Package ubic.gemma.persistence.util

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 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<Long,Collection<Long>>	getArrayDesignsUsedEEMap(Collection<Long> ees, Session session)
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)

Methods inherited from class java.lang.Object

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

Constructor Detail

CommonQueries

public CommonQueries()

Method Detail

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 BioAssaySet> ees,
                                                          Session session)

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

getArrayDesignsUsedEEMap

public static Map<Long,Collection<Long>> getArrayDesignsUsedEEMap(Collection<Long> ees,
                                                                        Session session)

Parameters:

ees - experiments

session - session

Returns:

map of experiment to collection of array design ids. If any of the ids given are for subsets, then the key in the return value will be for the subset, not the source experiment (so it is consistent with the input)

getCompositeSequences

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

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

Parameters:

session - session

gene - gene

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:

session - session

probes - probes

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)