public class OWLGraphWrapper extends OWLGraphWrapperEdgesAdvanced
OWLOntology
objects. One of these is designated
the sourceOntology, the others are designated support ontologies
(see OWLGraphWrapperBasic.getSourceOntology()
and OWLGraphWrapperBasic.getSupportOntologySet()
).
The source ontology may import the support
ontologies, but this is optional. Most OWLGraphWrapper methods operate over the union of the source ontology
and support ontologies. This is particularly useful for working with OBO Library ontologies, where axioms
connecting ontologies may be available as separate ontologies.
owltools.graph
OWLDataFactory
objects, these only return an object if it
has been declared in either the source ontology or a support ontology.
See for example
OWLGraphWrapperExtended.getOWLClass(String id)
OWLGraphWrapperExtended.getOWLClassByIdentifier(String id)
OWLGraphWrapperExtended.getOWLObjectByLabel(String label)
For maintenance purpose this class has been split into multiple classes:
OWLGraphWrapperBasic
Methods handling multiple OWLOntology
objects in one graphOWLGraphWrapperExtended
Methods to extract information about entities, includes OBO-style information OWLGraphWrapperEdges
Methods for handling edges and relationsOWLGraphWrapperEdgesAdvanced
Methods related GOlr and advanced graph traversal optionsOWLGraphUtil
Modifier and Type | Class and Description |
---|---|
static interface |
OWLGraphWrapper.ISynonym |
static class |
OWLGraphWrapper.Synonym |
OWLGraphWrapperEdges.Config
Modifier and Type | Field and Description |
---|---|
static String |
DEFAULT_IRI_PREFIX |
inferredEdgeBySource, profiler
sourceOntology, supportOntologySet
Constructor and Description |
---|
OWLGraphWrapper(org.semanticweb.owlapi.model.OWLOntology ontology)
Create a new wrapper for an OWLOntology
|
OWLGraphWrapper(org.semanticweb.owlapi.model.OWLOntology ontology,
boolean isMergeImportClosure)
Deprecated.
|
OWLGraphWrapper(String iri)
creates a new
OWLOntology as the source ontology |
Modifier and Type | Method and Description |
---|---|
void |
addQueryOntology(org.semanticweb.owlapi.model.OWLOntology extOnt)
Deprecated.
|
List<OWLGraphWrapper.ISynonym> |
getOBOSynonyms(org.semanticweb.owlapi.model.OWLObject c)
It returns list of synonyms as encoded by OBO2OWL.
|
List<String> |
getOBOSynonymStrings(org.semanticweb.owlapi.model.OWLObject c,
List<String> sargs)
It returns String Listof synonyms.
|
org.semanticweb.owlapi.model.OWLOntology |
getOntology()
Deprecated.
|
String[] |
getSynonymStrings(org.semanticweb.owlapi.model.OWLObject c)
Deprecated.
|
void |
setOntology(org.semanticweb.owlapi.model.OWLOntology ontology)
Deprecated.
|
void |
useImportClosureForQueries()
Deprecated.
|
addDirectDescendentsToShuntGraph, addPropertiesForMaterialization, addPropertyForMaterialization, addPropertyIdsForMaterialization, addStepwiseAncestorsToShuntGraph, addTransitiveAncestorsToShuntGraph, categorizeNamespace, categorizeObject, classifyRelationship, close, getCurrentEdgesAdvancedCacheSize, getDummyString, getDummyStrings, getIsaPartofClosureMap, getIsaPartofIDClosure, getIsaPartofIDClosure, getIsaPartofLabelClosure, getIsaPartofLabelClosure, getLineageShuntGraph, getLineageShuntGraphJSON, getOnlyInTaxon, getOnlyInTaxonClosure, getOnlyInTaxonClosureLabels, getOnlyInTaxonLabelMap, getOnlyInTaxonLabels, getRelationClosureMap, getRelationClosureMapEngine, getRelationIDClosure, getRelationLabelClosure, getSegmentShuntGraph, getSegmentShuntGraphJSON, getSubClassesNames, relationshipIDsToPropertySet, setEdgesAdvancedCacheSize
clearCachedEdges, combineEdgePairWithGCI, combineEdgePairWithSuperPropsAndGCI, edgeToSourceExpression, getAllOWLClasses, getAllOWLClassesFromSource, getAncestorsThroughIsA, getDescendantsThroughIsA, getGCIIncomingEdges, getGCIOutgoingEdges, getGCIOutgoingEdges, getIncomingEdgesWithGCI, getNamedAncestorsWithGCI, getNamedAncestorsWithGCI, getOntologyLeaves, getOntologyRoots, getOntologyRoots, getOutgoingEdgesClosureWithGCI, getOutgoingEdgesNamedClosureOverSupProps, getOutgoingEdgesNamedClosureOverSupPropsWithGCI, getOutgoingEdgesWithGCI, getOutgoingEdgesWithGCI, getOWLClassAncestors, getOWLClassAncestorsWithGCI, getOWLClassDescendants, getOWLClassDescendantsWithGCI, getOWLClassDescendantsWithGCI, getOWLClassDirectAncestors, getOWLClassDirectDescendants, getOWLClassDirectDescendantsWithGCI, getOWLGraphEdgeSubRelsReflexive, getSubAnnotationPropertiesOf, getSubAnnotationPropertyClosureOf, getSubAnnotationPropertyReflexiveClosureOf, getSubPropertiesOf, getSubPropertyClosureOf, getSubPropertyReflexiveClosureOf, getSuperPropertyReflexiveClosureOf, hasFirstEdgeMoreGeneralGCIParams, isOWLObjectInSubsets, isRealClass
cacheEdges, combinedQuantifiedPropertyPair, combineEdgePair, combineEdgePair, edgeToTargetExpression, expandRelationChain, filterEdges, getAncestors, getAncestors, getAncestors, getAncestorsReflexive, getAncestorsReflexive, getCompleteEdgesBetween, getCompleteOutgoingEdgesClosure, getConfig, getDescendants, getDescendantsReflexive, getEdgeLabel, getEdgesBetween, getIncomingEdges, getIncomingEdgesClosure, getIncomingEdgesClosure, getIndividualDescendants, getInstanceChainsFromClosure, getInstancesFromClosure, getNamedAncestors, getNamedAncestorsReflexive, getOutgoingEdges, getOutgoingEdges, getOutgoingEdges, getOutgoingEdgesClosure, getOutgoingEdgesClosure, getOutgoingEdgesClosure, getOutgoingEdgesClosureReflexive, getOutgoingEdgesClosureReflexive, getOWLGraphEdgeSubsumers, getOWLGraphEdgeSubsumers, getPrimitiveIncomingEdges, getPrimitiveOutgoingEdges, getPrimitiveOutgoingEdges, getProfiler, getReasoner, getRelationOrChain, getSubsumersFromClosure, getSuperPropertiesOf, getSuperPropertyClosureOf, isExcluded, isExcludeEdge, primitiveEdgeToFullEdges, queryDescendants, queryDescendants, queryDescendants, setConfig, setProfiler, setReasoner
getAllOWLObjectsByAltId, getAllUsedSubsets, getAltIds, getAnnotationProperty, getAnnotationPropertyValue, getAnnotationPropertyValue, getAnnotationPropertyValues, getAnnotationPropertyValues, getAnnotationValue, getAnnotationValues, getBuiltin, getComment, getComment, getComments, getComments, getConsider, getCreatedBy, getDef, getDef, getDefXref, getDefXref, getDomain, getIdentifier, getIdentifier, getIdentifier, getIdentifier, getIRIByIdentifier, getIRIByIdentifier, getIRIByLabel, getIRIByLabel, getIsAnonymous, getIsAntiSymmetric, getIsCyclic, getIsFunctional, getIsInverseFunctional, getIsMetaTag, getIsObsolete, getIsObsoleteBinaryString, getIsReflexive, getIsSymmetric, getIsTransitive, getLabel, getLabel, getLabelOrDisplayId, getNamespace, getNamespace, getObjectByAltId, getOntologyId, getOWLAnnotationProperty, getOWLClass, getOWLClass, getOWLClass, getOWLClassByIdentifier, getOWLClassByIdentifier, getOWLClassByIdentifierNoAltIds, getOWLClassesInSubset, getOWLIndividual, getOWLIndividual, getOWLIndividualByIdentifier, getOWLObject, getOWLObject, getOWLObjectByAltId, getOWLObjectByIdentifier, getOWLObjectByLabel, getOWLObjectProperty, getOWLObjectProperty, getOWLObjectPropertyByIdentifier, getOWLObjectsByAltId, getOWLObjectsInSubset, getRange, getReplacedBy, getSubsets, getSubsets, getVersions, getXref, getXref, isObsolete
addImport, addImportsFromSupportOntologies, addSupportOntologiesFromImportsClosure, addSupportOntologiesFromImportsClosure, addSupportOntology, getAllOntologies, getAllOWLObjects, getAllOWLSubClassOfAxiomsForSubClass, getAllOWLSubClassOfAxiomsForSuperClass, getDataFactory, getManager, getSourceOntology, getSupportOntologySet, mergeImportClosure, mergeImportClosure, mergeOntology, mergeOntology, mergeSpecificImport, mergeSupportOntology, mergeSupportOntology, mergeSupportOntology, mergeSupportOntology, remakeOntologiesFromImportsClosure, remakeOntologiesFromImportsClosure, removeSupportOntology, setSourceOntology, setSupportOntologySet
public static final String DEFAULT_IRI_PREFIX
public OWLGraphWrapper(org.semanticweb.owlapi.model.OWLOntology ontology)
ontology
- @Deprecated public OWLGraphWrapper(org.semanticweb.owlapi.model.OWLOntology ontology, boolean isMergeImportClosure) throws org.semanticweb.owlapi.model.UnknownOWLOntologyException, org.semanticweb.owlapi.model.OWLOntologyCreationException
ontology
- isMergeImportClosure
- org.semanticweb.owlapi.model.UnknownOWLOntologyException
org.semanticweb.owlapi.model.OWLOntologyCreationException
public OWLGraphWrapper(String iri) throws org.semanticweb.owlapi.model.OWLOntologyCreationException
OWLOntology
as the source ontologyiri
- org.semanticweb.owlapi.model.OWLOntologyCreationException
@Deprecated public void useImportClosureForQueries() throws org.semanticweb.owlapi.model.UnknownOWLOntologyException, org.semanticweb.owlapi.model.OWLOntologyCreationException
org.semanticweb.owlapi.model.UnknownOWLOntologyException
org.semanticweb.owlapi.model.OWLOntologyCreationException
@Deprecated public void addQueryOntology(org.semanticweb.owlapi.model.OWLOntology extOnt) throws org.semanticweb.owlapi.model.OWLOntologyCreationException
org.semanticweb.owlapi.model.OWLOntologyCreationException
@Deprecated public org.semanticweb.owlapi.model.OWLOntology getOntology()
@Deprecated public void setOntology(org.semanticweb.owlapi.model.OWLOntology ontology)
@Deprecated public String[] getSynonymStrings(org.semanticweb.owlapi.model.OWLObject c)
c
- public List<OWLGraphWrapper.ISynonym> getOBOSynonyms(org.semanticweb.owlapi.model.OWLObject c)
c
- Copyright © 2010–2016. All rights reserved.