- c - Variable in class owltools.sim2.FastOwlSim.ClassCount
-
- c - Variable in class owltools.sim2.scores.AttributePairScores
-
- c1 - Variable in class owltools.sim.OldSimpleOwlSim.OWLClassExpressionPair
-
- c1 - Variable in class owltools.sim.OWLClassExpressionPair
-
- c2 - Variable in class owltools.sim.OldSimpleOwlSim.OWLClassExpressionPair
-
- c2 - Variable in class owltools.sim.OWLClassExpressionPair
-
- cacheInformationContentInOntology() - Method in class owltools.sim2.AbstractOwlSim
-
- cacheInformationContentInOntology() - Method in interface owltools.sim2.OwlSim
-
Generates an ontology containing annotation assertion axioms connecting
a class to an IC value.
- calculate(SimEngine, OWLObject, OWLObject) - Method in class owltools.sim.AsymmetricJaccardSimilarity
-
- calculate(SimEngine, OWLObject, OWLObject) - Method in class owltools.sim.AvgInformationContentBestMatchesSimilarity
-
Deprecated.
- calculate(SimEngine, OWLObject, OWLObject) - Method in class owltools.sim.AvgInformationContentLCSSimilarity
-
Deprecated.
- calculate(SimEngine, OWLObject, OWLObject) - Method in class owltools.sim.CombinedJaccardConjunctiveSetSimilarity
-
- calculate(SimEngine, OWLObject, OWLObject) - Method in class owltools.sim.CombinedSimilarity
-
- calculate(SimEngine, OWLObject, OWLObject) - Method in class owltools.sim.CombinedSimilarity2
-
- calculate(SimEngine, OWLObject, OWLObject) - Method in class owltools.sim.ConjunctiveSetInformationContentRatioSimilarity
-
- calculate(SimEngine, OWLObject, OWLObject) - Method in class owltools.sim.ConjunctiveSetSimilarity
-
- calculate(SimEngine, OWLObject, OWLObject) - Method in class owltools.sim.DescriptionTreeSimilarity
-
- calculate(SimEngine, OWLObject, OWLObject) - Method in class owltools.sim.DisjunctiveSetSimilarity
-
- calculate(SimEngine, OWLObject, OWLObject) - Method in class owltools.sim.JaccardBloomSimilarity
-
- calculate(SimEngine, OWLObject, OWLObject) - Method in class owltools.sim.JaccardSimilarity
-
- calculate(SimEngine, OWLObject, OWLObject) - Method in class owltools.sim.MaximumInformationContentSimilarity
-
- calculate(SimEngine, OWLObject, OWLObject) - Method in class owltools.sim.MultiSimilarity
-
- calculate(SimEngine, OWLObject, OWLObject) - Method in class owltools.sim.OverlapSimilarity
-
- calculate(SimEngine, OWLObject, OWLObject) - Method in class owltools.sim.Similarity
-
- calculateAllByAllEnrichment(OWLClass, OWLClass, OWLClass) - Method in class owltools.sim.OldSimpleOwlSim
-
- calculateAllByAllEnrichment() - Method in class owltools.sim2.AbstractOwlSim
-
- calculateAllByAllEnrichment(OWLClass, OWLClass, OWLClass) - Method in class owltools.sim2.AbstractOwlSim
-
- calculateAllByAllEnrichment(OWLClass, OWLClass, OWLClass) - Method in interface owltools.sim2.OwlSim
-
For every c ∈ sample set, test c against all classes ∈ enriched class set.
- calculateAllByAllEnrichment() - Method in interface owltools.sim2.OwlSim
-
- calculateAllSimilarity(OWLObject, OWLObject) - Method in class owltools.sim.SimEngine
-
iterates through ALL similarity metrics and calculates
- calculateCombinedScore(ElementPairScores, double, double) - Method in class owltools.sim2.AbstractOwlSim
-
- calculateCombinedScore(ElementPairScores, double, double) - Method in interface owltools.sim2.OwlSim
-
- calculateCombinedScore(ElementPairScores, double, double) - Method in class owltools.sim2.SimpleOwlSim
-
- calculateCombinedScores(List<ElementPairScores>, double, double) - Method in class owltools.sim2.FastOwlSim
-
Given a set of scorings between an individual i, and a set of individuals j1 ..jn ∈ J,
calculate the combined score for each i,j pair where j ∈ J
- calculateCombinedScores(List<ElementPairScores>, double, double) - Method in interface owltools.sim2.OwlSim
-
- calculateCombinedScores(List<ElementPairScores>, double, double) - Method in class owltools.sim2.SimpleOwlSim
-
- calculateEnrichment(OWLClass, OWLClass) - Method in class owltools.sim.EnrichmentEngine
-
- calculateEnrichment(OWLClass, OWLClass) - Method in class owltools.sim.OldSimpleOwlSim
-
- calculateEnrichment(OWLClass, OWLClass) - Method in class owltools.sim2.AbstractOwlSim
-
- calculateEnrichment(OWLClass, OWLClass) - Method in interface owltools.sim2.OwlSim
-
- calculateGenusDifferentiaEnrichment(OWLClass, OWLClass, OWLClass) - Method in class owltools.sim2.ClassDifferentiaLearner
-
- calculateMetricStats(Set<OWLNamedIndividual>, Set<OWLNamedIndividual>) - Method in class owltools.sim2.FastOwlSim
-
- calculateMetricStats(Set<OWLNamedIndividual>, Set<OWLNamedIndividual>) - Method in interface owltools.sim2.OwlSim
-
- calculateMetricStats(Set<OWLNamedIndividual>, Set<OWLNamedIndividual>) - Method in class owltools.sim2.SimpleOwlSim
-
- calculateOverallAnnotationSufficiencyForAttributeSet(Set<OWLClass>) - Method in class owltools.sim2.AbstractOwlSim
-
- calculateOverallAnnotationSufficiencyForAttributeSet(Set<OWLClass>) - Method in interface owltools.sim2.OwlSim
-
- calculateOverallAnnotationSufficiencyForIndividual(OWLNamedIndividual) - Method in class owltools.sim2.AbstractOwlSim
-
- calculateOverallAnnotationSufficiencyForIndividual(OWLNamedIndividual) - Method in interface owltools.sim2.OwlSim
-
- calculatePairwiseEnrichment(OWLClass, OWLClass, OWLClass) - Method in class owltools.sim.OldSimpleOwlSim
-
- calculatePairwiseEnrichment(OWLClass, OWLClass, OWLClass) - Method in class owltools.sim2.AbstractOwlSim
-
- calculatePairwiseEnrichment(OWLClass, OWLClass, OWLClass) - Method in interface owltools.sim2.OwlSim
-
Pairwise enrichment test
- calculateSimilarity(Similarity, OWLObject, OWLObject) - Method in class owltools.sim.SimEngine
-
Calculates the similarity between two OWLObjects
this is the core method of the SimEngine
- calculateSimilarity(OWLObject, OWLObject) - Method in interface owltools.sim.SimilarityCalculator
-
given two objects, calculate their similarity, returning a number between zero (no similarity)
and 1 (equivalence)
- calculateSimilarityAllByAll(String, Double) - Method in class owltools.sim.SimEngine
-
- calculateSimilarityScore(Similarity, OWLObject, OWLObject) - Method in class owltools.sim.SimEngine
-
- calculateSubgraphAnnotationSufficiencyForAttributeSet(Set<OWLClass>, OWLClass) - Method in class owltools.sim2.AbstractOwlSim
-
- calculateSubgraphAnnotationSufficiencyForAttributeSet(Set<OWLClass>, OWLClass) - Method in interface owltools.sim2.OwlSim
-
- calculateSubgraphAnnotationSufficiencyForIndividual(OWLNamedIndividual, OWLClass) - Method in class owltools.sim2.AbstractOwlSim
-
- candidates - Variable in class owltools.sim.SimSearch
-
- ClassCount(OWLClass, Double) - Constructor for class owltools.sim2.FastOwlSim.ClassCount
-
- ClassCount(OWLClass, Integer) - Constructor for class owltools.sim2.FastOwlSim.ClassCount
-
- classCount - Variable in class owltools.sim2.OwlSimMetadata
-
- ClassCountComparator - Static variable in class owltools.sim2.FastOwlSim
-
- ClassDifferentiaLearner - Class in owltools.sim2
-
- ClassDifferentiaLearner(OwlSim) - Constructor for class owltools.sim2.ClassDifferentiaLearner
-
- ClassDifferentiaLearner.InferredClassDefinition - Class in owltools.sim2
-
- classesToSkip - Variable in class owltools.sim2.preprocessor.AbstractSimPreProcessor
-
- classIndexSize - Variable in class owltools.sim2.OwlSimMetadata
-
- classPairCount - Variable in class owltools.sim2.SimStats
-
- clearInformationContentCache() - Method in class owltools.sim2.AbstractOwlSim
-
- clearInformationContentCache() - Method in class owltools.sim2.FastOwlSim
-
- clearInformationContentCache() - Method in class owltools.sim2.SimpleOwlSim
-
- clearLCSCache() - Method in class owltools.sim2.FastOwlSim
-
- CombinedJaccardConjunctiveSetSimilarity - Class in owltools.sim
-
filters first based on SimJ, if passes threshold performs full ConjunctiveSetSimilarity
- CombinedJaccardConjunctiveSetSimilarity() - Constructor for class owltools.sim.CombinedJaccardConjunctiveSetSimilarity
-
- combinedScore - Variable in class owltools.sim2.scores.ElementPairScores
-
- CombinedSimilarity - Class in owltools.sim
-
- CombinedSimilarity() - Constructor for class owltools.sim.CombinedSimilarity
-
- CombinedSimilarity2 - Class in owltools.sim
-
- CombinedSimilarity2() - Constructor for class owltools.sim.CombinedSimilarity2
-
- compareAllAttributes(OWLClass, Set<OWLClass>) - Method in class owltools.sim2.FastOwlSim
-
- compareAllAttributes(OWLClass, Set<OWLClass>) - Method in interface owltools.sim2.OwlSim
-
- compareAllAttributes(OWLClass, Set<OWLClass>) - Method in class owltools.sim2.SimpleOwlSim
-
- compareAttributeSetPair(Set<OWLClass>, Set<OWLClass>) - Method in class owltools.sim2.SimJSONEngine
-
- compareAttributeSetPair(Set<OWLClass>, Set<OWLClass>, boolean) - Method in class owltools.sim2.SimJSONEngine
-
- compareLCSWithEnrichmentGrouping(OWLOntology, Double, OWLPrettyPrinter) - Static method in class owltools.sim2.OwlSimUtil
-
- compareTo(OldSimpleOwlSim.EnrichmentResult) - Method in class owltools.sim.OldSimpleOwlSim.EnrichmentResult
-
- compareTo(ClassDifferentiaLearner.InferredClassDefinition) - Method in class owltools.sim2.ClassDifferentiaLearner.InferredClassDefinition
-
- compareTo(EnrichmentResult) - Method in class owltools.sim2.EnrichmentResult
-
- compareTo(OwlSim.ScoreAttributeSetPair) - Method in class owltools.sim2.OwlSim.ScoreAttributeSetPair
-
- compareTo(ElementPairScores) - Method in class owltools.sim2.scores.ElementPairScores
-
- compareTo(SimpleOwlSim.ScoreAttributePair) - Method in class owltools.sim2.SimpleOwlSim.ScoreAttributePair
-
- comparisonClass - Variable in class owltools.sim.SimEngine
-
- comparisonProperty - Variable in class owltools.sim.SimEngine
-
- comparisonSuperclass - Variable in class owltools.sim.SimEngine
-
- COMPOSED_PRIMARILY_OF - Variable in class owltools.sim2.preprocessor.AbstractOBOSimPreProcessor
-
- compute(OWLClass, OWLClass) - Method in class owltools.sim2.ClassDifferentiaLearner
-
- computeAttributeSetSimilarityStats(Set<OWLClass>) - Method in class owltools.sim2.AbstractOwlSim
-
- computeAttributeSetSimilarityStats(Set<OWLClass>) - Method in interface owltools.sim2.OwlSim
-
- computeAttributeSetSimilarityStatsForSubgraph(Set<OWLClass>, OWLClass) - Method in class owltools.sim2.AbstractOwlSim
-
- computeAttributeSetSimilarityStatsForSubgraph(Set<OWLClass>, OWLClass) - Method in interface owltools.sim2.OwlSim
-
- computeDescriptiveStatistics(OWLNamedIndividual) - Method in class owltools.sim2.kb.OWLSimReferenceBasedStatistics
-
- computeDescriptiveStatistics(Set<OWLClass>) - Method in class owltools.sim2.kb.OWLSimReferenceBasedStatistics
-
- computeIndividualSimilarityStats(OWLNamedIndividual) - Method in class owltools.sim2.AbstractOwlSim
-
- computeIndividualStats(OWLNamedIndividual) - Method in class owltools.sim2.AbstractOwlSim
-
- computeIndividualStats(OWLNamedIndividual) - Method in interface owltools.sim2.OwlSim
-
This will compute the individual summary statistics over the
set of anntoated classes to an individual i.
- computeIndividualStats(OWLNamedIndividual) - Method in class owltools.sim2.SimpleOwlSim
-
- computeIndividualStatsForSubgraph(OWLNamedIndividual, OWLClass) - Method in class owltools.sim2.AbstractOwlSim
-
- computeSystemStats() - Method in class owltools.sim2.AbstractOwlSim
-
- computeSystemStats() - Method in interface owltools.sim2.OwlSim
-
This function will compute the IC-based summary statistics over the set of
individuals for direct annotations.
- computeSystemStats() - Method in class owltools.sim2.SimpleOwlSim
-
- computeSystemStatsForSubgraph(OWLClass) - Method in class owltools.sim2.AbstractOwlSim
-
- computeSystemStatsForSubgraph(OWLClass) - Method in interface owltools.sim2.OwlSim
-
- computeTFIDFMatrix(int[][], int, int[][], int) - Method in class owltools.sim2.FastOwlSim
-
- computeTFIDFMatrix(int[][], int, int[][], int) - Method in interface owltools.sim2.OwlSim
-
- computeTFIDFMatrix(int[][], int, int[][], int) - Method in class owltools.sim2.SimpleOwlSim
-
- ConjunctiveSetInformationContentRatioSimilarity - Class in owltools.sim
-
score is the IC of the intersection of all attributes divided my min IC of a or b
it's recommended this used as a sub-method of a MultiSimilarity check
- ConjunctiveSetInformationContentRatioSimilarity() - Constructor for class owltools.sim.ConjunctiveSetInformationContentRatioSimilarity
-
- ConjunctiveSetSimilarity - Class in owltools.sim
-
ConjunctiveSetSimilarity(a,b) = IC( LCA_1(a,b) ^ LCA_2(a,b) ...
- ConjunctiveSetSimilarity() - Constructor for class owltools.sim.ConjunctiveSetSimilarity
-
- convertCountMatrixToFrequency(int[][], int) - Method in class owltools.sim2.FastOwlSim
-
- convertCountMatrixToFrequency(int[][], int) - Method in interface owltools.sim2.OwlSim
-
- convertCountMatrixToFrequency(int[][], int) - Method in class owltools.sim2.SimpleOwlSim
-
- corpusSize - Variable in class owltools.sim2.AbstractOwlSim
-
- count - Variable in class owltools.sim2.FastOwlSim.ClassCount
-
- createElementAttributeMapFromOntology() - Method in class owltools.sim.OldSimpleOwlSim
-
assumes that the ontology contains both attributes (TBox) and elements + associations (ABox)
- createElementAttributeMapFromOntology() - Method in class owltools.sim2.FastOwlSim
-
- createElementAttributeMapFromOntology() - Method in interface owltools.sim2.OwlSim
-
This must be called prior to calculation of any similarity metrics.
- createElementAttributeMapFromOntology() - Method in class owltools.sim2.SimpleOwlSim
-
- createOWLOntologyFromResults() - Method in class owltools.sim.Similarity
-
- createOwlSim(OWLOntology) - Method in class owltools.sim2.FastOwlSimFactory
-
- createOwlSim(OWLOntology) - Method in interface owltools.sim2.OwlSimFactory
-
- createOwlSim(OWLOntology) - Method in class owltools.sim2.SimpleOwlSimFactory
-
- createOwlSimFromOntologyFile(String) - Static method in class owltools.sim2.OwlSimUtil
-
Generates an OwlSim object from an ontology file
does *not* call
- createOwlSimFromOntologyFile(File) - Static method in class owltools.sim2.OwlSimUtil
-
- createOwlSimFromOntologyFiles(String, Set<String>, Set<String>) - Static method in class owltools.sim2.OwlSimUtil
-
- createPropertyView(OWLObjectProperty) - Method in class owltools.sim2.preprocessor.AbstractSimPreProcessor
-
- createPropertyView(OWLObjectProperty, OWLClass, String) - Method in class owltools.sim2.preprocessor.AbstractSimPreProcessor
-
- createPropertyView(OWLObjectProperty, Set<OWLClass>) - Method in class owltools.sim2.preprocessor.AbstractSimPreProcessor
-
- createPropertyView(OWLObjectProperty, Set<OWLClass>, String) - Method in class owltools.sim2.preprocessor.AbstractSimPreProcessor
-
- createRandomClassAssertions(OWLOntology, int, int) - Static method in class owltools.sim2.preprocessor.ABoxUtils
-
- createUnionExpression(OWLObject, OWLObject, OWLObject) - Method in class owltools.sim.SimEngine
-
- cs - Variable in class owltools.sim2.scores.ElementPairScores
-
- CutoffException - Exception in owltools.sim2
-
- CutoffException(String, Double, Double) - Constructor for exception owltools.sim2.CutoffException
-
- CutoffException(String, Integer, Integer) - Constructor for exception owltools.sim2.CutoffException
-
- generateGroupingClasses() - Method in class owltools.sim.OldSimpleOwlSim
-
Deprecated.
- generateLabel(OWLClassExpression) - Method in class owltools.sim2.preprocessor.AbstractSimPreProcessor
-
- generateLeastCommonSubsumers(Set<OWLClass>) - Method in class owltools.sim2.preprocessor.LCSEnabledSimPreProcessor
-
generates new LCS grouping classes
- generateLeastCommonSubsumersForAttributeClasses() - Method in class owltools.sim2.preprocessor.LCSEnabledSimPreProcessor
-
- generatePropertyViews() - Method in class owltools.sim.OldSimpleOwlSim
-
Deprecated.
- generateSourcePropertyViews() - Method in class owltools.sim.OldSimpleOwlSim
-
Deprecated.
- getA() - Method in class owltools.sim.OWLObjectPair
-
- getA() - Method in class owltools.sim2.scores.AttributePairScores
-
- getA() - Method in class owltools.sim2.scores.ElementPairScores
-
- getA() - Method in interface owltools.sim2.scores.PairScores
-
- getAboxProperty() - Method in class owltools.sim2.preprocessor.AbstractSimPreProcessor
-
- getAboxProperty() - Method in class owltools.sim2.preprocessor.ExpressionSimPreProcessor
-
- getAboxProperty() - Method in class owltools.sim2.preprocessor.PropertyViewSimPreProcessor
-
- getAboxProperty() - Method in interface owltools.sim2.preprocessor.SimPreProcessor
-
- getAllAttributeClasses() - Method in class owltools.sim.OldSimpleOwlSim
-
returns all attribute classes - i.e.
- getAllAttributeClasses() - Method in class owltools.sim2.FastOwlSim
-
- getAllAttributeClasses() - Method in interface owltools.sim2.OwlSim
-
returns all attribute classes - i.e.
- getAllAttributeClasses() - Method in class owltools.sim2.SimpleOwlSim
-
- getAllByAllLowestCommonSubsumer() - Method in class owltools.sim.OldSimpleOwlSim
-
Deprecated.
- getAllElements() - Method in class owltools.sim.OldSimpleOwlSim
-
- getAllElements() - Method in class owltools.sim2.FastOwlSim
-
- getAllElements() - Method in interface owltools.sim2.OwlSim
-
- getAllElements() - Method in class owltools.sim2.SimpleOwlSim
-
- getAllSimilarityAlgorithmClasses() - Method in class owltools.sim.SimEngine
-
- getAnnotationSufficiencyScore(OWLNamedIndividual) - Method in class owltools.sim2.SimJSONEngine
-
- getAnnotationSufficiencyScore(Set<OWLClass>) - Method in class owltools.sim2.SimJSONEngine
-
- getAnnotationSufficiencyScore(Set<OWLClass>, OWLClass) - Method in class owltools.sim2.SimJSONEngine
-
- getAnovaPValue() - Method in class owltools.sim2.kb.PValue
-
- getAnyLabel(OWLEntity) - Method in class owltools.sim2.preprocessor.AbstractSimPreProcessor
-
- getArbitraryAttributeClass() - Method in class owltools.sim2.OwlSim.ScoreAttributeSetPair
-
Deprecated.
- getAsymmetricAttributeJaccardSimilarity(OWLClass, OWLClass) - Method in class owltools.sim2.FastOwlSim
-
- getAsymmetricAttributeJaccardSimilarity(OWLClass, OWLClass) - Method in interface owltools.sim2.OwlSim
-
SimJASym(c,d) = | anc(c) ∩ anc(d) | / | anc(d) |
- getAsymmetricAttributeJaccardSimilarity(OWLClass, OWLClass) - Method in class owltools.sim2.SimpleOwlSim
-
- getAsymmetricAttributeJaccardSimilarityAsPercent(OWLClass, OWLClass) - Method in class owltools.sim2.AbstractOwlSim
-
- getAsymmetricAttributeJaccardSimilarityAsPercent(OWLClass, OWLClass) - Method in interface owltools.sim2.OwlSim
-
- getAsymmetricElementGraphInformationContentSimilarity(OWLNamedIndividual, OWLNamedIndividual) - Method in class owltools.sim2.FastOwlSim
-
- getAsymmetricElementJaccardSimilarity(OWLNamedIndividual, OWLNamedIndividual) - Method in class owltools.sim2.FastOwlSim
-
- getAsymmetricElementJaccardSimilarity(OWLNamedIndividual, OWLNamedIndividual) - Method in interface owltools.sim2.OwlSim
-
SimJ(i,j) = | Type(i) ∩ Type(j) | / | Type(j) |
- getAsymmetricElementJaccardSimilarity(OWLNamedIndividual, OWLNamedIndividual) - Method in class owltools.sim2.SimpleOwlSim
-
- getAsymmetricElementJaccardSimilarityAsPercent(OWLNamedIndividual, OWLNamedIndividual) - Method in class owltools.sim2.AbstractOwlSim
-
- getAsymmetricElementJaccardSimilarityAsPercent(OWLNamedIndividual, OWLNamedIndividual) - Method in class owltools.sim2.FastOwlSim
-
- getAsymmetricElementJaccardSimilarityAsPercent(OWLNamedIndividual, OWLNamedIndividual) - Method in interface owltools.sim2.OwlSim
-
- getAttributeClasses() - Method in class owltools.sim2.preprocessor.AbstractSimPreProcessor
-
- getAttributeClosureFor(OWLObject) - Method in class owltools.sim.SimEngine
-
- getAttributeGraphInformationContentSimilarity(OWLClass, OWLClass) - Method in class owltools.sim2.FastOwlSim
-
- getAttributeGraphInformationContentSimilarity(OWLClass, OWLClass) - Method in interface owltools.sim2.OwlSim
-
sums of IC of the intersection attributes/ sum of IC of union attributes.
- getAttributeGraphInformationContentSimilarity(OWLClass, OWLClass) - Method in class owltools.sim2.SimpleOwlSim
-
- getAttributeInformationProfile(Set<OWLClass>) - Method in class owltools.sim2.SimJSONEngine
-
- getAttributeInformationProfile(Set<OWLClass>, Set<OWLClass>) - Method in class owltools.sim2.SimJSONEngine
-
- getAttributeJaccardSimilarity(OWLClassExpression, OWLClassExpression) - Method in class owltools.sim.OldSimpleOwlSim
-
- getAttributeJaccardSimilarity(OWLClass, OWLClass) - Method in class owltools.sim2.FastOwlSim
-
- getAttributeJaccardSimilarity(OWLClass, OWLClass) - Method in interface owltools.sim2.OwlSim
-
SimJ(a,b) = | anc(a) ∩ anc(b) | / | anc(a) ∪ anc(b) |
- getAttributeJaccardSimilarity(OWLClass, OWLClass) - Method in class owltools.sim2.SimpleOwlSim
-
- getAttributeJaccardSimilarityAsPercent(OWLClass, OWLClass) - Method in class owltools.sim2.AbstractOwlSim
-
- getAttributeJaccardSimilarityAsPercent(OWLClass, OWLClass) - Method in class owltools.sim2.FastOwlSim
-
- getAttributeJaccardSimilarityAsPercent(OWLClass, OWLClass) - Method in interface owltools.sim2.OwlSim
-
- getAttributes(IRI) - Method in class owltools.sim2.kb.OWLSimReferenceBasedStatistics
-
- getAttributesFor(OWLObject) - Method in class owltools.sim.SimEngine
-
- getAttributesForElement(OWLEntity) - Method in class owltools.sim.OldSimpleOwlSim
-
- getAttributesForElement(OWLNamedIndividual) - Method in class owltools.sim2.FastOwlSim
-
- getAttributesForElement(OWLNamedIndividual) - Method in interface owltools.sim2.OwlSim
-
Gets all attribute classes used to describe individual element e.
- getAttributesForElement(OWLNamedIndividual) - Method in class owltools.sim2.SimpleOwlSim
-
- getAttributeSimilarity(OWLClass, OWLClass, SimpleOwlSim.Metric) - Method in class owltools.sim2.FastOwlSim
-
- getAttributeSimilarity(OWLClass, OWLClass, SimpleOwlSim.Metric) - Method in interface owltools.sim2.OwlSim
-
This method provides a generic wrapper onto other attribute-based similarity
methods
Compares two classes (attributes) according to the specified metric
- getAttributeSimilarity(OWLClass, OWLClass, SimpleOwlSim.Metric) - Method in class owltools.sim2.SimpleOwlSim
-
- getB() - Method in class owltools.sim.OWLObjectPair
-
- getB() - Method in class owltools.sim2.scores.AttributePairScores
-
- getB() - Method in class owltools.sim2.scores.ElementPairScores
-
- getB() - Method in interface owltools.sim2.scores.PairScores
-
- getBaseFileName() - Method in class owltools.sim.OldSimpleOwlSim
-
- getCandidateBasicStatistics() - Method in class owltools.sim2.kb.ICDistribution
-
- getCandidateDistribution() - Method in class owltools.sim2.kb.ICDistribution
-
- getCoannotatedClassesForAttribute(OWLClass) - Method in class owltools.sim2.FastOwlSim
-
- getCoannotatedClassesForAttribute(OWLClass, int) - Method in class owltools.sim2.FastOwlSim
-
- getCoannotatedClassesForAttribute(OWLClass, Double, int) - Method in class owltools.sim2.FastOwlSim
-
- getCoannotatedClassesForAttribute(OWLClass, int) - Method in interface owltools.sim2.OwlSim
-
- getCoannotatedClassesForAttribute(OWLClass) - Method in interface owltools.sim2.OwlSim
-
- getCoannotatedClassesForAttribute(OWLClass, Double, int) - Method in interface owltools.sim2.OwlSim
-
- getCoannotatedClassesForAttribute(OWLClass, int) - Method in class owltools.sim2.SimpleOwlSim
-
- getCoannotatedClassesForAttribute(OWLClass, Double, int) - Method in class owltools.sim2.SimpleOwlSim
-
- getCoannotatedClassesForAttribute(OWLClass) - Method in class owltools.sim2.SimpleOwlSim
-
- getCoAnnotatedClassesForAttributes(Set<OWLClass>) - Method in class owltools.sim2.FastOwlSim
-
- getCoAnnotatedClassesForAttributes(Set<OWLClass>, int) - Method in class owltools.sim2.FastOwlSim
-
- getCoAnnotatedClassesForAttributes(Set<OWLClass>) - Method in interface owltools.sim2.OwlSim
-
- getCoAnnotatedClassesForAttributes(Set<OWLClass>, int) - Method in interface owltools.sim2.OwlSim
-
- getCoAnnotatedClassesForAttributes(Set<OWLClass>) - Method in class owltools.sim2.SimpleOwlSim
-
- getCoAnnotatedClassesForAttributes(Set<OWLClass>, int) - Method in class owltools.sim2.SimpleOwlSim
-
- getCoAnnotatedClassesForIndividual(OWLNamedIndividual) - Method in class owltools.sim2.FastOwlSim
-
- getCoAnnotatedClassesForIndividual(OWLNamedIndividual, int) - Method in class owltools.sim2.FastOwlSim
-
- getCoAnnotatedClassesForIndividual(OWLNamedIndividual) - Method in interface owltools.sim2.OwlSim
-
- getCoAnnotatedClassesForIndividual(OWLNamedIndividual, int) - Method in interface owltools.sim2.OwlSim
-
- getCoAnnotatedClassesForIndividual(OWLNamedIndividual) - Method in class owltools.sim2.SimpleOwlSim
-
- getCoAnnotatedClassesForIndividual(OWLNamedIndividual, int) - Method in class owltools.sim2.SimpleOwlSim
-
- getCoAnnotatedClassesForMatches(List<ElementPairScores>, Set<OWLClass>) - Method in class owltools.sim2.FastOwlSim
-
- getCoAnnotatedClassesForMatches(List<ElementPairScores>, Set<OWLClass>, int) - Method in class owltools.sim2.FastOwlSim
-
- getCoAnnotatedClassesForMatches(List<ElementPairScores>, Set<OWLClass>) - Method in interface owltools.sim2.OwlSim
-
- getCoAnnotatedClassesForMatches(List<ElementPairScores>, Set<OWLClass>) - Method in class owltools.sim2.SimpleOwlSim
-
- getCoAnnotationListForAttribute(OWLClass, int) - Method in class owltools.sim2.SimJSONEngine
-
- getCommonSubsumers(OWLObject, OWLObject) - Method in class owltools.sim.SimEngine
-
todo rename - actually gets common named ancestors
- getCommonSubsumersSize(OWLObject, OWLObject) - Method in class owltools.sim.SimEngine
-
- getConditionalProbability(OWLClass, OWLClass) - Method in class owltools.sim2.AbstractOwlSim
-
- getConditionalProbability(OWLClass, OWLClass) - Method in interface owltools.sim2.OwlSim
-
- getConditionalProbability(OWLClass, OWLClass) - Method in class owltools.sim2.SimpleOwlSim
-
- getCorpusSize() - Method in class owltools.sim.OldSimpleOwlSim
-
- getCorpusSize() - Method in class owltools.sim.SimEngine
-
- getCorpusSize() - Method in class owltools.sim2.AbstractOwlSim
-
- getCorpusSize() - Method in interface owltools.sim2.OwlSim
-
The number of entities in the entire set being analyzed.
- getCorpusSize() - Method in class owltools.sim2.SimpleOwlSim
-
- getDescendants(Set<OWLClass>) - Method in class owltools.sim2.kb.OWLSimReferenceBasedStatistics
-
- getDirectAttributeClassExpressions() - Method in class owltools.sim2.preprocessor.AbstractSimPreProcessor
-
Deprecated.
- getDistributionBasedPValue() - Method in class owltools.sim2.kb.PValue
-
- getDistributions() - Method in class owltools.sim2.kb.OwlSimICDistribution
-
- getElementGraphInformationContentSimilarity(OWLNamedIndividual, OWLNamedIndividual) - Method in class owltools.sim2.FastOwlSim
-
- getElementGraphInformationContentSimilarity(OWLNamedIndividual, OWLNamedIndividual) - Method in interface owltools.sim2.OwlSim
-
sums of IC of the intersection attributes/ sum of IC of union attributes.
- getElementGraphInformationContentSimilarity(OWLNamedIndividual, OWLNamedIndividual) - Method in class owltools.sim2.SimpleOwlSim
-
- getElementJaccardSimilarity(OWLNamedIndividual, OWLNamedIndividual) - Method in class owltools.sim.OldSimpleOwlSim
-
- getElementJaccardSimilarity(OWLNamedIndividual, OWLNamedIndividual) - Method in class owltools.sim2.FastOwlSim
-
- getElementJaccardSimilarity(OWLNamedIndividual, OWLNamedIndividual) - Method in interface owltools.sim2.OwlSim
-
SimJ(i,j) = | Type(i) ∩ Type(j) | / | Type(i) ∪ Type(j) |
- getElementJaccardSimilarity(OWLNamedIndividual, OWLNamedIndividual) - Method in class owltools.sim2.SimpleOwlSim
-
- getElementJaccardSimilarityAsPercent(OWLNamedIndividual, OWLNamedIndividual) - Method in class owltools.sim2.AbstractOwlSim
-
- getElementJaccardSimilarityAsPercent(OWLNamedIndividual, OWLNamedIndividual) - Method in class owltools.sim2.FastOwlSim
-
- getElementJaccardSimilarityAsPercent(OWLNamedIndividual, OWLNamedIndividual) - Method in interface owltools.sim2.OwlSim
-
- getElementsForAttribute(OWLClass) - Method in class owltools.sim.OldSimpleOwlSim
-
inferred
- getElementsForAttribute(OWLClass) - Method in class owltools.sim2.FastOwlSim
-
- getElementsForAttribute(OWLClass) - Method in interface owltools.sim2.OwlSim
-
inferred
- getElementsForAttribute(OWLClass) - Method in class owltools.sim2.SimpleOwlSim
-
- getElementToAttributesMap() - Method in class owltools.sim2.FastOwlSim
-
- getElementToAttributesMap() - Method in interface owltools.sim2.OwlSim
-
- getElementToAttributesMap() - Method in class owltools.sim2.SimpleOwlSim
-
- getEnrichmentConfig() - Method in class owltools.sim.OldSimpleOwlSim
-
- getEnrichmentConfig() - Method in class owltools.sim2.AbstractOwlSim
-
- getEnrichmentConfig() - Method in interface owltools.sim2.OwlSim
-
- getEntropy() - Method in class owltools.sim2.AbstractOwlSim
-
- getEntropy(Set<OWLClass>) - Method in class owltools.sim2.AbstractOwlSim
-
- getEntropy() - Method in interface owltools.sim2.OwlSim
-
- getEntropy(Set<OWLClass>) - Method in interface owltools.sim2.OwlSim
-
- getEntropy() - Method in class owltools.sim2.SimpleOwlSim
-
- getEntropy(Set<OWLClass>) - Method in class owltools.sim2.SimpleOwlSim
-
- getExcludedLabels() - Method in class owltools.sim.SimEngine
-
any class whose label matches any of the strings returned
here will be excluded from any analysis.
- getFrequency(OWLObject) - Method in class owltools.sim.SimEngine
-
- getFrequency(Set<OWLObject>) - Method in class owltools.sim.SimEngine
-
as getFrequency(obj), treats objs as a conjunction
- getGraph() - Method in class owltools.sim.SimEngine
-
- getGraph() - Method in interface owltools.sim.SimilarityCalculator
-
- getGraph() - Method in class owltools.sim2.io.AbstractRenderer
-
- getGraph() - Method in interface owltools.sim2.io.SimResultRenderer
-
- getGroupwiseSimilarity(OWLNamedIndividual, OWLNamedIndividual) - Method in class owltools.sim2.AbstractOwlSim
-
- getGroupwiseSimilarity(OWLNamedIndividual) - Method in class owltools.sim2.FastOwlSim
-
- getGroupwiseSimilarity(Set<OWLClass>, Set<OWLClass>) - Method in class owltools.sim2.FastOwlSim
-
- getGroupwiseSimilarity(OWLNamedIndividual, OWLNamedIndividual) - Method in class owltools.sim2.FastOwlSim
-
- getGroupwiseSimilarity(OWLNamedIndividual, OWLNamedIndividual, double, double) - Method in class owltools.sim2.FastOwlSim
-
- getGroupwiseSimilarity(Set<OWLClass>, OWLNamedIndividual) - Method in class owltools.sim2.FastOwlSim
-
- getGroupwiseSimilarity(Set<OWLClass>, OWLNamedIndividual, double, double) - Method in class owltools.sim2.FastOwlSim
-
- getGroupwiseSimilarity(Set<OWLClass>, Set<OWLClass>, double, double) - Method in class owltools.sim2.FastOwlSim
-
- getGroupwiseSimilarity(OWLNamedIndividual) - Method in interface owltools.sim2.OwlSim
-
Compare a named individual i
to itself.
- getGroupwiseSimilarity(OWLNamedIndividual, OWLNamedIndividual) - Method in interface owltools.sim2.OwlSim
-
Compare two named individuals (i,j)
.
- getGroupwiseSimilarity(OWLNamedIndividual, OWLNamedIndividual, double, double) - Method in interface owltools.sim2.OwlSim
-
Compare two named individuals i
, filtering on
minSimJ
and minMaxIC
- getGroupwiseSimilarity(Set<OWLClass>, OWLNamedIndividual) - Method in interface owltools.sim2.OwlSim
-
Compare a set of attributes against the named individual i
.
- getGroupwiseSimilarity(Set<OWLClass>, OWLNamedIndividual, double, double) - Method in interface owltools.sim2.OwlSim
-
Compare a set of attributes against the named individual i
.
- getGroupwiseSimilarity(Set<OWLClass>, Set<OWLClass>) - Method in interface owltools.sim2.OwlSim
-
- getGroupwiseSimilarity(Set<OWLClass>, Set<OWLClass>, double, double) - Method in interface owltools.sim2.OwlSim
-
- getGroupwiseSimilarity(OWLNamedIndividual) - Method in class owltools.sim2.SimpleOwlSim
-
- getGroupwiseSimilarity(OWLNamedIndividual, OWLNamedIndividual, double, double) - Method in class owltools.sim2.SimpleOwlSim
-
- getGroupwiseSimilarity(Set<OWLClass>, OWLNamedIndividual) - Method in class owltools.sim2.SimpleOwlSim
-
- getGroupwiseSimilarity(Set<OWLClass>, OWLNamedIndividual, double, double) - Method in class owltools.sim2.SimpleOwlSim
-
- getGroupwiseSimilarity(Set<OWLClass>, Set<OWLClass>) - Method in class owltools.sim2.SimpleOwlSim
-
- getGroupwiseSimilarity(Set<OWLClass>, Set<OWLClass>, double, double) - Method in class owltools.sim2.SimpleOwlSim
-
- getICDistribution(Set<OWLClass>, IRI, double) - Method in class owltools.sim2.kb.OWLSimReferenceBasedStatistics
-
- getICDistribution(Set<OWLClass>, IRI, Set<OWLClass>, double) - Method in class owltools.sim2.kb.OWLSimReferenceBasedStatistics
-
- getICSimDisj(OWLClass, OWLClass) - Method in class owltools.sim2.AbstractOwlSim
-
- getIgnoreSubClassesOf() - Method in class owltools.sim.OldSimpleOwlSim
-
- getIgnoreSubClassesOf() - Method in class owltools.sim2.SimpleOwlSim
-
- getInferredAttributes(OWLNamedIndividual) - Method in class owltools.sim2.FastOwlSim
-
- getInferredAttributes(OWLNamedIndividual) - Method in interface owltools.sim2.OwlSim
-
- getInferredAttributes(OWLNamedIndividual) - Method in class owltools.sim2.SimpleOwlSim
-
- getInformationContent(OWLObject) - Method in class owltools.sim.SimEngine
-
The IC of an OWLObject is
freq(Obj)/corpusSize
here the frequency of an object is the number of individuals with a graph path up to the object,
and the corpus size is the number of individuals in the graph
- getInformationContent(Set<OWLObject>) - Method in class owltools.sim.SimEngine
-
- getInformationContentForAttribute(OWLClass) - Method in class owltools.sim.OldSimpleOwlSim
-
- getInformationContentForAttribute(OWLClass) - Method in class owltools.sim2.FastOwlSim
-
- getInformationContentForAttribute(OWLClass) - Method in interface owltools.sim2.OwlSim
-
- getInformationContentForAttribute(OWLClass) - Method in class owltools.sim2.SimpleOwlSim
-
- getInputOntology() - Method in class owltools.sim2.preprocessor.AbstractSimPreProcessor
-
- getInputOntology() - Method in interface owltools.sim2.preprocessor.SimPreProcessor
-
- getIRIViaOBOSuffix(String) - Method in class owltools.sim2.preprocessor.AbstractOBOSimPreProcessor
-
- getKurtosis() - Method in class owltools.sim2.kb.BasicStatistics
-
- getLabel(OWLEntity, OWLOntology) - Method in class owltools.sim2.preprocessor.AbstractSimPreProcessor
-
- getLCS() - Method in class owltools.sim.ConjunctiveSetInformationContentRatioSimilarity
-
- getLeastCommonSubsumers(OWLObject, OWLObject) - Method in class owltools.sim.SimEngine
-
note that this performs caching by default
- getLeastCommonSubsumerSimpleClassExpression(OWLObject, OWLObject) - Method in class owltools.sim.SimEngine
-
- getLeastCommonSubsumerSimpleClassExpression(OWLObject, OWLObject, boolean) - Method in class owltools.sim.SimEngine
-
- getLeastCommonSubsumersSize(OWLObject, OWLObject) - Method in class owltools.sim.SimEngine
-
- getLowestCommonSubsumer(OWLClassExpression, OWLClassExpression) - Method in class owltools.sim.OldSimpleOwlSim
-
gets the LCS.
- getLowestCommonSubsumer(OWLClassExpression, OWLClassExpression) - Method in class owltools.sim2.preprocessor.AbstractSimPreProcessor
-
- getLowestCommonSubsumer(OWLClassExpression, OWLClassExpression) - Method in class owltools.sim2.preprocessor.LCSEnabledSimPreProcessor
-
gets the LCS.
- getLowestCommonSubsumer(OWLClassExpression, OWLClassExpression, Set<OWLClass>) - Method in class owltools.sim2.preprocessor.LCSEnabledSimPreProcessor
-
- getLowestCommonSubsumer(OWLClassExpression, OWLClassExpression) - Method in interface owltools.sim2.preprocessor.SimPreProcessor
-
Returns the LCS of a and b.
- getLowestCommonSubsumerClass(OWLClassExpression, OWLClassExpression) - Method in class owltools.sim.OldSimpleOwlSim
-
generates a LCS expression and makes it a class if it is a class expression
- getLowestCommonSubsumerClass(OWLClassExpression, OWLClassExpression, Set<OWLClass>) - Method in class owltools.sim2.preprocessor.LCSEnabledSimPreProcessor
-
generates a LCS expression and makes it a class if it is a class expression
- getLowestCommonSubsumerIC(OWLClassExpression, OWLClassExpression) - Method in class owltools.sim.OldSimpleOwlSim
-
- getLowestCommonSubsumerIC(OWLClass, OWLClass) - Method in class owltools.sim2.SimpleOwlSim
-
IC(c) = -log2(p(c))
p(c) = | Inst(c) | / | Inst(owl:Thing) |
- getLowestCommonSubsumerIC(OWLClass, OWLClass, Double) - Method in class owltools.sim2.SimpleOwlSim
-
- getLowestCommonSubsumerWithIC(OWLClass, OWLClass) - Method in class owltools.sim2.FastOwlSim
-
- getLowestCommonSubsumerWithIC(OWLClass, OWLClass, Double) - Method in class owltools.sim2.FastOwlSim
-
- getLowestCommonSubsumerWithIC(OWLClass, OWLClass) - Method in interface owltools.sim2.OwlSim
-
Resnick similarity measure, together with all LCSs (MICAs) that
have this as IC
- getLowestCommonSubsumerWithIC(OWLClass, OWLClass, Double) - Method in interface owltools.sim2.OwlSim
-
- getLowestCommonSubsumerWithIC(OWLClass, OWLClass) - Method in class owltools.sim2.SimpleOwlSim
-
- getLowestCommonSubsumerWithIC(OWLClass, OWLClass, Double) - Method in class owltools.sim2.SimpleOwlSim
-
- getLowestCommonSubsumerWithLinScore(OWLClass, OWLClass) - Method in class owltools.sim2.AbstractOwlSim
-
- getLowestCommonSubsumerWithLinScore(OWLClass, OWLClass) - Method in interface owltools.sim2.OwlSim
-
- getMax() - Method in class owltools.sim2.kb.BasicStatistics
-
- getMax(SimpleOwlSim.Metric) - Method in class owltools.sim2.SimStats
-
- getMaxHits() - Method in class owltools.sim.SimSearch
-
- getMean() - Method in class owltools.sim2.kb.BasicStatistics
-
- getMessage() - Method in exception owltools.sim2.CutoffException
-
- getMetadata() - Method in class owltools.sim2.AbstractOwlSim
-
- getMetadata() - Method in class owltools.sim2.FastOwlSim
-
- getMetadata() - Method in interface owltools.sim2.OwlSim
-
- getMetricStats(OwlSim.Stat) - Method in class owltools.sim2.AbstractOwlSim
-
- getMetricStats(OwlSim.Stat) - Method in interface owltools.sim2.OwlSim
-
- getMin() - Method in class owltools.sim2.kb.BasicStatistics
-
- getMinimumDistanceToAncestor(OWLClass, OWLClass) - Method in class owltools.sim2.AbstractOwlSim
-
- getMinimumDistanceViaMICA(OWLClass, OWLClass) - Method in class owltools.sim2.AbstractOwlSim
-
- getNamedCommonSubsumers(OWLClassExpression, OWLClassExpression) - Method in class owltools.sim.OldSimpleOwlSim
-
- getNamedCommonSubsumers(OWLNamedIndividual, OWLNamedIndividual) - Method in class owltools.sim.OldSimpleOwlSim
-
- getNamedCommonSubsumers(OWLClass, OWLClass) - Method in class owltools.sim2.FastOwlSim
-
- getNamedCommonSubsumers(OWLNamedIndividual, OWLNamedIndividual) - Method in class owltools.sim2.FastOwlSim
-
- getNamedCommonSubsumers(OWLClass, OWLClass) - Method in interface owltools.sim2.OwlSim
-
CS(a,b) = { c : c ∈ RSub(a), c ∈ RSub(b) }
- getNamedCommonSubsumers(OWLNamedIndividual, OWLNamedIndividual) - Method in interface owltools.sim2.OwlSim
-
CS(i,j) = { c : c ∈ Type(i), c ∈ Type(j) }
- getNamedCommonSubsumers(OWLClassExpression, OWLClassExpression) - Method in class owltools.sim2.preprocessor.LCSEnabledSimPreProcessor
-
- getNamedCommonSubsumers(OWLNamedIndividual, OWLNamedIndividual) - Method in class owltools.sim2.preprocessor.LCSEnabledSimPreProcessor
-
- getNamedCommonSubsumers(OWLClass, OWLClass) - Method in class owltools.sim2.SimpleOwlSim
-
- getNamedCommonSubsumers(OWLNamedIndividual, OWLNamedIndividual) - Method in class owltools.sim2.SimpleOwlSim
-
- getNamedCommonSubsumersCount(OWLClass, OWLClass) - Method in class owltools.sim2.FastOwlSim
-
- getNamedCommonSubsumersCount(OWLClass, OWLClass) - Method in interface owltools.sim2.OwlSim
-
| CS(i,j) | = | { c : c ∈ Type(i), c ∈ Type(j) } |
- getNamedCommonSubsumersCount(OWLClass, OWLClass) - Method in class owltools.sim2.SimpleOwlSim
-
- getNamedLowestCommonSubsumers(OWLClassExpression, OWLClassExpression) - Method in class owltools.sim.OldSimpleOwlSim
-
- getNamedLowestCommonSubsumers(OWLClass, OWLClass) - Method in class owltools.sim2.FastOwlSim
-
- getNamedLowestCommonSubsumers(OWLClass, OWLClass) - Method in interface owltools.sim2.OwlSim
-
CSredundant(a,b) = { c : c ∈ CS(a,b), &E; c' : c' ∈ CS(a,b), c' &in Sub(c) }
LCS(a,b) = CS(a,b) - CSredundant
- getNamedLowestCommonSubsumers(OWLClassExpression, OWLClassExpression) - Method in class owltools.sim2.preprocessor.LCSEnabledSimPreProcessor
-
- getNamedLowestCommonSubsumers(OWLClass, OWLClass) - Method in class owltools.sim2.SimpleOwlSim
-
- getNamedReflexiveSubsumers(OWLClassExpression) - Method in class owltools.sim.OldSimpleOwlSim
-
- getNamedReflexiveSubsumers(OWLClass) - Method in class owltools.sim2.FastOwlSim
-
- getNamedReflexiveSubsumers(OWLClass) - Method in interface owltools.sim2.OwlSim
-
- getNamedReflexiveSubsumers(OWLClassExpression) - Method in class owltools.sim2.preprocessor.LCSEnabledSimPreProcessor
-
- getNamedReflexiveSubsumers(OWLClass) - Method in class owltools.sim2.SimpleOwlSim
-
- getNamedSubsumers(OWLClassExpression) - Method in class owltools.sim.OldSimpleOwlSim
-
- getNamedSubsumers(OWLNamedIndividual) - Method in class owltools.sim.OldSimpleOwlSim
-
- getNamedSubsumers(OWLClass) - Method in class owltools.sim2.AbstractOwlSim
-
- getNamedSubsumers(OWLClass) - Method in interface owltools.sim2.OwlSim
-
- getNamedSubsumers(OWLClassExpression) - Method in class owltools.sim2.preprocessor.LCSEnabledSimPreProcessor
-
- getNamedSubsumers(OWLNamedIndividual) - Method in class owltools.sim2.preprocessor.LCSEnabledSimPreProcessor
-
- getNamedSubsumers(OWLClass) - Method in class owltools.sim2.SimpleOwlSim
-
- getNamedUnionSubsumers(OWLClass, OWLClass) - Method in class owltools.sim2.FastOwlSim
-
- getNumberOfAttributesForI() - Method in class owltools.sim2.scores.ElementPairScores
-
- getNumberOfAttributesForJ() - Method in class owltools.sim2.scores.ElementPairScores
-
- getNumElementsForAttribute(OWLClass) - Method in class owltools.sim.OldSimpleOwlSim
-
|{e|e in a(c)}|
- getNumElementsForAttribute(OWLClass) - Method in class owltools.sim2.FastOwlSim
-
- getNumElementsForAttribute(OWLClass) - Method in interface owltools.sim2.OwlSim
-
|{e : e ∈ Inst(c)}|
- getNumElementsForAttribute(OWLClass) - Method in class owltools.sim2.SimpleOwlSim
-
- getNumSharedElements(OWLClass, OWLClass) - Method in class owltools.sim2.AbstractOwlSim
-
- getNumSharedElements(OWLClass, OWLClass) - Method in class owltools.sim2.FastOwlSim
-
- getNumSharedElements(OWLClass, OWLClass, OWLClass) - Method in class owltools.sim2.FastOwlSim
-
- getOutputOntology() - Method in class owltools.sim2.preprocessor.AbstractSimPreProcessor
-
- getOutputOntology() - Method in interface owltools.sim2.preprocessor.SimPreProcessor
-
- getOWLClassFromShortId(String) - Method in class owltools.sim2.AbstractOwlSim
-
- getOWLClassViaOBOSuffix(String) - Method in class owltools.sim2.preprocessor.AbstractOBOSimPreProcessor
-
- getOWLObjectPropertyViaOBOSuffix(String) - Method in class owltools.sim2.preprocessor.AbstractOBOSimPreProcessor
-
- getPairwiseSimilarity(OWLClass, OWLClass) - Method in class owltools.sim2.FastOwlSim
-
- getPairwiseSimilarity(OWLClass, OWLClass) - Method in interface owltools.sim2.OwlSim
-
Deprecated.
- getPairwiseSimilarity(OWLClass, OWLClass) - Method in class owltools.sim2.SimpleOwlSim
-
- getPaths(OWLClass, OWLClass) - Method in class owltools.sim2.AbstractOwlSim
-
- getPhenotypeEntityClasses() - Method in class owltools.sim2.preprocessor.PhenoSimHQEPreProcessor
-
- getPreSimMethod() - Method in class owltools.sim.MultiSimilarity
-
- getProperty(SimpleOwlSim.SimConfigurationProperty) - Method in class owltools.sim2.AbstractOwlSim
-
- getProperty(String) - Method in class owltools.sim2.preprocessor.AbstractSimPreProcessor
-
- getPropertyAsBoolean(SimpleOwlSim.SimConfigurationProperty) - Method in class owltools.sim2.AbstractOwlSim
-
- getPropertyAsDouble(SimpleOwlSim.SimConfigurationProperty) - Method in class owltools.sim2.AbstractOwlSim
-
- getPropertyAsDouble(SimpleOwlSim.SimConfigurationProperty, Double) - Method in class owltools.sim2.AbstractOwlSim
-
- getPValue(Set<OWLClass>, IRI) - Method in class owltools.sim2.kb.OwlSimPValue
-
- getPValue(Set<OWLClass>, IRI, Set<OWLClass>) - Method in class owltools.sim2.kb.OwlSimPValue
-
- getPValue(Set<OWLClass>, IRI) - Method in class owltools.sim2.kb.OWLSimReferenceBasedStatistics
-
- getPValue(Set<OWLClass>, IRI, Set<OWLClass>) - Method in class owltools.sim2.kb.OWLSimReferenceBasedStatistics
-
- getQualityClasses() - Method in class owltools.sim2.preprocessor.PhenoSimHQEPreProcessor
-
- getReasoner() - Method in class owltools.sim.OldSimpleOwlSim
-
- getReasoner() - Method in class owltools.sim2.AbstractOwlSim
-
- getReasoner() - Method in interface owltools.sim2.OwlSim
-
- getReasoner() - Method in class owltools.sim2.preprocessor.AbstractSimPreProcessor
-
- getReasoner() - Method in interface owltools.sim2.preprocessor.SimPreProcessor
-
- getReasoner() - Method in class owltools.sim2.SimpleOwlSim
-
- getReasonerFactory() - Method in class owltools.sim.OldSimpleOwlSim
-
- getReferenceBasicStatistics() - Method in class owltools.sim2.kb.ICDistribution
-
- getReferenceDistribution() - Method in class owltools.sim2.kb.ICDistribution
-
- getReferenceStats() - Method in class owltools.sim2.kb.OWLSimReferenceBasedStatistics
-
- getReflexiveSubClasses(OWLClassExpression) - Method in class owltools.sim2.preprocessor.AbstractSimPreProcessor
-
- getResultOutStream() - Method in class owltools.sim2.io.AbstractRenderer
-
- getResultOutStream() - Method in interface owltools.sim2.io.SimResultRenderer
-
- getScore() - Method in class owltools.sim.Similarity
-
- getScoredAttributesForElement(OWLNamedIndividual) - Method in class owltools.sim2.SimpleOwlSim
-
Given an individual element, return all direct attribute classes that the individual instantiates,
combined with IC.
- getSharedElements(OWLClass, OWLClass) - Method in class owltools.sim2.AbstractOwlSim
-
- getShortId(OWLClass) - Method in class owltools.sim2.AbstractOwlSim
-
- getShortId(OWLClass) - Method in interface owltools.sim2.OwlSim
-
- getSimEngine() - Method in class owltools.sim.SimSearch
-
- getSimilarityAlgorithm(String) - Method in class owltools.sim.SimEngine
-
factory class for generating a Similarity instance based on its name
- getSimilarityAlgorithm(Class) - Method in class owltools.sim.SimEngine
-
- getSimilarityBestMatchAverage(OWLNamedIndividual, OWLNamedIndividual, SimpleOwlSim.Metric, SimpleOwlSim.Direction) - Method in class owltools.sim2.FastOwlSim
-
- getSimilarityBestMatchAverage(OWLNamedIndividual, OWLNamedIndividual, SimpleOwlSim.Metric, SimpleOwlSim.Direction) - Method in interface owltools.sim2.OwlSim
-
Deprecated.
- getSimilarityBestMatchAverage(OWLNamedIndividual, OWLNamedIndividual, SimpleOwlSim.Metric, SimpleOwlSim.Direction) - Method in class owltools.sim2.SimpleOwlSim
-
- getSimilarityBestMatchAverageAsym(OWLNamedIndividual, OWLNamedIndividual) - Method in class owltools.sim.OldSimpleOwlSim
-
Pesquita et al
- getSimilarityBestMatchAverageAsym(OWLNamedIndividual, OWLNamedIndividual) - Method in class owltools.sim2.FastOwlSim
-
- getSimilarityBestMatchAverageAsym(OWLNamedIndividual, OWLNamedIndividual, SimpleOwlSim.Metric) - Method in class owltools.sim2.FastOwlSim
-
- getSimilarityBestMatchAverageAsym(OWLNamedIndividual, OWLNamedIndividual) - Method in interface owltools.sim2.OwlSim
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Deprecated.
- getSimilarityBestMatchAverageAsym(OWLNamedIndividual, OWLNamedIndividual, SimpleOwlSim.Metric) - Method in interface owltools.sim2.OwlSim
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See: Pesquita et al
- getSimilarityBestMatchAverageAsym(OWLNamedIndividual, OWLNamedIndividual) - Method in class owltools.sim2.SimpleOwlSim
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- getSimilarityBestMatchAverageAsym(OWLNamedIndividual, OWLNamedIndividual, SimpleOwlSim.Metric) - Method in class owltools.sim2.SimpleOwlSim
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- getSimilarityMaxIC(OWLNamedIndividual, OWLNamedIndividual) - Method in class owltools.sim.OldSimpleOwlSim
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- getSimilarityMaxIC(OWLNamedIndividual, OWLNamedIndividual) - Method in class owltools.sim2.FastOwlSim
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- getSimilarityMaxIC(OWLNamedIndividual, OWLNamedIndividual) - Method in interface owltools.sim2.OwlSim
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Find the inferred attribute shared by both i and j that has highest IC.
- getSimilarityMaxIC(OWLNamedIndividual, OWLNamedIndividual) - Method in class owltools.sim2.SimpleOwlSim
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- getSimplePValue() - Method in class owltools.sim2.kb.PValue
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- getSimPreProcessor() - Method in class owltools.sim.OldSimpleOwlSim
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- getSimPreProcessor() - Method in class owltools.sim2.SimpleOwlSim
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- getSimProperties() - Method in class owltools.sim2.AbstractOwlSim
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- getSimProperties() - Method in interface owltools.sim2.OwlSim
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- getSimProperties() - Method in class owltools.sim2.preprocessor.AbstractSimPreProcessor
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- getSimStatistics() - Method in class owltools.sim2.AbstractOwlSim
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- getSimStatistics(String) - Method in class owltools.sim2.FastOwlSim
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- getSimStatistics(String) - Method in interface owltools.sim2.OwlSim
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- getSimStatistics(String) - Method in class owltools.sim2.SimpleOwlSim
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- getSimStats() - Method in class owltools.sim2.AbstractOwlSim
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- getSimStats() - Method in interface owltools.sim2.OwlSim
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- getSkewness() - Method in class owltools.sim2.kb.BasicStatistics
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- getSourceOntology() - Method in class owltools.sim2.AbstractOwlSim
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- getSourceOntology() - Method in interface owltools.sim2.OwlSim
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- getSourceOntology() - Method in class owltools.sim2.SimpleOwlSim
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- getSourceViewProperties() - Method in class owltools.sim.OldSimpleOwlSim
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Deprecated.
- getStandardDeviation() - Method in class owltools.sim2.kb.BasicStatistics
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- getSubClasses() - Method in class owltools.sim2.kb.SubclassRetriever
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- getSubsetCoannotationMatrix(Set<OWLNamedIndividual>) - Method in class owltools.sim2.FastOwlSim
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- getSubsetCoannotationMatrix(Set<OWLNamedIndividual>) - Method in interface owltools.sim2.OwlSim
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- getSubsetCoannotationMatrix(Set<OWLNamedIndividual>) - Method in class owltools.sim2.SimpleOwlSim
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- getSubSimMethod() - Method in class owltools.sim.MultiSimilarity
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- getSummaryStatistics() - Method in class owltools.sim2.AbstractOwlSim
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- getSummaryStatistics(OWLClass) - Method in class owltools.sim2.AbstractOwlSim
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- getSummaryStatistics() - Method in interface owltools.sim2.OwlSim
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Fetch the pre-computed summary values
- getSummaryStatistics(OWLClass) - Method in interface owltools.sim2.OwlSim
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- getSummaryStatistics() - Method in class owltools.sim2.SimpleOwlSim
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- getSummaryStatisticsForCollection(Collection<SummaryStatistics>, OwlSim.Stat) - Method in class owltools.sim2.AbstractOwlSim
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This function will take an aggregated collection of Summary Statistics
and will generate a derived SummaryStatistic
based on a flag for the
desired summation.
- getSystemStats() - Method in class owltools.sim2.AbstractOwlSim
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- getSystemStats() - Method in interface owltools.sim2.OwlSim
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- getTopNVariances(Set<OWLClass>, int) - Method in class owltools.sim2.kb.OWLSimReferenceBasedStatistics
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- getTopNVarianceValues(Set<OWLClass>, int) - Method in class owltools.sim2.kb.OwlSimVariance
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This implementation can be heavily optimized
- getUnionSubsumers(OWLObject, OWLObject) - Method in class owltools.sim.SimEngine
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- getUnionSubsumersSize(OWLObject, OWLObject) - Method in class owltools.sim.SimEngine
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- getVariance(Set<OWLClass>, IRI) - Method in class owltools.sim2.kb.OWLSimReferenceBasedStatistics
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- getVariance(Set<OWLClass>, IRI, Set<OWLClass>) - Method in class owltools.sim2.kb.OWLSimReferenceBasedStatistics
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- getVarianceValue(Set<OWLClass>, IRI) - Method in class owltools.sim2.kb.OwlSimVariance
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- getVarianceValue(Set<OWLClass>, IRI, Set<OWLClass>) - Method in class owltools.sim2.kb.OwlSimVariance
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- getViewClasses(OWLClass) - Method in class owltools.sim2.preprocessor.AbstractSimPreProcessor
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- getViewClasses(OWLClass) - Method in interface owltools.sim2.preprocessor.SimPreProcessor
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The pre-processor may generate view classes.
- getViewProperties() - Method in class owltools.sim.OldSimpleOwlSim
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- getX() - Method in class owltools.sim2.kb.ICDistributionValue
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- getY() - Method in class owltools.sim2.kb.ICDistributionValue
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- GOSimPreProcessor - Class in owltools.sim2.preprocessor
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- GOSimPreProcessor() - Constructor for class owltools.sim2.preprocessor.GOSimPreProcessor
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- graph - Variable in class owltools.sim.SimEngine
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- graph - Variable in class owltools.sim2.io.AbstractRenderer
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