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

A

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

au.csiro.ontology.importer.owl - package au.csiro.ontology.importer.owl

au.csiro.ontology.importer.rf1 - package au.csiro.ontology.importer.rf1

au.csiro.ontology.importer.rf2 - package au.csiro.ontology.importer.rf2

B

BaseImporter - Class in au.csiro.ontology.importer

BaseImporter() - Constructor for class au.csiro.ontology.importer.BaseImporter

BaseImporter.ImportEntry - Class in au.csiro.ontology.importer

BaseImporter.ImportEntry(String, String, Map<String, String>, Set<BaseImporter.Module>, Input) - Constructor for class au.csiro.ontology.importer.BaseImporter.ImportEntry

BaseImporter.Module - Class in au.csiro.ontology.importer

BaseImporter.Module(String, String) - Constructor for class au.csiro.ontology.importer.BaseImporter.Module

build() - Method in class au.csiro.ontology.importer.rf2.RF2Importer.OntologyBuilder

C

cdsMap - Variable in class au.csiro.ontology.importer.rf2.RF2Importer.OntologyBuilder

children - Variable in class au.csiro.ontology.importer.rf1.RF1Importer

children - Variable in class au.csiro.ontology.importer.rf2.RF2Importer.OntologyBuilder

ci - Variable in class au.csiro.ontology.importer.rf2.RF2Importer.OntologyBuilder

clear() - Method in class au.csiro.ontology.importer.owl.OWLImporter

Clears all the state in the importer.

clear() - Method in class au.csiro.ontology.importer.rf1.RF1Importer

compareTo(ConceptRow) - Method in class au.csiro.ontology.importer.rf2.ConceptRow

compareTo(DescriptionRow) - Method in class au.csiro.ontology.importer.rf2.DescriptionRow

compareTo(RelationshipRow) - Method in class au.csiro.ontology.importer.rf2.RelationshipRow

conceptDefinedId - Variable in class au.csiro.ontology.importer.rf2.RF2Importer.OntologyBuilder

conceptModelAttId - Variable in class au.csiro.ontology.importer.rf2.RF2Importer.OntologyBuilder

ConceptRow - Class in au.csiro.ontology.importer.rf1

Represents a row in an RF1 concepts file.

ConceptRow(String, String, String, String, String, String) - Constructor for class au.csiro.ontology.importer.rf1.ConceptRow

Creates a new ConceptRow.

ConceptRow - Class in au.csiro.ontology.importer.rf2

Represents a row in an RF2 concepts file.

ConceptRow(String, String, String, String, String) - Constructor for class au.csiro.ontology.importer.rf2.ConceptRow

Creates a new ConceptRow.

conceptRows - Variable in class au.csiro.ontology.importer.rf1.VersionRows

The concept rows in this version.

conceptRows - Variable in class au.csiro.ontology.importer.rf2.VersionRows

The concept rows in this version.

conceptsFile - Variable in class au.csiro.ontology.importer.rf1.RF1Importer

concreteDomainRows - Variable in class au.csiro.ontology.importer.rf2.VersionRows

The concrete domains reference set rows in this version.

D

definitionId - Variable in class au.csiro.ontology.importer.rf2.RF2Importer.OntologyBuilder

DescriptionRow - Class in au.csiro.ontology.importer.rf1

Represents a row in an RF1 descriptions file.

DescriptionRow(String, String, String, String, String, String, String) - Constructor for class au.csiro.ontology.importer.rf1.DescriptionRow

Creates a new DescriptionRow.

DescriptionRow - Class in au.csiro.ontology.importer.rf2

Represents a row in an RF2 descriptions file.

DescriptionRow(String, String, String, String, String, String, String, String, String) - Constructor for class au.csiro.ontology.importer.rf2.DescriptionRow

Creates a new DescriptionRow.

descriptionRows - Variable in class au.csiro.ontology.importer.rf1.VersionRows

The description rows in this version.

E

equals(Object) - Method in class au.csiro.ontology.importer.rf1.RF1Importer.RoleValuePair

equals(Object) - Method in class au.csiro.ontology.importer.rf2.ConceptRow

equals(Object) - Method in class au.csiro.ontology.importer.rf2.DescriptionRow

equals(Object) - Method in class au.csiro.ontology.importer.rf2.RelationshipRow

equals(Object) - Method in class au.csiro.ontology.importer.rf2.RF2Importer.RoleValuePair

equalsOperatorId - Variable in class au.csiro.ontology.importer.rf2.RF2Importer.OntologyBuilder

extractVersionRows() - Method in class au.csiro.ontology.importer.rf1.RF1Importer

Processes the raw RF1 files and generates a VersionRows.

F

featureType - Variable in class au.csiro.ontology.importer.rf2.RF2Importer.OntologyBuilder

fi - Variable in class au.csiro.ontology.importer.rf2.RF2Importer.OntologyBuilder

fsnId - Variable in class au.csiro.ontology.importer.rf2.RF2Importer.OntologyBuilder

G

getActive() - Method in class au.csiro.ontology.importer.rf2.ConceptRow

getActive() - Method in class au.csiro.ontology.importer.rf2.DescriptionRow

getActive() - Method in class au.csiro.ontology.importer.rf2.RelationshipRow

getBundle(BaseImporter.ImportEntry) - Method in class au.csiro.ontology.importer.rf2.RF2Importer

Returns a VersionRows object for an ImportEntry.

getCaseSignificanceId() - Method in class au.csiro.ontology.importer.rf2.DescriptionRow

getCharacteristicType() - Method in class au.csiro.ontology.importer.rf1.RelationshipRow

getCharacteristicTypeId() - Method in class au.csiro.ontology.importer.rf2.RelationshipRow

getConcept(String, Map<String, Concept>) - Method in class au.csiro.ontology.importer.rf2.RF2Importer

getConceptId() - Method in class au.csiro.ontology.importer.rf1.ConceptRow

getConceptId() - Method in class au.csiro.ontology.importer.rf1.DescriptionRow

getConceptId() - Method in class au.csiro.ontology.importer.rf2.DescriptionRow

getConceptId1() - Method in class au.csiro.ontology.importer.rf1.RelationshipRow

getConceptId2() - Method in class au.csiro.ontology.importer.rf1.RelationshipRow

getConceptRows() - Method in class au.csiro.ontology.importer.rf1.VersionRows

getConceptRows() - Method in class au.csiro.ontology.importer.rf2.VersionRows

getConceptStatus() - Method in class au.csiro.ontology.importer.rf1.ConceptRow

getConcreteDomainRows() - Method in class au.csiro.ontology.importer.rf2.VersionRows

getCtv3Id() - Method in class au.csiro.ontology.importer.rf1.ConceptRow

getDefinitionStatusId() - Method in class au.csiro.ontology.importer.rf2.ConceptRow

getDescriptionId() - Method in class au.csiro.ontology.importer.rf1.DescriptionRow

getDescriptionRows() - Method in class au.csiro.ontology.importer.rf1.VersionRows

getDescriptionStatus() - Method in class au.csiro.ontology.importer.rf1.DescriptionRow

getDescriptionType() - Method in class au.csiro.ontology.importer.rf1.DescriptionRow

getDestinationId() - Method in class au.csiro.ontology.importer.rf2.RelationshipRow

getEffectiveTime() - Method in class au.csiro.ontology.importer.rf2.ConceptRow

getEffectiveTime() - Method in class au.csiro.ontology.importer.rf2.DescriptionRow

getEffectiveTime() - Method in class au.csiro.ontology.importer.rf2.RelationshipRow

getFeature(String, Map<String, NamedFeature>) - Method in class au.csiro.ontology.importer.rf2.RF2Importer

getFullySpecifiedName() - Method in class au.csiro.ontology.importer.rf1.ConceptRow

getId() - Method in class au.csiro.ontology.importer.rf2.ConceptRow

getId() - Method in class au.csiro.ontology.importer.rf2.DescriptionRow

getId() - Method in class au.csiro.ontology.importer.rf2.Module

getId() - Method in class au.csiro.ontology.importer.rf2.RelationshipRow

getInitialCapitalStatus() - Method in class au.csiro.ontology.importer.rf1.DescriptionRow

getInput() - Method in class au.csiro.ontology.importer.BaseImporter.ImportEntry

getIsPrimitive() - Method in class au.csiro.ontology.importer.rf1.ConceptRow

getLanguageCode() - Method in class au.csiro.ontology.importer.rf1.DescriptionRow

getLanguageCode() - Method in class au.csiro.ontology.importer.rf2.DescriptionRow

getMetadata() - Method in class au.csiro.ontology.importer.BaseImporter.ImportEntry

getMetadata() - Method in class au.csiro.ontology.importer.rf1.RF1Importer

getModifierId() - Method in class au.csiro.ontology.importer.rf2.RelationshipRow

getModuleId() - Method in class au.csiro.ontology.importer.BaseImporter.Module

getModuleId() - Method in class au.csiro.ontology.importer.rf2.ConceptRow

getModuleId() - Method in class au.csiro.ontology.importer.rf2.DescriptionRow

getModuleId() - Method in class au.csiro.ontology.importer.rf2.RelationshipRow

getModules() - Method in class au.csiro.ontology.importer.BaseImporter.ImportEntry

getModuleVersion() - Method in class au.csiro.ontology.importer.BaseImporter.Module

getModuleVersionsToLoad(RF2Input) - Method in class au.csiro.ontology.importer.rf2.RF2Importer

Determines which modules and versions should be loaded based on the Inputs object.

getOntologyBuilder(VersionRows, String, String, Map<String, String>) - Method in class au.csiro.ontology.importer.rf2.RF2Importer

Hook method for subclasses to override.

getOntologyVersions(IProgressMonitor) - Method in interface au.csiro.ontology.importer.IImporter

There are several models used to represent ontologies that have been adopted by different groups.

getOntologyVersions(IProgressMonitor) - Method in class au.csiro.ontology.importer.owl.OWLImporter

getOntologyVersions(IProgressMonitor) - Method in class au.csiro.ontology.importer.rf1.RF1Importer

getOntologyVersions(IProgressMonitor) - Method in class au.csiro.ontology.importer.rf2.RF2Importer

getProblems() - Method in interface au.csiro.ontology.importer.IImporter

Returns a list of problems that happened during the import process.

getProblems() - Method in class au.csiro.ontology.importer.owl.OWLImporter

getProblems() - Method in class au.csiro.ontology.importer.rf1.RF1Importer

getProblems() - Method in class au.csiro.ontology.importer.rf2.RF2Importer

getRefinability() - Method in class au.csiro.ontology.importer.rf1.RelationshipRow

getRelationshipGroup() - Method in class au.csiro.ontology.importer.rf1.RelationshipRow

getRelationshipGroup() - Method in class au.csiro.ontology.importer.rf2.RelationshipRow

getRelationshipId() - Method in class au.csiro.ontology.importer.rf1.RelationshipRow

getRelationshipRows() - Method in class au.csiro.ontology.importer.rf1.VersionRows

getRelationshipRows() - Method in class au.csiro.ontology.importer.rf2.VersionRows

getRelationshipType() - Method in class au.csiro.ontology.importer.rf1.RelationshipRow

getRole(String, Map<String, NamedRole>) - Method in class au.csiro.ontology.importer.rf2.RF2Importer

getRootModuleId() - Method in class au.csiro.ontology.importer.BaseImporter.ImportEntry

getRootModuleVersion() - Method in class au.csiro.ontology.importer.BaseImporter.ImportEntry

getSnomedId() - Method in class au.csiro.ontology.importer.rf1.ConceptRow

getSourceId() - Method in class au.csiro.ontology.importer.rf2.RelationshipRow

getTerm() - Method in class au.csiro.ontology.importer.rf1.DescriptionRow

getTerm() - Method in class au.csiro.ontology.importer.rf2.DescriptionRow

getTypeId() - Method in class au.csiro.ontology.importer.rf2.DescriptionRow

getTypeId() - Method in class au.csiro.ontology.importer.rf2.RelationshipRow

getVersionName() - Method in class au.csiro.ontology.importer.rf1.VersionRows

Returns the name of this version.

getVersions() - Method in class au.csiro.ontology.importer.rf2.Module

groupRoles(List<String[]>) - Method in class au.csiro.ontology.importer.rf1.RF1Importer

groupRoles(List<String[]>) - Method in class au.csiro.ontology.importer.rf2.RF2Importer

H

hashCode() - Method in class au.csiro.ontology.importer.rf1.RF1Importer.RoleValuePair

hashCode() - Method in class au.csiro.ontology.importer.rf2.ConceptRow

hashCode() - Method in class au.csiro.ontology.importer.rf2.DescriptionRow

hashCode() - Method in class au.csiro.ontology.importer.rf2.RelationshipRow

hashCode() - Method in class au.csiro.ontology.importer.rf2.RF2Importer.RoleValuePair

I

id - Variable in class au.csiro.ontology.importer.rf2.Module

The id of this module.

IImporter - Interface in au.csiro.ontology.importer

Defines the methods that must be implemented by classes used to import ontologies defined in external formats into our internal format.

ImportException - Exception in au.csiro.ontology.importer

Exception thrown to indicate that a problem was found when importing a set of axioms into our internal format.

ImportException(String) - Constructor for exception au.csiro.ontology.importer.ImportException

ImportException(String, Throwable) - Constructor for exception au.csiro.ontology.importer.ImportException

importModuleDependencyRefset(Set<InputStream>) - Static method in class au.csiro.ontology.importer.rf2.RefsetImporter

Imports a module dependency reference set from a Set of InputStreams.

inputs - Variable in class au.csiro.ontology.importer.rf2.RF2Importer

Queue with the inputs to process.

isActive(String) - Method in class au.csiro.ontology.importer.rf2.RF2Importer.OntologyBuilder

isAId - Variable in class au.csiro.ontology.importer.rf2.RF2Importer.OntologyBuilder

isUseSimpleFloats() - Method in class au.csiro.ontology.importer.owl.OWLImporter

isUseSimpleInts() - Method in class au.csiro.ontology.importer.owl.OWLImporter

L

lateralityId - Variable in class au.csiro.ontology.importer.rf2.RF2Importer.OntologyBuilder

lateralizableConcepts - Variable in class au.csiro.ontology.importer.rf2.RF2Importer.OntologyBuilder

loadConceptRows(Map<String, String>, Map<String, ConceptRow>, InputStream) - Method in class au.csiro.ontology.importer.rf2.RF2Importer

loadModuleDependencies(RF2Input) - Method in class au.csiro.ontology.importer.rf2.RF2Importer

Loads all the module dependency information from all RF2 inputs into a single IModuleDependencyRefset.

loadReferenceSet(RF2Input, String, Map<String, String>, Map<String, R>, IRefsetFactory<R>) - Method in class au.csiro.ontology.importer.rf2.RF2Importer

loadRelationshipRows(Map<String, String>, Map<String, RelationshipRow>, InputStream) - Method in class au.csiro.ontology.importer.rf2.RF2Importer

M

mapDatatype(List<Concept>, String[]) - Method in class au.csiro.ontology.importer.rf2.RF2Importer.OntologyBuilder

mapRoles(List<Concept>, Set<RF2Importer.RoleValuePair>) - Method in class au.csiro.ontology.importer.rf2.RF2Importer.OntologyBuilder

measurementTypeFloat - Variable in class au.csiro.ontology.importer.rf2.RF2Importer.OntologyBuilder

measurementTypeInt - Variable in class au.csiro.ontology.importer.rf2.RF2Importer.OntologyBuilder

merge(VersionRows) - Method in class au.csiro.ontology.importer.rf2.VersionRows

Merges another VersionRows into this.

metadata - Variable in class au.csiro.ontology.importer.rf1.RF1Importer

Contains the meta-data necessary to transform the distribution form of SNOMED into a DL model.

Module - Class in au.csiro.ontology.importer.rf2

Represents an RF2 module.

Module(String) - Constructor for class au.csiro.ontology.importer.rf2.Module

Creates a new module.

N

neverGroupedIds - Variable in class au.csiro.ontology.importer.rf2.RF2Importer.OntologyBuilder

neverGroupedIdsString - Variable in class au.csiro.ontology.importer.rf2.RF2Importer.OntologyBuilder

NOTHING_IRI - Static variable in class au.csiro.ontology.importer.owl.OWLImporter

O

OWLImporter - Class in au.csiro.ontology.importer.owl

Imports axioms in OWL format into the internal representation used by Snorocket.

OWLImporter(OWLOntology) - Constructor for class au.csiro.ontology.importer.owl.OWLImporter

OWLImporter(List<OWLAxiom>) - Constructor for class au.csiro.ontology.importer.owl.OWLImporter

P

parents - Variable in class au.csiro.ontology.importer.rf1.RF1Importer

parents - Variable in class au.csiro.ontology.importer.rf2.RF2Importer.OntologyBuilder

populateCDs(Map<String, List<String[]>>, String, String, String, String, String) - Method in class au.csiro.ontology.importer.rf2.RF2Importer

Populates concrete domains information.

populateChildren(String, String) - Method in class au.csiro.ontology.importer.rf1.RF1Importer

populateChildren(String, String, Map<String, Set<String>>) - Method in class au.csiro.ontology.importer.rf2.RF2Importer

populateInactiveChildren(String, String, Map<String, Set<String>>) - Method in class au.csiro.ontology.importer.rf2.RF2Importer.OntologyBuilder

populateInactiveParent(String, String, Map<String, Set<String>>) - Method in class au.csiro.ontology.importer.rf2.RF2Importer.OntologyBuilder

populateInactiveRels(String, String, String, String, String, Map<String, List<String[]>>) - Method in class au.csiro.ontology.importer.rf2.RF2Importer.OntologyBuilder

populateInactiveRoleDef(String, String, String, Map<String, Map<String, String>>) - Method in class au.csiro.ontology.importer.rf2.RF2Importer.OntologyBuilder

populateInactiveRoles(Set<String>, String, String, String, Map<String, Set<String>>, Map<String, Map<String, String>>) - Method in class au.csiro.ontology.importer.rf2.RF2Importer.OntologyBuilder

populateParent(String, String) - Method in class au.csiro.ontology.importer.rf1.RF1Importer

populateParent(String, String, Map<String, Set<String>>) - Method in class au.csiro.ontology.importer.rf2.RF2Importer

populateRels(String, String, String, String) - Method in class au.csiro.ontology.importer.rf1.RF1Importer

populateRels(String, String, String, String, String, Map<String, List<String[]>>) - Method in class au.csiro.ontology.importer.rf2.RF2Importer

populateRoleDef(String, String, String) - Method in class au.csiro.ontology.importer.rf1.RF1Importer

populateRoleDef(String, String, String, Map<String, Map<String, String>>) - Method in class au.csiro.ontology.importer.rf2.RF2Importer

populateRoles(Set<String>, String) - Method in class au.csiro.ontology.importer.rf1.RF1Importer

populateRoles(Set<String>, String, String, Map<String, Set<String>>, Map<String, Map<String, String>>) - Method in class au.csiro.ontology.importer.rf2.RF2Importer

primitive - Variable in class au.csiro.ontology.importer.rf1.RF1Importer

primitive - Variable in class au.csiro.ontology.importer.rf2.RF2Importer.OntologyBuilder

problems - Variable in class au.csiro.ontology.importer.rf1.RF1Importer

problems - Variable in class au.csiro.ontology.importer.rf2.RF2Importer

List of problems found while importing.

R

RefsetImporter - Class in au.csiro.ontology.importer.rf2

Imports RF2 reference sets.

RefsetImporter() - Constructor for class au.csiro.ontology.importer.rf2.RefsetImporter

RelationshipRow - Class in au.csiro.ontology.importer.rf1

RelationshipRow(String, String, String, String, String, String, String) - Constructor for class au.csiro.ontology.importer.rf1.RelationshipRow

Creates a new RelationshipRow.

RelationshipRow - Class in au.csiro.ontology.importer.rf2

RelationshipRow(String, String, String, String, String, String, String, String, String, String) - Constructor for class au.csiro.ontology.importer.rf2.RelationshipRow

Creates a new RelationshipRow.

relationshipRows - Variable in class au.csiro.ontology.importer.rf1.VersionRows

The relationship rows in this version.

relationshipRows - Variable in class au.csiro.ontology.importer.rf2.VersionRows

The relationship rows in this version.

relationshipsFile - Variable in class au.csiro.ontology.importer.rf1.RF1Importer

rels - Variable in class au.csiro.ontology.importer.rf1.RF1Importer

rels - Variable in class au.csiro.ontology.importer.rf2.RF2Importer.OntologyBuilder

resolveFiller(Concept, String) - Method in class au.csiro.ontology.importer.rf2.RF2Importer.OntologyBuilder

RF1Importer - Class in au.csiro.ontology.importer.rf1

Transforms the native RF1 files used in SNOMED into the internal representation.

RF1Importer(InputStream, InputStream, String) - Constructor for class au.csiro.ontology.importer.rf1.RF1Importer

Creates a new RF1Importer.

RF1Importer.RoleValuePair - Class in au.csiro.ontology.importer.rf1

RF2Importer - Class in au.csiro.ontology.importer.rf2

Imports ontologies specified in RF2 format into the internal representation.

RF2Importer(RF2Input) - Constructor for class au.csiro.ontology.importer.rf2.RF2Importer

Imports an ontology using the supplied configuration object.

RF2Importer(Collection<Input>) - Constructor for class au.csiro.ontology.importer.rf2.RF2Importer

Imports a set of ontologies using the supplied configuration object.

RF2Importer.OntologyBuilder - Class in au.csiro.ontology.importer.rf2

Class that knows how to build an Ontology from a set of RF2 files.

RF2Importer.OntologyBuilder(VersionRows, String, String, Map<String, String>) - Constructor for class au.csiro.ontology.importer.rf2.RF2Importer.OntologyBuilder

RF2Importer.RoleValuePair - Class in au.csiro.ontology.importer.rf2

Represents a role-value pair.

ri - Variable in class au.csiro.ontology.importer.rf2.RF2Importer.OntologyBuilder

rightIdentityIds - Variable in class au.csiro.ontology.importer.rf2.RF2Importer.OntologyBuilder

roleGroupId - Variable in class au.csiro.ontology.importer.rf2.RF2Importer.OntologyBuilder

roles - Variable in class au.csiro.ontology.importer.rf1.RF1Importer

roles - Variable in class au.csiro.ontology.importer.rf2.RF2Importer.OntologyBuilder

rootModuleId - Variable in class au.csiro.ontology.importer.rf2.RF2Importer.OntologyBuilder

rootModuleVersion - Variable in class au.csiro.ontology.importer.rf2.RF2Importer.OntologyBuilder

S

setUseSimpleFloats(boolean) - Method in class au.csiro.ontology.importer.owl.OWLImporter

setUseSimpleInts(boolean) - Method in class au.csiro.ontology.importer.owl.OWLImporter

setVersionName(String) - Method in class au.csiro.ontology.importer.rf1.VersionRows

Sets the name of this version.

someId - Variable in class au.csiro.ontology.importer.rf2.RF2Importer.OntologyBuilder

statedAxioms - Variable in class au.csiro.ontology.importer.rf2.RF2Importer.OntologyBuilder

synonymId - Variable in class au.csiro.ontology.importer.rf2.RF2Importer.OntologyBuilder

T

THING_IRI - Static variable in class au.csiro.ontology.importer.owl.OWLImporter

toString() - Method in class au.csiro.ontology.importer.rf2.ConceptRow

toString() - Method in class au.csiro.ontology.importer.rf2.DescriptionRow

toString() - Method in class au.csiro.ontology.importer.rf2.RelationshipRow

U

unitRoleId - Variable in class au.csiro.ontology.importer.rf2.RF2Importer.OntologyBuilder

usesConcreteDomains() - Method in class au.csiro.ontology.importer.rf1.RF1Importer

V

version - Variable in class au.csiro.ontology.importer.rf1.RF1Importer

VersionRows - Class in au.csiro.ontology.importer.rf1

This class represents a collection of rows from the RF1 concepts, descriptions, and relationships tables that correspond to a logical version.

VersionRows(String) - Constructor for class au.csiro.ontology.importer.rf1.VersionRows

Builds a new VersionRows.

VersionRows - Class in au.csiro.ontology.importer.rf2

This class represents a collection of rows from the RF2 concepts, descriptions, and relationships tables that correspond to a logical version.

VersionRows() - Constructor for class au.csiro.ontology.importer.rf2.VersionRows

Builds a new VersionRows.

VersionRows(Collection<ConceptRow>, Collection<RelationshipRow>, Collection<RefsetRow>) - Constructor for class au.csiro.ontology.importer.rf2.VersionRows

versions - Variable in class au.csiro.ontology.importer.rf2.Module

A collection of rows from the RF2 tables for each version of this module.

vr - Variable in class au.csiro.ontology.importer.rf2.RF2Importer.OntologyBuilder

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