C D E F G H I M O P S 

C

createNonBufferingReasoner(OWLOntology) - Method in class org.geneontology.reasoner.ExpressionMaterializingReasonerFactory
 
createNonBufferingReasoner(OWLOntology, OWLReasonerConfiguration) - Method in class org.geneontology.reasoner.ExpressionMaterializingReasonerFactory
 
createNonBufferingReasoner(OWLOntology) - Method in interface org.geneontology.reasoner.OWLExtendedReasonerFactory
 
createNonBufferingReasoner(OWLOntology, OWLReasonerConfiguration) - Method in interface org.geneontology.reasoner.OWLExtendedReasonerFactory
 
createReasoner(OWLOntology) - Method in class org.geneontology.reasoner.ExpressionMaterializingReasonerFactory
 
createReasoner(OWLOntology, OWLReasonerConfiguration) - Method in class org.geneontology.reasoner.ExpressionMaterializingReasonerFactory
 
createReasoner(OWLOntology) - Method in interface org.geneontology.reasoner.OWLExtendedReasonerFactory
 
createReasoner(OWLOntology, OWLReasonerConfiguration) - Method in interface org.geneontology.reasoner.OWLExtendedReasonerFactory
 

D

dispose() - Method in class org.geneontology.reasoner.ExpressionMaterializingReasoner
 

E

ExpressionMaterializingReasoner - Class in org.geneontology.reasoner
This wraps an existing reasoner to implement OWLExtendedReasoner.
ExpressionMaterializingReasoner(OWLOntology, OWLReasonerFactory, OWLReasonerConfiguration, BufferingMode) - Constructor for class org.geneontology.reasoner.ExpressionMaterializingReasoner
 
ExpressionMaterializingReasoner(OWLOntology, OWLReasonerFactory) - Constructor for class org.geneontology.reasoner.ExpressionMaterializingReasoner
 
ExpressionMaterializingReasoner(OWLOntology, OWLReasonerFactory, BufferingMode) - Constructor for class org.geneontology.reasoner.ExpressionMaterializingReasoner
 
ExpressionMaterializingReasonerFactory - Class in org.geneontology.reasoner
Simple OWL-API OWLReasonerFactory for instantiating an ExpressionMaterializingReasoner.
ExpressionMaterializingReasonerFactory(OWLReasonerFactory) - Constructor for class org.geneontology.reasoner.ExpressionMaterializingReasonerFactory
 

F

flush() - Method in class org.geneontology.reasoner.ExpressionMaterializingReasoner
 

G

getBottomClassNode() - Method in class org.geneontology.reasoner.ExpressionMaterializingReasoner
 
getBottomDataPropertyNode() - Method in class org.geneontology.reasoner.ExpressionMaterializingReasoner
 
getBottomObjectPropertyNode() - Method in class org.geneontology.reasoner.ExpressionMaterializingReasoner
 
getBufferingMode() - Method in class org.geneontology.reasoner.ExpressionMaterializingReasoner
 
getDataPropertyDomains(OWLDataProperty, boolean) - Method in class org.geneontology.reasoner.ExpressionMaterializingReasoner
 
getDataPropertyValues(OWLNamedIndividual, OWLDataProperty) - Method in class org.geneontology.reasoner.ExpressionMaterializingReasoner
 
getDifferentIndividuals(OWLNamedIndividual) - Method in class org.geneontology.reasoner.ExpressionMaterializingReasoner
 
getDisjointClasses(OWLClassExpression) - Method in class org.geneontology.reasoner.ExpressionMaterializingReasoner
 
getDisjointDataProperties(OWLDataPropertyExpression) - Method in class org.geneontology.reasoner.ExpressionMaterializingReasoner
 
getDisjointObjectProperties(OWLObjectPropertyExpression) - Method in class org.geneontology.reasoner.ExpressionMaterializingReasoner
 
getEquivalentClasses(OWLClassExpression) - Method in class org.geneontology.reasoner.ExpressionMaterializingReasoner
 
getEquivalentDataProperties(OWLDataProperty) - Method in class org.geneontology.reasoner.ExpressionMaterializingReasoner
 
getEquivalentObjectProperties(OWLObjectPropertyExpression) - Method in class org.geneontology.reasoner.ExpressionMaterializingReasoner
 
getFreshEntityPolicy() - Method in class org.geneontology.reasoner.ExpressionMaterializingReasoner
 
getIndividualNodeSetPolicy() - Method in class org.geneontology.reasoner.ExpressionMaterializingReasoner
 
getInstances(OWLClassExpression, boolean) - Method in class org.geneontology.reasoner.ExpressionMaterializingReasoner
 
getInverseObjectProperties(OWLObjectPropertyExpression) - Method in class org.geneontology.reasoner.ExpressionMaterializingReasoner
 
getObjectPropertyDomains(OWLObjectPropertyExpression, boolean) - Method in class org.geneontology.reasoner.ExpressionMaterializingReasoner
 
getObjectPropertyRanges(OWLObjectPropertyExpression, boolean) - Method in class org.geneontology.reasoner.ExpressionMaterializingReasoner
 
getObjectPropertyValues(OWLNamedIndividual, OWLObjectPropertyExpression) - Method in class org.geneontology.reasoner.ExpressionMaterializingReasoner
 
getPendingAxiomAdditions() - Method in class org.geneontology.reasoner.ExpressionMaterializingReasoner
 
getPendingAxiomRemovals() - Method in class org.geneontology.reasoner.ExpressionMaterializingReasoner
 
getPendingChanges() - Method in class org.geneontology.reasoner.ExpressionMaterializingReasoner
 
getPrecomputableInferenceTypes() - Method in class org.geneontology.reasoner.ExpressionMaterializingReasoner
 
getReasonerName() - Method in class org.geneontology.reasoner.ExpressionMaterializingReasoner
 
getReasonerName() - Method in class org.geneontology.reasoner.ExpressionMaterializingReasonerFactory
 
getReasonerVersion() - Method in class org.geneontology.reasoner.ExpressionMaterializingReasoner
 
getRootOntology() - Method in class org.geneontology.reasoner.ExpressionMaterializingReasoner
 
getSameIndividuals(OWLNamedIndividual) - Method in class org.geneontology.reasoner.ExpressionMaterializingReasoner
 
getSubClasses(OWLClassExpression, boolean) - Method in class org.geneontology.reasoner.ExpressionMaterializingReasoner
 
getSubDataProperties(OWLDataProperty, boolean) - Method in class org.geneontology.reasoner.ExpressionMaterializingReasoner
 
getSubObjectProperties(OWLObjectPropertyExpression, boolean) - Method in class org.geneontology.reasoner.ExpressionMaterializingReasoner
 
getSuperClasses(OWLClassExpression, boolean) - Method in class org.geneontology.reasoner.ExpressionMaterializingReasoner
 
getSuperClassesOver(OWLClassExpression, OWLObjectProperty, boolean) - Method in class org.geneontology.reasoner.ExpressionMaterializingReasoner
 
getSuperClassesOver(OWLClassExpression, OWLObjectProperty, boolean) - Method in interface org.geneontology.reasoner.OWLExtendedReasoner
Note that this is not a standard reasoner method.
getSuperClassExpressions(OWLClassExpression, boolean) - Method in class org.geneontology.reasoner.ExpressionMaterializingReasoner
 
getSuperClassExpressions(OWLClassExpression, boolean) - Method in interface org.geneontology.reasoner.OWLExtendedReasoner
Note that this is not a standard reasoner method.
getSuperDataProperties(OWLDataProperty, boolean) - Method in class org.geneontology.reasoner.ExpressionMaterializingReasoner
 
getSuperObjectProperties(OWLObjectPropertyExpression, boolean) - Method in class org.geneontology.reasoner.ExpressionMaterializingReasoner
 
getTimeOut() - Method in class org.geneontology.reasoner.ExpressionMaterializingReasoner
 
getTopClassNode() - Method in class org.geneontology.reasoner.ExpressionMaterializingReasoner
 
getTopDataPropertyNode() - Method in class org.geneontology.reasoner.ExpressionMaterializingReasoner
 
getTopObjectPropertyNode() - Method in class org.geneontology.reasoner.ExpressionMaterializingReasoner
 
getTypes(OWLNamedIndividual, boolean) - Method in class org.geneontology.reasoner.ExpressionMaterializingReasoner
 
getUnsatisfiableClasses() - Method in class org.geneontology.reasoner.ExpressionMaterializingReasoner
 
getWrappedReasoner() - Method in class org.geneontology.reasoner.ExpressionMaterializingReasoner
 

H

handleChanges(Set<OWLAxiom>, Set<OWLAxiom>) - Method in class org.geneontology.reasoner.ExpressionMaterializingReasoner
 

I

interrupt() - Method in class org.geneontology.reasoner.ExpressionMaterializingReasoner
 
isConsistent() - Method in class org.geneontology.reasoner.ExpressionMaterializingReasoner
 
isEntailed(OWLAxiom) - Method in class org.geneontology.reasoner.ExpressionMaterializingReasoner
 
isEntailed(Set<? extends OWLAxiom>) - Method in class org.geneontology.reasoner.ExpressionMaterializingReasoner
 
isEntailmentCheckingSupported(AxiomType<?>) - Method in class org.geneontology.reasoner.ExpressionMaterializingReasoner
 
isIncludeImports() - Method in class org.geneontology.reasoner.ExpressionMaterializingReasoner
 
isPrecomputed(InferenceType) - Method in class org.geneontology.reasoner.ExpressionMaterializingReasoner
 
isSatisfiable(OWLClassExpression) - Method in class org.geneontology.reasoner.ExpressionMaterializingReasoner
 

M

materializeExpressions() - Method in class org.geneontology.reasoner.ExpressionMaterializingReasoner
Materialize expressions for all classes and properties in the ontology signature.
materializeExpressions(Collection<OWLObjectProperty>) - Method in class org.geneontology.reasoner.ExpressionMaterializingReasoner
Materialize expressions for a collection of properties and all classes in the ontology signature.
materializeExpressions(OWLObjectProperty) - Method in class org.geneontology.reasoner.ExpressionMaterializingReasoner
Materialize expressions a property and all classes in the ontology signature.

O

org.geneontology.reasoner - package org.geneontology.reasoner
 
OWLExtendedReasoner - Interface in org.geneontology.reasoner
Extends standard OWL reasoning to allow for querying of ancestor class expressions
OWLExtendedReasonerFactory<REASONER extends OWLExtendedReasoner> - Interface in org.geneontology.reasoner
 

P

precomputeInferences(InferenceType...) - Method in class org.geneontology.reasoner.ExpressionMaterializingReasoner
 

S

setIncludeImports(boolean) - Method in class org.geneontology.reasoner.ExpressionMaterializingReasoner
 
C D E F G H I M O P S 

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