A B C D E F G H I J L M N O P Q R S T U V 

A

a - Variable in class owltools.sim2.io.SimResultRenderer.AttributesSimScores
 
ABNORMAL - Variable in class owltools.sim2.preprocessor.PhenoSimHQEPreProcessor
 
ABoxUtils - Class in owltools.sim2.preprocessor
 
ABoxUtils() - Constructor for class owltools.sim2.preprocessor.ABoxUtils
 
AbstractOBOSimPreProcessor - Class in owltools.sim2.preprocessor
 
AbstractOBOSimPreProcessor() - Constructor for class owltools.sim2.preprocessor.AbstractOBOSimPreProcessor
 
AbstractOwlSim - Class in owltools.sim2
 
AbstractOwlSim() - Constructor for class owltools.sim2.AbstractOwlSim
 
AbstractRenderer - Class in owltools.sim2.io
 
AbstractRenderer() - Constructor for class owltools.sim2.io.AbstractRenderer
 
AbstractSimPreProcessor - Class in owltools.sim2.preprocessor
 
AbstractSimPreProcessor() - Constructor for class owltools.sim2.preprocessor.AbstractSimPreProcessor
 
addAttributeClass(OWLClassExpression) - Method in class owltools.sim.OldSimpleOwlSim.ScoreAttributesPair
 
addAttributeClass(OWLClass) - Method in class owltools.sim2.OwlSim.ScoreAttributeSetPair
Adds am attribute to set (first creating empty set if not already present)
addAttributeIC(double) - Method in class owltools.sim2.SimStats
 
addAxiomsToOutput(Set<OWLAxiom>, boolean) - Method in class owltools.sim2.preprocessor.AbstractSimPreProcessor
 
addAxiomToOutput(OWLAxiom, boolean) - Method in class owltools.sim2.preprocessor.AbstractSimPreProcessor
 
addElementLabels(OWLOntology, String) - Static method in class owltools.sim2.OwlSimUtil
 
addElementLabels(OWLOntology, File) - Static method in class owltools.sim2.OwlSimUtil
 
addElementToAttributeAssociationsFromFile(OWLOntology, File) - Static method in class owltools.sim2.OwlSimUtil
 
addIgnoreSubClassesOf(OWLClass) - Method in class owltools.sim.OldSimpleOwlSim
 
addIgnoreSubClassesOf(IRI) - Method in class owltools.sim.OldSimpleOwlSim
 
addIgnoreSubClassesOf(OWLClass) - Method in class owltools.sim2.SimpleOwlSim
e.g.
addIgnoreSubClassesOf(IRI) - Method in class owltools.sim2.SimpleOwlSim
 
addIndividualIC(double) - Method in class owltools.sim2.SimStats
 
addPropertyChain(String, String, String) - Method in class owltools.sim2.preprocessor.AbstractOBOSimPreProcessor
 
addResultsToOWLOntology(OWLOntology) - Method in class owltools.sim.Similarity
translates similarity results into OWL Axioms and saves axioms into an OWL Ontology
addSourceViewProperty(OWLObjectProperty) - Method in class owltools.sim.OldSimpleOwlSim
Deprecated.
addSourceViewProperty(IRI) - Method in class owltools.sim.OldSimpleOwlSim
 
addViewMapping(OWLClass, OWLObjectProperty, OWLClass) - Method in class owltools.sim2.preprocessor.AbstractSimPreProcessor
 
addViewProperty(OWLObjectProperty) - Method in class owltools.sim.OldSimpleOwlSim
Deprecated.
addViewProperty(IRI) - Method in class owltools.sim.OldSimpleOwlSim
Deprecated.
aggregate - Variable in class owltools.sim2.OwlSim.StatsPerIndividual
 
allTypesDirectCount - Variable in class owltools.sim2.OwlSimMetadata
 
allTypesInferredCount - Variable in class owltools.sim2.OwlSimMetadata
 
analysisRelation - Variable in class owltools.sim2.preprocessor.PropertyViewSimPreProcessor
 
analysisStats - Variable in class owltools.sim2.SimStats
 
annotationIRI(String) - Method in class owltools.sim.Similarity
 
aScore - Variable in class owltools.sim.MultiSimilarity
 
assertInferences(boolean) - Method in class owltools.sim.OldSimpleOwlSim
 
assertInferredForAttributeClasses() - Method in class owltools.sim2.preprocessor.AbstractSimPreProcessor
 
assignDefaultInformationContentForAllClasses() - Method in class owltools.sim2.AbstractOwlSim
 
assignDefaultInformationContentForAllClasses() - Method in class owltools.sim2.FastOwlSim
 
AsymmetricJaccardSimilarity - Class in owltools.sim
 
AsymmetricJaccardSimilarity() - Constructor for class owltools.sim.AsymmetricJaccardSimilarity
 
asymmetricSimGIC - Variable in class owltools.sim2.scores.ElementPairScores
 
asymmetricSimjScore - Variable in class owltools.sim2.scores.AttributePairScores
 
asymmetricSimjScore - Variable in class owltools.sim2.scores.ElementPairScores
 
AsymSimJScore - Variable in class owltools.sim2.io.SimResultRenderer.AttributesSimScores
 
AsymSimJScoreLabel - Variable in class owltools.sim2.io.SimResultRenderer.AttributesSimScores
 
attributeClass - Variable in class owltools.sim.OldSimpleOwlSim.ScoreAttributePair
 
attributeClass - Variable in class owltools.sim2.SimpleOwlSim.ScoreAttributePair
 
attributeClassSet - Variable in class owltools.sim.OldSimpleOwlSim.ScoreAttributesPair
 
attributeClassSet - Variable in class owltools.sim2.OwlSim.ScoreAttributeSetPair
Set of attributes that have the score
attributeInformationContentCutoff - Variable in class owltools.sim.OldSimpleOwlSim.EnrichmentConfig
 
attributeInformationContentCutoff - Variable in class owltools.sim2.EnrichmentConfig
 
AttributePairScores - Class in owltools.sim2.scores
A set of scores for any given pair of attributes classes
AttributePairScores(OWLClass, OWLClass) - Constructor for class owltools.sim2.scores.AttributePairScores
 
attributesIC - Variable in class owltools.sim2.SimStats
 
AutomaticSimPreProcessor - Class in owltools.sim2.preprocessor
uses all properties as view properties, no role chains
AutomaticSimPreProcessor() - Constructor for class owltools.sim2.preprocessor.AutomaticSimPreProcessor
 
avgIC - Variable in class owltools.sim2.scores.ElementPairScores
 
AvgInformationContentBestMatchesSimilarity - Class in owltools.sim
Deprecated.
AvgInformationContentBestMatchesSimilarity() - Constructor for class owltools.sim.AvgInformationContentBestMatchesSimilarity
Deprecated.
 
AvgInformationContentLCSSimilarity - Class in owltools.sim
Deprecated.
AvgInformationContentLCSSimilarity() - Constructor for class owltools.sim.AvgInformationContentLCSSimilarity
Deprecated.
 

B

b - Variable in class owltools.sim2.io.SimResultRenderer.AttributesSimScores
 
baseFileName - Variable in class owltools.sim.OldSimpleOwlSim
 
BasicStatistics - Class in owltools.sim2.kb
 
BasicStatistics(DescriptiveStatistics) - Constructor for class owltools.sim2.kb.BasicStatistics
 
bestForC - Variable in class owltools.sim2.scores.ScoreMatrix
 
bestForD - Variable in class owltools.sim2.scores.ScoreMatrix
 
bestSubsumers - Variable in class owltools.sim.ConjunctiveSetSimilarity
 
bestSubsumers - Variable in class owltools.sim.DisjunctiveSetSimilarity
 
bestSubsumers - Variable in class owltools.sim.MaximumInformationContentSimilarity
 
bloomFilter - Variable in class owltools.sim.SimSearch
 
bmaAsymIC - Variable in class owltools.sim2.io.SimResultRenderer.IndividualSimScores
 
bmaAsymIC - Variable in class owltools.sim2.scores.ElementPairScores
 
bmaAsymICLabel - Variable in class owltools.sim2.io.SimResultRenderer.IndividualSimScores
 
bmaAsymJ - Variable in class owltools.sim2.io.SimResultRenderer.IndividualSimScores
 
bmaAsymJLabel - Variable in class owltools.sim2.io.SimResultRenderer.IndividualSimScores
 
bmaInverseAsymIC - Variable in class owltools.sim2.scores.ElementPairScores
 
bmaSymIC - Variable in class owltools.sim2.io.SimResultRenderer.IndividualSimScores
 
bmaSymIC - Variable in class owltools.sim2.scores.ElementPairScores
 
bmaSymICLabel - Variable in class owltools.sim2.io.SimResultRenderer.IndividualSimScores
 
bmaSymJ - Variable in class owltools.sim2.io.SimResultRenderer.IndividualSimScores
 
bmaSymJLabel - Variable in class owltools.sim2.io.SimResultRenderer.IndividualSimScores
 
BruteForceSimPreProcessor - Class in owltools.sim2.preprocessor
uses ClassAssertions to determine view property
BruteForceSimPreProcessor() - Constructor for class owltools.sim2.preprocessor.BruteForceSimPreProcessor
 
bScore - Variable in class owltools.sim.MultiSimilarity
 
buildDescription(OWLObject, OWLObject) - Method in class owltools.sim.DescriptionTreeSimilarity
Recursively build a class expression that subsumes a and b.
buildDescription(OWLObject, OWLObject, Set<OWLObject>) - Method in class owltools.sim.DescriptionTreeSimilarity
 

C

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 - 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
 
ClassDifferentiaLearner.InferredClassDefinition(OWLClass, OWLClass, OWLClass, Double) - Constructor for class owltools.sim2.ClassDifferentiaLearner.InferredClassDefinition
 
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
 

D

d - Variable in class owltools.sim2.scores.AttributePairScores
 
debugClass - Variable in class owltools.sim2.FastOwlSim
 
deepSimMethods - Variable in class owltools.sim.MultiSimilarity
 
defaultLCSElementFrequencyThreshold - Variable in class owltools.sim2.preprocessor.LCSEnabledSimPreProcessor
 
defaultNewIntersectionSimJThreshold - Variable in class owltools.sim2.preprocessor.LCSEnabledSimPreProcessor
 
defaultValue() - Method in enum owltools.sim2.SimpleOwlSim.SimConfigurationProperty
 
DelimitedLineRenderer - Class in owltools.sim2.io
 
DelimitedLineRenderer(PrintStream, String, String) - Constructor for class owltools.sim2.io.DelimitedLineRenderer
 
DelimitedLineRenderer(PrintStream) - Constructor for class owltools.sim2.io.DelimitedLineRenderer
 
DEPENDS_ON - Variable in class owltools.sim2.preprocessor.AbstractOBOSimPreProcessor
 
DescriptionTreeSimilarity - Class in owltools.sim
A similarity between two entities constructed by threading two description trees together.
DescriptionTreeSimilarity() - Constructor for class owltools.sim.DescriptionTreeSimilarity
 
DEVELOPS_FROM - Variable in class owltools.sim2.preprocessor.AbstractOBOSimPreProcessor
 
DisjunctiveSetSimilarity - Class in owltools.sim
 
DisjunctiveSetSimilarity() - Constructor for class owltools.sim.DisjunctiveSetSimilarity
 
dispose() - Method in class owltools.sim2.AbstractOwlSim
 
dispose() - Method in class owltools.sim2.FastOwlSim
 
dispose() - Method in class owltools.sim2.io.AbstractRenderer
 
dispose() - Method in class owltools.sim2.io.JSONRenderer
 
dispose() - Method in class owltools.sim2.io.OWLRenderer
 
dispose() - Method in interface owltools.sim2.io.SimResultRenderer
 
dispose() - Method in interface owltools.sim2.OwlSim
call when owlsim object is no longer required
dispose() - Method in class owltools.sim2.preprocessor.AbstractSimPreProcessor
 
dispose() - Method in interface owltools.sim2.preprocessor.SimPreProcessor
Clean the current instance, i.e.
ds - Variable in class owltools.sim2.scores.ElementPairScores
 

E

edgeSetToExpression(Set<OWLGraphEdge>) - Method in class owltools.sim.SimEngine
 
eiSetSize - Variable in class owltools.sim2.EnrichmentResult
 
ElementPairScores - Class in owltools.sim2.scores
A pair of scores for any given pair of individuals
ElementPairScores(OWLNamedIndividual, OWLNamedIndividual) - Constructor for class owltools.sim2.scores.ElementPairScores
 
enrichedClass - Variable in class owltools.sim.OldSimpleOwlSim.EnrichmentResult
 
enrichedClass - Variable in class owltools.sim2.EnrichmentResult
 
enrichedClassSize - Variable in class owltools.sim2.EnrichmentResult
 
enrichmentConfig - Variable in class owltools.sim.OldSimpleOwlSim
 
enrichmentConfig - Variable in class owltools.sim2.AbstractOwlSim
 
EnrichmentConfig - Class in owltools.sim2
 
EnrichmentConfig() - Constructor for class owltools.sim2.EnrichmentConfig
 
EnrichmentEngine - Class in owltools.sim
 
EnrichmentEngine() - Constructor for class owltools.sim.EnrichmentEngine
 
EnrichmentResult - Class in owltools.sim2
 
EnrichmentResult(OWLClass, OWLClass, double, double) - Constructor for class owltools.sim2.EnrichmentResult
 
EnrichmentResult(OWLClass, OWLClass, double, double, int, int, int, int) - Constructor for class owltools.sim2.EnrichmentResult
 
equals(Object) - Method in class owltools.sim.OldSimpleOwlSim.OWLClassExpressionPair
 
equals(Object) - Method in class owltools.sim.OWLClassExpressionPair
 
equals(Object) - Method in class owltools.sim.OWLObjectPair
 
equals(Object) - Method in class owltools.sim2.EnrichmentResult
 
equals(Object) - Method in class owltools.sim2.io.SimResultRenderer.AttributesSimScores
 
equals(Object) - Method in class owltools.sim2.scores.ElementPairScores
 
excludeClassesInComparison - Variable in class owltools.sim.SimEngine
 
EXPRESSED_IN - Variable in class owltools.sim2.preprocessor.AbstractOBOSimPreProcessor
 
ExpressionSimPreProcessor - Class in owltools.sim2.preprocessor
 
ExpressionSimPreProcessor() - Constructor for class owltools.sim2.preprocessor.ExpressionSimPreProcessor
 
extendEdge(OWLGraphEdge) - Method in class owltools.sim.SimEngine
 
extractClassesFromDeclarations(Set<OWLAxiom>) - Method in class owltools.sim2.preprocessor.AbstractSimPreProcessor
 

F

FastOwlSim - Class in owltools.sim2
Faster implementation of OwlSim Makes use of integers to index classes, and bitmaps to represent class sets.
FastOwlSim(OWLOntology) - Constructor for class owltools.sim2.FastOwlSim
 
FastOwlSim(OWLReasoner) - Constructor for class owltools.sim2.FastOwlSim
 
FastOwlSim.ClassCount - Class in owltools.sim2
 
FastOwlSim.ClassCount(OWLClass, Double) - Constructor for class owltools.sim2.FastOwlSim.ClassCount
 
FastOwlSim.ClassCount(OWLClass, Integer) - Constructor for class owltools.sim2.FastOwlSim.ClassCount
 
FastOwlSimFactory - Class in owltools.sim2
 
FastOwlSimFactory() - Constructor for class owltools.sim2.FastOwlSimFactory
 
featureToAttributeMap - Variable in class owltools.sim.MultiSimilarity
 
filterByDirectProperty(Set<OWLClass>, OWLObjectProperty) - Method in class owltools.sim2.preprocessor.PhenoSimHQEPreProcessor
Note: if the ontology contains Z SubClassOf df some Z2, Z2 SubClassOf U then Z2 will be retained, but U will not.
filterEnrichmentResults(List<EnrichmentResult>) - Method in class owltools.sim2.AbstractOwlSim
 
filterObjects(Set<OWLObject>) - Method in class owltools.sim.SimEngine
 
filterUnused(Set<OWLAxiom>) - Method in class owltools.sim2.preprocessor.AbstractSimPreProcessor
Call after createPropertyView() if the view contains a class C' = P some C, and C' does not classify and individuals or classes in the ontology (excluding other view classes in this set), then C' and related axioms are removed TODO: note that in general this should not be used if P is reflexive, as there will trivially be subclasses of the view class
findDifferentia(OWLClass, OWLClass, OWLClass) - Method in class owltools.sim2.ClassDifferentiaLearner
 
findMatches(Set<OWLClass>, String) - Method in class owltools.sim2.AbstractOwlSim
 
findMatches(OWLNamedIndividual, String) - Method in class owltools.sim2.AbstractOwlSim
 
findMatches(OWLNamedIndividual, String, double, double) - Method in class owltools.sim2.AbstractOwlSim
 
findMatches(Set<OWLClass>, String, double, double) - Method in class owltools.sim2.FastOwlSim
 
findMatches(Set<OWLClass>, String) - Method in interface owltools.sim2.OwlSim
Find all similar matches to a pseudo-individual with a set of attributes when compared to loaded individuals using getGroupwiseSimilarity with default cutoffs.
findMatches(Set<OWLClass>, String, double, double) - Method in interface owltools.sim2.OwlSim
Find all similar matches to a pseudo-individual with a set of attributes when compared to loaded individuals using getGroupwiseSimilarity with minSimJPct and minMaxIC cutoffs.
findMatches(OWLNamedIndividual, String) - Method in interface owltools.sim2.OwlSim
 
findMatches(OWLNamedIndividual, String, double, double) - Method in interface owltools.sim2.OwlSim
 
findMatches(Set<OWLClass>, String) - Method in class owltools.sim2.SimpleOwlSim
 
findMatches(Set<OWLClass>, String, double, double) - Method in class owltools.sim2.SimpleOwlSim
 
findMatchesRefactored(Set<OWLClass>, String) - Method in class owltools.sim2.FastOwlSim
 
findMatchesRefactored(Set<OWLClass>, String, double, double) - Method in class owltools.sim2.FastOwlSim
 
findMatchesWithin(OWLNamedIndividual, Set<OWLNamedIndividual>) - Method in class owltools.sim2.FastOwlSim
 
findMatchesWithin(Set<OWLClass>, Set<OWLNamedIndividual>, double, double) - Method in class owltools.sim2.FastOwlSim
 
findMatchesWithin(OWLNamedIndividual, Set<OWLNamedIndividual>) - Method in interface owltools.sim2.OwlSim
 
findMatchesWithin(OWLNamedIndividual, Set<OWLNamedIndividual>) - Method in class owltools.sim2.SimpleOwlSim
 
flush() - Method in class owltools.sim2.preprocessor.AbstractSimPreProcessor
 
forceReflexivePropertyCreation - Variable in class owltools.sim.DescriptionTreeSimilarity
 
FormattedRenderer - Class in owltools.sim2.io
 
FormattedRenderer(PrintStream, OWLPrettyPrinter) - Constructor for class owltools.sim2.io.FormattedRenderer
 
FormattedRenderer(OWLPrettyPrinter) - Constructor for class owltools.sim2.io.FormattedRenderer
 
FormattedRenderer(OWLGraphWrapper) - Constructor for class owltools.sim2.io.FormattedRenderer
 
FormattedRenderer(OWLGraphWrapper, PrintStream) - Constructor for class owltools.sim2.io.FormattedRenderer
 

G

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
IC = -(log OwlSim.getNumElementsForAttribute(OWLClass) / corpus size) / log(2)
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
Deprecated.
getSimilarityBestMatchAverageAsym(OWLNamedIndividual, OWLNamedIndividual, SimpleOwlSim.Metric) - Method in interface owltools.sim2.OwlSim
See: Pesquita et al
getSimilarityBestMatchAverageAsym(OWLNamedIndividual, OWLNamedIndividual) - Method in class owltools.sim2.SimpleOwlSim
 
getSimilarityBestMatchAverageAsym(OWLNamedIndividual, OWLNamedIndividual, SimpleOwlSim.Metric) - Method in class owltools.sim2.SimpleOwlSim
 
getSimilarityMaxIC(OWLNamedIndividual, OWLNamedIndividual) - Method in class owltools.sim.OldSimpleOwlSim
 
getSimilarityMaxIC(OWLNamedIndividual, OWLNamedIndividual) - Method in class owltools.sim2.FastOwlSim
 
getSimilarityMaxIC(OWLNamedIndividual, OWLNamedIndividual) - Method in interface owltools.sim2.OwlSim
Find the inferred attribute shared by both i and j that has highest IC.
getSimilarityMaxIC(OWLNamedIndividual, OWLNamedIndividual) - Method in class owltools.sim2.SimpleOwlSim
 
getSimplePValue() - Method in class owltools.sim2.kb.PValue
 
getSimPreProcessor() - Method in class owltools.sim.OldSimpleOwlSim
 
getSimPreProcessor() - Method in class owltools.sim2.SimpleOwlSim
 
getSimProperties() - Method in class owltools.sim2.AbstractOwlSim
 
getSimProperties() - Method in interface owltools.sim2.OwlSim
 
getSimProperties() - Method in class owltools.sim2.preprocessor.AbstractSimPreProcessor
 
getSimStatistics() - Method in class owltools.sim2.AbstractOwlSim
 
getSimStatistics(String) - Method in class owltools.sim2.FastOwlSim
 
getSimStatistics(String) - Method in interface owltools.sim2.OwlSim
 
getSimStatistics(String) - Method in class owltools.sim2.SimpleOwlSim
 
getSimStats() - Method in class owltools.sim2.AbstractOwlSim
 
getSimStats() - Method in interface owltools.sim2.OwlSim
 
getSkewness() - Method in class owltools.sim2.kb.BasicStatistics
 
getSourceOntology() - Method in class owltools.sim2.AbstractOwlSim
 
getSourceOntology() - Method in interface owltools.sim2.OwlSim
 
getSourceOntology() - Method in class owltools.sim2.SimpleOwlSim
 
getSourceViewProperties() - Method in class owltools.sim.OldSimpleOwlSim
Deprecated.
getStandardDeviation() - Method in class owltools.sim2.kb.BasicStatistics
 
getSubClasses() - Method in class owltools.sim2.kb.SubclassRetriever
 
getSubsetCoannotationMatrix(Set<OWLNamedIndividual>) - Method in class owltools.sim2.FastOwlSim
 
getSubsetCoannotationMatrix(Set<OWLNamedIndividual>) - Method in interface owltools.sim2.OwlSim
 
getSubsetCoannotationMatrix(Set<OWLNamedIndividual>) - Method in class owltools.sim2.SimpleOwlSim
 
getSubSimMethod() - Method in class owltools.sim.MultiSimilarity
 
getSummaryStatistics() - Method in class owltools.sim2.AbstractOwlSim
 
getSummaryStatistics(OWLClass) - Method in class owltools.sim2.AbstractOwlSim
 
getSummaryStatistics() - Method in interface owltools.sim2.OwlSim
Fetch the pre-computed summary values
getSummaryStatistics(OWLClass) - Method in interface owltools.sim2.OwlSim
OwlSim.StatsPerIndividual summary statistic calculations using OWLClass c as the root node
getSummaryStatistics() - Method in class owltools.sim2.SimpleOwlSim
 
getSummaryStatisticsForCollection(Collection<SummaryStatistics>, OwlSim.Stat) - Method in class owltools.sim2.AbstractOwlSim
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
 
getSystemStats() - Method in interface owltools.sim2.OwlSim
 
getTopNVariances(Set<OWLClass>, int) - Method in class owltools.sim2.kb.OWLSimReferenceBasedStatistics
 
getTopNVarianceValues(Set<OWLClass>, int) - Method in class owltools.sim2.kb.OwlSimVariance
This implementation can be heavily optimized
getUnionSubsumers(OWLObject, OWLObject) - Method in class owltools.sim.SimEngine
 
getUnionSubsumersSize(OWLObject, OWLObject) - Method in class owltools.sim.SimEngine
 
getVariance(Set<OWLClass>, IRI) - Method in class owltools.sim2.kb.OWLSimReferenceBasedStatistics
 
getVariance(Set<OWLClass>, IRI, Set<OWLClass>) - Method in class owltools.sim2.kb.OWLSimReferenceBasedStatistics
 
getVarianceValue(Set<OWLClass>, IRI) - Method in class owltools.sim2.kb.OwlSimVariance
 
getVarianceValue(Set<OWLClass>, IRI, Set<OWLClass>) - Method in class owltools.sim2.kb.OwlSimVariance
 
getViewClasses(OWLClass) - Method in class owltools.sim2.preprocessor.AbstractSimPreProcessor
 
getViewClasses(OWLClass) - Method in interface owltools.sim2.preprocessor.SimPreProcessor
The pre-processor may generate view classes.
getViewProperties() - Method in class owltools.sim.OldSimpleOwlSim
 
getX() - Method in class owltools.sim2.kb.ICDistributionValue
 
getY() - Method in class owltools.sim2.kb.ICDistributionValue
 
GOSimPreProcessor - Class in owltools.sim2.preprocessor
 
GOSimPreProcessor() - Constructor for class owltools.sim2.preprocessor.GOSimPreProcessor
 
graph - Variable in class owltools.sim.SimEngine
 
graph - Variable in class owltools.sim2.io.AbstractRenderer
 

H

HAS_PART - Variable in class owltools.sim2.preprocessor.AbstractOBOSimPreProcessor
 
HAS_PHENOTYPE - Variable in class owltools.sim2.preprocessor.AbstractOBOSimPreProcessor
 
hashCode() - Method in class owltools.sim.OldSimpleOwlSim.OWLClassExpressionPair
 
hashCode() - Method in class owltools.sim.OWLClassExpressionPair
 
hashCode() - Method in class owltools.sim.OWLObjectPair
 
hashCode() - Method in class owltools.sim2.EnrichmentResult
 
hashCode() - Method in class owltools.sim2.io.SimResultRenderer.AttributesSimScores
 
hashCode() - Method in class owltools.sim2.scores.ElementPairScores
 
hasInformationContent(OWLObject) - Method in class owltools.sim.SimEngine
 

I

i - Variable in class owltools.sim2.io.SimResultRenderer.IndividualSimScores
 
i - Variable in class owltools.sim2.scores.ElementPairScores
 
ICDistribution - Class in owltools.sim2.kb
 
ICDistribution(double[], DescriptiveStatistics, double) - Constructor for class owltools.sim2.kb.ICDistribution
 
ICDistributionValue - Class in owltools.sim2.kb
 
ICDistributionValue(double, double) - Constructor for class owltools.sim2.kb.ICDistributionValue
 
icIRIString - Variable in class owltools.sim2.AbstractOwlSim
 
iclcsMatrix - Variable in class owltools.sim2.scores.ElementPairScores
 
ignoreClasses(Set<String>) - Method in class owltools.sim2.preprocessor.AbstractSimPreProcessor
 
incrementClassPairCount(int) - Method in class owltools.sim2.SimStats
 
incrementIndividualPairCount() - Method in class owltools.sim2.SimStats
 
incrementUniqueClassPairCount() - Method in class owltools.sim2.SimStats
 
individualCount - Variable in class owltools.sim2.OwlSimMetadata
 
individualPairCount - Variable in class owltools.sim2.SimStats
 
individualsIC - Variable in class owltools.sim2.SimStats
 
INHERES_IN - Variable in class owltools.sim2.preprocessor.AbstractOBOSimPreProcessor
 
INHERES_IN_PART_OF - Variable in class owltools.sim2.preprocessor.AbstractOBOSimPreProcessor
 
init() - Method in class owltools.sim2.SimStats
 
initCoannotationMatrix(int[][]) - Method in class owltools.sim2.FastOwlSim
 
initCoannotationMatrix(int[][]) - Method in interface owltools.sim2.OwlSim
 
initCoannotationMatrix(int[][]) - Method in class owltools.sim2.SimpleOwlSim
 
inverseAsymmetricSimGIC - Variable in class owltools.sim2.scores.ElementPairScores
 
inverseAsymmetricSimjScore - Variable in class owltools.sim2.scores.AttributePairScores
 
inverseAsymmetricSimjScore - Variable in class owltools.sim2.scores.ElementPairScores
 
isAboveMinScore() - Method in class owltools.sim.Similarity
 
isBestMatch - Variable in class owltools.sim2.io.SimResultRenderer.AttributesSimScores
 
isBestMatchForI - Variable in class owltools.sim2.scores.AttributePairScores
 
isDisableLCSCache - Variable in class owltools.sim2.AbstractOwlSim
 
isDisableLCSCache() - Method in class owltools.sim2.AbstractOwlSim
 
isExcludedFromAnalysis(OWLObject) - Method in class owltools.sim.SimEngine
A class is excluded from the analysis if: it is a named entity, and the label for that entity matches the exclude labels list OR: it is a class expression, and the signature contains an excluded class
isFiltered - Variable in class owltools.sim2.io.SimResultRenderer.AttributesSimScores
 
isICmetric(String) - Static method in enum owltools.sim2.SimpleOwlSim.Metric
 
isJmetric(String) - Static method in enum owltools.sim2.SimpleOwlSim.Metric
 
isLCSCacheFullyPopulated - Variable in class owltools.sim2.AbstractOwlSim
 
isMultiSpecies - Variable in class owltools.sim2.preprocessor.PhenoSimHQEPreProcessor
 
isNoLookupForLCSCache - Variable in class owltools.sim2.AbstractOwlSim
 
isNoLookupForLCSCache() - Method in class owltools.sim2.AbstractOwlSim
 
isUpperLevel(OWLClass) - Method in class owltools.sim2.preprocessor.AbstractSimPreProcessor
 
isVerbotenEntity(OWLClass) - Method in class owltools.sim2.preprocessor.PhenoSimHQEPreProcessor
 

J

j - Variable in class owltools.sim2.io.SimResultRenderer.IndividualSimScores
 
j - Variable in class owltools.sim2.scores.ElementPairScores
 
JaccardBloomSimilarity - Class in owltools.sim
 
JaccardBloomSimilarity() - Constructor for class owltools.sim.JaccardBloomSimilarity
 
JaccardSimilarity - Class in owltools.sim
 
JaccardSimilarity() - Constructor for class owltools.sim.JaccardSimilarity
 
JSONRenderer - Class in owltools.sim2.io
 
JSONRenderer(PrintStream, String, String) - Constructor for class owltools.sim2.io.JSONRenderer
 
JSONRenderer(PrintStream) - Constructor for class owltools.sim2.io.JSONRenderer
 

L

label(OWLObject) - Method in class owltools.sim.SimEngine
 
lcsCache - Variable in class owltools.sim2.preprocessor.LCSEnabledSimPreProcessor
 
lcsCacheWidth - Variable in class owltools.sim2.OwlSimMetadata
 
LCSEnabledSimPreProcessor - Class in owltools.sim2.preprocessor
 
LCSEnabledSimPreProcessor() - Constructor for class owltools.sim2.preprocessor.LCSEnabledSimPreProcessor
 
lcsIC - Variable in class owltools.sim2.scores.AttributePairScores
 
lcsIntersectionSet - Variable in class owltools.sim.ConjunctiveSetInformationContentRatioSimilarity
 
lcsScore - Variable in class owltools.sim2.io.SimResultRenderer.AttributesSimScores
 
lcsScorePrefix - Variable in class owltools.sim2.io.SimResultRenderer.AttributesSimScores
 
lcsSet - Variable in class owltools.sim2.scores.AttributePairScores
 
loadLCSCache(String) - Method in class owltools.sim2.FastOwlSim
 
loadLCSCache(String) - Method in interface owltools.sim2.OwlSim
Loads a pregenerated IC cache.
loadLCSCache(String) - Method in class owltools.sim2.SimpleOwlSim
 
LOG - Variable in class owltools.sim2.preprocessor.AbstractSimPreProcessor
 
logCountMatrix(int[][]) - Method in class owltools.sim2.FastOwlSim
 

M

makeAllByAllLowestCommonSubsumer() - Method in class owltools.sim.OldSimpleOwlSim
 
makeClass(OWLObjectIntersectionOf) - Method in class owltools.sim.OldSimpleOwlSim
given a CE of the form A1 and A2 and ...
makeClass(OWLObjectIntersectionOf) - Method in class owltools.sim2.preprocessor.LCSEnabledSimPreProcessor
given a CE of the form A1 and A2 and ...
makeDefaultIndividuals(OWLOntology) - Static method in class owltools.sim2.preprocessor.ABoxUtils
Creates a "fake" individual for every class.
makeDefaultIndividuals(OWLOntology, String) - Static method in class owltools.sim2.preprocessor.ABoxUtils
Creates a "fake" individual for every class.
makeDevelopmentMorphologyLinks() - Method in class owltools.sim2.preprocessor.PhenoSimHQEPreProcessor
In MP we have + abn.
makeHasPhenotypeInstancesDirect() - Method in class owltools.sim2.preprocessor.PhenoSimHQEPreProcessor
 
makeIndividualSummaryStatistics(SummaryStatistics) - Method in class owltools.sim2.SimJSONEngine
 
makeIntersectionPair(OWLClassExpression, OWLClassExpression) - Method in class owltools.sim.SimEngine
 
makeLCSTriple(OWLObject, OWLObject, OWLObject) - Method in class owltools.sim2.SimJSONEngine
 
makeNonRedundant(Set<OWLObject>) - Method in class owltools.sim.SimEngine
An object x is redundant with a set S if: there exists an element y of S, such that y
makeNonRedundant(Set<OWLObject>, boolean) - Method in class owltools.sim.SimEngine
 
makeObj(OWLObject) - Method in class owltools.sim2.SimJSONEngine
 
makeObjAndSet(Map<String, Object>, String, OWLObject) - Method in class owltools.sim2.SimJSONEngine
 
makePartOfReflexive() - Method in class owltools.sim2.preprocessor.AbstractOBOSimPreProcessor
 
makeReflexive(String) - Method in class owltools.sim2.preprocessor.AbstractOBOSimPreProcessor
 
makeReflexive(OWLObjectProperty) - Method in class owltools.sim2.preprocessor.AbstractSimPreProcessor
 
makeReflexive(OWLObjectProperty, OWLClass) - Method in class owltools.sim2.preprocessor.AbstractSimPreProcessor
makes class and all subclasses reflexive
makeSummaryStatistics(OwlSim.StatsPerIndividual) - Method in class owltools.sim2.SimJSONEngine
 
makeSummaryStatistics(OWLClass) - Method in class owltools.sim2.SimJSONEngine
 
makeSummaryStatistics() - Method in class owltools.sim2.SimJSONEngine
 
makeUnionPair(OWLClassExpression, OWLClassExpression) - Method in class owltools.sim.SimEngine
 
makeUniqAttSet(List<Map>) - Method in class owltools.sim2.SimJSONEngine
 
makeViewClassIRI(IRI, IRI) - Method in class owltools.sim2.preprocessor.AbstractSimPreProcessor
 
makeViewClassIRI(IRI, IRI, String, boolean, boolean) - Method in class owltools.sim2.preprocessor.AbstractSimPreProcessor
 
mapClassAssertionsUp(OWLOntology, OWLReasoner, Set<OWLClass>, Set<OWLClass>) - Static method in class owltools.sim2.preprocessor.ABoxUtils
 
materializeClassExpression(OWLClassExpression) - Method in class owltools.sim2.preprocessor.AbstractSimPreProcessor
 
materializeClassExpressions(Set<OWLClassExpression>) - Method in class owltools.sim2.preprocessor.AbstractSimPreProcessor
Note: does not flush
materializeClassExpressionsReferencedBy(OWLObjectProperty) - Method in class owltools.sim2.preprocessor.AbstractSimPreProcessor
 
materializedClassExpressionMap - Variable in class owltools.sim2.preprocessor.AbstractSimPreProcessor
 
matrix - Variable in class owltools.sim2.scores.ScoreMatrix
 
max - Variable in class owltools.sim2.OwlSim.StatsPerIndividual
 
maxHits - Variable in class owltools.sim.SimSearch
 
maxIC - Variable in class owltools.sim2.io.SimResultRenderer.IndividualSimScores
 
maxIC - Variable in class owltools.sim2.scores.ElementPairScores
 
maxICLabel - Variable in class owltools.sim2.io.SimResultRenderer.IndividualSimScores
 
maxICwitness - Variable in class owltools.sim2.scores.ElementPairScores
 
maximumClassSize - Variable in class owltools.sim2.EnrichmentConfig
 
MaximumInformationContentSimilarity - Class in owltools.sim
MaximumInformationContentSimilarity(a,b) = max { IC(LCA_1(a,b)) ...
MaximumInformationContentSimilarity() - Constructor for class owltools.sim.MaximumInformationContentSimilarity
 
MD5(String) - Method in class owltools.sim2.preprocessor.AbstractSimPreProcessor
 
mean - Variable in class owltools.sim2.OwlSim.StatsPerIndividual
 
metrics - Static variable in interface owltools.sim2.OwlSim
 
metricStatMaxes - Variable in class owltools.sim2.AbstractOwlSim
 
metricStatMeans - Variable in class owltools.sim2.AbstractOwlSim
 
metricStatMins - Variable in class owltools.sim2.AbstractOwlSim
 
min - Variable in class owltools.sim2.OwlSim.StatsPerIndividual
 
minIC - Variable in class owltools.sim.SimSearch
 
minimumIC - Variable in class owltools.sim.SimEngine
 
minScore - Variable in class owltools.sim.Similarity
 
minScore - Variable in class owltools.sim.SimSearch
 
MultiSimilarity - Class in owltools.sim
This is the standard method to use when comparing entities with multiple attributes.
MultiSimilarity() - Constructor for class owltools.sim.MultiSimilarity
 

N

n - Variable in class owltools.sim2.OwlSim.StatsPerIndividual
 
NoElementAttributeMapException - Exception in owltools.sim2
 
NoElementAttributeMapException() - Constructor for exception owltools.sim2.NoElementAttributeMapException
 
nonSignificantObjects() - Method in class owltools.sim.SimEngine
 
NullSimPreProcessor - Class in owltools.sim2.preprocessor
uses ClassAssertions to determine view property
NullSimPreProcessor() - Constructor for class owltools.sim2.preprocessor.NullSimPreProcessor
 
numberOfElementsI - Variable in class owltools.sim2.io.SimResultRenderer.IndividualSimScores
 
numberOfElementsJ - Variable in class owltools.sim2.io.SimResultRenderer.IndividualSimScores
 

O

OldSimpleOwlSim - Class in owltools.sim
Inputs
OldSimpleOwlSim(OWLOntology) - Constructor for class owltools.sim.OldSimpleOwlSim
 
OldSimpleOwlSim.EnrichmentConfig - Class in owltools.sim
 
OldSimpleOwlSim.EnrichmentConfig() - Constructor for class owltools.sim.OldSimpleOwlSim.EnrichmentConfig
 
OldSimpleOwlSim.EnrichmentResult - Class in owltools.sim
 
OldSimpleOwlSim.EnrichmentResult(OWLClass, OWLClass, double, double) - Constructor for class owltools.sim.OldSimpleOwlSim.EnrichmentResult
 
OldSimpleOwlSim.OWLClassExpressionPair - Class in owltools.sim
 
OldSimpleOwlSim.OWLClassExpressionPair(OWLClassExpression, OWLClassExpression) - Constructor for class owltools.sim.OldSimpleOwlSim.OWLClassExpressionPair
 
OldSimpleOwlSim.ScoreAttributePair - Class in owltools.sim
 
OldSimpleOwlSim.ScoreAttributePair(Double, OWLClassExpression) - Constructor for class owltools.sim.OldSimpleOwlSim.ScoreAttributePair
 
OldSimpleOwlSim.ScoreAttributesPair - Class in owltools.sim
 
OldSimpleOwlSim.ScoreAttributesPair(Double, OWLClassExpression) - Constructor for class owltools.sim.OldSimpleOwlSim.ScoreAttributesPair
 
OldSimpleOwlSim.ScoreAttributesPair(Double, Set<OWLClassExpression>) - Constructor for class owltools.sim.OldSimpleOwlSim.ScoreAttributesPair
 
OldSimpleOwlSim.ScoreAttributesPair(double) - Constructor for class owltools.sim.OldSimpleOwlSim.ScoreAttributesPair
 
OldSimpleOwlSim.Stage - Enum in owltools.sim
 
overallStats - Variable in class owltools.sim2.AbstractOwlSim
 
overallSummaryStatsPerIndividual - Variable in class owltools.sim2.AbstractOwlSim
 
OverlapSimilarity - Class in owltools.sim
 
OverlapSimilarity() - Constructor for class owltools.sim.OverlapSimilarity
 
OWLClassExpressionPair - Class in owltools.sim
 
OWLClassExpressionPair(OWLClassExpression, OWLClassExpression) - Constructor for class owltools.sim.OWLClassExpressionPair
 
OWLObjectPair - Class in owltools.sim
 
OWLObjectPair(OWLObject, OWLObject) - Constructor for class owltools.sim.OWLObjectPair
 
OWLObjectPair(OWLObject, OWLObject, boolean) - Constructor for class owltools.sim.OWLObjectPair
 
owlpp - Variable in class owltools.sim.OldSimpleOwlSim
 
owlpp - Variable in class owltools.sim2.io.AbstractRenderer
 
OWLRenderer - Class in owltools.sim2.io
 
OWLRenderer(PrintStream) - Constructor for class owltools.sim2.io.OWLRenderer
 
OWLResultsManager - Class in owltools.sim
 
OWLResultsManager() - Constructor for class owltools.sim.OWLResultsManager
 
OwlSim - Interface in owltools.sim2
Semantic Similarity
OwlSim.ScoreAttributeSetPair - Class in owltools.sim2
A pair consisting of a set of equal-scoring attributes, and a score
OwlSim.ScoreAttributeSetPair(double, OWLClass) - Constructor for class owltools.sim2.OwlSim.ScoreAttributeSetPair
 
OwlSim.ScoreAttributeSetPair(double, Set<OWLClass>) - Constructor for class owltools.sim2.OwlSim.ScoreAttributeSetPair
 
OwlSim.ScoreAttributeSetPair(double) - Constructor for class owltools.sim2.OwlSim.ScoreAttributeSetPair
Combined/Summary score May vary depending on the method used
OwlSim.Stat - Enum in owltools.sim2
 
OwlSim.StatsPerIndividual - Class in owltools.sim2
 
OwlSim.StatsPerIndividual() - Constructor for class owltools.sim2.OwlSim.StatsPerIndividual
 
OwlSimFactory - Interface in owltools.sim2
Factory for creating OwlSim engines
OwlSimICDistribution - Class in owltools.sim2.kb
 
OwlSimICDistribution(OWLSimReferenceBasedStatistics, double[], IRI, Set<OWLClass>, double) - Constructor for class owltools.sim2.kb.OwlSimICDistribution
 
OwlSimMetadata - Class in owltools.sim2
 
OwlSimMetadata() - Constructor for class owltools.sim2.OwlSimMetadata
 
OwlSimPValue - Class in owltools.sim2.kb
 
OwlSimPValue(OWLSimReferenceBasedStatistics) - Constructor for class owltools.sim2.kb.OwlSimPValue
 
OWLSimReferenceBasedStatistics - Class in owltools.sim2.kb
 
OWLSimReferenceBasedStatistics(OwlSim, OWLOntology, OWLGraphWrapper) - Constructor for class owltools.sim2.kb.OWLSimReferenceBasedStatistics
Assuming owlsim, ontologyGraph and sourceOntology objects already initialized
OwlSimUtil - Class in owltools.sim2
Utility methods wrapping OwlSim Most of this functionality duplicates code found elsewhere in OWLTools, but using these static methods may be more straightforward.
OwlSimUtil() - Constructor for class owltools.sim2.OwlSimUtil
 
OwlSimVariance - Class in owltools.sim2.kb
 
OwlSimVariance(OWLSimReferenceBasedStatistics) - Constructor for class owltools.sim2.kb.OwlSimVariance
 
OwlSimVarianceEntityReferenceNotFoundException - Exception in owltools.sim2.kb
 
OwlSimVarianceEntityReferenceNotFoundException(IRI) - Constructor for exception owltools.sim2.kb.OwlSimVarianceEntityReferenceNotFoundException
 
owlThing() - Method in class owltools.sim2.FastOwlSim
Convenience method.
owlThingNode() - Method in class owltools.sim2.FastOwlSim
Convenience method.
owltools.sim - package owltools.sim
OWLSim -- Semantic Similarity over OWL ontologies
owltools.sim2 - package owltools.sim2
 
owltools.sim2.io - package owltools.sim2.io
 
owltools.sim2.kb - package owltools.sim2.kb
 
owltools.sim2.preprocessor - package owltools.sim2.preprocessor
 
owltools.sim2.scores - package owltools.sim2.scores
 

P

PairScores<T> - Interface in owltools.sim2.scores
A set of scores for any pair of objects
PART_OF - Variable in class owltools.sim2.preprocessor.AbstractOBOSimPreProcessor
 
PhenoSimHQEPreProcessor - Class in owltools.sim2.preprocessor
 
PhenoSimHQEPreProcessor() - Constructor for class owltools.sim2.preprocessor.PhenoSimHQEPreProcessor
 
populateFullCoannotationMatrix() - Method in class owltools.sim2.FastOwlSim
 
populateFullCoannotationMatrix() - Method in interface owltools.sim2.OwlSim
 
populateFullCoannotationMatrix() - Method in class owltools.sim2.SimpleOwlSim
 
populateSimilarityMatrix(OWLNamedIndividual, OWLNamedIndividual, ElementPairScores) - Method in class owltools.sim2.FastOwlSim
 
populationClassSize - Variable in class owltools.sim2.EnrichmentResult
 
precomputeAttributeAllByAll() - Method in class owltools.sim2.AbstractOwlSim
 
precomputeAttributeAllByAll() - Method in interface owltools.sim2.OwlSim
For implementations that use a cache, this performs an all by all comparison of all attributes and caches the results.
precomputeAttributeElementCount() - Method in class owltools.sim.OldSimpleOwlSim
 
precomputeAttributeElementCount() - Method in class owltools.sim2.SimpleOwlSim
Mapping between an attribute (e.g.
preprocess() - Method in class owltools.sim.OldSimpleOwlSim
NEW: externalize preprocessing to separate class
preprocess() - Method in class owltools.sim2.preprocessor.AbstractSimPreProcessor
 
preprocess() - Method in class owltools.sim2.preprocessor.AutomaticSimPreProcessor
 
preprocess() - Method in class owltools.sim2.preprocessor.BruteForceSimPreProcessor
 
preprocess() - Method in class owltools.sim2.preprocessor.ExpressionSimPreProcessor
 
preprocess() - Method in class owltools.sim2.preprocessor.GOSimPreProcessor
 
preprocess() - Method in class owltools.sim2.preprocessor.NullSimPreProcessor
 
preprocess() - Method in class owltools.sim2.preprocessor.PhenoSimHQEPreProcessor
 
preprocess() - Method in class owltools.sim2.preprocessor.PropertyViewSimPreProcessor
 
preprocess() - Method in interface owltools.sim2.preprocessor.SimPreProcessor
Generate output ontology
preSimMethod - Variable in class owltools.sim.MultiSimilarity
 
print(PrintStream) - Method in class owltools.sim.AvgInformationContentBestMatchesSimilarity
Deprecated.
 
print(PrintStream) - Method in class owltools.sim.AvgInformationContentLCSSimilarity
Deprecated.
 
print(PrintStream) - Method in class owltools.sim.CombinedJaccardConjunctiveSetSimilarity
 
print(PrintStream) - Method in class owltools.sim.CombinedSimilarity
 
print(PrintStream) - Method in class owltools.sim.CombinedSimilarity2
 
print(PrintStream) - Method in class owltools.sim.ConjunctiveSetInformationContentRatioSimilarity
 
print(PrintStream) - Method in class owltools.sim.ConjunctiveSetSimilarity
 
print(PrintStream) - Method in class owltools.sim.DescriptionTreeSimilarity
 
print(PrintStream) - Method in class owltools.sim.DisjunctiveSetSimilarity
 
print(PrintStream) - Method in class owltools.sim.MultiSimilarity
 
print() - Method in class owltools.sim.Similarity
 
print(PrintStream) - Method in class owltools.sim.Similarity
 
print(PrintStream, OWLObject) - Method in class owltools.sim.Similarity
 
printAttributeSim(SimResultRenderer.AttributesSimScores, OWLGraphWrapper, OWLPrettyPrinter) - Method in class owltools.sim2.io.DelimitedLineRenderer
 
printAttributeSim(SimResultRenderer.AttributesSimScores, OWLGraphWrapper) - Method in class owltools.sim2.io.DelimitedLineRenderer
 
printAttributeSim(SimResultRenderer.AttributesSimScores, OWLGraphWrapper, OWLPrettyPrinter) - Method in class owltools.sim2.io.FormattedRenderer
 
printAttributeSim(SimResultRenderer.AttributesSimScores, OWLGraphWrapper) - Method in class owltools.sim2.io.FormattedRenderer
 
printAttributeSim(SimResultRenderer.AttributesSimScores, OWLGraphWrapper) - Method in class owltools.sim2.io.JSONRenderer
 
printAttributeSim(SimResultRenderer.AttributesSimScores, OWLGraphWrapper, OWLPrettyPrinter) - Method in class owltools.sim2.io.JSONRenderer
 
printAttributeSim(SimResultRenderer.AttributesSimScores, OWLGraphWrapper) - Method in class owltools.sim2.io.OWLRenderer
Deprecated.
printAttributeSim(SimResultRenderer.AttributesSimScores, OWLGraphWrapper, OWLPrettyPrinter) - Method in class owltools.sim2.io.OWLRenderer
 
printAttributeSim(SimResultRenderer.AttributesSimScores, OWLGraphWrapper) - Method in interface owltools.sim2.io.SimResultRenderer
 
printAttributeSim(SimResultRenderer.AttributesSimScores, OWLGraphWrapper, OWLPrettyPrinter) - Method in interface owltools.sim2.io.SimResultRenderer
 
printAttributeSim(SimResultRenderer.AttributesSimScores, OWLGraphWrapper) - Method in class owltools.sim2.io.TabularRenderer
 
printAttributeSim(SimResultRenderer.AttributesSimScores, OWLGraphWrapper, OWLPrettyPrinter) - Method in class owltools.sim2.io.TabularRenderer
 
printAttributeSimWithIndividuals(SimResultRenderer.AttributesSimScores, OWLPrettyPrinter, OWLGraphWrapper, OWLNamedIndividual, OWLNamedIndividual) - Method in class owltools.sim2.io.DelimitedLineRenderer
 
printAttributeSimWithIndividuals(SimResultRenderer.AttributesSimScores, OWLPrettyPrinter, OWLGraphWrapper, OWLNamedIndividual, OWLNamedIndividual) - Method in class owltools.sim2.io.FormattedRenderer
 
printAttributeSimWithIndividuals(SimResultRenderer.AttributesSimScores, OWLPrettyPrinter, OWLGraphWrapper, OWLNamedIndividual, OWLNamedIndividual) - Method in class owltools.sim2.io.JSONRenderer
 
printAttributeSimWithIndividuals(SimResultRenderer.AttributesSimScores, OWLPrettyPrinter, OWLGraphWrapper, OWLNamedIndividual, OWLNamedIndividual) - Method in class owltools.sim2.io.OWLRenderer
 
printAttributeSimWithIndividuals(SimResultRenderer.AttributesSimScores, OWLPrettyPrinter, OWLGraphWrapper, OWLNamedIndividual, OWLNamedIndividual) - Method in interface owltools.sim2.io.SimResultRenderer
 
printAttributeSimWithIndividuals(SimResultRenderer.AttributesSimScores, OWLPrettyPrinter, OWLGraphWrapper, OWLNamedIndividual, OWLNamedIndividual) - Method in class owltools.sim2.io.TabularRenderer
 
printComment(CharSequence) - Method in class owltools.sim2.io.DelimitedLineRenderer
 
printComment(CharSequence) - Method in class owltools.sim2.io.FormattedRenderer
 
printComment(CharSequence) - Method in class owltools.sim2.io.JSONRenderer
 
printComment(CharSequence) - Method in class owltools.sim2.io.OWLRenderer
 
printComment(CharSequence) - Method in interface owltools.sim2.io.SimResultRenderer
 
printComment(CharSequence) - Method in class owltools.sim2.io.TabularRenderer
 
printDescription(PrintStream, OWLObject) - Method in class owltools.sim.Similarity
 
printDescription(PrintStream, OWLObject, int) - Method in class owltools.sim.Similarity
 
printIndividualPairSim(SimResultRenderer.IndividualSimScores, OWLPrettyPrinter, OWLGraphWrapper) - Method in class owltools.sim2.io.DelimitedLineRenderer
 
printIndividualPairSim(SimResultRenderer.IndividualSimScores, OWLPrettyPrinter, OWLGraphWrapper) - Method in class owltools.sim2.io.FormattedRenderer
 
printIndividualPairSim(SimResultRenderer.IndividualSimScores, OWLPrettyPrinter, OWLGraphWrapper) - Method in class owltools.sim2.io.JSONRenderer
 
printIndividualPairSim(SimResultRenderer.IndividualSimScores, OWLPrettyPrinter, OWLGraphWrapper) - Method in class owltools.sim2.io.OWLRenderer
 
printIndividualPairSim(SimResultRenderer.IndividualSimScores, OWLPrettyPrinter, OWLGraphWrapper) - Method in interface owltools.sim2.io.SimResultRenderer
 
printIndividualPairSim(SimResultRenderer.IndividualSimScores, OWLPrettyPrinter, OWLGraphWrapper) - Method in class owltools.sim2.io.TabularRenderer
 
printPairScores(ElementPairScores) - Method in class owltools.sim2.io.DelimitedLineRenderer
 
printPairScores(AttributePairScores) - Method in class owltools.sim2.io.DelimitedLineRenderer
 
printPairScores(ElementPairScores) - Method in class owltools.sim2.io.FormattedRenderer
 
printPairScores(AttributePairScores) - Method in class owltools.sim2.io.FormattedRenderer
 
printPairScores(ElementPairScores) - Method in class owltools.sim2.io.JSONRenderer
 
printPairScores(AttributePairScores) - Method in class owltools.sim2.io.JSONRenderer
 
printPairScores(ElementPairScores) - Method in class owltools.sim2.io.OWLRenderer
 
printPairScores(AttributePairScores) - Method in class owltools.sim2.io.OWLRenderer
 
printPairScores(ElementPairScores) - Method in interface owltools.sim2.io.SimResultRenderer
 
printPairScores(AttributePairScores) - Method in interface owltools.sim2.io.SimResultRenderer
 
printPairScores(ElementPairScores) - Method in class owltools.sim2.io.TabularRenderer
 
printPairScores(AttributePairScores) - Method in class owltools.sim2.io.TabularRenderer
 
printX(PrintStream, OWLObject) - Method in class owltools.sim.DescriptionTreeSimilarity
 
printX(PrintStream, OWLObject, int) - Method in class owltools.sim.DescriptionTreeSimilarity
 
PropertyViewSimPreProcessor - Class in owltools.sim2.preprocessor
 
PropertyViewSimPreProcessor() - Constructor for class owltools.sim2.preprocessor.PropertyViewSimPreProcessor
 
pValue - Variable in class owltools.sim.OldSimpleOwlSim.EnrichmentResult
 
pValue - Variable in class owltools.sim2.EnrichmentResult
 
PValue - Class in owltools.sim2.kb
 
PValue(double, double, double) - Constructor for class owltools.sim2.kb.PValue
 
pValueCorrected - Variable in class owltools.sim.OldSimpleOwlSim.EnrichmentResult
 
pValueCorrected - Variable in class owltools.sim2.EnrichmentResult
 
pValueCorrectedCutoff - Variable in class owltools.sim.OldSimpleOwlSim.EnrichmentConfig
 
pValueCorrectedCutoff - Variable in class owltools.sim2.EnrichmentConfig
 

Q

QUALIFIER - Variable in class owltools.sim2.preprocessor.AbstractOBOSimPreProcessor
 
QUALITY - Variable in class owltools.sim2.preprocessor.PhenoSimHQEPreProcessor
 
quickScore(Set<OWLObject>, Set<OWLObject>) - Method in class owltools.sim.DescriptionTreeSimilarity
 

R

randomizeClassAssertions(OWLOntology, int) - Static method in class owltools.sim2.preprocessor.ABoxUtils
 
rank - Variable in class owltools.sim2.scores.ElementPairScores
 
reason() - Method in class owltools.sim.OldSimpleOwlSim
 
reasoner - Variable in class owltools.sim2.AbstractOwlSim
 
reasonerClass - Variable in class owltools.sim2.OwlSimMetadata
 
removeAxiomsFromOutput(Set<OWLAxiom>, boolean) - Method in class owltools.sim2.preprocessor.AbstractSimPreProcessor
 
removeDisjointClassesAxioms() - Method in class owltools.sim2.preprocessor.AbstractSimPreProcessor
 
removeUnreachableAxioms() - Method in class owltools.sim.OldSimpleOwlSim
If a node cannot be reached on the existential graph, then remove it.
removeUnreachableAxioms() - Method in class owltools.sim2.preprocessor.AbstractSimPreProcessor
note: approximation used, may end up removing too many.
render(OWLPrettyPrinter) - Method in class owltools.sim2.ClassDifferentiaLearner
 
render(Set<OWLClass>) - Method in class owltools.sim2.io.FormattedRenderer
 
render(OWLClass) - Method in class owltools.sim2.io.FormattedRenderer
 
render(OWLNamedIndividual) - Method in class owltools.sim2.io.FormattedRenderer
 
renderAttScore(String, double, OWLClass, OWLClass, OWLGraphWrapper, OWLPrettyPrinter) - Method in class owltools.sim2.io.DelimitedLineRenderer
 
renderAttScoreWithIndividuals(String, double, OWLClass, OWLClass, OWLNamedIndividual, OWLNamedIndividual, OWLGraphWrapper, OWLPrettyPrinter) - Method in class owltools.sim2.io.DelimitedLineRenderer
 
renderIndividualScore(String, double, Set<OWLClass>, OWLNamedIndividual, OWLNamedIndividual, OWLPrettyPrinter) - Method in class owltools.sim2.io.DelimitedLineRenderer
 
renderPair(OWLNamedIndividual, OWLNamedIndividual, OWLPrettyPrinter) - Method in class owltools.sim2.io.DelimitedLineRenderer
 
renderPair(OWLNamedIndividual, OWLNamedIndividual, OWLPrettyPrinter) - Method in class owltools.sim2.io.JSONRenderer
 
renderPair(OWLNamedIndividual, OWLNamedIndividual, OWLPrettyPrinter) - Method in class owltools.sim2.io.TabularRenderer
 
report(Reporter) - Method in class owltools.sim.AsymmetricJaccardSimilarity
 
report(Reporter) - Method in class owltools.sim.ConjunctiveSetInformationContentRatioSimilarity
 
report(Reporter) - Method in class owltools.sim.JaccardSimilarity
 
report(Reporter) - Method in class owltools.sim.MultiSimilarity
 
report(Object...) - Method in class owltools.sim.Reporter
 
report(Reporter) - Method in class owltools.sim.Similarity
 
Reporter - Class in owltools.sim
 
Reporter(PrintStream, OWLGraphWrapper) - Constructor for class owltools.sim.Reporter
 
Reporter(OWLGraphWrapper) - Constructor for class owltools.sim.Reporter
 
reporter - Variable in class owltools.sim.SimSearch
 
resultOutStream - Variable in class owltools.sim2.io.AbstractRenderer
 
RESULTS_IN_DEVELOPMENT_OF - Variable in class owltools.sim2.preprocessor.AbstractOBOSimPreProcessor
 
RESULTS_IN_MORPHOGENESIS_OF - Variable in class owltools.sim2.preprocessor.AbstractOBOSimPreProcessor
 
retrieveCandidatesIC(Set<OWLClass>) - Method in class owltools.sim2.kb.OWLSimReferenceBasedStatistics
 

S

sampleSetClass - Variable in class owltools.sim.OldSimpleOwlSim.EnrichmentResult
 
sampleSetClass - Variable in class owltools.sim2.EnrichmentResult
 
sampleSetClassSize - Variable in class owltools.sim2.EnrichmentResult
 
saveIntermediateStates - Variable in class owltools.sim2.preprocessor.AbstractSimPreProcessor
 
saveLCSCache(String) - Method in class owltools.sim2.AbstractOwlSim
 
saveLCSCache(String, Double) - Method in class owltools.sim2.FastOwlSim
 
saveLCSCache(String) - Method in interface owltools.sim2.OwlSim
Saves the contents of the LCS-IC cache Assumes that this has already been filled by comparing all classes by all classes.
saveLCSCache(String, Double) - Method in interface owltools.sim2.OwlSim
As OwlSim.saveLCSCache(String), but do not write a line for any LCS whose IC falls below the threshold.
saveLCSCache(String, Double) - Method in class owltools.sim2.SimpleOwlSim
 
saveOntology(OldSimpleOwlSim.Stage) - Method in class owltools.sim.OldSimpleOwlSim
 
saveOntology(String) - Method in class owltools.sim.OldSimpleOwlSim
 
saveState(String) - Method in class owltools.sim2.AbstractOwlSim
 
saveState(String) - Method in class owltools.sim2.FastOwlSim
 
saveState(String) - Method in interface owltools.sim2.OwlSim
Experimental: save internal state of object
saveState(String) - Method in class owltools.sim2.preprocessor.AbstractSimPreProcessor
 
scaleFactor - Variable in class owltools.sim2.OwlSimMetadata
 
score - Variable in class owltools.sim.OldSimpleOwlSim.ScoreAttributePair
 
score - Variable in class owltools.sim.OldSimpleOwlSim.ScoreAttributesPair
 
score - Variable in class owltools.sim2.FastOwlSim.ClassCount
 
score - Variable in class owltools.sim2.OwlSim.ScoreAttributeSetPair
Score shared by all attributes in attribute set
score - Variable in class owltools.sim2.SimpleOwlSim.ScoreAttributePair
 
ScoreMatrix<T> - Class in owltools.sim2.scores
A matrix of scores or scored entities for two groups of attributes
ScoreMatrix() - Constructor for class owltools.sim2.scores.ScoreMatrix
 
search(OWLObject) - Method in class owltools.sim.SimSearch
Given a query object (e.g.
search(Set<OWLClass>, String, boolean) - Method in class owltools.sim2.SimJSONEngine
 
search(Set<OWLClass>, String, boolean, boolean) - Method in class owltools.sim2.SimJSONEngine
 
search(Set<OWLClass>, String, boolean, Integer) - Method in class owltools.sim2.SimJSONEngine
 
search(Set<OWLClass>, String, boolean, Integer, boolean) - Method in class owltools.sim2.SimJSONEngine
 
search(Set<OWLClass>, SimpleOwlSim.Metric) - Method in class owltools.sim2.SimpleOwlSim
 
setAttributeClassSet(Set<OWLClass>) - Method in class owltools.sim2.OwlSim.ScoreAttributeSetPair
Setter
setAttributesFromOntology(OWLOntology) - Method in class owltools.sim.OldSimpleOwlSim
Deprecated.
setBaseFileName(String) - Method in class owltools.sim.OldSimpleOwlSim
 
setCandidates(Set<OWLObject>) - Method in class owltools.sim.SimSearch
 
setCorpusSize(int) - Method in class owltools.sim.OldSimpleOwlSim
 
setCorpusSize(int) - Method in class owltools.sim2.AbstractOwlSim
 
setCorpusSize(int) - Method in interface owltools.sim2.OwlSim
Sets the number of entities in domain.
setCorpusSize(int) - Method in class owltools.sim2.SimpleOwlSim
 
setDisableLCSCache(boolean) - Method in class owltools.sim2.AbstractOwlSim
 
setDisableLCSCache(boolean) - Method in interface owltools.sim2.OwlSim
if set, the cache is neither read nor written to.
setEnrichmentConfig(OldSimpleOwlSim.EnrichmentConfig) - Method in class owltools.sim.OldSimpleOwlSim
 
setEnrichmentConfig(EnrichmentConfig) - Method in class owltools.sim2.AbstractOwlSim
 
setEnrichmentConfig(EnrichmentConfig) - Method in interface owltools.sim2.OwlSim
 
setGraph(OWLGraphWrapper) - Method in class owltools.sim.SimEngine
 
setGraph(OWLGraphWrapper) - Method in interface owltools.sim.SimilarityCalculator
 
setGraph(OWLGraphWrapper) - Method in class owltools.sim2.io.AbstractRenderer
 
setGraph(OWLGraphWrapper) - Method in interface owltools.sim2.io.SimResultRenderer
 
setIgnoreSubClassesOf(Set<OWLClass>) - Method in class owltools.sim.OldSimpleOwlSim
 
setIgnoreSubClassesOf(Set<OWLClass>) - Method in class owltools.sim2.SimpleOwlSim
 
setInformationContentFromOntology(OWLOntology) - Method in class owltools.sim2.AbstractOwlSim
 
setInformationContentFromOntology(OWLOntology) - Method in interface owltools.sim2.OwlSim
Populate the IC cache from an ontology of class-IC mappings.
setInformtionContectForAttribute(OWLClass, Double) - Method in class owltools.sim2.AbstractOwlSim
 
setInformtionContectForAttribute(OWLClass, Double) - Method in class owltools.sim2.FastOwlSim
 
setInformtionContectForAttribute(OWLClass, Double) - Method in class owltools.sim2.SimpleOwlSim
 
setInputOntology(OWLOntology) - Method in class owltools.sim2.preprocessor.AbstractSimPreProcessor
 
setInputOntology(OWLOntology) - Method in interface owltools.sim2.preprocessor.SimPreProcessor
sets the input ontology.
setMaxHits(int) - Method in class owltools.sim.SimSearch
 
setNoLookupForLCSCache(boolean) - Method in class owltools.sim2.AbstractOwlSim
 
setNoLookupForLCSCache(boolean) - Method in interface owltools.sim2.OwlSim
Ff set, the cache is written to but not read from.
setOutputOntology(OWLOntology) - Method in class owltools.sim2.preprocessor.AbstractSimPreProcessor
 
setOutputOntology(OWLOntology) - Method in interface owltools.sim2.preprocessor.SimPreProcessor
sets the output ontology.
setOWLPrettyPrinter(OWLPrettyPrinter) - Method in class owltools.sim2.preprocessor.AbstractSimPreProcessor
 
setOWLPrettyPrinter(OWLPrettyPrinter) - Method in interface owltools.sim2.preprocessor.SimPreProcessor
 
setPreSimMethod(String) - Method in class owltools.sim.MultiSimilarity
 
setReasoner(OWLReasoner) - Method in class owltools.sim.OldSimpleOwlSim
 
setReasoner(OWLReasoner) - Method in class owltools.sim2.preprocessor.AbstractSimPreProcessor
 
setReasoner(OWLReasoner) - Method in interface owltools.sim2.preprocessor.SimPreProcessor
Sets the reasoner.
setReasoner(OWLReasoner) - Method in class owltools.sim2.SimpleOwlSim
 
setReasonerFactory(OWLReasonerFactory) - Method in class owltools.sim.OldSimpleOwlSim
 
setReasonerFactory(OWLReasonerFactory) - Method in class owltools.sim2.preprocessor.AbstractSimPreProcessor
 
setReasonerFactory(OWLReasonerFactory) - Method in interface owltools.sim2.preprocessor.SimPreProcessor
Sets the reasoner factory.
setResultOutStream(PrintStream) - Method in class owltools.sim2.io.AbstractRenderer
 
setScore(Double) - Method in class owltools.sim.Similarity
 
setScore(int) - Method in class owltools.sim.Similarity
 
setSimEngine(SimEngine) - Method in class owltools.sim.SimSearch
 
setSimPreProcessor(SimPreProcessor) - Method in class owltools.sim.OldSimpleOwlSim
 
setSimPreProcessor(SimPreProcessor) - Method in class owltools.sim2.SimpleOwlSim
 
setSimProperties(Properties) - Method in class owltools.sim2.AbstractOwlSim
 
setSimProperties(Properties) - Method in interface owltools.sim2.OwlSim
 
setSimProperties(Properties) - Method in class owltools.sim2.preprocessor.AbstractSimPreProcessor
 
setSimProperties(Properties) - Method in interface owltools.sim2.preprocessor.SimPreProcessor
 
setSimStats(SimStats) - Method in class owltools.sim2.AbstractOwlSim
 
setSourceOntology(OWLOntology) - Method in class owltools.sim2.SimpleOwlSim
 
setSourceViewProperties(List<OWLObjectProperty>) - Method in class owltools.sim.OldSimpleOwlSim
Deprecated.
setSubSimMethod(String) - Method in class owltools.sim.MultiSimilarity
 
setValue(SimpleOwlSim.Metric, double) - Method in class owltools.sim2.SimStats
 
setViewProperties(Set<OWLObjectProperty>) - Method in class owltools.sim.OldSimpleOwlSim
Deprecated.
show(Set<OWLClassExpression>, OWLPrettyPrinter) - Method in class owltools.sim2.io.JSONRenderer
 
show(Set<OWLClass>, OWLPrettyPrinter) - Method in class owltools.sim2.io.TabularRenderer
 
showTimings() - Method in class owltools.sim2.AbstractOwlSim
 
showTimings() - Method in interface owltools.sim2.OwlSim
Writes timing information using log4j.
showTimingsAndReset() - Method in class owltools.sim2.AbstractOwlSim
 
SimEngine - Class in owltools.sim
SimEngine provides access to multiple similarity calculation procedures (see Similarity).
SimEngine(OWLGraphWrapper) - Constructor for class owltools.sim.SimEngine
 
simEngine - Variable in class owltools.sim.SimSearch
 
SimEngine.SimilarityAlgorithmException - Exception in owltools.sim
 
SimEngine.SimilarityAlgorithmException(String) - Constructor for exception owltools.sim.SimEngine.SimilarityAlgorithmException
 
simGIC - Variable in class owltools.sim2.io.SimResultRenderer.IndividualSimScores
 
simGIC - Variable in class owltools.sim2.scores.AttributePairScores
 
simGIC - Variable in class owltools.sim2.scores.ElementPairScores
 
simGICLabel - Variable in class owltools.sim2.io.SimResultRenderer.IndividualSimScores
 
Similarity - Class in owltools.sim
Represents a pairwise similarity between two OWLObjects.
Similarity() - Constructor for class owltools.sim.Similarity
 
SimilarityCalculator - Interface in owltools.sim
 
simJScore - Variable in class owltools.sim2.io.SimResultRenderer.AttributesSimScores
 
simjScore - Variable in class owltools.sim2.io.SimResultRenderer.IndividualSimScores
 
simjScore - Variable in class owltools.sim2.scores.AttributePairScores
 
simjScore - Variable in class owltools.sim2.scores.ElementPairScores
 
simjScoreLabel - Variable in class owltools.sim2.io.SimResultRenderer.AttributesSimScores
 
simjScoreLabel - Variable in class owltools.sim2.io.SimResultRenderer.IndividualSimScores
 
SimJSONEngine - Class in owltools.sim2
 
SimJSONEngine(OWLGraphWrapper, OwlSim) - Constructor for class owltools.sim2.SimJSONEngine
 
SimpleOwlSim - Class in owltools.sim2
Soon to be deprecated implementation of OwlSim
SimpleOwlSim(OWLOntology) - Constructor for class owltools.sim2.SimpleOwlSim
 
SimpleOwlSim.Direction - Enum in owltools.sim2
Asymmetric metrics can be applied in either of two directions, or both can be aggregated
SimpleOwlSim.Metric - Enum in owltools.sim2
Base similarity metric - may be applied at individual or class level
SimpleOwlSim.OutputFormat - Enum in owltools.sim2
The OutputFormat enumerates the different styles of output for sim results, and maps 1:1 with different renderers.
SimpleOwlSim.ScoreAttributePair - Class in owltools.sim2
A pair consisting of an attribute class, and a score for that class
SimpleOwlSim.ScoreAttributePair(double, OWLClass) - Constructor for class owltools.sim2.SimpleOwlSim.ScoreAttributePair
 
SimpleOwlSim.SimConfigurationProperty - Enum in owltools.sim2
Set of tags that can be used in configuration
SimpleOwlSimFactory - Class in owltools.sim2
 
SimpleOwlSimFactory() - Constructor for class owltools.sim2.SimpleOwlSimFactory
 
SimPreProcessor - Interface in owltools.sim2.preprocessor
An ontology pre-processor will take an input ontology, apply a series of transforms, and generate an output ontology The output ontology may in many cases be the same as the input ontology
simProperties - Variable in class owltools.sim2.preprocessor.AbstractSimPreProcessor
 
SimResultRenderer - Interface in owltools.sim2.io
 
SimResultRenderer.AttributesSimScores - Class in owltools.sim2.io
 
SimResultRenderer.AttributesSimScores(OWLClass, OWLClass) - Constructor for class owltools.sim2.io.SimResultRenderer.AttributesSimScores
 
SimResultRenderer.IndividualSimScores - Class in owltools.sim2.io
 
SimResultRenderer.IndividualSimScores(OWLNamedIndividual, OWLNamedIndividual) - Constructor for class owltools.sim2.io.SimResultRenderer.IndividualSimScores
 
SimSearch - Class in owltools.sim
quick search for best matches
SimSearch(SimEngine) - Constructor for class owltools.sim.SimSearch
 
SimSearch(SimEngine, Reporter) - Constructor for class owltools.sim.SimSearch
 
simStats - Variable in class owltools.sim2.AbstractOwlSim
 
SimStats - Class in owltools.sim2
Will keep track of the overall stats of analysis in data sets.
SimStats() - Constructor for class owltools.sim2.SimStats
 
simStatsPerIndividual - Variable in class owltools.sim2.AbstractOwlSim
 
sortMapByScore(Map<OWLObject, Similarity>) - Method in class owltools.sim.MultiSimilarity
 
splitIRI(IRI) - Method in class owltools.sim.Similarity
 
storeResult(OWLNamedIndividual, OWLNamedIndividual, OwlSim.ScoreAttributeSetPair, String) - Method in class owltools.sim.OWLResultsManager
 
SubclassRetriever - Class in owltools.sim2.kb
 
SubclassRetriever(OWLClass, OWLOntology) - Constructor for class owltools.sim2.kb.SubclassRetriever
 
subgraphSummaryStatsPerIndividual - Variable in class owltools.sim2.AbstractOwlSim
 
subSimMethod - Variable in class owltools.sim.MultiSimilarity
 
sum - Variable in class owltools.sim2.OwlSim.StatsPerIndividual
 

T

TabularRenderer - Class in owltools.sim2.io
 
TabularRenderer(PrintStream, String, String) - Constructor for class owltools.sim2.io.TabularRenderer
 
TabularRenderer(PrintStream) - Constructor for class owltools.sim2.io.TabularRenderer
 
tdelta(long) - Method in class owltools.sim2.AbstractOwlSim
 
toString() - Method in class owltools.sim.ConjunctiveSetInformationContentRatioSimilarity
 
toString() - Method in class owltools.sim.ConjunctiveSetSimilarity
 
toString() - Method in class owltools.sim.DisjunctiveSetSimilarity
 
toString() - Method in class owltools.sim.MaximumInformationContentSimilarity
 
toString() - Method in class owltools.sim.OldSimpleOwlSim.EnrichmentResult
 
toString() - Method in class owltools.sim.OWLObjectPair
 
toString() - Method in class owltools.sim.Similarity
 
toString() - Method in class owltools.sim2.ClassDifferentiaLearner.InferredClassDefinition
 
toString() - Method in class owltools.sim2.ClassDifferentiaLearner
 
toString() - Method in class owltools.sim2.EnrichmentResult
 
toString() - Method in class owltools.sim2.OwlSim.StatsPerIndividual
 
toString() - Method in class owltools.sim2.scores.ElementPairScores
 
translateABoxToTBox(OWLOntology) - Static method in class owltools.sim2.preprocessor.ABoxUtils
generates SubClassOf axioms from ClassAssertion axioms Note that property assertions are currently ignored
translateResultsToOWLAxioms(String, OWLNamedIndividual, Set<OWLAxiom>) - Method in class owltools.sim.AsymmetricJaccardSimilarity
 
translateResultsToOWLAxioms(String, OWLNamedIndividual, Set<OWLAxiom>) - Method in class owltools.sim.AvgInformationContentBestMatchesSimilarity
Deprecated.
 
translateResultsToOWLAxioms(String, OWLNamedIndividual, Set<OWLAxiom>) - Method in class owltools.sim.AvgInformationContentLCSSimilarity
Deprecated.
 
translateResultsToOWLAxioms(String, OWLNamedIndividual, Set<OWLAxiom>) - Method in class owltools.sim.CombinedJaccardConjunctiveSetSimilarity
 
translateResultsToOWLAxioms(String, OWLNamedIndividual, Set<OWLAxiom>) - Method in class owltools.sim.CombinedSimilarity
 
translateResultsToOWLAxioms(String, OWLNamedIndividual, Set<OWLAxiom>) - Method in class owltools.sim.CombinedSimilarity2
 
translateResultsToOWLAxioms(String, OWLNamedIndividual, Set<OWLAxiom>) - Method in class owltools.sim.ConjunctiveSetInformationContentRatioSimilarity
 
translateResultsToOWLAxioms(String, OWLNamedIndividual, Set<OWLAxiom>) - Method in class owltools.sim.ConjunctiveSetSimilarity
 
translateResultsToOWLAxioms(String, OWLNamedIndividual, Set<OWLAxiom>) - Method in class owltools.sim.DescriptionTreeSimilarity
adds additional axioms specific to this method.
translateResultsToOWLAxioms(String, OWLNamedIndividual, Set<OWLAxiom>) - Method in class owltools.sim.DisjunctiveSetSimilarity
 
translateResultsToOWLAxioms(String, OWLNamedIndividual, Set<OWLAxiom>) - Method in class owltools.sim.JaccardBloomSimilarity
 
translateResultsToOWLAxioms(String, OWLNamedIndividual, Set<OWLAxiom>) - Method in class owltools.sim.JaccardSimilarity
 
translateResultsToOWLAxioms(String, OWLNamedIndividual, Set<OWLAxiom>) - Method in class owltools.sim.MaximumInformationContentSimilarity
 
translateResultsToOWLAxioms(String, OWLNamedIndividual, Set<OWLAxiom>) - Method in class owltools.sim.MultiSimilarity
adds additional axioms specific to this method.
translateResultsToOWLAxioms(String, OWLNamedIndividual, Set<OWLAxiom>) - Method in class owltools.sim.OverlapSimilarity
 
translateResultsToOWLAxioms() - Method in class owltools.sim.Similarity
 
translateResultsToOWLAxioms(String, OWLNamedIndividual, Set<OWLAxiom>) - Method in class owltools.sim.Similarity
 
trim() - Method in class owltools.sim2.preprocessor.AbstractSimPreProcessor
 

U

uniqueClassCount - Variable in class owltools.sim2.SimStats
 
uniqueClassPairCount - Variable in class owltools.sim2.SimStats
 
UnknownOWLClassException - Exception in owltools.sim2
 
UnknownOWLClassException(OWLClass) - Constructor for exception owltools.sim2.UnknownOWLClassException
 

V

valueOf(String) - Static method in enum owltools.sim.OldSimpleOwlSim.Stage
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum owltools.sim2.OwlSim.Stat
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum owltools.sim2.SimpleOwlSim.Direction
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum owltools.sim2.SimpleOwlSim.Metric
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum owltools.sim2.SimpleOwlSim.OutputFormat
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum owltools.sim2.SimpleOwlSim.SimConfigurationProperty
Returns the enum constant of this type with the specified name.
values() - Static method in enum owltools.sim.OldSimpleOwlSim.Stage
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum owltools.sim2.OwlSim.Stat
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum owltools.sim2.SimpleOwlSim.Direction
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum owltools.sim2.SimpleOwlSim.Metric
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum owltools.sim2.SimpleOwlSim.OutputFormat
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum owltools.sim2.SimpleOwlSim.SimConfigurationProperty
Returns an array containing the constants of this enum type, in the order they are declared.
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