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

A

accept(Ontology, Traversal.Visitor...) - Method in interface au.csiro.ontology.util.Traversal

accept(Node, Traversal.Visitor...) - Method in interface au.csiro.ontology.util.Traversal

active - Variable in class au.csiro.ontology.snomed.refset.rf2.ModuleDependencyRow

active - Variable in class au.csiro.ontology.snomed.refset.rf2.RefsetRow

annotationRefsetFiles - Variable in class au.csiro.ontology.input.RF2Input

associationRefsetFiles - Variable in class au.csiro.ontology.input.RF2Input

attributeDomainRefsetFiles - Variable in class au.csiro.ontology.input.RF2Input

attributeValueRefsetFiles - Variable in class au.csiro.ontology.input.RF2Input

au.csiro.ontology - package au.csiro.ontology

au.csiro.ontology.classification - package au.csiro.ontology.classification

au.csiro.ontology.input - package au.csiro.ontology.input

au.csiro.ontology.model - package au.csiro.ontology.model

au.csiro.ontology.snomed.refset.rf2 - package au.csiro.ontology.snomed.refset.rf2

au.csiro.ontology.util - package au.csiro.ontology.util

Axiom - Class in au.csiro.ontology.model

Base class for axioms.

Axiom() - Constructor for class au.csiro.ontology.model.Axiom

AxiomUtils - Class in au.csiro.ontology.util

Several utilities for axioms.

AxiomUtils() - Constructor for class au.csiro.ontology.util.AxiomUtils

B

base - Variable in class au.csiro.ontology.input.Input

BFS_MAX - Static variable in interface au.csiro.ontology.util.Traversal

A level-order traversal where the level is the max distance from the root.

BFS_MIN - Static variable in interface au.csiro.ontology.util.Traversal

A level-order traversal where the level is the min distance from the root.

BigIntegerLiteral - Class in au.csiro.ontology.model

This class represents a double literal.

BigIntegerLiteral() - Constructor for class au.csiro.ontology.model.BigIntegerLiteral

BigIntegerLiteral(BigInteger) - Constructor for class au.csiro.ontology.model.BigIntegerLiteral

BigIntegerLiteral(long) - Constructor for class au.csiro.ontology.model.BigIntegerLiteral

BooleanLiteral - Class in au.csiro.ontology.model

Deprecated.

BooleanLiteral() - Constructor for class au.csiro.ontology.model.BooleanLiteral

Deprecated.

BooleanLiteral(boolean) - Constructor for class au.csiro.ontology.model.BooleanLiteral

Deprecated.

BOTTOM - Static variable in class au.csiro.ontology.model.NamedConcept

Represents the bottom concept.

BOTTOM_CONCEPT - Static variable in class au.csiro.ontology.model.NamedConcept

The bottom concept.

C

children - Variable in class au.csiro.ontology.Node

Set of child nodes.

classify() - Method in interface au.csiro.ontology.classification.IReasoner

Classifies the current axioms.

close() - Method in class au.csiro.ontology.input.Input

Release internal state.

compareTo(Literal) - Method in class au.csiro.ontology.model.BigIntegerLiteral

compareTo(Literal) - Method in class au.csiro.ontology.model.BooleanLiteral

Deprecated.

compareTo(Axiom) - Method in class au.csiro.ontology.model.ConceptInclusion

compareTo(Concept) - Method in class au.csiro.ontology.model.Conjunction

compareTo(Concept) - Method in class au.csiro.ontology.model.Datatype

compareTo(Literal) - Method in class au.csiro.ontology.model.DateLiteral

compareTo(Literal) - Method in class au.csiro.ontology.model.DecimalLiteral

compareTo(Literal) - Method in class au.csiro.ontology.model.DoubleLiteral

Deprecated.

compareTo(Concept) - Method in class au.csiro.ontology.model.Existential

compareTo(Literal) - Method in class au.csiro.ontology.model.FloatLiteral

compareTo(Axiom) - Method in class au.csiro.ontology.model.FunctionalFeature

compareTo(Literal) - Method in class au.csiro.ontology.model.IntegerLiteral

compareTo(Literal) - Method in class au.csiro.ontology.model.LongLiteral

compareTo(Concept) - Method in class au.csiro.ontology.model.NamedConcept

compareTo(Feature) - Method in class au.csiro.ontology.model.NamedFeature

compareTo(Role) - Method in class au.csiro.ontology.model.NamedRole

compareTo(Axiom) - Method in class au.csiro.ontology.model.RoleInclusion

compareTo(Literal) - Method in class au.csiro.ontology.model.StringLiteral

compareTo(RefsetRow) - Method in class au.csiro.ontology.snomed.refset.rf2.RefsetRow

complexMapRefsetFiles - Variable in class au.csiro.ontology.input.RF2Input

computeStats(Ontology) - Static method in class au.csiro.ontology.util.Traversal.Stats

Traverses the ontology to compute min and max path length to root for each node.

Concept - Class in au.csiro.ontology.model

Base interface for concepts.

Concept() - Constructor for class au.csiro.ontology.model.Concept

ConceptInclusion - Class in au.csiro.ontology.model

This class represents a concept inclusion axiom (also known as a SubClassOf axiom in OWL).

ConceptInclusion() - Constructor for class au.csiro.ontology.model.ConceptInclusion

ConceptInclusion(Concept, Concept) - Constructor for class au.csiro.ontology.model.ConceptInclusion

Creates a new ConceptInclusion.

conceptsFiles - Variable in class au.csiro.ontology.input.RF2Input

concreteDomainRefsetFiles - Variable in class au.csiro.ontology.input.RF2Input

Conjunction - Class in au.csiro.ontology.model

This class represents a conjunction (also referred to as an ObjectIntersectionOf in OWL).

Conjunction() - Constructor for class au.csiro.ontology.model.Conjunction

Conjunction(Concept[]) - Constructor for class au.csiro.ontology.model.Conjunction

Conjunction(Collection<? extends Concept>) - Constructor for class au.csiro.ontology.model.Conjunction

createBigIntegerLiteral(long) - Static method in class au.csiro.ontology.Factory

createBigIntegerLiteral(BigInteger) - Static method in class au.csiro.ontology.Factory

createBooleanLiteral(boolean) - Static method in class au.csiro.ontology.Factory

Deprecated.

createConceptInclusion(Concept, Concept) - Static method in class au.csiro.ontology.Factory

createConjunction(Concept...) - Static method in class au.csiro.ontology.Factory

createDatatype(Feature, Operator, Literal) - Static method in class au.csiro.ontology.Factory

createDateLiteral(Calendar) - Static method in class au.csiro.ontology.Factory

createDecimalLiteral(double) - Static method in class au.csiro.ontology.Factory

createDecimalLiteral(BigDecimal) - Static method in class au.csiro.ontology.Factory

createDoubleLiteral(double) - Static method in class au.csiro.ontology.Factory

Deprecated.

createExistential(Role, Concept) - Static method in class au.csiro.ontology.Factory

createFloatLiteral(float) - Static method in class au.csiro.ontology.Factory

createIntegerLiteral(int) - Static method in class au.csiro.ontology.Factory

createLongLiteral(long) - Static method in class au.csiro.ontology.Factory

createNamedConcept(String) - Static method in class au.csiro.ontology.Factory

createNamedFeature(String) - Static method in class au.csiro.ontology.Factory

createNamedRole(String) - Static method in class au.csiro.ontology.Factory

createRoleInclusion(Role[], Role) - Static method in class au.csiro.ontology.Factory

createStringLiteral(String) - Static method in class au.csiro.ontology.Factory

D

Datatype - Class in au.csiro.ontology.model

A datatype expression that represents a set of individuals that have a property with a certain value.

Datatype() - Constructor for class au.csiro.ontology.model.Datatype

Datatype(Feature, Operator, Literal) - Constructor for class au.csiro.ontology.model.Datatype

DateLiteral - Class in au.csiro.ontology.model

This class represents a date literal.

DateLiteral() - Constructor for class au.csiro.ontology.model.DateLiteral

DateLiteral(Calendar) - Constructor for class au.csiro.ontology.model.DateLiteral

DecimalLiteral - Class in au.csiro.ontology.model

This class represents a double literal.

DecimalLiteral() - Constructor for class au.csiro.ontology.model.DecimalLiteral

DecimalLiteral(BigDecimal) - Constructor for class au.csiro.ontology.model.DecimalLiteral

DecimalLiteral(double) - Constructor for class au.csiro.ontology.model.DecimalLiteral

dependencies - Variable in class au.csiro.ontology.snomed.refset.rf2.ModuleDependency

dependencies - Variable in class au.csiro.ontology.snomed.refset.rf2.ModuleDependencyRefset

descriptionFormatRefsetFiles - Variable in class au.csiro.ontology.input.RF2Input

descriptionsFiles - Variable in class au.csiro.ontology.input.RF2Input

deserialise(String) - Static method in class au.csiro.ontology.util.AxiomUtils

Transforms a string representation of an axiom into an Axiom.

deserialiseConcept(String) - Static method in class au.csiro.ontology.util.AxiomUtils

Transforms a string representation of a concept into an Concept.

displayName - Variable in class au.csiro.ontology.snomed.refset.rf2.Refset

DoubleLiteral - Class in au.csiro.ontology.model

Deprecated.

DoubleLiteral() - Constructor for class au.csiro.ontology.model.DoubleLiteral

Deprecated.

DoubleLiteral(double) - Constructor for class au.csiro.ontology.model.DoubleLiteral

Deprecated.

E

effectiveTime - Variable in class au.csiro.ontology.snomed.refset.rf2.ModuleDependencyRow

effectiveTime - Variable in class au.csiro.ontology.snomed.refset.rf2.RefsetRow

equals(Object) - Method in class au.csiro.ontology.model.BigIntegerLiteral

equals(Object) - Method in class au.csiro.ontology.model.BooleanLiteral

Deprecated.

equals(Object) - Method in class au.csiro.ontology.model.Concept

equals(Object) - Method in class au.csiro.ontology.model.ConceptInclusion

equals(Object) - Method in class au.csiro.ontology.model.Conjunction

equals(Object) - Method in class au.csiro.ontology.model.Datatype

equals(Object) - Method in class au.csiro.ontology.model.DateLiteral

equals(Object) - Method in class au.csiro.ontology.model.DecimalLiteral

equals(Object) - Method in class au.csiro.ontology.model.DoubleLiteral

Deprecated.

equals(Object) - Method in class au.csiro.ontology.model.Existential

equals(Object) - Method in class au.csiro.ontology.model.Feature

equals(Object) - Method in class au.csiro.ontology.model.FloatLiteral

equals(Object) - Method in class au.csiro.ontology.model.FunctionalFeature

equals(Object) - Method in class au.csiro.ontology.model.IntegerLiteral

equals(Object) - Method in class au.csiro.ontology.model.Literal

equals(Object) - Method in class au.csiro.ontology.model.LongLiteral

equals(Object) - Method in class au.csiro.ontology.model.NamedConcept

equals(Object) - Method in class au.csiro.ontology.model.NamedFeature

equals(Object) - Method in class au.csiro.ontology.model.NamedRole

equals(Object) - Method in class au.csiro.ontology.model.Role

equals(Object) - Method in class au.csiro.ontology.model.StringLiteral

equals(Object) - Method in class au.csiro.ontology.snomed.refset.rf2.ModuleDependency

equals(Object) - Method in class au.csiro.ontology.snomed.refset.rf2.ModuleDependencyRow

equals(Object) - Method in class au.csiro.ontology.snomed.refset.rf2.RefsetRow

equivalentConcepts - Variable in class au.csiro.ontology.Node

Set of equivalent concepts in this node.

Existential - Class in au.csiro.ontology.model

This class represents an existential (also known as an ObjectSomeValuesFrom in OWL).

Existential() - Constructor for class au.csiro.ontology.model.Existential

Existential(Role, Concept) - Constructor for class au.csiro.ontology.model.Existential

extras - Variable in class au.csiro.ontology.snomed.refset.rf2.RefsetRow

F

Factory - Class in au.csiro.ontology

Concrete implementation of IFactory.

Factory() - Constructor for class au.csiro.ontology.Factory

Feature - Class in au.csiro.ontology.model

Base class for features.

Feature() - Constructor for class au.csiro.ontology.model.Feature

FloatLiteral - Class in au.csiro.ontology.model

This class represents a float literal.

FloatLiteral() - Constructor for class au.csiro.ontology.model.FloatLiteral

FloatLiteral(float) - Constructor for class au.csiro.ontology.model.FloatLiteral

FunctionalFeature - Class in au.csiro.ontology.model

FunctionalFeature() - Constructor for class au.csiro.ontology.model.FunctionalFeature

FunctionalFeature(Feature) - Constructor for class au.csiro.ontology.model.FunctionalFeature

G

getActive() - Method in class au.csiro.ontology.snomed.refset.rf2.RefsetRow

getAffectedNodes() - Method in class au.csiro.ontology.Ontology

getAnnotationRefsetFiles() - Method in class au.csiro.ontology.input.RF2Input

getAssociationRefsetFiles() - Method in class au.csiro.ontology.input.RF2Input

getAttributeDomainRefsetFiles() - Method in class au.csiro.ontology.input.RF2Input

getAttributeValueRefsetFiles() - Method in class au.csiro.ontology.input.RF2Input

getBase() - Method in class au.csiro.ontology.input.Input

Optional base for resolving names against when Input#getInputType() is InputType#EXTERNAL.

getBottomNode() - Method in class au.csiro.ontology.Ontology

getChildren() - Method in class au.csiro.ontology.Node

getClassifiedOntology() - Method in interface au.csiro.ontology.classification.IReasoner

Returns an IOntology that represents the generated taxonomy.

getClassifiedOntology(Ontology) - Method in interface au.csiro.ontology.classification.IReasoner

Returns an IOntology that represents the generated taxonomy.

getColumns() - Method in class au.csiro.ontology.snomed.refset.rf2.RefsetRow

getComplexMapRefsetFiles() - Method in class au.csiro.ontology.input.RF2Input

getConcept() - Method in class au.csiro.ontology.model.Existential

getConceptDefinedId() - Method in class au.csiro.ontology.util.SnomedMetadata

Returns the id of the enumeration in SNOMED used to indicate that a concept is fully defined.

getConceptModelAttId() - Method in class au.csiro.ontology.util.SnomedMetadata

Returns the root concept id for roles.

getConcepts() - Method in class au.csiro.ontology.model.Conjunction

getConceptsFiles() - Method in class au.csiro.ontology.input.RF2Input

getConcreteDomainRefsetFiles() - Method in class au.csiro.ontology.input.RF2Input

getDefinitionId() - Method in class au.csiro.ontology.util.SnomedMetadata

Returns the id of the enumeration in SNOMED used to indicate that a description is a definition.

getDependencies() - Method in class au.csiro.ontology.snomed.refset.rf2.ModuleDependency

getDescriptionFormatRefsetFiles() - Method in class au.csiro.ontology.input.RF2Input

getDescriptionsFiles() - Method in class au.csiro.ontology.input.RF2Input

getDisplayName() - Method in interface au.csiro.ontology.snomed.refset.rf2.IRefset

Returns the name of this reference set.

getDisplayName() - Method in class au.csiro.ontology.snomed.refset.rf2.Refset

getEffectiveTime() - Method in class au.csiro.ontology.snomed.refset.rf2.ModuleDependencyRow

getEffectiveTime() - Method in class au.csiro.ontology.snomed.refset.rf2.RefsetRow

getEquivalentConcepts() - Method in class au.csiro.ontology.Node

getExtras() - Method in class au.csiro.ontology.snomed.refset.rf2.RefsetRow

getFeature() - Method in class au.csiro.ontology.model.Datatype

getFeature() - Method in class au.csiro.ontology.model.FunctionalFeature

getFsnId() - Method in class au.csiro.ontology.util.SnomedMetadata

Returns the id of the enumeration in SNOMED used to indicate that a description is a fully specified name.

getId() - Method in class au.csiro.ontology.input.ModuleInfo

getId() - Method in class au.csiro.ontology.input.Version

getId() - Method in class au.csiro.ontology.model.NamedConcept

Returns this concept's identifier.

getId() - Method in class au.csiro.ontology.model.NamedFeature

Returns this concept's identifier.

getId() - Method in class au.csiro.ontology.model.NamedRole

Returns this role's identifier.

getId() - Method in class au.csiro.ontology.Ontology

getId() - Method in interface au.csiro.ontology.snomed.refset.rf2.IRefset

Returns the id of this refset.

getId() - Method in class au.csiro.ontology.snomed.refset.rf2.ModuleDependency

getId() - Method in class au.csiro.ontology.snomed.refset.rf2.ModuleDependencyRow

getId() - Method in class au.csiro.ontology.snomed.refset.rf2.Refset

getId() - Method in class au.csiro.ontology.snomed.refset.rf2.RefsetRow

getIdentifiersFiles() - Method in class au.csiro.ontology.input.RF2Input

getInferredAxioms() - Method in class au.csiro.ontology.Ontology

getInputs() - Method in class au.csiro.ontology.input.Inputs

getInputStream(String) - Method in class au.csiro.ontology.input.Input

getInputType() - Method in class au.csiro.ontology.input.Input

getIsAId() - Method in class au.csiro.ontology.util.SnomedMetadata

Returns the role id for is-a relationships.

getLanguageRefsetFiles() - Method in class au.csiro.ontology.input.RF2Input

getLateralityId() - Method in class au.csiro.ontology.util.SnomedMetadata

getLhs() - Method in class au.csiro.ontology.model.ConceptInclusion

getLhs() - Method in class au.csiro.ontology.model.RoleInclusion

getLiteral() - Method in class au.csiro.ontology.model.Datatype

getMetadata() - Method in class au.csiro.ontology.input.Version

getModuleDependencies() - Method in interface au.csiro.ontology.snomed.refset.rf2.IModuleDependencyRefset

Returns a Map of root module ids and a Map of IModules indexed by version.

getModuleDependencies() - Method in class au.csiro.ontology.snomed.refset.rf2.ModuleDependencyRefset

getModuleDependenciesRefsetFiles() - Method in class au.csiro.ontology.input.RF2Input

getModuleId() - Method in class au.csiro.ontology.snomed.refset.rf2.ModuleDependencyRow

getModuleId() - Method in class au.csiro.ontology.snomed.refset.rf2.RefsetRow

getModules() - Method in class au.csiro.ontology.input.RF2Input

getNames() - Method in class au.csiro.ontology.util.Statistics

Returns the names of the performance measures.

getNeverGroupedIds() - Method in class au.csiro.ontology.util.SnomedMetadata

Returns the set of ids of SNOMED roles that should never be placed in a role group.

getNeverGroupedIdsString() - Method in class au.csiro.ontology.util.SnomedMetadata

Returns the raw property value for the never grouped ids.

getNode(String) - Method in class au.csiro.ontology.Ontology

getNode(String) - Method in class au.csiro.ontology.Taxonomy

Deprecated.

Returns the Node in the taxonomy that contains a specified concept or null if such Node does not exist.

getNodeMap() - Method in class au.csiro.ontology.Ontology

getOperator() - Method in class au.csiro.ontology.model.Datatype

getOrderedRefsetFiles() - Method in class au.csiro.ontology.input.RF2Input

getOwlAxiomRefsetFiles() - Method in class au.csiro.ontology.input.RF2Input

getOwlFile() - Method in class au.csiro.ontology.input.OWLInput

getOwlOntologyRefsetFiles() - Method in class au.csiro.ontology.input.RF2Input

getOwlReasonerFactory() - Method in class au.csiro.ontology.input.OWLInput

getParents() - Method in class au.csiro.ontology.Node

getQuerySpecificationRefsetFiles() - Method in class au.csiro.ontology.input.RF2Input

getReferencedComponentId() - Method in class au.csiro.ontology.snomed.refset.rf2.ModuleDependencyRow

getReferencedComponentId() - Method in class au.csiro.ontology.snomed.refset.rf2.RefsetRow

getRefsetDescriptorRefsetFiles() - Method in class au.csiro.ontology.input.RF2Input

getRefsetId() - Method in class au.csiro.ontology.snomed.refset.rf2.ModuleDependencyRow

getRefsetId() - Method in class au.csiro.ontology.snomed.refset.rf2.RefsetRow

getRelationshipsFiles() - Method in class au.csiro.ontology.input.RF2Input

getReleaseType() - Method in class au.csiro.ontology.input.RF2Input

getRhs() - Method in class au.csiro.ontology.model.ConceptInclusion

getRhs() - Method in class au.csiro.ontology.model.RoleInclusion

getRightIdentityIds() - Method in class au.csiro.ontology.util.SnomedMetadata

Returns the right identity axioms that cannot be represented in RF1 or RF2 formats.

getRightIdentityIdsString() - Method in class au.csiro.ontology.util.SnomedMetadata

Returns the raw property value for the right identity ids.

getRole() - Method in class au.csiro.ontology.model.Existential

getRoleGroupId() - Method in class au.csiro.ontology.util.SnomedMetadata

Returns the id for the "role group" role.

getSimpleMapRefsetFiles() - Method in class au.csiro.ontology.input.RF2Input

getSimpleRefsetFiles() - Method in class au.csiro.ontology.input.RF2Input

getSomeId() - Method in class au.csiro.ontology.util.SnomedMetadata

Returns the id of the enumeration in SNOMED used to represent an existential quantification.

getSourceEffectiveTime() - Method in class au.csiro.ontology.snomed.refset.rf2.ModuleDependencyRow

getStatedAxioms() - Method in class au.csiro.ontology.Ontology

getStatedRelationshipsFiles() - Method in class au.csiro.ontology.input.RF2Input

getStatistics() - Method in class au.csiro.ontology.util.Statistics

Returns a string with all the current statistics.

getSynonymId() - Method in class au.csiro.ontology.util.SnomedMetadata

Returns the id of the enumeration in SNOMED used to indicate that a description is a synonym.

getTargetEffectiveTime() - Method in class au.csiro.ontology.snomed.refset.rf2.ModuleDependencyRow

getTextDefinitionsFiles() - Method in class au.csiro.ontology.input.RF2Input

getTime(String) - Method in class au.csiro.ontology.util.Statistics

Gets a time for a performance measurement.

getTopNode() - Method in class au.csiro.ontology.Ontology

getTotalTime() - Method in class au.csiro.ontology.util.Statistics

getValue() - Method in class au.csiro.ontology.model.BigIntegerLiteral

getValue() - Method in class au.csiro.ontology.model.BooleanLiteral

Deprecated.

getValue() - Method in class au.csiro.ontology.model.DateLiteral

getValue() - Method in class au.csiro.ontology.model.DecimalLiteral

getValue() - Method in class au.csiro.ontology.model.DoubleLiteral

Deprecated.

getValue() - Method in class au.csiro.ontology.model.FloatLiteral

getValue() - Method in class au.csiro.ontology.model.IntegerLiteral

getValue() - Method in class au.csiro.ontology.model.LongLiteral

getValue() - Method in class au.csiro.ontology.model.StringLiteral

getVersion() - Method in class au.csiro.ontology.Ontology

getVersion() - Method in class au.csiro.ontology.snomed.refset.rf2.ModuleDependency

getVersions() - Method in class au.csiro.ontology.input.ModuleInfo

H

hashCode() - Method in class au.csiro.ontology.model.BigIntegerLiteral

hashCode() - Method in class au.csiro.ontology.model.BooleanLiteral

Deprecated.

hashCode() - Method in class au.csiro.ontology.model.Concept

hashCode() - Method in class au.csiro.ontology.model.ConceptInclusion

hashCode() - Method in class au.csiro.ontology.model.Conjunction

hashCode() - Method in class au.csiro.ontology.model.Datatype

hashCode() - Method in class au.csiro.ontology.model.DateLiteral

hashCode() - Method in class au.csiro.ontology.model.DecimalLiteral

hashCode() - Method in class au.csiro.ontology.model.DoubleLiteral

Deprecated.

hashCode() - Method in class au.csiro.ontology.model.Existential

hashCode() - Method in class au.csiro.ontology.model.Feature

hashCode() - Method in class au.csiro.ontology.model.FloatLiteral

hashCode() - Method in class au.csiro.ontology.model.FunctionalFeature

hashCode() - Method in class au.csiro.ontology.model.IntegerLiteral

hashCode() - Method in class au.csiro.ontology.model.Literal

hashCode() - Method in class au.csiro.ontology.model.LongLiteral

hashCode() - Method in class au.csiro.ontology.model.NamedConcept

hashCode() - Method in class au.csiro.ontology.model.NamedFeature

hashCode() - Method in class au.csiro.ontology.model.NamedRole

hashCode() - Method in class au.csiro.ontology.model.Role

hashCode() - Method in class au.csiro.ontology.model.StringLiteral

hashCode() - Method in class au.csiro.ontology.snomed.refset.rf2.ModuleDependency

hashCode() - Method in class au.csiro.ontology.snomed.refset.rf2.ModuleDependencyRow

hashCode() - Method in class au.csiro.ontology.snomed.refset.rf2.RefsetRow

I

id - Variable in class au.csiro.ontology.input.ModuleInfo

id - Variable in class au.csiro.ontology.input.Version

id - Variable in class au.csiro.ontology.model.NamedConcept

String identifier of this concept.

id - Variable in class au.csiro.ontology.model.NamedRole

String identifier of this concept.

id - Variable in class au.csiro.ontology.Ontology

The id of the ontology.

id - Variable in class au.csiro.ontology.snomed.refset.rf2.ModuleDependency

id - Variable in class au.csiro.ontology.snomed.refset.rf2.ModuleDependencyRow

id - Variable in class au.csiro.ontology.snomed.refset.rf2.Refset

id - Variable in class au.csiro.ontology.snomed.refset.rf2.RefsetRow

identifiersFiles - Variable in class au.csiro.ontology.input.RF2Input

IModuleDependencyRefset - Interface in au.csiro.ontology.snomed.refset.rf2

inferredAxioms - Variable in class au.csiro.ontology.Ontology

The collection of inferred axioms that form the ontology.

Input - Class in au.csiro.ontology.input

Base class for inputs.

Input() - Constructor for class au.csiro.ontology.input.Input

Input.InputType - Enum in au.csiro.ontology.input

Indicates if the files should be loaded from an external file system or the class path.

Inputs - Class in au.csiro.ontology.input

This class is able to process a configuration file that specifies a set of input ontologies potentially in different formats.

Inputs() - Constructor for class au.csiro.ontology.input.Inputs

Constructor.

inputs - Variable in class au.csiro.ontology.input.Inputs

List of input files.

Inputs.ReleaseType - Enum in au.csiro.ontology.input

Indicates the type of SNOMED release.

InputsUtil - Class in au.csiro.ontology.input

Utility class to create XML input file programmatically.

InputsUtil() - Constructor for class au.csiro.ontology.input.InputsUtil

inputType - Variable in class au.csiro.ontology.input.Input

INSTANCE - Static variable in class au.csiro.ontology.util.SnomedMetadata

INSTANCE - Static variable in class au.csiro.ontology.util.Statistics

Singleton instance.

IntegerLiteral - Class in au.csiro.ontology.model

This class represents an integer literal.

IntegerLiteral() - Constructor for class au.csiro.ontology.model.IntegerLiteral

IntegerLiteral(int) - Constructor for class au.csiro.ontology.model.IntegerLiteral

Constructor.

IProgressMonitor - Interface in au.csiro.ontology.util

This interface should be implemented by objects that wish to monitor the progress of a task.

IReasoner - Interface in au.csiro.ontology.classification

This interface represents the functionality of a reasoner.

IRefset - Interface in au.csiro.ontology.snomed.refset.rf2

An RF2 reference set.

isActive() - Method in class au.csiro.ontology.snomed.refset.rf2.ModuleDependencyRow

isClassified() - Method in interface au.csiro.ontology.classification.IReasoner

Determines if the ontology has been classified.

iterator() - Method in class au.csiro.ontology.Taxonomy

Deprecated.

Returns an Iterator for all the nodes in the Taxonomy.

L

languageRefsetFiles - Variable in class au.csiro.ontology.input.RF2Input

lastAffectedNodes - Variable in class au.csiro.ontology.Ontology

Set of Nodes potentially affected by the last incremental classification.

lhs - Variable in class au.csiro.ontology.model.RoleInclusion

The left hand side of the expression.

Literal - Class in au.csiro.ontology.model

This interface represents a literal (also known as a Literal in OWL).

Literal() - Constructor for class au.csiro.ontology.model.Literal

load(InputStream) - Static method in class au.csiro.ontology.input.Inputs

Loads an Inputs object from am XML file.

loadAxioms(Set<Axiom>) - Method in interface au.csiro.ontology.classification.IReasoner

Loads and indexes the supplied axioms.

loadAxioms(Iterator<Axiom>) - Method in interface au.csiro.ontology.classification.IReasoner

Loads and indexes the supplied axioms.

loadAxioms(Ontology) - Method in interface au.csiro.ontology.classification.IReasoner

Loads and indexes the supplied axioms.

LongLiteral - Class in au.csiro.ontology.model

This class represents a long literal.

LongLiteral() - Constructor for class au.csiro.ontology.model.LongLiteral

LongLiteral(long) - Constructor for class au.csiro.ontology.model.LongLiteral

M

main(String[]) - Static method in class au.csiro.ontology.input.InputsUtil

metadata - Variable in class au.csiro.ontology.input.Version

moduleDependenciesRefsetFiles - Variable in class au.csiro.ontology.input.RF2Input

ModuleDependency - Class in au.csiro.ontology.snomed.refset.rf2

Contains information about modules and their dependencies.

ModuleDependency(String, String) - Constructor for class au.csiro.ontology.snomed.refset.rf2.ModuleDependency

Creates a new module.

ModuleDependencyRefset - Class in au.csiro.ontology.snomed.refset.rf2

This class represents a module dependency reference set.

ModuleDependencyRefset(Set<ModuleDependencyRow>, boolean) - Constructor for class au.csiro.ontology.snomed.refset.rf2.ModuleDependencyRefset

Creates a new module dependency reference set.

ModuleDependencyRow - Class in au.csiro.ontology.snomed.refset.rf2

Simple implementation of a module dependency refset member.

ModuleDependencyRow(String, String, boolean, String, String, String, String, String) - Constructor for class au.csiro.ontology.snomed.refset.rf2.ModuleDependencyRow

moduleId - Variable in class au.csiro.ontology.snomed.refset.rf2.ModuleDependencyRow

moduleId - Variable in class au.csiro.ontology.snomed.refset.rf2.RefsetRow

ModuleInfo - Class in au.csiro.ontology.input

Contains a module id and a list of versions that should be imported.

ModuleInfo() - Constructor for class au.csiro.ontology.input.ModuleInfo

ModuleInfo(String) - Constructor for class au.csiro.ontology.input.ModuleInfo

modules - Variable in class au.csiro.ontology.input.RF2Input

N

NamedConcept - Class in au.csiro.ontology.model

This class represents a named concept (also referred to as a class in OWL).

NamedConcept() - Constructor for class au.csiro.ontology.model.NamedConcept

No args constructor.

NamedConcept(String) - Constructor for class au.csiro.ontology.model.NamedConcept

Creates a new Concept.

NamedFeature - Class in au.csiro.ontology.model

This class represents a feature (also referred to as a data property in OWL).

NamedFeature() - Constructor for class au.csiro.ontology.model.NamedFeature

NamedFeature(String) - Constructor for class au.csiro.ontology.model.NamedFeature

Creates a new Concept.

NamedRole - Class in au.csiro.ontology.model

This class represents a role (also referred to as an object property in OWL).

NamedRole() - Constructor for class au.csiro.ontology.model.NamedRole

NamedRole(String) - Constructor for class au.csiro.ontology.model.NamedRole

Creates a new Role.

neverGroupedIds - Variable in class au.csiro.ontology.util.SnomedMetadata

Node - Class in au.csiro.ontology

Represents a node in the taxonomy generated after classifying an ontology.

Node() - Constructor for class au.csiro.ontology.Node

nodeIterator() - Method in class au.csiro.ontology.Ontology

nodeMap - Variable in class au.csiro.ontology.Ontology

A map that contains references to all the nodes in the taxonomy indexed by id.

nodeMap - Variable in class au.csiro.ontology.Taxonomy

Deprecated.

A map that contains references to all the nodes in the taxonomy indexed by id.

NullProgressMonitor - Class in au.csiro.ontology.util

Implementation of IProgressMonitor that does nothing.

NullProgressMonitor() - Constructor for class au.csiro.ontology.util.NullProgressMonitor

O

Ontology - Class in au.csiro.ontology

Represents an ontology in our internal format.

Ontology(String, String, Collection<Axiom>, Map<String, Node>, Set<Node>) - Constructor for class au.csiro.ontology.Ontology

Builds a new ontology.

Ontology(String, String, Collection<Axiom>, Map<String, Node>) - Constructor for class au.csiro.ontology.Ontology

Builds a new ontology.

Operator - Enum in au.csiro.ontology.model

orderedRefsetFiles - Variable in class au.csiro.ontology.input.RF2Input

owlAxiomRefsetFiles - Variable in class au.csiro.ontology.input.RF2Input

owlFile - Variable in class au.csiro.ontology.input.OWLInput

OWLInput - Class in au.csiro.ontology.input

OWLInput() - Constructor for class au.csiro.ontology.input.OWLInput

owlOntologyRefsetFiles - Variable in class au.csiro.ontology.input.RF2Input

P

parents - Variable in class au.csiro.ontology.Node

Set of parents nodes.

props - Variable in class au.csiro.ontology.util.SnomedMetadata

prune() - Method in interface au.csiro.ontology.classification.IReasoner

Removes all the state in the classifier except the taxonomy generated after classification.

Q

querySpecificationRefsetFiles - Variable in class au.csiro.ontology.input.RF2Input

R

referencedComponentId - Variable in class au.csiro.ontology.snomed.refset.rf2.ModuleDependencyRow

referencedComponentId - Variable in class au.csiro.ontology.snomed.refset.rf2.RefsetRow

Refset - Class in au.csiro.ontology.snomed.refset.rf2

Refset() - Constructor for class au.csiro.ontology.snomed.refset.rf2.Refset

refsetDescriptorRefsetFiles - Variable in class au.csiro.ontology.input.RF2Input

refsetId - Variable in class au.csiro.ontology.snomed.refset.rf2.ModuleDependencyRow

refsetId - Variable in class au.csiro.ontology.snomed.refset.rf2.RefsetRow

RefsetRow - Class in au.csiro.ontology.snomed.refset.rf2

RefsetRow(String, String, String, String, String, String, String...) - Constructor for class au.csiro.ontology.snomed.refset.rf2.RefsetRow

Constructor.

relationshipsFiles - Variable in class au.csiro.ontology.input.RF2Input

releaseType - Variable in class au.csiro.ontology.input.RF2Input

RF2Input - Class in au.csiro.ontology.input

An RF set of input files.

RF2Input() - Constructor for class au.csiro.ontology.input.RF2Input

Constructor.

rhs - Variable in class au.csiro.ontology.model.RoleInclusion

The right hand side of the expression.

rightIdentities - Variable in class au.csiro.ontology.util.SnomedMetadata

Role - Class in au.csiro.ontology.model

Base class for features.

Role() - Constructor for class au.csiro.ontology.model.Role

RoleInclusion - Class in au.csiro.ontology.model

This class represents a role inclusion axiom (also known as a SubObjectPropertyOf axiom in OWL).

RoleInclusion() - Constructor for class au.csiro.ontology.model.RoleInclusion

RoleInclusion(Role[], Role) - Constructor for class au.csiro.ontology.model.RoleInclusion

Creates a new RoleInclusion.

RoleInclusion(Role, Role) - Constructor for class au.csiro.ontology.model.RoleInclusion

Creates a new RoleInclusion.

S

save(OutputStream) - Method in interface au.csiro.ontology.classification.IReasoner

Saves this reasoner to the specified OutputStream.

serialise(Axiom) - Static method in class au.csiro.ontology.util.AxiomUtils

Transforms an axiom into a String representation.

serialiseConcept(Concept) - Static method in class au.csiro.ontology.util.AxiomUtils

Transforms a concept into a String representation.

serialiseLiteral(Literal) - Static method in class au.csiro.ontology.util.AxiomUtils

setAffectedNodes(Set<Node>) - Method in class au.csiro.ontology.Ontology

setAnnotationRefsetFiles(Set<String>) - Method in class au.csiro.ontology.input.RF2Input

setAssociationRefsetFiles(Set<String>) - Method in class au.csiro.ontology.input.RF2Input

setAttributeDomainRefsetFiles(Set<String>) - Method in class au.csiro.ontology.input.RF2Input

setAttributeValueRefsetFiles(Set<String>) - Method in class au.csiro.ontology.input.RF2Input

setBase(String) - Method in class au.csiro.ontology.input.Input

setComplexMapRefsetFiles(Set<String>) - Method in class au.csiro.ontology.input.RF2Input

setConcept(Concept) - Method in class au.csiro.ontology.model.Existential

setConcepts(Concept[]) - Method in class au.csiro.ontology.model.Conjunction

setConceptsFiles(Set<String>) - Method in class au.csiro.ontology.input.RF2Input

setConcreteDomainRefsetFiles(Set<String>) - Method in class au.csiro.ontology.input.RF2Input

setDescriptionFormatRefsetFiles(Set<String>) - Method in class au.csiro.ontology.input.RF2Input

setDescriptionsFiles(Set<String>) - Method in class au.csiro.ontology.input.RF2Input

setDisplayName(String) - Method in interface au.csiro.ontology.snomed.refset.rf2.IRefset

Sets the display name for this reference set.

setDisplayName(String) - Method in class au.csiro.ontology.snomed.refset.rf2.Refset

setFeature(Feature) - Method in class au.csiro.ontology.model.Datatype

setFeature(Feature) - Method in class au.csiro.ontology.model.FunctionalFeature

setId(String) - Method in class au.csiro.ontology.input.ModuleInfo

setId(String) - Method in class au.csiro.ontology.input.Version

setId(String) - Method in class au.csiro.ontology.model.NamedConcept

setId(String) - Method in class au.csiro.ontology.model.NamedFeature

setId(String) - Method in class au.csiro.ontology.model.NamedRole

setIdentifiersFiles(Set<String>) - Method in class au.csiro.ontology.input.RF2Input

setInputs(List<Input>) - Method in class au.csiro.ontology.input.Inputs

setInputType(Input.InputType) - Method in class au.csiro.ontology.input.Input

setLanguageRefsetFiles(Set<String>) - Method in class au.csiro.ontology.input.RF2Input

setLhs(Concept) - Method in class au.csiro.ontology.model.ConceptInclusion

setLhs(Role[]) - Method in class au.csiro.ontology.model.RoleInclusion

setLiteral(Literal) - Method in class au.csiro.ontology.model.Datatype

setMetadata(Map<String, String>) - Method in class au.csiro.ontology.input.Version

setModuleDependenciesRefsetFiles(Set<String>) - Method in class au.csiro.ontology.input.RF2Input

setModules(List<ModuleInfo>) - Method in class au.csiro.ontology.input.RF2Input

setNodeMap(Map<String, Node>) - Method in class au.csiro.ontology.Ontology

setOperator(Operator) - Method in class au.csiro.ontology.model.Datatype

setOrderedRefsetFiles(Set<String>) - Method in class au.csiro.ontology.input.RF2Input

setOwlAxiomRefsetFiles(Set<String>) - Method in class au.csiro.ontology.input.RF2Input

setOwlFile(String) - Method in class au.csiro.ontology.input.OWLInput

setOwlOntologyRefsetFiles(Set<String>) - Method in class au.csiro.ontology.input.RF2Input

setOwlReasonerFactory(String) - Method in class au.csiro.ontology.input.OWLInput

setQuerySpecificationRefsetFiles(Set<String>) - Method in class au.csiro.ontology.input.RF2Input

setRefsetDescriptorRefsetFiles(Set<String>) - Method in class au.csiro.ontology.input.RF2Input

setRelationshipsFiles(Set<String>) - Method in class au.csiro.ontology.input.RF2Input

setReleaseType(Inputs.ReleaseType) - Method in class au.csiro.ontology.input.RF2Input

setRhs(Concept) - Method in class au.csiro.ontology.model.ConceptInclusion

setRhs(Role) - Method in class au.csiro.ontology.model.RoleInclusion

setRole(Role) - Method in class au.csiro.ontology.model.Existential

setSimpleMapRefsetFiles(Set<String>) - Method in class au.csiro.ontology.input.RF2Input

setSimpleRefsetFiles(Set<String>) - Method in class au.csiro.ontology.input.RF2Input

setStatedRelationshipsFiles(Set<String>) - Method in class au.csiro.ontology.input.RF2Input

setTextDefinitionsFile(Set<String>) - Method in class au.csiro.ontology.input.RF2Input

setTime(String, long) - Method in class au.csiro.ontology.util.Statistics

Sets a time for a performance measurement.

setValue(BigInteger) - Method in class au.csiro.ontology.model.BigIntegerLiteral

setValue(boolean) - Method in class au.csiro.ontology.model.BooleanLiteral

Deprecated.

setValue(Calendar) - Method in class au.csiro.ontology.model.DateLiteral

setValue(BigDecimal) - Method in class au.csiro.ontology.model.DecimalLiteral

setValue(double) - Method in class au.csiro.ontology.model.DoubleLiteral

Deprecated.

setValue(float) - Method in class au.csiro.ontology.model.FloatLiteral

setValue(int) - Method in class au.csiro.ontology.model.IntegerLiteral

setValue(long) - Method in class au.csiro.ontology.model.LongLiteral

setValue(String) - Method in class au.csiro.ontology.model.StringLiteral

setVersions(List<Version>) - Method in class au.csiro.ontology.input.ModuleInfo

simpleMapRefsetFiles - Variable in class au.csiro.ontology.input.RF2Input

simpleRefsetFiles - Variable in class au.csiro.ontology.input.RF2Input

SnomedMetadata - Class in au.csiro.ontology.util

This class contains the default meta-data that is necessary to successfully import the SNOMED distribution files into a DL model.

sourceEffectiveTime - Variable in class au.csiro.ontology.snomed.refset.rf2.ModuleDependencyRow

statedAxioms - Variable in class au.csiro.ontology.Ontology

The collection of stated axioms that form the ontology.

statedRelationshipsFiles - Variable in class au.csiro.ontology.input.RF2Input

Statistics - Class in au.csiro.ontology.util

Generic class used to collect performance statistics.

Stats() - Constructor for class au.csiro.ontology.util.Traversal.Stats

step(int, int) - Method in interface au.csiro.ontology.util.IProgressMonitor

Indicates that there has been progress in a task.

step(int, int) - Method in class au.csiro.ontology.util.NullProgressMonitor

StringLiteral - Class in au.csiro.ontology.model

This class represents a literal that is best stored as a Java string.

StringLiteral() - Constructor for class au.csiro.ontology.model.StringLiteral

StringLiteral(String) - Constructor for class au.csiro.ontology.model.StringLiteral

T

targetEffectiveTime - Variable in class au.csiro.ontology.snomed.refset.rf2.ModuleDependencyRow

taskBusy() - Method in interface au.csiro.ontology.util.IProgressMonitor

Indicates that there is a task in progress whose length cannot be determined.

taskBusy() - Method in class au.csiro.ontology.util.NullProgressMonitor

taskEnded() - Method in interface au.csiro.ontology.util.IProgressMonitor

Indicates that the previously started task has now ended.

taskEnded() - Method in class au.csiro.ontology.util.NullProgressMonitor

taskStarted(String) - Method in interface au.csiro.ontology.util.IProgressMonitor

Indicates that some task has started.

taskStarted(String) - Method in class au.csiro.ontology.util.NullProgressMonitor

Taxonomy - Class in au.csiro.ontology

Deprecated.

Use IOntology instead.

Taxonomy(Map<String, Node>) - Constructor for class au.csiro.ontology.Taxonomy

Deprecated.

Creates a new Taxonomy.

textDefinitionsFiles - Variable in class au.csiro.ontology.input.RF2Input

TOP - Static variable in class au.csiro.ontology.model.NamedConcept

Represents the top concept.

TOP_CONCEPT - Static variable in class au.csiro.ontology.model.NamedConcept

The top concept.

toString() - Method in class au.csiro.ontology.model.BigIntegerLiteral

toString() - Method in class au.csiro.ontology.model.BooleanLiteral

Deprecated.

toString() - Method in class au.csiro.ontology.model.Concept

toString() - Method in class au.csiro.ontology.model.ConceptInclusion

toString() - Method in class au.csiro.ontology.model.Conjunction

toString() - Method in class au.csiro.ontology.model.Datatype

toString() - Method in class au.csiro.ontology.model.DateLiteral

toString() - Method in class au.csiro.ontology.model.DecimalLiteral

toString() - Method in class au.csiro.ontology.model.DoubleLiteral

Deprecated.

toString() - Method in class au.csiro.ontology.model.Existential

toString() - Method in class au.csiro.ontology.model.Feature

toString() - Method in class au.csiro.ontology.model.FloatLiteral

toString() - Method in class au.csiro.ontology.model.IntegerLiteral

toString() - Method in class au.csiro.ontology.model.Literal

toString() - Method in class au.csiro.ontology.model.LongLiteral

toString() - Method in class au.csiro.ontology.model.NamedConcept

toString() - Method in class au.csiro.ontology.model.NamedFeature

toString() - Method in class au.csiro.ontology.model.NamedRole

toString() - Method in class au.csiro.ontology.model.Role

toString() - Method in class au.csiro.ontology.model.RoleInclusion

toString() - Method in class au.csiro.ontology.model.StringLiteral

toString() - Method in class au.csiro.ontology.Node

toString() - Method in class au.csiro.ontology.snomed.refset.rf2.ModuleDependency

toString() - Method in class au.csiro.ontology.snomed.refset.rf2.ModuleDependencyRow

Traversal - Interface in au.csiro.ontology.util

Traversal.Stats - Class in au.csiro.ontology.util

Traversal.Visitor - Interface in au.csiro.ontology.util

V

ValidationException - Exception in au.csiro.ontology.snomed.refset.rf2

ValidationException(String, Collection<String>) - Constructor for exception au.csiro.ontology.snomed.refset.rf2.ValidationException

valueOf(String) - Static method in enum au.csiro.ontology.input.Input.InputType

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

valueOf(String) - Static method in enum au.csiro.ontology.input.Inputs.ReleaseType

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

valueOf(String) - Static method in enum au.csiro.ontology.model.Operator

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

values() - Static method in enum au.csiro.ontology.input.Input.InputType

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

values() - Static method in enum au.csiro.ontology.input.Inputs.ReleaseType

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

values() - Static method in enum au.csiro.ontology.model.Operator

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

Version - Class in au.csiro.ontology.input

Contains the id of a version and the meta-data associated with it.

Version() - Constructor for class au.csiro.ontology.input.Version

Version(String) - Constructor for class au.csiro.ontology.input.Version

version - Variable in class au.csiro.ontology.Ontology

The version of the ontology.

version - Variable in class au.csiro.ontology.snomed.refset.rf2.ModuleDependency

versions - Variable in class au.csiro.ontology.input.ModuleInfo

visit(Node) - Method in interface au.csiro.ontology.util.Traversal.Visitor

Z

zip - Variable in class au.csiro.ontology.input.Input

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