Package ubic.gemma.core.ontology

Class GoMetricImpl

java.lang.Object

ubic.gemma.core.ontology.GoMetricImpl

All Implemented Interfaces:

GoMetric

@Component
public class GoMetricImpl
extends Object
implements GoMetric

Author:

meeta

Nested Class Summary

Nested classes/interfaces inherited from interface ubic.gemma.core.ontology.GoMetric

GoMetric.Metric

Constructor Summary

Constructors

Constructor	Description
GoMetricImpl()

Method Summary

Modifier and Type	Method	Description
Double	computeMatrixSimilarity(Gene gene1, Gene gene2, DoubleMatrix<Long,String> gene2TermMatrix, GoMetric.Metric metric)
Double	computeMaxSimilarity(Gene queryGene, Gene targetGene, Map<String,Double> GOProbMap, GoMetric.Metric metric)
Double	computeMergedOverlap(List<Gene> sameGenes1, List<Gene> sameGenes2, Map<Long,Collection<String>> geneGoMap)	Tailored to handle computing overlap between two gene lists which may contain duplicate genes of the same name but different IDs.
Double	computeSimilarity(Gene queryGene, Gene targetGene, Map<String,Double> GOProbMap, GoMetric.Metric metric)
Double	computeSimpleOverlap(Gene g, Gene coexpG, Map<Long,Collection<String>> geneGoMap)
DoubleMatrix<Long,String>	createVectorMatrix(Map<Long,Collection<String>> gene2go, boolean weight)
Integer	getChildrenOccurrence(Map<String,Integer> termCountMap, String term)
protected void	logIds(String prefix, Collection<OntologyTerm> terms)
void	setGene2GOAssociationService(Gene2GOAssociationService gene2GOAssociationService)
void	setGeneOntologyService(GeneOntologyService geneOntologyService)

Methods inherited from class java.lang.Object

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

Constructor Detail

GoMetricImpl

public GoMetricImpl()

Method Detail

computeMatrixSimilarity

public Double computeMatrixSimilarity(Gene gene1,
                                      Gene gene2,
                                      DoubleMatrix<Long,String> gene2TermMatrix,
                                      GoMetric.Metric metric)

Specified by:

computeMatrixSimilarity in interface GoMetric

computeMaxSimilarity

public Double computeMaxSimilarity(Gene queryGene,
                                   Gene targetGene,
                                   Map<String,Double> GOProbMap,
                                   GoMetric.Metric metric)

Specified by:

computeMaxSimilarity in interface GoMetric

Parameters:

metric - metric

GOProbMap - go prob map

queryGene - query gene

targetGene - target gene

Returns:

the MAX overlap score between two genes

computeMergedOverlap

public Double computeMergedOverlap(List<Gene> sameGenes1,
                                   List<Gene> sameGenes2,
                                   Map<Long,Collection<String>> geneGoMap)

Tailored to handle computing overlap between two gene lists which may contain duplicate genes of the same name but different IDs. If gene lists do not contain duplicates (size = 1) the result will be the same as that of computing simple overlap.

Specified by:

computeMergedOverlap in interface GoMetric

Parameters:

geneGoMap - gene go map

sameGenes1 - same genes 1

sameGenes2 - same genes 2

Returns:

number of overlapping terms between merged sets of GO terms for duplicate gene lists

computeSimilarity

public Double computeSimilarity(Gene queryGene,
                                Gene targetGene,
                                Map<String,Double> GOProbMap,
                                GoMetric.Metric metric)

Specified by:

computeSimilarity in interface GoMetric

Parameters:

metric - metric

GOProbMap - go prob map

queryGene - query gene

targetGene - target gene

Returns:

the overlap score between two genes

computeSimpleOverlap

public Double computeSimpleOverlap(Gene g,
                                   Gene coexpG,
                                   Map<Long,Collection<String>> geneGoMap)

Specified by:

computeSimpleOverlap in interface GoMetric

Parameters:

g - g

coexpG - coexp g

geneGoMap - gene go map

Returns:

number of overlapping terms

createVectorMatrix

public DoubleMatrix<Long,String> createVectorMatrix(Map<Long,Collection<String>> gene2go,
                                                          boolean weight)

Specified by:

createVectorMatrix in interface GoMetric

Parameters:

gene2go - Map

weight - weight

Returns:

Sparse matrix of genes x GOTerms

getChildrenOccurrence

public Integer getChildrenOccurrence(Map<String,Integer> termCountMap,
                                     String term)

Specified by:

getChildrenOccurrence in interface GoMetric

Parameters:

termCountMap - each GO term uri mapped to the number of its occurrence in the corpus

term - the uri of the query GO term

Returns:

the number of times the query GO term occurs in addition to the number of times its children occur in the corpus

setGene2GOAssociationService

public void setGene2GOAssociationService(Gene2GOAssociationService gene2GOAssociationService)

Specified by:

setGene2GOAssociationService in interface GoMetric

Parameters:

gene2GOAssociationService - the gene2GOAssociationService to set

setGeneOntologyService

public void setGeneOntologyService(GeneOntologyService geneOntologyService)

Specified by:

setGeneOntologyService in interface GoMetric

Parameters:

geneOntologyService - the geneOntologyService to set

logIds

protected void logIds(String prefix,
                      Collection<OntologyTerm> terms)