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

A

AbstractCompositeOntologyChange - Class in org.semanticweb.owlapi

Author: Matthew Horridge
The University Of Manchester
Bio-Health Informatics Group
Date: 23-Jul-2007

AbstractCompositeOntologyChange(OWLDataFactory) - Constructor for class org.semanticweb.owlapi.AbstractCompositeOntologyChange

AbstractOWLDebugger - Class in org.semanticweb.owlapi.debugging

Author: Matthew Horridge
The University Of Manchester
Bio-Health Informatics Group
Date: 24-Nov-2006

An abstract debugger which provides common infrastructure for finding multiple justification.

AbstractOWLDebugger(OWLOntologyManager, OWLOntology) - Constructor for class org.semanticweb.owlapi.debugging.AbstractOWLDebugger

AbstractOWLMetric<M> - Class in org.semanticweb.owlapi.metrics

Author: Matthew Horridge
The University Of Manchester
Bio-Health Informatics Group
Date: 27-Jul-2007

AbstractOWLMetric(OWLOntologyManager) - Constructor for class org.semanticweb.owlapi.metrics.AbstractOWLMetric

addAxiom(OWLAxiom, Set<OWLOntology>, OWLOntologyManager) - Static method in class com.clarkparsia.owlapi.explanation.util.OntologyUtils

Add the axiom to all the given ontologies.

addChild(MutableTree<N>) - Method in class uk.ac.manchester.cs.bhig.util.MutableTree

addChild(MutableTree<N>, Object) - Method in class uk.ac.manchester.cs.bhig.util.MutableTree

AddClassExpressionClosureAxiom - Class in org.semanticweb.owlapi

Author: Matthew Horridge
The University Of Manchester
Bio-Health Informatics Group
Date: 24-Jul-2007

This composite change adds a 'closure' axiom to an ontology for a given class and object property.

AddClassExpressionClosureAxiom(OWLDataFactory, OWLClass, OWLObjectPropertyExpression, Set<OWLOntology>, OWLOntology) - Constructor for class org.semanticweb.owlapi.AddClassExpressionClosureAxiom

Creates a composite change that will add a closure axiom for a given class along a specified property.

AlphaExplanationOrderer - Class in uk.ac.manchester.cs.owl.explanation.ordering

Author: Matthew Horridge
The University Of Manchester
Bio-Health Informatics Group
Date: 22-Jan-2008

Orders an explanation in a flat list, sorting axioms alphabetically.

AlphaExplanationOrderer(OWLObjectRenderer) - Constructor for class uk.ac.manchester.cs.owl.explanation.ordering.AlphaExplanationOrderer

AmalgamateSubClassAxioms - Class in org.semanticweb.owlapi

Author: Matthew Horridge
The University Of Manchester
Bio-Health Informatics Group
Date: 15-Aug-2007

Given a set of ontologies S, for each ontology, O, in S, this change combines multiple subclass axioms with a common left hand side into one subclass axiom.

AmalgamateSubClassAxioms(Set<OWLOntology>, OWLDataFactory) - Constructor for class org.semanticweb.owlapi.AmalgamateSubClassAxioms

AverageAssertedNamedSuperclassCount - Class in org.semanticweb.owlapi.metrics

Author: Matthew Horridge
The University Of Manchester
Bio-Health Informatics Group
Date: 27-Jul-2007

AverageAssertedNamedSuperclassCount(OWLOntologyManager) - Constructor for class org.semanticweb.owlapi.metrics.AverageAssertedNamedSuperclassCount

AxiomCount - Class in org.semanticweb.owlapi.metrics

Author: Matthew Horridge
The University Of Manchester
Bio-Health Informatics Group
Date: 27-Jul-2007

AxiomCount(OWLOntologyManager) - Constructor for class org.semanticweb.owlapi.metrics.AxiomCount

AxiomCountMetric - Class in org.semanticweb.owlapi.metrics

Author: Matthew Horridge
The University Of Manchester
Bio-Health Informatics Group
Date: 20-Dec-2007

AxiomCountMetric(OWLOntologyManager) - Constructor for class org.semanticweb.owlapi.metrics.AxiomCountMetric

AxiomTypeCountMetricFactory - Class in org.semanticweb.owlapi.metrics

Author: Matthew Horridge
The University Of Manchester
Bio-Health Informatics Group
Date: 27-Jul-2007

AxiomTypeCountMetricFactory() - Constructor for class org.semanticweb.owlapi.metrics.AxiomTypeCountMetricFactory

AxiomTypeMetric - Class in org.semanticweb.owlapi.metrics

Author: Matthew Horridge
The University Of Manchester
Bio-Health Informatics Group
Date: 27-Jul-2007

AxiomTypeMetric(OWLOntologyManager, AxiomType<?>) - Constructor for class org.semanticweb.owlapi.metrics.AxiomTypeMetric

B

beginTransaction() - Method in class com.clarkparsia.owlapi.explanation.SingleExplanationGeneratorImpl

beginTransaction() - Method in interface com.clarkparsia.owlapi.explanation.TransactionAwareSingleExpGen

Indicates to the explanation generator that a transaction which may modify the ontology state is starting.

BlackBoxExplanation - Class in com.clarkparsia.owlapi.explanation

A black box explanation

BlackBoxExplanation(OWLOntology, OWLReasonerFactory, OWLReasoner) - Constructor for class com.clarkparsia.owlapi.explanation.BlackBoxExplanation

BlackBoxOWLDebugger - Class in org.semanticweb.owlapi.debugging

Author: Matthew Horridge
The University Of Manchester
Bio-Health Informatics Group
Date: 24-Nov-2006

This is an implementation of a blackbox debugger.

BlackBoxOWLDebugger(OWLOntologyManager, OWLOntology, OWLReasonerFactory) - Constructor for class org.semanticweb.owlapi.debugging.BlackBoxOWLDebugger

C

clearChildren() - Method in class uk.ac.manchester.cs.bhig.util.MutableTree

remove all children

CoerceConstantsIntoDataPropertyRange - Class in org.semanticweb.owlapi

Author: Matthew Horridge
The University Of Manchester
Bio-Health Informatics Group
Date: 13-Aug-2007

Coerces constants to have the same type as the range of a property in axioms where the two are used.

CoerceConstantsIntoDataPropertyRange(OWLDataFactory, Set<OWLOntology>) - Constructor for class org.semanticweb.owlapi.CoerceConstantsIntoDataPropertyRange

com.clarkparsia.owlapi.explanation - package com.clarkparsia.owlapi.explanation

com.clarkparsia.owlapi.explanation.io - package com.clarkparsia.owlapi.explanation.io

com.clarkparsia.owlapi.explanation.util - package com.clarkparsia.owlapi.explanation.util

com.clarkparsia.owlapi.modularity.locality - package com.clarkparsia.owlapi.modularity.locality

ConciseExplanationRenderer - Class in com.clarkparsia.owlapi.explanation.io

Explanation renderer in concise form

ConciseExplanationRenderer() - Constructor for class com.clarkparsia.owlapi.explanation.io.ConciseExplanationRenderer

constructHittingSetTree(Set<OWLAxiom>, Set<Set<OWLAxiom>>, Set<Set<OWLAxiom>>, Set<OWLAxiom>) - Method in class org.semanticweb.owlapi.debugging.AbstractOWLDebugger

This is a recursive method that builds a hitting set tree to obtain all justifications for an unsatisfiable class.

containsUnreferencedEntity(OWLOntology, OWLClassExpression) - Static method in class com.clarkparsia.owlapi.explanation.util.OntologyUtils

Determines if a class description contains any unreferenced entities with respect to the ontology that contains the entailments which are being explained.

convert(OWLAxiom) - Method in class com.clarkparsia.owlapi.explanation.SatisfiabilityConverter

ConvertEquivalentClassesToSuperClasses - Class in org.semanticweb.owlapi

Author: Matthew Horridge
The University Of Manchester
Bio-Health Informatics Group
Date: 23-Jul-2007

This composite change will convert a defined class to a primitive class by replacing equivalent classes axioms where the class in question is a class in the equivalent classes axioms to a set of subclass axioms whose superclasses are the set of classes which were originally equivalent to the class in question.

ConvertEquivalentClassesToSuperClasses(OWLDataFactory, OWLClass, Set<OWLOntology>, OWLOntology, boolean) - Constructor for class org.semanticweb.owlapi.ConvertEquivalentClassesToSuperClasses

ConvertPropertyAssertionsToAnnotations - Class in org.semanticweb.owlapi

Author: Matthew Horridge
The University Of Manchester
Bio-Health Informatics Group
Date: 23-Jul-2007

Given a set of ontologies, this composite change will convert all property assertion axioms whose subject is a 'punned' individual (i.e.

ConvertPropertyAssertionsToAnnotations(OWLDataFactory, Set<OWLOntology>) - Constructor for class org.semanticweb.owlapi.ConvertPropertyAssertionsToAnnotations

ConvertSuperClassesToEquivalentClass - Class in org.semanticweb.owlapi

Author: Matthew Horridge
The University Of Manchester
Bio-Health Informatics Group
Date: 23-Jul-2007

This composite change will convert a primitive class to a defined class by replacing subclass axioms where the class in question is on the left hand side of the subclass axiom to an equivalent classes axiom which makes the class equivalent to the intersection of its superclasses.

ConvertSuperClassesToEquivalentClass(OWLDataFactory, OWLClass, Set<OWLOntology>, OWLOntology) - Constructor for class org.semanticweb.owlapi.ConvertSuperClassesToEquivalentClass

convertToNormalForm(OWLClassExpression) - Method in class org.semanticweb.owlapi.normalform.NegationalNormalFormConverter

convertToNormalForm(OWLClassExpression) - Method in interface org.semanticweb.owlapi.normalform.NormalFormRewriter

createMetrics(OWLOntologyManager) - Static method in class org.semanticweb.owlapi.metrics.AxiomTypeCountMetricFactory

CreateValuePartition - Class in org.semanticweb.owlapi

Author: Matthew Horridge
The University Of Manchester
Bio-Health Informatics Group
Date: 23-Jul-2007

This composite change will create a value partion - see "pattern 2" in "Representing Specified Values in OWL: "value partitions" and "value sets"" (http://www.w3.org/TR/swbp-specified-values.)

A value partition is an ontology design pattern which is used to represent a set of closed values for a particular property.

CreateValuePartition(OWLDataFactory, OWLClass, Set<OWLClass>, OWLObjectProperty, OWLOntology) - Constructor for class org.semanticweb.owlapi.CreateValuePartition

Creates a composite change that will create a value partition.

D

DebuggerClassExpressionGenerator - Class in org.semanticweb.owlapi.debugging

Author: Matthew Horridge
The University Of Manchester
Bio-Health Informatics Group
Date: 01-Mar-2007

DebuggerClassExpressionGenerator(OWLDataFactory) - Constructor for class org.semanticweb.owlapi.debugging.DebuggerClassExpressionGenerator

debuggingAxioms - Variable in class com.clarkparsia.owlapi.explanation.BlackBoxExplanation

DEFAULT_INITIAL_EXPANSION_LIMIT - Static variable in class com.clarkparsia.owlapi.explanation.BlackBoxExplanation

default expansion limit

DEFAULT_INITIAL_EXPANSION_LIMIT - Static variable in class org.semanticweb.owlapi.debugging.BlackBoxOWLDebugger

default expansion limit

DefaultExplanationGenerator - Class in com.clarkparsia.owlapi.explanation

Author: Matthew Horridge
Clark & Parsia, LLC
Bio-Health Informatics Group
Date: 24-Jan-2008

DefaultExplanationGenerator(OWLOntologyManager, OWLReasonerFactory, OWLOntology, ExplanationProgressMonitor) - Constructor for class com.clarkparsia.owlapi.explanation.DefaultExplanationGenerator

DefaultExplanationGenerator(OWLOntologyManager, OWLReasonerFactory, OWLOntology, OWLReasoner, ExplanationProgressMonitor) - Constructor for class com.clarkparsia.owlapi.explanation.DefaultExplanationGenerator

DefinitionTracker - Class in com.clarkparsia.owlapi.explanation.util

Tracker for definitions

DefinitionTracker(OWLOntology) - Constructor for class com.clarkparsia.owlapi.explanation.util.DefinitionTracker

df - Variable in class com.clarkparsia.owlapi.modularity.locality.SemanticLocalityEvaluator

dispose() - Method in class com.clarkparsia.owlapi.explanation.BlackBoxExplanation

dispose() - Method in class org.semanticweb.owlapi.debugging.BlackBoxOWLDebugger

dispose() - Method in interface org.semanticweb.owlapi.debugging.OWLDebugger

dispose of resources locked such as reasoners

dispose() - Method in class org.semanticweb.owlapi.metrics.AbstractOWLMetric

dispose() - Method in interface org.semanticweb.owlapi.metrics.OWLMetric

Diposes of the metric.

disposeMetric() - Method in class org.semanticweb.owlapi.metrics.AbstractOWLMetric

disposeMetric() - Method in class org.semanticweb.owlapi.metrics.AverageAssertedNamedSuperclassCount

disposeMetric() - Method in class org.semanticweb.owlapi.metrics.AxiomCount

disposeMetric() - Method in class org.semanticweb.owlapi.metrics.DLExpressivity

disposeMetric() - Method in class org.semanticweb.owlapi.metrics.HiddenGCICount

disposeMetric() - Method in class org.semanticweb.owlapi.metrics.ImportClosureSize

disposeMetric() - Method in class org.semanticweb.owlapi.metrics.MaximumNumberOfNamedSuperclasses

disposeMetric() - Method in class org.semanticweb.owlapi.metrics.NumberOfClassesWithMultipleInheritance

disposeMetric() - Method in class org.semanticweb.owlapi.metrics.ObjectCountMetric

disposeMetric() - Method in class org.semanticweb.owlapi.metrics.UnsatisfiableClassCountMetric

DLExpressivity - Class in org.semanticweb.owlapi.metrics

Author: Matthew Horridge
The University Of Manchester
Bio-Health Informatics Group
Date: 27-Jul-2007

DLExpressivity(OWLOntologyManager) - Constructor for class org.semanticweb.owlapi.metrics.DLExpressivity

DoubleValuedMetric - Class in org.semanticweb.owlapi.metrics

Author: Matthew Horridge
The University Of Manchester
Bio-Health Informatics Group
Date: 27-Jul-2007

DoubleValuedMetric(OWLOntologyManager) - Constructor for class org.semanticweb.owlapi.metrics.DoubleValuedMetric

dump(PrintWriter) - Method in class uk.ac.manchester.cs.bhig.util.MutableTree

dump(PrintWriter, int) - Method in class uk.ac.manchester.cs.bhig.util.MutableTree

dump(PrintWriter) - Method in interface uk.ac.manchester.cs.bhig.util.Tree

dump(PrintWriter, int) - Method in interface uk.ac.manchester.cs.bhig.util.Tree

E

endRendering() - Method in class com.clarkparsia.owlapi.explanation.io.ConciseExplanationRenderer

endRendering() - Method in interface com.clarkparsia.owlapi.explanation.io.ExplanationRenderer

end of rendering

endRendering() - Method in class com.clarkparsia.owlapi.explanation.io.SilentExplanationRenderer

endTransaction() - Method in class com.clarkparsia.owlapi.explanation.SingleExplanationGeneratorImpl

endTransaction() - Method in interface com.clarkparsia.owlapi.explanation.TransactionAwareSingleExpGen

End a transaction.

EntailedAxiomTree - Class in uk.ac.manchester.cs.owl.explanation.ordering

Author: Matthew Horridge
The University Of Manchester
Bio-Health Informatics Group
Date: 22-Jan-2008

EntailedAxiomTree(OWLAxiom) - Constructor for class uk.ac.manchester.cs.owl.explanation.ordering.EntailedAxiomTree

ExplanationGenerator - Interface in com.clarkparsia.owlapi.explanation

a generator for explanations

ExplanationOrderer - Interface in uk.ac.manchester.cs.owl.explanation.ordering

Author: Matthew Horridge
The University Of Manchester
Bio-Health Informatics Group
Date: 11-Jan-2008

ExplanationOrdererImpl - Class in uk.ac.manchester.cs.owl.explanation.ordering

Author: Matthew Horridge
The University Of Manchester
Bio-Health Informatics Group
Date: 11-Jan-2008

Provides ordering and indenting of explanations based on various ordering heuristics.

ExplanationOrdererImpl(OWLOntologyManager) - Constructor for class uk.ac.manchester.cs.owl.explanation.ordering.ExplanationOrdererImpl

ExplanationProgressMonitor - Interface in com.clarkparsia.owlapi.explanation.util

Author: Matthew Horridge
Clark & Parsia, LLC
Bio-Health Informatics Group
Date: 26-Nov-2007

A progress monitor for an explanation generator.

ExplanationRenderer - Interface in com.clarkparsia.owlapi.explanation.io

Renderer for explanations

ExplanationTree - Class in uk.ac.manchester.cs.owl.explanation.ordering

Author: Matthew Horridge
The University Of Manchester
Bio-Health Informatics Group
Date: 22-Jan-2008

ExplanationTree(OWLAxiom) - Constructor for class uk.ac.manchester.cs.owl.explanation.ordering.ExplanationTree

extract(Set<OWLEntity>) - Method in interface org.semanticweb.owlapi.modularity.OntologySegmenter

Returns a set of axioms that is a segment of the ontology associated with this segmenter.

extract(Set<OWLEntity>, int, int, OWLReasoner) - Method in interface org.semanticweb.owlapi.modularity.OntologySegmenter

Returns a set of axioms that is a segment of the ontology associated with this segmenter.

extract(Set<OWLEntity>) - Method in class uk.ac.manchester.cs.owlapi.modularity.SyntacticLocalityModuleExtractor

extract(Set<OWLEntity>, int, int, OWLReasoner) - Method in class uk.ac.manchester.cs.owlapi.modularity.SyntacticLocalityModuleExtractor

extract(Set<OWLEntity>, int, int, OWLReasoner, boolean) - Method in class uk.ac.manchester.cs.owlapi.modularity.SyntacticLocalityModuleExtractor

Extracts a module from the associated ontology for a given signature and the associated module type, and returns the module as a set of axioms.

extractAsOntology(Set<OWLEntity>, IRI) - Method in interface org.semanticweb.owlapi.modularity.OntologySegmenter

Returns an ontology that is a segment of the ontology associated with this segmenter.

extractAsOntology(Set<OWLEntity>, IRI, int, int, OWLReasoner) - Method in interface org.semanticweb.owlapi.modularity.OntologySegmenter

Returns an ontology that is a segment of the ontology associated with this segmenter.

extractAsOntology(Set<OWLEntity>, IRI) - Method in class uk.ac.manchester.cs.owlapi.modularity.SyntacticLocalityModuleExtractor

extractAsOntology(Set<OWLEntity>, IRI, int, int, OWLReasoner) - Method in class uk.ac.manchester.cs.owlapi.modularity.SyntacticLocalityModuleExtractor

F

factory - Variable in class com.clarkparsia.owlapi.explanation.SatisfiabilityConverter

fillDepthFirst() - Method in class uk.ac.manchester.cs.bhig.util.MutableTree

fillDepthFirst() - Method in interface uk.ac.manchester.cs.bhig.util.Tree

foundAllExplanations() - Method in interface com.clarkparsia.owlapi.explanation.util.ExplanationProgressMonitor

Called when all explanations have been found.

foundAllExplanations() - Method in class com.clarkparsia.owlapi.explanation.util.SilentExplanationProgressMonitor

foundExplanation(Set<OWLAxiom>) - Method in interface com.clarkparsia.owlapi.explanation.util.ExplanationProgressMonitor

Called when an explanation has been found.

foundExplanation(Set<OWLAxiom>) - Method in class com.clarkparsia.owlapi.explanation.util.SilentExplanationProgressMonitor

G

GCICount - Class in org.semanticweb.owlapi.metrics

Author: Matthew Horridge
The University Of Manchester
Bio-Health Informatics Group
Date: 27-Jul-2007

GCICount(OWLOntologyManager) - Constructor for class org.semanticweb.owlapi.metrics.GCICount

getAllSOSForIncosistentClass(OWLClassExpression) - Method in class org.semanticweb.owlapi.debugging.AbstractOWLDebugger

getAllSOSForIncosistentClass(OWLClassExpression) - Method in interface org.semanticweb.owlapi.debugging.OWLDebugger

getAxioms() - Method in class org.semanticweb.owlapi.metrics.AxiomCountMetric

getAxiomsForLHS(OWLEntity) - Method in class uk.ac.manchester.cs.owl.explanation.ordering.ExplanationOrdererImpl

Gets axioms that have a LHS corresponding to the specified entity.

getAxiomType() - Method in class org.semanticweb.owlapi.metrics.AxiomTypeMetric

getChanges() - Method in class org.semanticweb.owlapi.AddClassExpressionClosureAxiom

getChanges() - Method in class org.semanticweb.owlapi.AmalgamateSubClassAxioms

getChanges() - Method in class org.semanticweb.owlapi.CoerceConstantsIntoDataPropertyRange

getChanges() - Method in class org.semanticweb.owlapi.ConvertEquivalentClassesToSuperClasses

getChanges() - Method in class org.semanticweb.owlapi.ConvertPropertyAssertionsToAnnotations

getChanges() - Method in class org.semanticweb.owlapi.ConvertSuperClassesToEquivalentClass

getChanges() - Method in class org.semanticweb.owlapi.CreateValuePartition

getChanges() - Method in class org.semanticweb.owlapi.MakeClassesMutuallyDisjoint

getChanges() - Method in class org.semanticweb.owlapi.MakePrimitiveSubClassesMutuallyDisjoint

getChanges() - Method in interface org.semanticweb.owlapi.OWLCompositeOntologyChange

Gets the changes which compose this composite change.

getChanges() - Method in class org.semanticweb.owlapi.RemoveAllDisjointAxioms

getChanges() - Method in class org.semanticweb.owlapi.ShortForm2AnnotationGenerator

getChanges() - Method in class org.semanticweb.owlapi.SplitSubClassAxioms

getChildAxioms(OWLAxiom) - Method in class org.semanticweb.owlapi.debugging.JustificationMap

getChildCount() - Method in class uk.ac.manchester.cs.bhig.util.MutableTree

getChildCount() - Method in interface uk.ac.manchester.cs.bhig.util.Tree

A convenience method that gets the number of child nodes that this node has.

getChildren() - Method in class uk.ac.manchester.cs.bhig.util.MutableTree

getChildren() - Method in interface uk.ac.manchester.cs.bhig.util.Tree

Gets the children of this tree node.

getComplementedClassExpressions(OWLClassExpression) - Method in class org.semanticweb.owlapi.normalform.OWLObjectComplementOfExtractor

getCurrentClass() - Method in class org.semanticweb.owlapi.debugging.AbstractOWLDebugger

getCurrentClass() - Method in class org.semanticweb.owlapi.debugging.BlackBoxOWLDebugger

getDataFactory() - Method in class org.semanticweb.owlapi.AbstractCompositeOntologyChange

getDebuggerClassExpression() - Method in class org.semanticweb.owlapi.debugging.DebuggerClassExpressionGenerator

getDefinitionTracker() - Method in class com.clarkparsia.owlapi.explanation.SingleExplanationGeneratorImpl

getEdge(Tree<N>) - Method in class uk.ac.manchester.cs.bhig.util.MutableTree

getEdge(Tree<N>) - Method in interface uk.ac.manchester.cs.bhig.util.Tree

getExplanation(OWLClassExpression) - Method in class com.clarkparsia.owlapi.explanation.BlackBoxExplanation

getExplanation(OWLClassExpression) - Method in class com.clarkparsia.owlapi.explanation.DefaultExplanationGenerator

getExplanation(OWLAxiom) - Method in class com.clarkparsia.owlapi.explanation.DefaultExplanationGenerator

getExplanation(OWLClassExpression) - Method in interface com.clarkparsia.owlapi.explanation.ExplanationGenerator

Returns a single explanation for the given unsatisfiable class.

getExplanation(OWLClassExpression) - Method in class com.clarkparsia.owlapi.explanation.HSTExplanationGenerator

getExplanation(OWLClassExpression) - Method in interface com.clarkparsia.owlapi.explanation.SingleExplanationGenerator

Get a single explanation for an arbitrary class expression, or empty set if the given expression is satisfiable.

getExplanations(OWLClassExpression) - Method in class com.clarkparsia.owlapi.explanation.DefaultExplanationGenerator

getExplanations(OWLAxiom) - Method in class com.clarkparsia.owlapi.explanation.DefaultExplanationGenerator

getExplanations(OWLClassExpression, int) - Method in class com.clarkparsia.owlapi.explanation.DefaultExplanationGenerator

getExplanations(OWLAxiom, int) - Method in class com.clarkparsia.owlapi.explanation.DefaultExplanationGenerator

getExplanations(OWLClassExpression) - Method in interface com.clarkparsia.owlapi.explanation.ExplanationGenerator

Returns all the explanations for the given unsatisfiable class.

getExplanations(OWLClassExpression, int) - Method in interface com.clarkparsia.owlapi.explanation.ExplanationGenerator

Return a specified number of explanations for the given unsatisfiable class.

getExplanations(OWLClassExpression) - Method in class com.clarkparsia.owlapi.explanation.HSTExplanationGenerator

getExplanations(OWLClassExpression, int) - Method in class com.clarkparsia.owlapi.explanation.HSTExplanationGenerator

getManager() - Method in class org.semanticweb.owlapi.metrics.AbstractOWLMetric

getManager() - Method in interface org.semanticweb.owlapi.metrics.OWLMetric

Gets the ontology manager which, amongst other things can be used to obtain the imports closure of the current ontology.

getMaxDepth() - Method in class uk.ac.manchester.cs.bhig.util.MutableTree

getMetrics() - Method in class org.semanticweb.owlapi.metrics.OWLMetricManager

getModuleType() - Method in class uk.ac.manchester.cs.owlapi.modularity.SyntacticLocalityModuleExtractor

Returns the module type for this extractor.

getName() - Method in class org.semanticweb.owlapi.metrics.AverageAssertedNamedSuperclassCount

getName() - Method in class org.semanticweb.owlapi.metrics.AxiomCount

getName() - Method in class org.semanticweb.owlapi.metrics.DLExpressivity

getName() - Method in class org.semanticweb.owlapi.metrics.HiddenGCICount

getName() - Method in class org.semanticweb.owlapi.metrics.ImportClosureSize

getName() - Method in class org.semanticweb.owlapi.metrics.MaximumNumberOfNamedSuperclasses

getName() - Method in class org.semanticweb.owlapi.metrics.NumberOfClassesWithMultipleInheritance

getName() - Method in class org.semanticweb.owlapi.metrics.ObjectCountMetric

getName() - Method in interface org.semanticweb.owlapi.metrics.OWLMetric

Gets the human readable name of this metric

getName() - Method in class org.semanticweb.owlapi.metrics.UnsatisfiableClassCountMetric

getObjects(OWLOntology) - Method in class org.semanticweb.owlapi.metrics.AxiomTypeMetric

getObjects(OWLOntology) - Method in class org.semanticweb.owlapi.metrics.GCICount

getObjects(OWLOntology) - Method in class org.semanticweb.owlapi.metrics.LogicalAxiomCount

getObjects(OWLOntology) - Method in class org.semanticweb.owlapi.metrics.ObjectCountMetric

getObjects() - Method in class org.semanticweb.owlapi.metrics.ObjectCountMetric

getObjects(OWLOntology) - Method in class org.semanticweb.owlapi.metrics.ReferencedClassCount

getObjects(OWLOntology) - Method in class org.semanticweb.owlapi.metrics.ReferencedDataPropertyCount

getObjects(OWLOntology) - Method in class org.semanticweb.owlapi.metrics.ReferencedIndividualCount

getObjects(OWLOntology) - Method in class org.semanticweb.owlapi.metrics.ReferencedObjectPropertyCount

getObjectTypeName() - Method in class org.semanticweb.owlapi.metrics.AxiomTypeMetric

getObjectTypeName() - Method in class org.semanticweb.owlapi.metrics.GCICount

getObjectTypeName() - Method in class org.semanticweb.owlapi.metrics.LogicalAxiomCount

getObjectTypeName() - Method in class org.semanticweb.owlapi.metrics.ObjectCountMetric

getObjectTypeName() - Method in class org.semanticweb.owlapi.metrics.ReferencedClassCount

getObjectTypeName() - Method in class org.semanticweb.owlapi.metrics.ReferencedDataPropertyCount

getObjectTypeName() - Method in class org.semanticweb.owlapi.metrics.ReferencedIndividualCount

getObjectTypeName() - Method in class org.semanticweb.owlapi.metrics.ReferencedObjectPropertyCount

getOccurrences(OWLAxiom, Set<Set<OWLAxiom>>) - Static method in class com.clarkparsia.owlapi.explanation.HSTExplanationGenerator

Given an axiom and a set of axioms this method determines how many sets contain the axiom.

getOntologies() - Method in class org.semanticweb.owlapi.metrics.AbstractOWLMetric

getOntology() - Method in class com.clarkparsia.owlapi.explanation.HSTExplanationGenerator

getOntology() - Method in interface com.clarkparsia.owlapi.explanation.SingleExplanationGenerator

getOntology() - Method in class com.clarkparsia.owlapi.explanation.SingleExplanationGeneratorImpl

getOntology() - Method in class org.semanticweb.owlapi.metrics.AbstractOWLMetric

getOntology() - Method in interface org.semanticweb.owlapi.metrics.OWLMetric

Gets the ontology which the value of the metric should be based on.

getOntologyManager() - Method in class com.clarkparsia.owlapi.explanation.HSTExplanationGenerator

getOntologyManager() - Method in interface com.clarkparsia.owlapi.explanation.SingleExplanationGenerator

getOntologyManager() - Method in class com.clarkparsia.owlapi.explanation.SingleExplanationGeneratorImpl

getOrderedExplanation(OWLAxiom, Set<OWLAxiom>) - Method in class uk.ac.manchester.cs.owl.explanation.ordering.AlphaExplanationOrderer

getOrderedExplanation(OWLAxiom, Set<OWLAxiom>) - Method in interface uk.ac.manchester.cs.owl.explanation.ordering.ExplanationOrderer

Gets an ordered (and possibly indented) explanation.

getOrderedExplanation(OWLAxiom, Set<OWLAxiom>) - Method in class uk.ac.manchester.cs.owl.explanation.ordering.ExplanationOrdererImpl

getOrderedExplanation(OWLAxiom, Set<OWLAxiom>) - Method in class uk.ac.manchester.cs.owl.explanation.ordering.NullExplanationOrderer

getOWLOntology() - Method in class org.semanticweb.owlapi.debugging.AbstractOWLDebugger

getOWLOntology() - Method in interface org.semanticweb.owlapi.debugging.OWLDebugger

getOWLOntologyManager() - Method in class org.semanticweb.owlapi.debugging.AbstractOWLDebugger

getParent() - Method in class uk.ac.manchester.cs.bhig.util.MutableTree

getParent() - Method in interface uk.ac.manchester.cs.bhig.util.Tree

Gets the parent of this tree node.

getPathToRoot() - Method in class uk.ac.manchester.cs.bhig.util.MutableTree

getPathToRoot() - Method in interface uk.ac.manchester.cs.bhig.util.Tree

getReasoner() - Method in class com.clarkparsia.owlapi.explanation.HSTExplanationGenerator

getReasoner() - Method in interface com.clarkparsia.owlapi.explanation.SingleExplanationGenerator

getReasoner() - Method in class com.clarkparsia.owlapi.explanation.SingleExplanationGeneratorImpl

getReasonerFactory() - Method in class com.clarkparsia.owlapi.explanation.HSTExplanationGenerator

getReasonerFactory() - Method in interface com.clarkparsia.owlapi.explanation.SingleExplanationGenerator

getReasonerFactory() - Method in class com.clarkparsia.owlapi.explanation.SingleExplanationGeneratorImpl

getRoot() - Method in class uk.ac.manchester.cs.bhig.util.MutableTree

getRoot() - Method in interface uk.ac.manchester.cs.bhig.util.Tree

A convenience method that gets the root of this tree.

getRootAxioms() - Method in class org.semanticweb.owlapi.debugging.JustificationMap

getSingleExplanationGenerator() - Method in class com.clarkparsia.owlapi.explanation.HSTExplanationGenerator

getSize() - Method in class uk.ac.manchester.cs.bhig.util.MutableTree

getSOSForIncosistentClass(OWLClassExpression) - Method in class org.semanticweb.owlapi.debugging.BlackBoxOWLDebugger

getSOSForIncosistentClass(OWLClassExpression) - Method in interface org.semanticweb.owlapi.debugging.OWLDebugger

getUserObject() - Method in class uk.ac.manchester.cs.bhig.util.MutableTree

getUserObject() - Method in interface uk.ac.manchester.cs.bhig.util.Tree

Gets the "content" of this tree node.

getUserObjectClosure() - Method in class uk.ac.manchester.cs.bhig.util.MutableTree

getUserObjectClosure() - Method in interface uk.ac.manchester.cs.bhig.util.Tree

getUserObjectPathToRoot() - Method in class uk.ac.manchester.cs.bhig.util.MutableTree

getUserObjectPathToRoot() - Method in interface uk.ac.manchester.cs.bhig.util.Tree

getValue() - Method in class org.semanticweb.owlapi.metrics.AbstractOWLMetric

getValue() - Method in interface org.semanticweb.owlapi.metrics.OWLMetric

Gets the value of this metric.

H

HiddenGCICount - Class in org.semanticweb.owlapi.metrics

Author: Matthew Horridge
The University Of Manchester
Bio-Health Informatics Group
Date: 13-Aug-2007

Counts the number of "hidden" GCIs in an ontology imports closure.

HiddenGCICount(OWLOntologyManager) - Constructor for class org.semanticweb.owlapi.metrics.HiddenGCICount

HSTExplanationGenerator - Class in com.clarkparsia.owlapi.explanation

HST explanation generator

HSTExplanationGenerator(TransactionAwareSingleExpGen) - Constructor for class com.clarkparsia.owlapi.explanation.HSTExplanationGenerator

I

ImportClosureSize - Class in org.semanticweb.owlapi.metrics

Author: Matthew Horridge
The University Of Manchester
Bio-Health Informatics Group
Date: 17-Jan-2008

ImportClosureSize(OWLOntologyManager) - Constructor for class org.semanticweb.owlapi.metrics.ImportClosureSize

indexAxiomsByRHSEntities(OWLObject, OWLAxiom) - Method in class uk.ac.manchester.cs.owl.explanation.ordering.ExplanationOrdererImpl

IntegerValuedMetric - Class in org.semanticweb.owlapi.metrics

Author: Matthew Horridge
The University Of Manchester
Bio-Health Informatics Group
Date: 27-Jul-2007

An OWLMetric that returns an integer value

IntegerValuedMetric(OWLOntologyManager) - Constructor for class org.semanticweb.owlapi.metrics.IntegerValuedMetric

isCancelled() - Method in interface com.clarkparsia.owlapi.explanation.util.ExplanationProgressMonitor

Determines if the process of generating explanations has been cancelled.

isCancelled() - Method in class com.clarkparsia.owlapi.explanation.util.SilentExplanationProgressMonitor

isDefined(OWLEntity) - Method in class com.clarkparsia.owlapi.explanation.util.DefinitionTracker

Checks if this entity is referred by a logical axiom in the imports closure of the designated ontology.

isDefined(OWLClassExpression) - Method in class com.clarkparsia.owlapi.explanation.util.DefinitionTracker

Checks if all the entities referred in the given concept are also referred by a logical axiom in the imports closure of the designated ontology.

isEntailed() - Method in class uk.ac.manchester.cs.owl.explanation.ordering.EntailedAxiomTree

isEntailed() - Method in class uk.ac.manchester.cs.owl.explanation.ordering.ExplanationTree

isFirstExplanation() - Method in class com.clarkparsia.owlapi.explanation.SingleExplanationGeneratorImpl

isImportsClosureUsed() - Method in class org.semanticweb.owlapi.metrics.AbstractOWLMetric

isImportsClosureUsed() - Method in interface org.semanticweb.owlapi.metrics.OWLMetric

Determines if the computation of the metric should take into account the imports closure of the current ontology.

isInNormalForm(OWLClassExpression) - Method in class org.semanticweb.owlapi.normalform.NegationalNormalFormConverter

isInNormalForm(OWLClassExpression) - Method in interface org.semanticweb.owlapi.normalform.NormalFormRewriter

isLeaf() - Method in class uk.ac.manchester.cs.bhig.util.MutableTree

isLeaf() - Method in interface uk.ac.manchester.cs.bhig.util.Tree

A convenience method that determines if this node is a leaf node (because it has no children).

isLocal(OWLAxiom, Set<? extends OWLEntity>) - Method in interface com.clarkparsia.owlapi.modularity.locality.LocalityEvaluator

Tests whether a given axiom is local with respect to a given signature.

isLocal(OWLAxiom, Set<? extends OWLEntity>) - Method in class com.clarkparsia.owlapi.modularity.locality.SemanticLocalityEvaluator

isLocal(OWLAxiom, Set<? extends OWLEntity>) - Method in class com.clarkparsia.owlapi.modularity.locality.SyntacticLocalityEvaluator

isMetricInvalidated(List<? extends OWLOntologyChange>) - Method in class org.semanticweb.owlapi.metrics.AbstractOWLMetric

Determines if the specified list of changes will cause the value of this metric to be invalid.

isMetricInvalidated(List<? extends OWLOntologyChange>) - Method in class org.semanticweb.owlapi.metrics.AverageAssertedNamedSuperclassCount

isMetricInvalidated(List<? extends OWLOntologyChange>) - Method in class org.semanticweb.owlapi.metrics.AxiomCount

isMetricInvalidated(List<? extends OWLOntologyChange>) - Method in class org.semanticweb.owlapi.metrics.DLExpressivity

isMetricInvalidated(List<? extends OWLOntologyChange>) - Method in class org.semanticweb.owlapi.metrics.HiddenGCICount

isMetricInvalidated(List<? extends OWLOntologyChange>) - Method in class org.semanticweb.owlapi.metrics.ImportClosureSize

isMetricInvalidated(List<? extends OWLOntologyChange>) - Method in class org.semanticweb.owlapi.metrics.MaximumNumberOfNamedSuperclasses

isMetricInvalidated(List<? extends OWLOntologyChange>) - Method in class org.semanticweb.owlapi.metrics.NumberOfClassesWithMultipleInheritance

isMetricInvalidated(List<? extends OWLOntologyChange>) - Method in class org.semanticweb.owlapi.metrics.ObjectCountMetric

isMetricInvalidated(List<? extends OWLOntologyChange>) - Method in class org.semanticweb.owlapi.metrics.UnsatisfiableClassCountMetric

isRoot() - Method in class uk.ac.manchester.cs.bhig.util.MutableTree

isRoot() - Method in interface uk.ac.manchester.cs.bhig.util.Tree

A convenience method that determines if this is a root node (because it has no parent node)

isTopOrBuiltInDatatype(OWLDataRange) - Static method in class com.clarkparsia.owlapi.modularity.locality.SyntacticLocalityEvaluator

This is a convenience method for determining whether a given data range expression is the top datatype or a built-in datatype.

isTopOrBuiltInInfiniteDatatype(OWLDataRange) - Static method in class com.clarkparsia.owlapi.modularity.locality.SyntacticLocalityEvaluator

This is a convenience method for determining whether a given data range expression is the top datatype or a built-in infinite datatype.

J

JustificationMap - Class in org.semanticweb.owlapi.debugging

Author: Matthew Horridge
The University Of Manchester
Bio-Health Informatics Group
Date: 30-Apr-2007

JustificationMap(OWLClassExpression, Set<OWLAxiom>) - Constructor for class org.semanticweb.owlapi.debugging.JustificationMap

L

LocalityClass - Enum in com.clarkparsia.owlapi.modularity.locality

Types of locality classes that can be used

localityCls - Variable in class com.clarkparsia.owlapi.modularity.locality.SyntacticLocalityEvaluator

LocalityEvaluator - Interface in com.clarkparsia.owlapi.modularity.locality

A locality evaluator

log - Static variable in class com.clarkparsia.owlapi.modularity.locality.SemanticLocalityEvaluator

logger - Static variable in class com.clarkparsia.owlapi.explanation.SatisfiabilityConverter

LogicalAxiomCount - Class in org.semanticweb.owlapi.metrics

Author: Matthew Horridge
The University Of Manchester
Bio-Health Informatics Group
Date: 27-Jul-2007

LogicalAxiomCount(OWLOntologyManager) - Constructor for class org.semanticweb.owlapi.metrics.LogicalAxiomCount

M

MakeClassesMutuallyDisjoint - Class in org.semanticweb.owlapi

Author: Matthew Horridge
The University Of Manchester
Bio-Health Informatics Group
Date: 24-Jul-2007

Given a set of class expressions, this composite change will make them mutually disjoint.

MakeClassesMutuallyDisjoint(OWLDataFactory, Set<? extends OWLClassExpression>, boolean, OWLOntology) - Constructor for class org.semanticweb.owlapi.MakeClassesMutuallyDisjoint

Creates a composite change which makes a set of classes mutually disjoint

MakePrimitiveSubClassesMutuallyDisjoint - Class in org.semanticweb.owlapi

Author: Matthew Horridge
The University Of Manchester
Bio-Health Informatics Group
Date: 24-Jul-2007

For a given class, this composite change makes its told primitive subclasses mutually disjoint.

MakePrimitiveSubClassesMutuallyDisjoint(OWLDataFactory, OWLClass, Set<OWLOntology>, OWLOntology) - Constructor for class org.semanticweb.owlapi.MakePrimitiveSubClassesMutuallyDisjoint

MakePrimitiveSubClassesMutuallyDisjoint(OWLDataFactory, OWLClass, Set<OWLOntology>, OWLOntology, boolean) - Constructor for class org.semanticweb.owlapi.MakePrimitiveSubClassesMutuallyDisjoint

map - Variable in class org.semanticweb.owlapi.CoerceConstantsIntoDataPropertyRange

MaximumNumberOfNamedSuperclasses - Class in org.semanticweb.owlapi.metrics

Author: Matthew Horridge
The University Of Manchester
Bio-Health Informatics Group
Date: 27-Jul-2007

MaximumNumberOfNamedSuperclasses(OWLOntologyManager) - Constructor for class org.semanticweb.owlapi.metrics.MaximumNumberOfNamedSuperclasses

ModuleType - Enum in uk.ac.manchester.cs.owlapi.modularity

Enumeration for module types.

MultipleExplanationGenerator - Interface in com.clarkparsia.owlapi.explanation

multiple explanation generator

MutableTree<N> - Class in uk.ac.manchester.cs.bhig.util

Author: Matthew Horridge
The University Of Manchester
Bio-Health Informatics Group
Date: 22-Jan-2008

MutableTree(N) - Constructor for class uk.ac.manchester.cs.bhig.util.MutableTree

N

NegationalNormalFormConverter - Class in org.semanticweb.owlapi.normalform

Author: Matthew Horridge
The University Of Manchester
Bio-Health Informatics Group
Date: 24-Sep-2007

NegationalNormalFormConverter(OWLDataFactory) - Constructor for class org.semanticweb.owlapi.normalform.NegationalNormalFormConverter

NodeRenderer<N> - Interface in uk.ac.manchester.cs.bhig.util

Author: Matthew Horridge
The University of Manchester
Information Management Group
Date: 27-Nov-2008

NormalFormRewriter - Interface in org.semanticweb.owlapi.normalform

Author: Matthew Horridge
The University Of Manchester
Bio-Health Informatics Group
Date: 24-Sep-2007

NullExplanationOrderer - Class in uk.ac.manchester.cs.owl.explanation.ordering

Author: Matthew Horridge
The University Of Manchester
Bio-Health Informatics Group
Date: 22-Jan-2008

An implementation of an explanation order, which doesn't really do any ordering!

NullExplanationOrderer() - Constructor for class uk.ac.manchester.cs.owl.explanation.ordering.NullExplanationOrderer

NumberOfClassesWithMultipleInheritance - Class in org.semanticweb.owlapi.metrics

Author: Matthew Horridge
The University Of Manchester
Bio-Health Informatics Group
Date: 27-Jul-2007

NumberOfClassesWithMultipleInheritance(OWLOntologyManager) - Constructor for class org.semanticweb.owlapi.metrics.NumberOfClassesWithMultipleInheritance

O

ObjectCountMetric<E> - Class in org.semanticweb.owlapi.metrics

Author: Matthew Horridge
The University Of Manchester
Bio-Health Informatics Group
Date: 27-Jul-2007

ObjectCountMetric(OWLOntologyManager) - Constructor for class org.semanticweb.owlapi.metrics.ObjectCountMetric

ontologiesChanged(List<? extends OWLOntologyChange>) - Method in class com.clarkparsia.owlapi.explanation.util.DefinitionTracker

ontologiesChanged(List<? extends OWLOntologyChange>) - Method in class org.semanticweb.owlapi.metrics.AbstractOWLMetric

OntologySegmenter - Interface in org.semanticweb.owlapi.modularity

An interface for any class implementing ontology segmentation or modularisation.

OntologyUtils - Class in com.clarkparsia.owlapi.explanation.util

Some ontology utils methods

OntologyUtils() - Constructor for class com.clarkparsia.owlapi.explanation.util.OntologyUtils

org.semanticweb.owlapi - package org.semanticweb.owlapi

org.semanticweb.owlapi.debugging - package org.semanticweb.owlapi.debugging

org.semanticweb.owlapi.metrics - package org.semanticweb.owlapi.metrics

org.semanticweb.owlapi.modularity - package org.semanticweb.owlapi.modularity

org.semanticweb.owlapi.normalform - package org.semanticweb.owlapi.normalform

OWLCompositeOntologyChange - Interface in org.semanticweb.owlapi

Author: Matthew Horridge
The University Of Manchester
Bio-Health Informatics Group
Date: 23-Jul-2007

A composite ontology change encapsulates a list of ontology changes, which should be applied as a logical unit.

OWLDebugger - Interface in org.semanticweb.owlapi.debugging

Author: Matthew Horridge
The University Of Manchester
Bio-Health Informatics Group
Date: 24-Nov-2006

OWLMetric<M> - Interface in org.semanticweb.owlapi.metrics

Author: Matthew Horridge
The University Of Manchester
Bio-Health Informatics Group
Date: 27-Jul-2007

Represents a metric about some aspect of an ontology and possibly its imports closure.

OWLMetricManager - Class in org.semanticweb.owlapi.metrics

Author: Matthew Horridge
The University Of Manchester
Bio-Health Informatics Group
Date: 27-Jul-2007

OWLMetricManager(List<OWLMetric<?>>) - Constructor for class org.semanticweb.owlapi.metrics.OWLMetricManager

OWLObjectComplementOfExtractor - Class in org.semanticweb.owlapi.normalform

Author: Matthew Horridge
The University Of Manchester
Bio-Health Informatics Group
Date: 13-Oct-2007

Extracts the parts of a class expression which are negated.

OWLObjectComplementOfExtractor() - Constructor for class org.semanticweb.owlapi.normalform.OWLObjectComplementOfExtractor

P

property - Variable in class org.semanticweb.owlapi.AddClassExpressionClosureAxiom

pruneUntilMinimal(OWLClassExpression) - Method in class com.clarkparsia.owlapi.explanation.BlackBoxExplanation

R

reasoner - Variable in class com.clarkparsia.owlapi.modularity.locality.SemanticLocalityEvaluator

recomputeMetric() - Method in class org.semanticweb.owlapi.metrics.AbstractOWLMetric

recomputeMetric() - Method in class org.semanticweb.owlapi.metrics.AverageAssertedNamedSuperclassCount

recomputeMetric() - Method in class org.semanticweb.owlapi.metrics.AxiomCount

recomputeMetric() - Method in class org.semanticweb.owlapi.metrics.DLExpressivity

recomputeMetric() - Method in class org.semanticweb.owlapi.metrics.HiddenGCICount

recomputeMetric() - Method in class org.semanticweb.owlapi.metrics.ImportClosureSize

recomputeMetric() - Method in class org.semanticweb.owlapi.metrics.MaximumNumberOfNamedSuperclasses

recomputeMetric() - Method in class org.semanticweb.owlapi.metrics.NumberOfClassesWithMultipleInheritance

recomputeMetric() - Method in class org.semanticweb.owlapi.metrics.ObjectCountMetric

recomputeMetric() - Method in class org.semanticweb.owlapi.metrics.UnsatisfiableClassCountMetric

ReferencedClassCount - Class in org.semanticweb.owlapi.metrics

Author: Matthew Horridge
The University Of Manchester
Bio-Health Informatics Group
Date: 27-Jul-2007

ReferencedClassCount(OWLOntologyManager) - Constructor for class org.semanticweb.owlapi.metrics.ReferencedClassCount

ReferencedDataPropertyCount - Class in org.semanticweb.owlapi.metrics

Author: Matthew Horridge
The University Of Manchester
Bio-Health Informatics Group
Date: 27-Jul-2007

ReferencedDataPropertyCount(OWLOntologyManager) - Constructor for class org.semanticweb.owlapi.metrics.ReferencedDataPropertyCount

ReferencedIndividualCount - Class in org.semanticweb.owlapi.metrics

Author: Matthew Horridge
The University Of Manchester
Bio-Health Informatics Group
Date: 27-Jul-2007

ReferencedIndividualCount(OWLOntologyManager) - Constructor for class org.semanticweb.owlapi.metrics.ReferencedIndividualCount

ReferencedObjectPropertyCount - Class in org.semanticweb.owlapi.metrics

Author: Matthew Horridge
The University Of Manchester
Bio-Health Informatics Group
Date: 27-Jul-2007

ReferencedObjectPropertyCount(OWLOntologyManager) - Constructor for class org.semanticweb.owlapi.metrics.ReferencedObjectPropertyCount

RemoveAllDisjointAxioms - Class in org.semanticweb.owlapi

Author: Matthew Horridge
The University Of Manchester
Bio-Health Informatics Group
Date: 24-Jul-2007

Given a set of ontologies, this composite change will remove all disjoint classes axioms from these ontologies.

RemoveAllDisjointAxioms(OWLDataFactory, Set<OWLOntology>) - Constructor for class org.semanticweb.owlapi.RemoveAllDisjointAxioms

removeAxiom(OWLAxiom, Set<OWLOntology>, OWLOntologyManager) - Static method in class com.clarkparsia.owlapi.explanation.util.OntologyUtils

Removes an axiom from all the given ontologies that contains the axiom and returns those ontologies.

removeChild(MutableTree<N>) - Method in class uk.ac.manchester.cs.bhig.util.MutableTree

render(OWLAxiom, Set<Set<OWLAxiom>>) - Method in class com.clarkparsia.owlapi.explanation.io.ConciseExplanationRenderer

render(OWLAxiom, Set<Set<OWLAxiom>>) - Method in interface com.clarkparsia.owlapi.explanation.io.ExplanationRenderer

render(OWLAxiom, Set<Set<OWLAxiom>>) - Method in class com.clarkparsia.owlapi.explanation.io.SilentExplanationRenderer

render(Tree<N>) - Method in interface uk.ac.manchester.cs.bhig.util.NodeRenderer

renderer - Variable in class uk.ac.manchester.cs.owl.explanation.ordering.AlphaExplanationOrderer

replace(MutableTree<N>) - Method in class uk.ac.manchester.cs.bhig.util.MutableTree

Deprecated.

this method is not in the public interface and is unused.

reset() - Method in class org.semanticweb.owlapi.normalform.OWLObjectComplementOfExtractor

clear the visitor

S

SatisfiabilityConverter - Class in com.clarkparsia.owlapi.explanation

Satisfiability converter

SatisfiabilityConverter(OWLDataFactory) - Constructor for class com.clarkparsia.owlapi.explanation.SatisfiabilityConverter

SemanticLocalityEvaluator - Class in com.clarkparsia.owlapi.modularity.locality

Semantic locality evaluator

SemanticLocalityEvaluator(OWLOntologyManager, OWLReasonerFactory) - Constructor for class com.clarkparsia.owlapi.modularity.locality.SemanticLocalityEvaluator

setImportsClosureUsed(boolean) - Method in class org.semanticweb.owlapi.metrics.AbstractOWLMetric

setImportsClosureUsed(boolean) - Method in interface org.semanticweb.owlapi.metrics.OWLMetric

Sets whether this metric uses the imports closure of the current ontology

setModuleType(ModuleType) - Method in class uk.ac.manchester.cs.owlapi.modularity.SyntacticLocalityModuleExtractor

Changes the module type for this extractor without deleting the stored referenced entities.

setNodeRenderer(NodeRenderer<N>) - Method in class uk.ac.manchester.cs.bhig.util.MutableTree

setNodeRenderer(NodeRenderer<N>) - Method in interface uk.ac.manchester.cs.bhig.util.Tree

setOntology(OWLOntology) - Method in class org.semanticweb.owlapi.metrics.AbstractOWLMetric

setOntology(OWLOntology) - Method in interface org.semanticweb.owlapi.metrics.OWLMetric

Sets the "root" ontology.

setOntology(OWLOntology) - Method in class org.semanticweb.owlapi.metrics.OWLMetricManager

setParent(MutableTree<N>) - Method in class uk.ac.manchester.cs.bhig.util.MutableTree

setProgressMonitor(ExplanationProgressMonitor) - Method in class com.clarkparsia.owlapi.explanation.HSTExplanationGenerator

setProgressMonitor(ExplanationProgressMonitor) - Method in interface com.clarkparsia.owlapi.explanation.MultipleExplanationGenerator

Sets the progress monitor for this multiple explanation generator.

ShortForm2AnnotationGenerator - Class in org.semanticweb.owlapi

Author: Matthew Horridge
The University Of Manchester
Bio-Health Informatics Group
Date: 15-Feb-2008

ShortForm2AnnotationGenerator(OWLOntologyManager, OWLOntology, ShortFormProvider, IRI, String) - Constructor for class org.semanticweb.owlapi.ShortForm2AnnotationGenerator

ShortForm2AnnotationGenerator(OWLOntologyManager, OWLOntology, ShortFormProvider, IRI) - Constructor for class org.semanticweb.owlapi.ShortForm2AnnotationGenerator

SilentExplanationProgressMonitor - Class in com.clarkparsia.owlapi.explanation.util

Author: Matthew Horridge
Clark & Parsia, LLC
Bio-Health Informatics Group
Date: 26-Nov-2007

SilentExplanationProgressMonitor() - Constructor for class com.clarkparsia.owlapi.explanation.util.SilentExplanationProgressMonitor

SilentExplanationRenderer - Class in com.clarkparsia.owlapi.explanation.io

Null implementation

SilentExplanationRenderer() - Constructor for class com.clarkparsia.owlapi.explanation.io.SilentExplanationRenderer

SingleExplanationGenerator - Interface in com.clarkparsia.owlapi.explanation

Explanation generator for a single explanation

SingleExplanationGeneratorImpl - Class in com.clarkparsia.owlapi.explanation

SingleExplanationGeneratorImpl(OWLOntology, OWLReasonerFactory, OWLReasoner) - Constructor for class com.clarkparsia.owlapi.explanation.SingleExplanationGeneratorImpl

sortChildren(Comparator<Tree<N>>) - Method in class uk.ac.manchester.cs.bhig.util.MutableTree

sortChildren(Comparator<Tree<N>>) - Method in interface uk.ac.manchester.cs.bhig.util.Tree

Sorts the children using the specified comparator

SplitSubClassAxioms - Class in org.semanticweb.owlapi

Author: Matthew Horridge
The University Of Manchester
Bio-Health Informatics Group
Date: 15-Aug-2007

Given a set of ontologies, this composite change will replace all subclass axioms in each ontology, whose super class is an object intersection (conjuction) with multiple subclass axioms - one for each conjunct.

SplitSubClassAxioms(Set<OWLOntology>, OWLDataFactory) - Constructor for class org.semanticweb.owlapi.SplitSubClassAxioms

Creates a composite change to split subclass axioms into multiple more fine grained subclass axioms.

startRendering(Writer) - Method in class com.clarkparsia.owlapi.explanation.io.ConciseExplanationRenderer

startRendering(Writer) - Method in interface com.clarkparsia.owlapi.explanation.io.ExplanationRenderer

startRendering(Writer) - Method in class com.clarkparsia.owlapi.explanation.io.SilentExplanationRenderer

supportedLocalityClasses() - Method in class com.clarkparsia.owlapi.modularity.locality.SyntacticLocalityEvaluator

Returns all supported locality classes.

SyntacticLocalityEvaluator - Class in com.clarkparsia.owlapi.modularity.locality

Syntactic locality evaluator

SyntacticLocalityEvaluator(LocalityClass) - Constructor for class com.clarkparsia.owlapi.modularity.locality.SyntacticLocalityEvaluator

Constructs a new locality evaluator for the given locality class.

SyntacticLocalityModuleExtractor - Class in uk.ac.manchester.cs.owlapi.modularity

Implementation of module extraction based on syntactic locality.

SyntacticLocalityModuleExtractor(OWLOntologyManager, OWLOntology, Set<OWLAxiom>, ModuleType) - Constructor for class uk.ac.manchester.cs.owlapi.modularity.SyntacticLocalityModuleExtractor

Creates a new module extractor for a subset of a given ontology, its manager, and a specified type of locality.

SyntacticLocalityModuleExtractor(OWLOntologyManager, OWLOntology, ModuleType) - Constructor for class uk.ac.manchester.cs.owlapi.modularity.SyntacticLocalityModuleExtractor

Creates a new module extractor for a given ontology, its manager, and a specified type of locality.

T

toString() - Method in class com.clarkparsia.owlapi.explanation.BlackBoxExplanation

toString() - Method in class org.semanticweb.owlapi.metrics.AbstractOWLMetric

toString() - Method in class org.semanticweb.owlapi.metrics.OWLMetricManager

toString() - Method in class uk.ac.manchester.cs.bhig.util.MutableTree

toString() - Method in enum uk.ac.manchester.cs.owlapi.modularity.ModuleType

TransactionAwareSingleExpGen - Interface in com.clarkparsia.owlapi.explanation

transactional support for single explanation generator

Tree<N> - Interface in uk.ac.manchester.cs.bhig.util

Author: Matthew Horridge
The University Of Manchester
Bio-Health Informatics Group
Date: 22-Jan-2008

U

uk.ac.manchester.cs.bhig.util - package uk.ac.manchester.cs.bhig.util

uk.ac.manchester.cs.owl.explanation.ordering - package uk.ac.manchester.cs.owl.explanation.ordering

uk.ac.manchester.cs.owlapi.modularity - package uk.ac.manchester.cs.owlapi.modularity

UnsatisfiableClassCountMetric - Class in org.semanticweb.owlapi.metrics

Author: Matthew Horridge
The University Of Manchester
Bio-Health Informatics Group
Date: 17-Jan-2008

UnsatisfiableClassCountMetric(OWLReasoner, OWLOntologyManager) - Constructor for class org.semanticweb.owlapi.metrics.UnsatisfiableClassCountMetric

V

valueOf(String) - Static method in enum com.clarkparsia.owlapi.modularity.locality.LocalityClass

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum uk.ac.manchester.cs.owlapi.modularity.ModuleType

Returns the enum constant of this type with the specified name.

values() - Static method in enum com.clarkparsia.owlapi.modularity.locality.LocalityClass

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum uk.ac.manchester.cs.owlapi.modularity.ModuleType

Returns an array containing the constants of this enum type, in the order they are declared.

visit(OWLSubClassOfAxiom) - Method in class org.semanticweb.owlapi.debugging.DebuggerClassExpressionGenerator

visit(OWLNegativeObjectPropertyAssertionAxiom) - Method in class org.semanticweb.owlapi.debugging.DebuggerClassExpressionGenerator

visit(OWLAsymmetricObjectPropertyAxiom) - Method in class org.semanticweb.owlapi.debugging.DebuggerClassExpressionGenerator

visit(OWLReflexiveObjectPropertyAxiom) - Method in class org.semanticweb.owlapi.debugging.DebuggerClassExpressionGenerator

visit(OWLDisjointClassesAxiom) - Method in class org.semanticweb.owlapi.debugging.DebuggerClassExpressionGenerator

visit(OWLDataPropertyDomainAxiom) - Method in class org.semanticweb.owlapi.debugging.DebuggerClassExpressionGenerator

visit(OWLImportsDeclaration) - Method in class org.semanticweb.owlapi.debugging.DebuggerClassExpressionGenerator

visit(OWLObjectPropertyDomainAxiom) - Method in class org.semanticweb.owlapi.debugging.DebuggerClassExpressionGenerator

visit(OWLEquivalentObjectPropertiesAxiom) - Method in class org.semanticweb.owlapi.debugging.DebuggerClassExpressionGenerator

visit(OWLNegativeDataPropertyAssertionAxiom) - Method in class org.semanticweb.owlapi.debugging.DebuggerClassExpressionGenerator

visit(OWLDifferentIndividualsAxiom) - Method in class org.semanticweb.owlapi.debugging.DebuggerClassExpressionGenerator

visit(OWLDisjointDataPropertiesAxiom) - Method in class org.semanticweb.owlapi.debugging.DebuggerClassExpressionGenerator

visit(OWLDisjointObjectPropertiesAxiom) - Method in class org.semanticweb.owlapi.debugging.DebuggerClassExpressionGenerator

visit(OWLObjectPropertyRangeAxiom) - Method in class org.semanticweb.owlapi.debugging.DebuggerClassExpressionGenerator

visit(OWLObjectPropertyAssertionAxiom) - Method in class org.semanticweb.owlapi.debugging.DebuggerClassExpressionGenerator

visit(OWLFunctionalObjectPropertyAxiom) - Method in class org.semanticweb.owlapi.debugging.DebuggerClassExpressionGenerator

visit(OWLSubObjectPropertyOfAxiom) - Method in class org.semanticweb.owlapi.debugging.DebuggerClassExpressionGenerator

visit(OWLDisjointUnionAxiom) - Method in class org.semanticweb.owlapi.debugging.DebuggerClassExpressionGenerator

visit(OWLDeclarationAxiom) - Method in class org.semanticweb.owlapi.debugging.DebuggerClassExpressionGenerator

visit(OWLAnnotationAssertionAxiom) - Method in class org.semanticweb.owlapi.debugging.DebuggerClassExpressionGenerator

visit(OWLSymmetricObjectPropertyAxiom) - Method in class org.semanticweb.owlapi.debugging.DebuggerClassExpressionGenerator

visit(OWLDataPropertyRangeAxiom) - Method in class org.semanticweb.owlapi.debugging.DebuggerClassExpressionGenerator

visit(OWLFunctionalDataPropertyAxiom) - Method in class org.semanticweb.owlapi.debugging.DebuggerClassExpressionGenerator

visit(OWLEquivalentDataPropertiesAxiom) - Method in class org.semanticweb.owlapi.debugging.DebuggerClassExpressionGenerator

visit(OWLClassAssertionAxiom) - Method in class org.semanticweb.owlapi.debugging.DebuggerClassExpressionGenerator

visit(OWLEquivalentClassesAxiom) - Method in class org.semanticweb.owlapi.debugging.DebuggerClassExpressionGenerator

visit(OWLDataPropertyAssertionAxiom) - Method in class org.semanticweb.owlapi.debugging.DebuggerClassExpressionGenerator

visit(OWLTransitiveObjectPropertyAxiom) - Method in class org.semanticweb.owlapi.debugging.DebuggerClassExpressionGenerator

visit(OWLIrreflexiveObjectPropertyAxiom) - Method in class org.semanticweb.owlapi.debugging.DebuggerClassExpressionGenerator

visit(OWLSubDataPropertyOfAxiom) - Method in class org.semanticweb.owlapi.debugging.DebuggerClassExpressionGenerator

visit(OWLInverseFunctionalObjectPropertyAxiom) - Method in class org.semanticweb.owlapi.debugging.DebuggerClassExpressionGenerator

visit(OWLSameIndividualAxiom) - Method in class org.semanticweb.owlapi.debugging.DebuggerClassExpressionGenerator

visit(OWLSubPropertyChainOfAxiom) - Method in class org.semanticweb.owlapi.debugging.DebuggerClassExpressionGenerator

visit(OWLInverseObjectPropertiesAxiom) - Method in class org.semanticweb.owlapi.debugging.DebuggerClassExpressionGenerator

visit(SWRLRule) - Method in class org.semanticweb.owlapi.debugging.DebuggerClassExpressionGenerator

visit(OWLHasKeyAxiom) - Method in class org.semanticweb.owlapi.debugging.DebuggerClassExpressionGenerator

visit(OWLAnnotationPropertyDomainAxiom) - Method in class org.semanticweb.owlapi.debugging.DebuggerClassExpressionGenerator

visit(OWLAnnotationPropertyRangeAxiom) - Method in class org.semanticweb.owlapi.debugging.DebuggerClassExpressionGenerator

visit(OWLSubAnnotationPropertyOfAxiom) - Method in class org.semanticweb.owlapi.debugging.DebuggerClassExpressionGenerator

visit(OWLDatatypeDefinitionAxiom) - Method in class org.semanticweb.owlapi.debugging.DebuggerClassExpressionGenerator

visit(OWLClass) - Method in class org.semanticweb.owlapi.normalform.OWLObjectComplementOfExtractor

visit(OWLDataAllValuesFrom) - Method in class org.semanticweb.owlapi.normalform.OWLObjectComplementOfExtractor

visit(OWLDataExactCardinality) - Method in class org.semanticweb.owlapi.normalform.OWLObjectComplementOfExtractor

visit(OWLDataMaxCardinality) - Method in class org.semanticweb.owlapi.normalform.OWLObjectComplementOfExtractor

visit(OWLDataMinCardinality) - Method in class org.semanticweb.owlapi.normalform.OWLObjectComplementOfExtractor

visit(OWLDataSomeValuesFrom) - Method in class org.semanticweb.owlapi.normalform.OWLObjectComplementOfExtractor

visit(OWLDataHasValue) - Method in class org.semanticweb.owlapi.normalform.OWLObjectComplementOfExtractor

visit(OWLObjectAllValuesFrom) - Method in class org.semanticweb.owlapi.normalform.OWLObjectComplementOfExtractor

visit(OWLObjectComplementOf) - Method in class org.semanticweb.owlapi.normalform.OWLObjectComplementOfExtractor

visit(OWLObjectExactCardinality) - Method in class org.semanticweb.owlapi.normalform.OWLObjectComplementOfExtractor

visit(OWLObjectIntersectionOf) - Method in class org.semanticweb.owlapi.normalform.OWLObjectComplementOfExtractor

visit(OWLObjectMaxCardinality) - Method in class org.semanticweb.owlapi.normalform.OWLObjectComplementOfExtractor

visit(OWLObjectMinCardinality) - Method in class org.semanticweb.owlapi.normalform.OWLObjectComplementOfExtractor

visit(OWLObjectOneOf) - Method in class org.semanticweb.owlapi.normalform.OWLObjectComplementOfExtractor

visit(OWLObjectHasSelf) - Method in class org.semanticweb.owlapi.normalform.OWLObjectComplementOfExtractor

visit(OWLObjectSomeValuesFrom) - Method in class org.semanticweb.owlapi.normalform.OWLObjectComplementOfExtractor

visit(OWLObjectUnionOf) - Method in class org.semanticweb.owlapi.normalform.OWLObjectComplementOfExtractor

visit(OWLObjectHasValue) - Method in class org.semanticweb.owlapi.normalform.OWLObjectComplementOfExtractor

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