Package ubic.gemma.core.ontology

Interface GoMetric

All Known Implementing Classes:

GoMetricImpl

public interface GoMetric

Nested Class Summary

Nested Classes

Modifier and Type	Interface	Description
static class	GoMetric.Metric

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)
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)
void	setGene2GOAssociationService(Gene2GOAssociationService gene2GOAssociationService)
void	setGeneOntologyService(GeneOntologyService geneOntologyService)

Method Detail

computeMatrixSimilarity

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

computeMaxSimilarity

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

computeMergedOverlap

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

computeSimilarity

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

computeSimpleOverlap

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

createVectorMatrix

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

getChildrenOccurrence

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

setGene2GOAssociationService

void setGene2GOAssociationService(Gene2GOAssociationService gene2GOAssociationService)

setGeneOntologyService

void setGeneOntologyService(GeneOntologyService geneOntologyService)