ubic.gemma.core.ontology

Interface GoMetric

All Known Implementing Classes:

GoMetricImpl

public interface GoMetric

Nested Class Summary

Nested Classes

Modifier and Type	Interface and Description
static class	GoMetric.Metric

Method Summary

Modifier and Type	Method and Description
Double	computeMatrixSimilarity(Gene gene1, Gene gene2, ubic.basecode.dataStructure.matrix.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)
ubic.basecode.dataStructure.matrix.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,
                               ubic.basecode.dataStructure.matrix.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

ubic.basecode.dataStructure.matrix.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)