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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
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