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A

AbstractModuleExtractor - Class in com.clarkparsia.modularity

Title:

AbstractModuleExtractor() - Constructor for class com.clarkparsia.modularity.AbstractModuleExtractor

AbstractModuleExtractor(LocalityClass) - Constructor for class com.clarkparsia.modularity.AbstractModuleExtractor

AbstractModuleExtractor(AbstractModuleExtractor) - Constructor for class com.clarkparsia.modularity.AbstractModuleExtractor

add(T) - Method in class com.clarkparsia.reachability.PairSet

addAxiom(OWLAxiom) - Method in class com.clarkparsia.modularity.AbstractModuleExtractor

addAxiom(OWLAxiom) - Method in class com.clarkparsia.modularity.GraphBuilder

addAxiom(OWLAxiom) - Method in interface com.clarkparsia.modularity.ModuleExtractor

Adds an axiom to the extractor.

addEntities(Set<E>) - Method in class com.clarkparsia.reachability.EntityNode

addEntity(E) - Method in class com.clarkparsia.reachability.EntityNode

addOutput(Node) - Method in class com.clarkparsia.reachability.Node

AndNode - Class in com.clarkparsia.reachability

AndNode(int) - Constructor for class com.clarkparsia.reachability.AndNode

applyChanges(Taxonomy<OWLClass>) - Method in class com.clarkparsia.modularity.AbstractModuleExtractor

applyChanges(Taxonomy<OWLClass>) - Method in interface com.clarkparsia.modularity.ModuleExtractor

Update the modules with the changes that have been put into the queue so far.

areSame() - Method in class com.clarkparsia.modularity.OntologyDiff

Checks whether the two compared ontologies were the same (i.e., there are no differences).

AxiomBasedModuleExtractor - Class in com.clarkparsia.modularity

Title:

AxiomBasedModuleExtractor() - Constructor for class com.clarkparsia.modularity.AxiomBasedModuleExtractor

AxiomBasedModuleExtractor(LocalityClass) - Constructor for class com.clarkparsia.modularity.AxiomBasedModuleExtractor

B

buffering(BufferingMode) - Method in class com.clarkparsia.modularity.IncrementalReasonerConfiguration

buffering(boolean) - Method in class com.clarkparsia.modularity.IncrementalReasonerConfiguration

build() - Method in class com.clarkparsia.modularity.GraphBuilder

buildClassHierarchy(OWLReasoner) - Static method in class com.clarkparsia.modularity.IncrementalReasoner

Build the class hierarchy based on the results from the reasoner

C

canUpdate() - Method in class com.clarkparsia.modularity.AbstractModuleExtractor

Returns if the extracted modules can be updated.

canUpdate() - Method in interface com.clarkparsia.modularity.ModuleExtractor

Returns if the extracted modules can be updated.

changes - Variable in class com.clarkparsia.modularity.AbstractModuleExtractor

The types of changes that are pending in additions and deletions

ChangeTypeDetector - Class in com.clarkparsia.modularity

Detects what kind of type of a change (i.e., TBox, RBox or ABox change) an addition or a deletion of an OWLAxiom introduces.

ChangeTypeDetector() - Constructor for class com.clarkparsia.modularity.ChangeTypeDetector

classify() - Method in class com.clarkparsia.modularity.IncrementalReasoner

close() - Method in class com.clarkparsia.modularity.io.UncloseableOutputStream

Captures the close request, and does NOT forward it to the underlying stream.

com.clarkparsia.modularity - package com.clarkparsia.modularity

com.clarkparsia.modularity.io - package com.clarkparsia.modularity.io

com.clarkparsia.reachability - package com.clarkparsia.reachability

compare(OWLClass, OWLClass) - Method in class com.clarkparsia.modularity.IncrementalReasoner.DisjointClassComparator

computeReachable(Iterable<E>) - Method in class com.clarkparsia.reachability.Reachability

computeSCC(ReachabilityGraph<E>) - Static method in class com.clarkparsia.reachability.SCC

Computes the strongly connected components of a graph.

config() - Static method in class com.clarkparsia.modularity.IncrementalReasoner

contains(Object) - Method in class com.clarkparsia.reachability.PairSet

contains(E) - Method in class com.clarkparsia.reachability.Reachability

copy() - Method in class com.clarkparsia.modularity.AxiomBasedModuleExtractor

copy() - Method in class com.clarkparsia.modularity.GraphBasedModuleExtractor

copy() - Method in class com.clarkparsia.modularity.IncrementalReasoner

copy() - Method in interface com.clarkparsia.modularity.ModuleExtractor

createAndNode(Set<Node>) - Method in class com.clarkparsia.reachability.ReachabilityGraph

createEntityNode(E) - Method in class com.clarkparsia.reachability.ReachabilityGraph

createIncrementalReasoner() - Method in class com.clarkparsia.modularity.IncrementalReasonerConfiguration

createIncrementalReasoner(OWLOntology) - Method in class com.clarkparsia.modularity.IncrementalReasonerConfiguration

createModuleExtractor() - Static method in class com.clarkparsia.modularity.ModuleExtractorFactory

createNonBufferingReasoner(OWLOntology) - Method in class com.clarkparsia.modularity.IncremantalReasonerFactory

createNonBufferingReasoner(OWLOntology, OWLReasonerConfiguration) - Method in class com.clarkparsia.modularity.IncremantalReasonerFactory

createOrNode(Set<Node>) - Method in class com.clarkparsia.reachability.ReachabilityGraph

createReasoner(OWLOntology) - Method in class com.clarkparsia.modularity.IncremantalReasonerFactory

createReasoner(OWLOntology, OWLReasonerConfiguration) - Method in class com.clarkparsia.modularity.IncremantalReasonerFactory

D

deleteAxiom(OWLAxiom) - Method in class com.clarkparsia.modularity.AbstractModuleExtractor

deleteAxiom(OWLAxiom) - Method in interface com.clarkparsia.modularity.ModuleExtractor

Deletes an axiom from the extractor.

diffAxioms(Collection<OWLAxiom>, Collection<OWLAxiom>) - Static method in class com.clarkparsia.modularity.OntologyDiff

Computes the difference between two sets of axioms.

diffAxiomsWithOntologies(Collection<OWLAxiom>, Collection<OWLOntology>) - Static method in class com.clarkparsia.modularity.OntologyDiff

Computes the difference between a set of axioms and an ontology.

diffOntologies(OWLOntology, OWLOntology) - Static method in class com.clarkparsia.modularity.OntologyDiff

Computes the difference between two ontologies.

diffOntologiesWithAxioms(Collection<OWLOntology>, Collection<OWLAxiom>) - Static method in class com.clarkparsia.modularity.OntologyDiff

Computes the difference between a collection of ontologies and a collection of axioms

DisjointClassComparator(Taxonomy<OWLClass>, OWLClassExpression) - Constructor for class com.clarkparsia.modularity.IncrementalReasoner.DisjointClassComparator

dispose() - Method in class com.clarkparsia.modularity.IncrementalReasoner

E

EntailmentChecker - Class in com.clarkparsia.modularity

Title:

EntailmentChecker(IncrementalReasoner) - Constructor for class com.clarkparsia.modularity.EntailmentChecker

entityAxioms - Variable in class com.clarkparsia.modularity.AbstractModuleExtractor

Map to find axioms that references an axiom

EntityNode<E> - Class in com.clarkparsia.reachability

EntityNode(E) - Constructor for class com.clarkparsia.reachability.EntityNode

extractModule(Set<? extends OWLEntity>) - Method in class com.clarkparsia.modularity.AxiomBasedModuleExtractor

Extract the module for a given set of entities.

extractModule(Set<? extends OWLEntity>) - Method in class com.clarkparsia.modularity.GraphBasedModuleExtractor

extractModule(OWLOntology, Set<OWLEntity>, ModuleType) - Static method in class com.clarkparsia.modularity.ModularityUtils

Extract the module from the imports closure of the given ontology for the given signature.

extractModule(Set<OWLOntology>, Set<OWLEntity>, ModuleType) - Static method in class com.clarkparsia.modularity.ModularityUtils

Extract the module from a given set of ontologies (but not their imports) for the given signature.

extractModule(Set<? extends OWLEntity>) - Method in interface com.clarkparsia.modularity.ModuleExtractor

Extract the module for a given set of entities.

extractModules() - Method in class com.clarkparsia.modularity.AbstractModuleExtractor

Extract modules from scratch

extractModules() - Method in interface com.clarkparsia.modularity.ModuleExtractor

Extract modules for all classes from scratch

extractModuleSignatures(Set<? extends OWLEntity>, ProgressMonitor) - Method in class com.clarkparsia.modularity.AbstractModuleExtractor

extractModuleSignatures(Set<? extends OWLEntity>, ProgressMonitor) - Method in class com.clarkparsia.modularity.AxiomBasedModuleExtractor

extractModuleSignatures(Set<? extends OWLEntity>, ProgressMonitor) - Method in class com.clarkparsia.modularity.GraphBasedModuleExtractor

extractor(ModuleExtractor) - Method in class com.clarkparsia.modularity.IncrementalReasonerConfiguration

F

file(File) - Method in class com.clarkparsia.modularity.IncrementalReasonerConfiguration

flush() - Method in class com.clarkparsia.modularity.IncrementalReasoner

flush() - Method in class com.clarkparsia.modularity.io.UncloseableOutputStream

Forwards the call to the underlying stream.

G

getAdditions() - Method in class com.clarkparsia.modularity.OntologyDiff

Gets the list of axioms that were added to the second ontology with respect to the first ontology.

getAxioms(OWLEntity) - Method in class com.clarkparsia.modularity.AbstractModuleExtractor

Return the axioms which references this entity

getAxioms() - Method in class com.clarkparsia.modularity.AbstractModuleExtractor

getAxioms() - Method in interface com.clarkparsia.modularity.ModuleExtractor

Returns all the axioms loaded in the extractor.

getAxioms(OWLEntity) - Method in interface com.clarkparsia.modularity.ModuleExtractor

Return the axioms which references this entity

getBottomClassNode() - Method in class com.clarkparsia.modularity.IncrementalReasoner

getBottomDataPropertyNode() - Method in class com.clarkparsia.modularity.IncrementalReasoner

getBottomObjectPropertyNode() - Method in class com.clarkparsia.modularity.IncrementalReasoner

getBufferingMode() - Method in class com.clarkparsia.modularity.IncrementalReasoner

getChanges(OWLOntology) - Method in class com.clarkparsia.modularity.OntologyDiff

Produces a list of ontology change objects that if applied to the initial ontology, would convert that initial ontology into the final ontology.

getChanges(Collection<OWLOntology>) - Method in class com.clarkparsia.modularity.OntologyDiff

Produces a list of ontology change objects that if applied to the set of initial ontologies, would convert that set of ontologies into the final ontology.

getComplementRepresentation() - Method in class com.clarkparsia.modularity.IncrementalReasoner.DisjointClassComparator

getDataPropertyDomains(OWLDataProperty, boolean) - Method in class com.clarkparsia.modularity.IncrementalReasoner

getDataPropertyValues(OWLNamedIndividual, OWLDataProperty) - Method in class com.clarkparsia.modularity.IncrementalReasoner

getDeletions() - Method in class com.clarkparsia.modularity.OntologyDiff

Gets the list of axioms that were deleted in the second ontology with respect to the first ontology.

getDiffCount() - Method in class com.clarkparsia.modularity.OntologyDiff

Gets the number of differences (in terms of numbers of axioms) between the compared ontologies.

getDifferentIndividuals(OWLNamedIndividual) - Method in class com.clarkparsia.modularity.IncrementalReasoner

getDisjointClasses(OWLClassExpression) - Method in class com.clarkparsia.modularity.IncrementalReasoner

getDisjointDataProperties(OWLDataPropertyExpression) - Method in class com.clarkparsia.modularity.IncrementalReasoner

getDisjointObjectProperties(OWLObjectPropertyExpression) - Method in class com.clarkparsia.modularity.IncrementalReasoner

getEntities() - Method in class com.clarkparsia.modularity.AbstractModuleExtractor

getEntities() - Method in interface com.clarkparsia.modularity.ModuleExtractor

Returns all the entities referenced in loaded axioms.

getEntities() - Method in class com.clarkparsia.reachability.EntityNode

getEntities() - Method in class com.clarkparsia.reachability.ReachabilityGraph

getEntityNodes() - Method in class com.clarkparsia.reachability.ReachabilityGraph

getEquivalentClasses(OWLClassExpression) - Method in class com.clarkparsia.modularity.IncrementalReasoner

getEquivalentDataProperties(OWLDataProperty) - Method in class com.clarkparsia.modularity.IncrementalReasoner

getEquivalentObjectProperties(OWLObjectPropertyExpression) - Method in class com.clarkparsia.modularity.IncrementalReasoner

getFile() - Method in class com.clarkparsia.modularity.IncrementalReasonerConfiguration

getFreshEntityPolicy() - Method in class com.clarkparsia.modularity.IncrementalReasoner

getGraph() - Method in class com.clarkparsia.reachability.Reachability

getIndividualNodeSetPolicy() - Method in class com.clarkparsia.modularity.IncrementalReasoner

getInputs() - Method in class com.clarkparsia.reachability.Node

getInstance() - Static method in class com.clarkparsia.modularity.IncremantalReasonerFactory

Returns a static factory instance that can be used to create reasoners.

getInstances(OWLClassExpression, boolean) - Method in class com.clarkparsia.modularity.IncrementalReasoner

getInverseObjectProperties(OWLObjectPropertyExpression) - Method in class com.clarkparsia.modularity.IncrementalReasoner

getManager() - Method in class com.clarkparsia.modularity.IncrementalReasoner

getModuleAxioms(Set<OWLEntity>) - Method in class com.clarkparsia.modularity.AbstractModuleExtractor

getModuleEntities(OWLEntity) - Method in class com.clarkparsia.modularity.AbstractModuleExtractor

getModuleEntities(OWLEntity) - Method in interface com.clarkparsia.modularity.ModuleExtractor

getModuleExtractor() - Method in class com.clarkparsia.modularity.IncrementalReasoner

Get the module extractor

getModuleExtractor() - Method in class com.clarkparsia.modularity.IncrementalReasonerConfiguration

getModuleFromSignature(Set<OWLEntity>) - Method in class com.clarkparsia.modularity.AbstractModuleExtractor

Returns a new ontology that contains the axioms that are in the module for given set of entities

getModuleFromSignature(Set<OWLEntity>) - Method in interface com.clarkparsia.modularity.ModuleExtractor

Returns a new ontology that contains the axioms that are in the module for given set of entities

getNode(E) - Method in class com.clarkparsia.reachability.ReachabilityGraph

getNullNode() - Method in class com.clarkparsia.reachability.ReachabilityGraph

getObjectPropertyDomains(OWLObjectPropertyExpression, boolean) - Method in class com.clarkparsia.modularity.IncrementalReasoner

getObjectPropertyRanges(OWLObjectPropertyExpression, boolean) - Method in class com.clarkparsia.modularity.IncrementalReasoner

getObjectPropertyValues(OWLNamedIndividual, OWLObjectPropertyExpression) - Method in class com.clarkparsia.modularity.IncrementalReasoner

getOutputs() - Method in class com.clarkparsia.reachability.Node

getPendingAxiomAdditions() - Method in class com.clarkparsia.modularity.IncrementalReasoner

getPendingAxiomRemovals() - Method in class com.clarkparsia.modularity.IncrementalReasoner

getPendingChanges() - Method in class com.clarkparsia.modularity.IncrementalReasoner

getPrecomputableInferenceTypes() - Method in class com.clarkparsia.modularity.IncrementalReasoner

getReasoner() - Method in class com.clarkparsia.modularity.IncrementalReasoner

Get the underlying reasoner

getReasoner() - Method in class com.clarkparsia.modularity.IncrementalReasonerConfiguration

getReasonerName() - Method in class com.clarkparsia.modularity.IncremantalReasonerFactory

getReasonerName() - Method in class com.clarkparsia.modularity.IncrementalReasoner

getReasonerVersion() - Method in class com.clarkparsia.modularity.IncrementalReasoner

getRootOntology() - Method in class com.clarkparsia.modularity.IncrementalReasoner

getSameIndividuals(OWLNamedIndividual) - Method in class com.clarkparsia.modularity.IncrementalReasoner

getStartNode() - Method in class com.clarkparsia.reachability.ReachabilityGraph

getSubClasses(OWLClassExpression, boolean) - Method in class com.clarkparsia.modularity.IncrementalReasoner

getSubDataProperties(OWLDataProperty, boolean) - Method in class com.clarkparsia.modularity.IncrementalReasoner

getSubObjectProperties(OWLObjectPropertyExpression, boolean) - Method in class com.clarkparsia.modularity.IncrementalReasoner

getSuperClasses(OWLClassExpression, boolean) - Method in class com.clarkparsia.modularity.IncrementalReasoner

getSuperDataProperties(OWLDataProperty, boolean) - Method in class com.clarkparsia.modularity.IncrementalReasoner

getSuperObjectProperties(OWLObjectPropertyExpression, boolean) - Method in class com.clarkparsia.modularity.IncrementalReasoner

getTaxonomy() - Method in class com.clarkparsia.modularity.IncrementalReasoner

getTimeOut() - Method in class com.clarkparsia.modularity.IncrementalReasoner

getTimers() - Method in class com.clarkparsia.modularity.AbstractModuleExtractor

getTimers() - Method in interface com.clarkparsia.modularity.ModuleExtractor

Returns the timers used by this extractor to collect statistics about performance.

getTopClassNode() - Method in class com.clarkparsia.modularity.IncrementalReasoner

getTopDataPropertyNode() - Method in class com.clarkparsia.modularity.IncrementalReasoner

getTopObjectPropertyNode() - Method in class com.clarkparsia.modularity.IncrementalReasoner

getTypes(OWLNamedIndividual, boolean) - Method in class com.clarkparsia.modularity.IncrementalReasoner

getUnderlyingStream() - Method in class com.clarkparsia.modularity.io.UncloseableOutputStream

Gets the underlying stream.

getUnsatisfiableClasses() - Method in class com.clarkparsia.modularity.IncrementalReasoner

GraphBasedModuleExtractor - Class in com.clarkparsia.modularity

GraphBasedModuleExtractor() - Constructor for class com.clarkparsia.modularity.GraphBasedModuleExtractor

GraphBuilder - Class in com.clarkparsia.modularity

GraphBuilder() - Constructor for class com.clarkparsia.modularity.GraphBuilder

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hasNext() - Method in class com.clarkparsia.reachability.PairSet.PairIterator

hasOutput(Node) - Method in class com.clarkparsia.reachability.Node

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IncremantalReasonerFactory - Class in com.clarkparsia.modularity

Title:

IncremantalReasonerFactory() - Constructor for class com.clarkparsia.modularity.IncremantalReasonerFactory

IncrementalReasoner - Class in com.clarkparsia.modularity

Title:

IncrementalReasoner(OWLOntology, IncrementalReasonerConfiguration) - Constructor for class com.clarkparsia.modularity.IncrementalReasoner

IncrementalReasoner.DisjointClassComparator - Class in com.clarkparsia.modularity

IncrementalReasonerConfiguration - Class in com.clarkparsia.modularity

IncrementalReasonerConfiguration() - Constructor for class com.clarkparsia.modularity.IncrementalReasonerConfiguration

IncrementalReasonerConfiguration(OWLReasonerConfiguration) - Constructor for class com.clarkparsia.modularity.IncrementalReasonerConfiguration

inputActivated() - Method in class com.clarkparsia.reachability.AndNode

inputActivated() - Method in class com.clarkparsia.reachability.EntityNode

inputActivated() - Method in class com.clarkparsia.reachability.Node

inputActivated() - Method in class com.clarkparsia.reachability.OrNode

inputs - Variable in class com.clarkparsia.reachability.Node

interrupt() - Method in class com.clarkparsia.modularity.IncrementalReasoner

isABoxAxiom(OWLAxiom) - Static method in class com.clarkparsia.modularity.ChangeTypeDetector

Checks whether the given OWLAxiom is a ABox axiom

isABoxChanged() - Method in class com.clarkparsia.modularity.AbstractModuleExtractor

Checks whether there are unapplied changes to the ABox

isActive() - Method in class com.clarkparsia.reachability.AndNode

isActive() - Method in class com.clarkparsia.reachability.EntityNode

isActive() - Method in class com.clarkparsia.reachability.Node

isActive() - Method in class com.clarkparsia.reachability.OrNode

isChanged() - Method in class com.clarkparsia.modularity.AbstractModuleExtractor

Checks if axioms have been added/removed and modules need to be updated

isChanged() - Method in interface com.clarkparsia.modularity.ModuleExtractor

Checks if axioms have been added/removed and modules need to be updated

isClassificationNeeded(Expressivity) - Method in class com.clarkparsia.modularity.AbstractModuleExtractor

isClassificationNeeded(Expressivity) - Method in interface com.clarkparsia.modularity.ModuleExtractor

Checks if the changes that has not yet been updated require re-classification

isClassified() - Method in class com.clarkparsia.modularity.IncrementalReasoner

isConsistent() - Method in class com.clarkparsia.modularity.IncrementalReasoner

isEntailed(Set<? extends OWLAxiom>) - Method in class com.clarkparsia.modularity.EntailmentChecker

isEntailed(OWLAxiom) - Method in class com.clarkparsia.modularity.EntailmentChecker

isEntailed(OWLAxiom) - Method in class com.clarkparsia.modularity.IncrementalReasoner

isEntailed(Set<? extends OWLAxiom>) - Method in class com.clarkparsia.modularity.IncrementalReasoner

isEntailmentCheckingSupported(AxiomType<?>) - Method in class com.clarkparsia.modularity.IncrementalReasoner

isLocal(OWLAxiom, Set<OWLEntity>) - Method in class com.clarkparsia.modularity.AbstractModuleExtractor

isMultiThreaded() - Method in class com.clarkparsia.modularity.IncrementalReasonerConfiguration

isOptimizeForSharedModules() - Method in class com.clarkparsia.modularity.AxiomBasedModuleExtractor

Returns if shared modules optimization is on.

isPrecomputed(InferenceType) - Method in class com.clarkparsia.modularity.IncrementalReasoner

isRBoxAxiom(OWLAxiom) - Static method in class com.clarkparsia.modularity.ChangeTypeDetector

Checks whether the given OWLAxiom is a RBox axiom

isRBoxChanged() - Method in class com.clarkparsia.modularity.AbstractModuleExtractor

Checks whether there are unapplied changes to the RBox

isRealized() - Method in class com.clarkparsia.modularity.IncrementalReasoner

isRedundant() - Method in class com.clarkparsia.reachability.AndNode

isRedundant() - Method in class com.clarkparsia.reachability.Node

isRedundant() - Method in class com.clarkparsia.reachability.OrNode

isSatisfiable(OWLClassExpression) - Method in class com.clarkparsia.modularity.IncrementalReasoner

isTBoxAxiom(OWLAxiom) - Static method in class com.clarkparsia.modularity.ChangeTypeDetector

Checks whether the given OWLAxiom is a TBox axiom

isTBoxChanged() - Method in class com.clarkparsia.modularity.AbstractModuleExtractor

Checks whether there are unapplied changes to the TBox

iterator() - Method in class com.clarkparsia.reachability.PairSet

L

listenChanges(boolean) - Method in class com.clarkparsia.modularity.IncrementalReasonerConfiguration

load(ZipInputStream) - Method in class com.clarkparsia.modularity.AbstractModuleExtractor

load(InputStream) - Static method in class com.clarkparsia.modularity.io.TaxonomyPersistence

Loads the taxonomy from a stream

load(ZipInputStream) - Method in interface com.clarkparsia.modularity.ModuleExtractor

Restores the previously saved state of the ModuleExtractor from a stream.

loadModules(InputStream) - Static method in class com.clarkparsia.modularity.io.ModuleExtractorPersistence

Reads information about the modules from the input stream that has the information stored in a form of ontology.

log - Static variable in class com.clarkparsia.modularity.AbstractModuleExtractor

log - Static variable in class com.clarkparsia.modularity.AxiomBasedModuleExtractor

log - Static variable in class com.clarkparsia.modularity.EntailmentChecker

log - Static variable in class com.clarkparsia.modularity.GraphBasedModuleExtractor

log - Static variable in class com.clarkparsia.modularity.GraphBuilder

log - Static variable in class com.clarkparsia.modularity.IncrementalReasoner

log - Static variable in class com.clarkparsia.modularity.io.ModuleExtractorPersistence

log - Static variable in class com.clarkparsia.modularity.io.TaxonomyPersistence

log - Static variable in class com.clarkparsia.reachability.Reachability

log - Static variable in class com.clarkparsia.reachability.ReachabilityGraph

M

manager(OWLOntologyManager) - Method in class com.clarkparsia.modularity.IncrementalReasonerConfiguration

ModularityUtils - Class in com.clarkparsia.modularity

ModularityUtils() - Constructor for class com.clarkparsia.modularity.ModularityUtils

ModuleExtractor - Interface in com.clarkparsia.modularity

Title:

ModuleExtractorFactory - Class in com.clarkparsia.modularity

Title:

ModuleExtractorFactory() - Constructor for class com.clarkparsia.modularity.ModuleExtractorFactory

ModuleExtractorPersistence - Class in com.clarkparsia.modularity.io

Title:

ModuleExtractorPersistence() - Constructor for class com.clarkparsia.modularity.io.ModuleExtractorPersistence

modules - Variable in class com.clarkparsia.modularity.AbstractModuleExtractor

multiThreaded(boolean) - Method in class com.clarkparsia.modularity.IncrementalReasonerConfiguration

Sets the multi-threading option.

N

next() - Method in class com.clarkparsia.reachability.PairSet.PairIterator

Node - Class in com.clarkparsia.reachability

Node() - Constructor for class com.clarkparsia.reachability.Node

O

ontologiesChanged(List<? extends OWLOntologyChange>) - Method in class com.clarkparsia.modularity.IncrementalReasoner

OntologyDiff - Class in com.clarkparsia.modularity

Computes differences between two ontologies, sets of ontologies or collections of axioms.

OrNode - Class in com.clarkparsia.reachability

OrNode(int) - Constructor for class com.clarkparsia.reachability.OrNode

outputs - Variable in class com.clarkparsia.reachability.Node

P

PairIterator() - Constructor for class com.clarkparsia.reachability.PairSet.PairIterator

PairSet<T> - Class in com.clarkparsia.reachability

An unmodifiable Set implementation that is a wrapper around a pair of sets without additional storage for set elements.

PairSet(Set<T>, Set<T>) - Constructor for class com.clarkparsia.reachability.PairSet

PairSet.PairIterator - Class in com.clarkparsia.reachability

Iterate through first and second set filtering any duplicates that might be in both sets.

precomputeInferences(InferenceType...) - Method in class com.clarkparsia.modularity.IncrementalReasoner

prepareReasoner() - Method in class com.clarkparsia.modularity.IncrementalReasoner

progressMonitor(ReasonerProgressMonitor) - Method in class com.clarkparsia.modularity.IncrementalReasonerConfiguration

R

Reachability<E> - Class in com.clarkparsia.reachability

Computes reachability in a directed graph with and/or nodes.

Reachability(ReachabilityGraph<E>) - Constructor for class com.clarkparsia.reachability.Reachability

ReachabilityGraph<E> - Class in com.clarkparsia.reachability

Graph with and/or nodes designed to compute reachability

ReachabilityGraph() - Constructor for class com.clarkparsia.reachability.ReachabilityGraph

reasoner(PelletReasoner) - Method in class com.clarkparsia.modularity.IncrementalReasonerConfiguration

remove() - Method in class com.clarkparsia.reachability.Node

remove() - Method in class com.clarkparsia.reachability.PairSet.PairIterator

remove(Object) - Method in class com.clarkparsia.reachability.PairSet

removeInOuts() - Method in class com.clarkparsia.reachability.Node

removeOutput(Node) - Method in class com.clarkparsia.reachability.Node

reset() - Method in class com.clarkparsia.reachability.AndNode

reset() - Method in class com.clarkparsia.reachability.EntityNode

reset() - Method in class com.clarkparsia.reachability.Node

reset() - Method in class com.clarkparsia.reachability.OrNode

resetModules() - Method in class com.clarkparsia.modularity.AbstractModuleExtractor

S

save(ZipOutputStream) - Method in class com.clarkparsia.modularity.AbstractModuleExtractor

save(File) - Method in class com.clarkparsia.modularity.IncrementalReasoner

save(Taxonomy<OWLClass>, OutputStream) - Static method in class com.clarkparsia.modularity.io.TaxonomyPersistence

Saves a taxonomy into a stream.

save(ZipOutputStream) - Method in interface com.clarkparsia.modularity.ModuleExtractor

Save the current state of the ModuleExtractor.

saveAxioms(Collection<OWLAxiom>, OutputStream) - Static method in class com.clarkparsia.modularity.io.ModuleExtractorPersistence

Saves the axioms from the ModuleExtractor in the form of an ontology containing these axioms.

saveModules(Map<OWLEntity, Set<OWLEntity>>, OutputStream) - Static method in class com.clarkparsia.modularity.io.ModuleExtractorPersistence

Saves the information about modules from ModuleExtractor to an output stream as an ontology of modules annotated with URIs of the OWL entities that belong to the respective modules.

SCC - Class in com.clarkparsia.reachability

setOptimizeForSharedModules(boolean) - Method in class com.clarkparsia.modularity.AxiomBasedModuleExtractor

Sets the the option to optimize for shared modules during module extraction.

simplify() - Method in class com.clarkparsia.reachability.ReachabilityGraph

size() - Method in class com.clarkparsia.reachability.PairSet

T

TaxonomyPersistence - Class in com.clarkparsia.modularity.io

Title: Stores and restores a taxonomy to a stream.

TaxonomyPersistence() - Constructor for class com.clarkparsia.modularity.io.TaxonomyPersistence

timeout(long) - Method in class com.clarkparsia.modularity.IncrementalReasonerConfiguration

timers - Variable in class com.clarkparsia.modularity.IncrementalReasoner

toString() - Method in class com.clarkparsia.modularity.IncremantalReasonerFactory

toString() - Method in class com.clarkparsia.reachability.AndNode

toString() - Method in class com.clarkparsia.reachability.EntityNode

toString() - Method in class com.clarkparsia.reachability.OrNode

U

UncloseableOutputStream - Class in com.clarkparsia.modularity.io

Title:

UncloseableOutputStream(OutputStream) - Constructor for class com.clarkparsia.modularity.io.UncloseableOutputStream

Wraps an output stream with a wrapper that does not allow the underlying stream to be closed.

V

visit(OWLSubClassOfAxiom) - Method in class com.clarkparsia.modularity.EntailmentChecker

visit(OWLEquivalentClassesAxiom) - Method in class com.clarkparsia.modularity.EntailmentChecker

visit(OWLSameIndividualAxiom) - Method in class com.clarkparsia.modularity.EntailmentChecker

visit(OWLDisjointClassesAxiom) - Method in class com.clarkparsia.modularity.EntailmentChecker

visit(OWLClassAssertionAxiom) - Method in class com.clarkparsia.modularity.EntailmentChecker

visit(OWLDeclarationAxiom) - Method in class com.clarkparsia.modularity.EntailmentChecker

visit(OWLNegativeObjectPropertyAssertionAxiom) - Method in class com.clarkparsia.modularity.EntailmentChecker

visit(OWLAsymmetricObjectPropertyAxiom) - Method in class com.clarkparsia.modularity.EntailmentChecker

visit(OWLReflexiveObjectPropertyAxiom) - Method in class com.clarkparsia.modularity.EntailmentChecker

visit(OWLDataPropertyDomainAxiom) - Method in class com.clarkparsia.modularity.EntailmentChecker

visit(OWLObjectPropertyDomainAxiom) - Method in class com.clarkparsia.modularity.EntailmentChecker

visit(OWLEquivalentObjectPropertiesAxiom) - Method in class com.clarkparsia.modularity.EntailmentChecker

visit(OWLNegativeDataPropertyAssertionAxiom) - Method in class com.clarkparsia.modularity.EntailmentChecker

visit(OWLDifferentIndividualsAxiom) - Method in class com.clarkparsia.modularity.EntailmentChecker

visit(OWLDisjointDataPropertiesAxiom) - Method in class com.clarkparsia.modularity.EntailmentChecker

visit(OWLDisjointObjectPropertiesAxiom) - Method in class com.clarkparsia.modularity.EntailmentChecker

visit(OWLObjectPropertyRangeAxiom) - Method in class com.clarkparsia.modularity.EntailmentChecker

visit(OWLObjectPropertyAssertionAxiom) - Method in class com.clarkparsia.modularity.EntailmentChecker

visit(OWLFunctionalObjectPropertyAxiom) - Method in class com.clarkparsia.modularity.EntailmentChecker

visit(OWLSubObjectPropertyOfAxiom) - Method in class com.clarkparsia.modularity.EntailmentChecker

visit(OWLDisjointUnionAxiom) - Method in class com.clarkparsia.modularity.EntailmentChecker

visit(OWLSymmetricObjectPropertyAxiom) - Method in class com.clarkparsia.modularity.EntailmentChecker

visit(OWLDataPropertyRangeAxiom) - Method in class com.clarkparsia.modularity.EntailmentChecker

visit(OWLFunctionalDataPropertyAxiom) - Method in class com.clarkparsia.modularity.EntailmentChecker

visit(OWLEquivalentDataPropertiesAxiom) - Method in class com.clarkparsia.modularity.EntailmentChecker

visit(OWLDataPropertyAssertionAxiom) - Method in class com.clarkparsia.modularity.EntailmentChecker

visit(OWLTransitiveObjectPropertyAxiom) - Method in class com.clarkparsia.modularity.EntailmentChecker

visit(OWLIrreflexiveObjectPropertyAxiom) - Method in class com.clarkparsia.modularity.EntailmentChecker

visit(OWLSubDataPropertyOfAxiom) - Method in class com.clarkparsia.modularity.EntailmentChecker

visit(OWLInverseFunctionalObjectPropertyAxiom) - Method in class com.clarkparsia.modularity.EntailmentChecker

visit(OWLSubPropertyChainOfAxiom) - Method in class com.clarkparsia.modularity.EntailmentChecker

visit(OWLInverseObjectPropertiesAxiom) - Method in class com.clarkparsia.modularity.EntailmentChecker

visit(OWLHasKeyAxiom) - Method in class com.clarkparsia.modularity.EntailmentChecker

visit(OWLDatatypeDefinitionAxiom) - Method in class com.clarkparsia.modularity.EntailmentChecker

visit(SWRLRule) - Method in class com.clarkparsia.modularity.EntailmentChecker

W

write(byte[]) - Method in class com.clarkparsia.modularity.io.UncloseableOutputStream

Forwards the call to the underlying stream.

write(byte[], int, int) - Method in class com.clarkparsia.modularity.io.UncloseableOutputStream

Forwards the call to the underlying stream.

write(int) - Method in class com.clarkparsia.modularity.io.UncloseableOutputStream

Forwards the call to the underlying stream.

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