nor a subset

getCompositeSequences

public static Collection<CompositeSequence> getCompositeSequences(Gene gene,
 Session session)

Given a gene, get all the composite sequences that map to it.

Parameters:

gene - gene

session - session

Returns:

composite sequences

getCs2GeneMap

public static Map<CompositeSequence, Collection<Gene>> getCs2GeneMap(Collection<Gene> genes,
 Collection<ArrayDesign> arrayDesigns,
 Session session)

getCs2GeneMap

public static Map<CompositeSequence, Collection<Gene>> getCs2GeneMap(Collection<Gene> genes,
 Session session)

Parameters:

genes - genes

session - session

Returns:

map of probes to input genes they map to. Other genes those probes might detect are not included.

getCs2GeneIdMapForGenes

public static Map<Long, Collection<Long>> getCs2GeneIdMapForGenes(Collection<Long> genes,
 Collection<Long> arrayDesigns,
 Session session)

Obtain a mapping of probe to gene IDs for the given gene IDs and platforms IDs.

getCs2GeneMapForProbes

public static Map<Long, Collection<Long>> getCs2GeneMapForProbes(Collection<Long> probes,
 Session session)

Parameters:

probes - probes

session - session

Returns:

map of probes to all the genes 'detected' by those probes. Probes that don't map to genes will have an empty gene collection.

filterProbesByPlatform

public static Collection<Long> filterProbesByPlatform(Collection<Long> probes,
 Collection<Long> arrayDesignIds,
 Session session)