Package ubic.gemma.persistence.service.association.coexpression

Class CoexpressionDaoImpl

java.lang.Object

ubic.gemma.persistence.service.association.coexpression.CoexpressionDaoImpl

All Implemented Interfaces:

CoexpressionDao

@Repository
public class CoexpressionDaoImpl
extends Object
implements CoexpressionDao

Manages and queries coexpression 'links' between genes.

Author:

klc, paul

See Also:

• Gene2GeneCoexpression

Constructor Summary

Constructors

Constructor	Description
CoexpressionDaoImpl()

Method Summary

Modifier and Type	Method	Description
Integer	countLinks(Gene gene, ExpressionExperiment ee)
Map<Gene,Integer>	countOldLinks(Collection<Gene> genes)
void	createOrUpdate(ExpressionExperiment ee, List<NonPersistentNonOrderedCoexpLink> links, LinkCreator c, Set<Gene> genesTested)
void	deleteLinks(Taxon t, ExpressionExperiment experiment)
List<CoexpressionValueObject>	findCoexpressionRelationships(Gene gene, Collection<Long> bas, int maxResults, boolean quick)	Find coexpression links for a gene that are common to all the given datasets.
Map<Long,List<CoexpressionValueObject>>	findCoexpressionRelationships(Taxon taxon, Collection<Long> genes, Collection<Long> bas, int maxResults, boolean quick)	Find coexpression links for the genes that are common to all the given datasets, so stringency = bas.size().
Map<Long,List<CoexpressionValueObject>>	findCoexpressionRelationships(Taxon t, Collection<Long> genes, Collection<Long> bas, int stringency, int maxResults, boolean quick)
Map<Long,List<CoexpressionValueObject>>	findInterCoexpressionRelationships(Taxon taxon, Collection<Long> genes, Collection<Long> bas, int stringency, boolean quick)	Return coexpression relationships among the given genes, limited to the given data sets.
Collection<CoexpressionValueObject>	getCoexpression(Taxon taxon, ExpressionExperiment experiment, boolean quick)
List<Object[]>	getRawCoexpressionFromDbViaGenes(Collection<Long> geneIds, Taxon t, int stringency)
boolean	hasLinks(Taxon taxon, ExpressionExperiment ee)
Map<SupportDetails,Gene2GeneCoexpression>	initializeFromOldData(Gene gene, Map<Long,Gene> geneIdMap, Map<NonPersistentNonOrderedCoexpLink,SupportDetails> linksSoFar, Set<Long> skipGenes)
int	queryAndCache(Gene gene)
void	updateModifiedSupportDetails(ExpressionExperiment experiment, Collection<SupportDetails> supportDetailsToDelete, Collection<SupportDetails> supportDetailsToUpdate)
GeneCoexpressionNodeDegreeValueObject	updateNodeDegree(Gene g, GeneCoexpressionNodeDegree nd)	This is a maintenance method.
void	updateRelativeNodeDegrees(Map<Long,List<Double>> relRanksPerGenePositive, Map<Long,List<Double>> relRanksPerGeneNegative)

Methods inherited from class java.lang.Object

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

Constructor Details

CoexpressionDaoImpl

public CoexpressionDaoImpl()

Method Details

hasLinks

public boolean hasLinks(Taxon taxon,
 ExpressionExperiment ee)

Specified by:

hasLinks in interface CoexpressionDao

countLinks

public Integer countLinks(Gene gene,
 ExpressionExperiment ee)

Specified by:

countLinks in interface CoexpressionDao

createOrUpdate

public void createOrUpdate(ExpressionExperiment ee,
 List<NonPersistentNonOrderedCoexpLink> links,
 LinkCreator c,
 Set<Gene> genesTested)

Specified by:

createOrUpdate in interface CoexpressionDao

Parameters:

ee - bio assay set

links - in gene order

c - link creator

genesTested - genes tested

deleteLinks

public void deleteLinks(Taxon t,
 ExpressionExperiment experiment)

Specified by:

deleteLinks in interface CoexpressionDao

findCoexpressionRelationships

public List<CoexpressionValueObject> findCoexpressionRelationships(Gene gene,
 Collection<Long> bas,
 int maxResults,
 boolean quick)

Description copied from interface: CoexpressionDao

Find coexpression links for a gene that are common to all the given datasets. That is the stringency is bas.size().

Specified by:

findCoexpressionRelationships in interface CoexpressionDao

Parameters:

gene - gene

bas - bio assays

maxResults - max results

quick - quick

Returns:

coexpression VO

findCoexpressionRelationships

public Map<Long,List<CoexpressionValueObject>> findCoexpressionRelationships(Taxon taxon,
 Collection<Long> genes,
 Collection<Long> bas,
 int maxResults,
 boolean quick)

Description copied from interface: CoexpressionDao

Find coexpression links for the genes that are common to all the given datasets, so stringency = bas.size().

Specified by:

findCoexpressionRelationships in interface CoexpressionDao

Parameters:

taxon - taxon

genes - genes

bas - bio assays

maxResults - max results

quick - quick

Returns:

map of ids to coexp. VOs

findCoexpressionRelationships

public Map<Long,List<CoexpressionValueObject>> findCoexpressionRelationships(Taxon t,
 Collection<Long> genes,
 Collection<Long> bas,
 int stringency,
 int maxResults,
 boolean quick)

Specified by:

findCoexpressionRelationships in interface CoexpressionDao

Parameters:

t - taxon

genes - genes

bas - limit on which data sets to query, or null (or empty) for no limit.

stringency - minimum number of the datasets the link must be supported by

maxResults - maximum results per gene.

quick - quick

Returns:

map of ids to coexp. VOs

findInterCoexpressionRelationships

public Map<Long,List<CoexpressionValueObject>> findInterCoexpressionRelationships(Taxon taxon,
 Collection<Long> genes,
 Collection<Long> bas,
 int stringency,
 boolean quick)

Description copied from interface: CoexpressionDao

Return coexpression relationships among the given genes, limited to the given data sets.

Specified by:

findInterCoexpressionRelationships in interface CoexpressionDao

Parameters:

taxon - taxon

genes - genes

bas - bio assays

stringency - stringency

quick - quick

Returns:

map of ids to coexp. VOs

updateNodeDegree

public GeneCoexpressionNodeDegreeValueObject updateNodeDegree(Gene g,
 GeneCoexpressionNodeDegree nd)

Description copied from interface: CoexpressionDao

This is a maintenance method. This requires doing a coexpression query for the gene, and updating (or, if need be, creating) the associated GeneCoexpressionNodeDegree object.

Specified by:

updateNodeDegree in interface CoexpressionDao

Parameters:

g - gene

nd - node degree

Returns:

updated value object

getCoexpression

public Collection<CoexpressionValueObject> getCoexpression(Taxon taxon,
 ExpressionExperiment experiment,
 boolean quick)

Specified by:

getCoexpression in interface CoexpressionDao

Parameters:

taxon - taxon

experiment - experiment

quick - quick

Returns:

links, but not including flipped versions

queryAndCache

public int queryAndCache(Gene gene)

Specified by:

queryAndCache in interface CoexpressionDao

Parameters:

gene - gene

Returns:

number of links that were cached

initializeFromOldData

public Map<SupportDetails,Gene2GeneCoexpression> initializeFromOldData(Gene gene,
 Map<Long,Gene> geneIdMap,
 Map<NonPersistentNonOrderedCoexpLink,SupportDetails> linksSoFar,
 Set<Long> skipGenes)

Specified by:

initializeFromOldData in interface CoexpressionDao

countOldLinks

public Map<Gene,Integer> countOldLinks(Collection<Gene> genes)

Specified by:

countOldLinks in interface CoexpressionDao

updateRelativeNodeDegrees

public void updateRelativeNodeDegrees(Map<Long,List<Double>> relRanksPerGenePositive,
 Map<Long,List<Double>> relRanksPerGeneNegative)

Specified by:

updateRelativeNodeDegrees in interface CoexpressionDao

updateModifiedSupportDetails

public void updateModifiedSupportDetails(ExpressionExperiment experiment,
 Collection<SupportDetails> supportDetailsToDelete,
 Collection<SupportDetails> supportDetailsToUpdate)

getRawCoexpressionFromDbViaGenes

public List<Object[]> getRawCoexpressionFromDbViaGenes(Collection<Long> geneIds,
 Taxon t,
 int stringency)