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java.lang.Objectowltools.graph.OWLGraphWrapper
public class OWLGraphWrapper
Wraps one or more OWLOntology objects providing convenient OBO-like operations
OWLOntology
objects. One of these is designated
the sourceOntology, the others are designated support ontologies
(see getSourceOntology()
and 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
OWLGraphUtil
Nested Class Summary | |
---|---|
class |
OWLGraphWrapper.Config
Configuration options. |
static interface |
OWLGraphWrapper.ISynonym
|
static class |
OWLGraphWrapper.Synonym
|
Field Summary | |
---|---|
static String |
DEFAULT_IRI_PREFIX
|
Map<org.semanticweb.owlapi.model.OWLObject,Set<OWLGraphEdge>> |
inferredEdgeBySource
|
Constructor Summary | |
---|---|
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 |
Method Summary | |
---|---|
OWLShuntGraph |
addAncestorsToShuntGraph(org.semanticweb.owlapi.model.OWLObject x,
OWLShuntGraph g)
Add a set of edges, as ancestors to x in OWLShuntGraph g. |
OWLShuntGraph |
addDirectDescendentsToShuntGraph(org.semanticweb.owlapi.model.OWLObject x,
OWLShuntGraph g)
Add a set of edges, as descendents to x in OWLShuntGraph g. |
void |
addImport(org.semanticweb.owlapi.model.OWLOntology extOnt)
adds an imports declaration between the source ontology and extOnt |
void |
addImportsFromSupportOntologies()
|
void |
addQueryOntology(org.semanticweb.owlapi.model.OWLOntology extOnt)
Deprecated. |
void |
addSupportOntologiesFromImportsClosure()
Each ontology in the import closure of the source ontology is added to the list of support ontologies |
void |
addSupportOntologiesFromImportsClosure(boolean doForAllSupportOntologies)
Each ontology in the import closure of the source ontology (and the import closure of each existing support ontology, if doForAllSupportOntologies is true) is added to the list of support ontologies |
void |
addSupportOntology(org.semanticweb.owlapi.model.OWLOntology o)
|
void |
cacheEdges()
caches full outgoing and incoming edges in general you should not need to call this directly; used internally by this class. |
OWLGraphEdge |
combineEdgePair(org.semanticweb.owlapi.model.OWLObject s,
OWLGraphEdge ne,
OWLGraphEdge extEdge,
int nextDist)
Composes two graph edges into a new edge, using axioms in the ontology to determine the correct composition For example, Edge(x,SUBCLASS_OF,y) * Edge(y,SUBCLASS_OF,z) yields Edge(x,SUBCLASS_OF,z) Note that property chains of length>2 are currently ignored |
org.semanticweb.owlapi.model.OWLObject |
edgeToTargetExpression(OWLGraphEdge e)
pack/translate an edge (either asserted or a graph closure edge) into an OWL class expression according to the OWLGraph to OWLOntology translation rules. |
Set<org.semanticweb.owlapi.model.OWLOntology> |
getAllOntologies()
in general application code need not call this - it is mostly used internally |
Set<org.semanticweb.owlapi.model.OWLObject> |
getAllOWLObjects()
fetches all classes, individuals and object properties in all ontologies |
Set<String> |
getAllUsedSubsets()
fetches all subset names that are used |
List<String> |
getAltIds(org.semanticweb.owlapi.model.OWLObject c)
It returns the values of the alt_id tag |
Set<org.semanticweb.owlapi.model.OWLObject> |
getAncestors(org.semanticweb.owlapi.model.OWLObject x)
returns all ancestors of an object. |
Set<org.semanticweb.owlapi.model.OWLObject> |
getAncestors(org.semanticweb.owlapi.model.OWLObject x,
Set<org.semanticweb.owlapi.model.OWLPropertyExpression> overProps)
returns all ancestors that can be reached over subclass or the specified set of relations |
Set<org.semanticweb.owlapi.model.OWLObject> |
getAncestorsReflexive(org.semanticweb.owlapi.model.OWLObject x)
|
Set<org.semanticweb.owlapi.model.OWLObject> |
getAncestorsReflexive(org.semanticweb.owlapi.model.OWLObject x,
Set<org.semanticweb.owlapi.model.OWLPropertyExpression> overProps)
|
org.semanticweb.owlapi.model.OWLAnnotationProperty |
getAnnotationProperty(String tag)
It translates a oboformat tag into an OWL annotation property |
String |
getAnnotationValue(org.semanticweb.owlapi.model.OWLObject c,
org.semanticweb.owlapi.model.OWLAnnotationProperty lap)
fetches the value of a single-valued annotation property for an OWLObject TODO: provide a flag that determines behavior in the case of >1 value |
List<String> |
getAnnotationValues(org.semanticweb.owlapi.model.OWLObject c,
org.semanticweb.owlapi.model.OWLAnnotationProperty lap)
gets the values of all annotation assertions to an OWLObject for a particular annotation property |
boolean |
getBuiltin(org.semanticweb.owlapi.model.OWLObject c)
Deprecated. |
String |
getComment(org.semanticweb.owlapi.model.OWLObject c)
gets the value of rdfs:comment for an OWLObject |
Set<OWLGraphEdge> |
getCompleteEdgesBetween(org.semanticweb.owlapi.model.OWLObject s,
org.semanticweb.owlapi.model.OWLObject t)
|
Set<OWLGraphEdge> |
getCompleteOutgoingEdgesClosure(org.semanticweb.owlapi.model.OWLObject s)
See getIncomingEdgesClosure(OWLObject s, boolean isComplete) |
OWLGraphWrapper.Config |
getConfig()
|
List<String> |
getConsider(org.semanticweb.owlapi.model.OWLObject c)
It returns the values of the consider tag. |
String |
getCreatedBy(org.semanticweb.owlapi.model.OWLObject c)
It returns the value of the created_by tag |
org.semanticweb.owlapi.model.OWLDataFactory |
getDataFactory()
|
String |
getDef(org.semanticweb.owlapi.model.OWLObject c)
Gets the textual definition of an OWLObject assumes zero or one def It returns the definition text (encoded as def in obo format and IAO_0000115 annotation property in OWL format) of a class |
List<String> |
getDefXref(org.semanticweb.owlapi.model.OWLObject c)
Get the definition xrefs (IAO_0000115) |
Set<org.semanticweb.owlapi.model.OWLObject> |
getDescendants(org.semanticweb.owlapi.model.OWLObject x)
gets all descendants d of x, where d is reachable by any path. |
Set<org.semanticweb.owlapi.model.OWLObject> |
getDescendantsReflexive(org.semanticweb.owlapi.model.OWLObject x)
gets all reflexive descendants d of x, where d is reachable by any path. |
String |
getDomain(org.semanticweb.owlapi.model.OWLObjectProperty prop)
It returns the value of the domain tag |
String |
getEdgeLabel(OWLGraphEdge e)
Get the human readable label for an edge. |
Set<OWLGraphEdge> |
getEdgesBetween(org.semanticweb.owlapi.model.OWLObject s,
org.semanticweb.owlapi.model.OWLObject t)
|
String |
getIdentifier(org.semanticweb.owlapi.model.IRI iriId)
gets the OBO-style ID of the specified object. |
String |
getIdentifier(org.semanticweb.owlapi.model.OWLObject owlObject)
gets the OBO-style ID of the specified object. |
Set<OWLGraphEdge> |
getIncomingEdges(org.semanticweb.owlapi.model.OWLObject t)
|
Set<OWLGraphEdge> |
getIncomingEdgesClosure(org.semanticweb.owlapi.model.OWLObject t)
gets all inferred edges coming in to the target edge for every s, if t is reachable from s, then include the inferred edge between s and t. |
Set<OWLGraphEdge> |
getIncomingEdgesClosure(org.semanticweb.owlapi.model.OWLObject t,
boolean isComplete)
As getIncomingEdgesClosure(OWLObject t) , but allows the option of including
'complete' edge list. |
Set<org.semanticweb.owlapi.model.OWLObject> |
getIndividualDescendants(org.semanticweb.owlapi.model.OWLObject x)
return all individuals i where x is reachable from i |
Set<OWLGraphEdge> |
getInstanceChainsFromClosure(org.semanticweb.owlapi.model.OWLClass c)
Finds all edges between an instance i and he given class c. |
Set<org.semanticweb.owlapi.model.OWLIndividual> |
getInstancesFromClosure(org.semanticweb.owlapi.model.OWLClass c)
Find all edges of the form [i INST c] in the graph closure. |
org.semanticweb.owlapi.model.IRI |
getIRIByIdentifier(String id)
|
org.semanticweb.owlapi.model.IRI |
getIRIByLabel(String label)
fetches an OWL IRI by rdfs:label |
org.semanticweb.owlapi.model.IRI |
getIRIByLabel(String label,
boolean isEnforceUnivocal)
fetches an OWL IRI by rdfs:label, optionally testing for uniqueness TODO: index labels. |
boolean |
getIsAnonymous(org.semanticweb.owlapi.model.OWLObject c)
Deprecated. |
boolean |
getIsAntiSymmetric(org.semanticweb.owlapi.model.OWLObject c)
It returns the value of the is_anti_symmetric tag or IAO_0000427 annotation |
Map<String,String> |
getIsaPartofClosureMap(org.semanticweb.owlapi.model.OWLObject c)
Return a overlaps with getIsaPartofLabelClosure and stuff in GafSolrDocumentLoader. |
List<String> |
getIsaPartofIDClosure(org.semanticweb.owlapi.model.OWLObject c)
Return a overlaps with getIsaPartofLabelClosure and stuff in GafSolrDocumentLoader. |
List<String> |
getIsaPartofLabelClosure(org.semanticweb.owlapi.model.OWLObject c)
Return a overlaps with getIsaPartofIDClosure and stuff in GafSolrDocumentLoader. |
boolean |
getIsCyclic(org.semanticweb.owlapi.model.OWLObject c)
It returns the value of the is_cyclic tag |
boolean |
getIsFunctional(org.semanticweb.owlapi.model.OWLObjectProperty c)
true if c is functional in the source ontology |
boolean |
getIsInverseFunctional(org.semanticweb.owlapi.model.OWLObjectProperty c)
|
boolean |
getIsMetaTag(org.semanticweb.owlapi.model.OWLObject c)
It returns the value of the is_metadata_tag tag. |
boolean |
getIsObsolete(org.semanticweb.owlapi.model.OWLObject c)
It returns the value of the is-obsolete tag. |
String |
getIsObsoleteBinaryString(org.semanticweb.owlapi.model.OWLObject c)
It returns the value of the is-obsolete tag. |
boolean |
getIsReflexive(org.semanticweb.owlapi.model.OWLObjectProperty c)
|
boolean |
getIsSymmetric(org.semanticweb.owlapi.model.OWLObjectProperty c)
|
boolean |
getIsTransitive(org.semanticweb.owlapi.model.OWLObjectProperty c)
true if c is transitive in the source ontology |
String |
getLabel(org.semanticweb.owlapi.model.OWLObject c)
fetches the rdfs:label for an OWLObject assumes zero or one rdfs:label |
String |
getLabelOrDisplayId(org.semanticweb.owlapi.model.OWLObject c)
|
org.semanticweb.owlapi.model.OWLOntologyManager |
getManager()
|
Set<org.semanticweb.owlapi.model.OWLObject> |
getNamedAncestors(org.semanticweb.owlapi.model.OWLObject x)
Gets all ancestors that are OWLNamedObjects i.e. |
Set<org.semanticweb.owlapi.model.OWLObject> |
getNamedAncestorsReflexive(org.semanticweb.owlapi.model.OWLObject x)
|
String |
getNamespace(org.semanticweb.owlapi.model.OWLObject c)
It returns the value of the OBO-namespace tag Example: if the OWLObject is the GO class GO:0008150, this would return "biological_process" |
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)
It returns String Listof synonyms. |
org.semanticweb.owlapi.model.OWLOntology |
getOntology()
Deprecated. |
String |
getOntologyId()
gets the OBO-style ID of the source ontology IRI. |
Set<OWLGraphEdge> |
getOutgoingEdges(org.semanticweb.owlapi.model.OWLObject cls)
retrieves direct edges from a source to the direct **named** target e.g. |
Set<OWLGraphEdge> |
getOutgoingEdges(org.semanticweb.owlapi.model.OWLObject obj,
boolean isClosure,
boolean isReflexive)
|
Set<OWLGraphEdge> |
getOutgoingEdgesClosure(org.semanticweb.owlapi.model.OWLObject s)
Retrieves the graph closure originating from source. |
Set<OWLGraphEdge> |
getOutgoingEdgesClosure(org.semanticweb.owlapi.model.OWLObject s,
boolean isComplete)
See getIncomingEdgesClosure(OWLObject s, boolean isComplete) |
Set<OWLGraphEdge> |
getOutgoingEdgesClosureReflexive(org.semanticweb.owlapi.model.OWLObject s)
as getOutgoingEdgesClosure(s), but also includes an identity edge |
org.semanticweb.owlapi.model.OWLAnnotationProperty |
getOWLAnnotationProperty(org.semanticweb.owlapi.model.IRI iri)
|
org.semanticweb.owlapi.model.OWLClass |
getOWLClass(org.semanticweb.owlapi.model.IRI iri)
Returns an OWLClass given an IRI the class must be declared in either the source ontology, or in a support ontology, otherwise null is returned |
org.semanticweb.owlapi.model.OWLClass |
getOWLClass(org.semanticweb.owlapi.model.OWLObject x)
|
org.semanticweb.owlapi.model.OWLClass |
getOWLClass(String s)
Returns an OWLClass given an IRI string the class must be declared in either the source ontology, or in a support ontology, otherwise null is returned |
org.semanticweb.owlapi.model.OWLClass |
getOWLClassByIdentifier(String id)
Given an OBO-style ID, return the corresponding OWLClass, if it is declared - otherwise null |
Set<org.semanticweb.owlapi.model.OWLClass> |
getOWLClassesInSubset(String subset)
given a subset name, find all OWLClasses assigned to that subset |
Set<OWLGraphEdge> |
getOWLGraphEdgeSubsumers(OWLGraphEdge e)
generalizes over quantified properties |
Set<OWLGraphEdge> |
getOWLGraphEdgeSubsumers(OWLGraphEdge e,
int i)
|
org.semanticweb.owlapi.model.OWLNamedIndividual |
getOWLIndividual(org.semanticweb.owlapi.model.IRI iri)
Returns an OWLNamedIndividual with this IRI if it has been declared in the source or support ontologies. |
org.semanticweb.owlapi.model.OWLNamedIndividual |
getOWLIndividual(String s)
|
org.semanticweb.owlapi.model.OWLNamedIndividual |
getOWLIndividualByIdentifier(String id)
Given an OBO-style ID, return the corresponding OWLNamedIndividual, if it is declared - otherwise null |
org.semanticweb.owlapi.model.OWLObject |
getOWLObject(org.semanticweb.owlapi.model.IRI s)
Returns the OWLObject with this IRI Must have been declared in one of the ontologies Currently OWLObject must be one of OWLClass, OWLObjectProperty or OWLNamedIndividual If the ontology employs punning and there different entities with the same IRI, then the order of precedence is OWLClass then OWLObjectProperty then OWLNamedIndividual |
org.semanticweb.owlapi.model.OWLObject |
getOWLObject(String s)
Returns the OWLObject with this IRI (where IRI is specified as a string - e.g http://purl.obolibrary.org/obo/GO_0008150) |
org.semanticweb.owlapi.model.OWLObject |
getOWLObjectByIdentifier(String id)
Given an OBO-style ID, return the corresponding OWLObject, if it is declared - otherwise null |
org.semanticweb.owlapi.model.OWLObject |
getOWLObjectByLabel(String label)
fetches an OWL Object by rdfs:label if there is >1 match, return the first one encountered |
org.semanticweb.owlapi.model.OWLObjectProperty |
getOWLObjectProperty(org.semanticweb.owlapi.model.IRI iri)
|
org.semanticweb.owlapi.model.OWLObjectProperty |
getOWLObjectProperty(String iri)
Returns the OWLObjectProperty with this IRI Must have been declared in one of the ontologies |
org.semanticweb.owlapi.model.OWLObjectProperty |
getOWLObjectPropertyByIdentifier(String id)
Given an OBO-style ID, return the corresponding OWLObjectProperty, if it is declared - otherwise null |
Set<org.semanticweb.owlapi.model.OWLObject> |
getOWLObjectsInSubset(String subset)
given a subset name, find all OWLObjects (typically OWLClasses) assigned to that subset |
Set<OWLGraphEdge> |
getPrimitiveIncomingEdges(org.semanticweb.owlapi.model.OWLObject t)
|
Set<OWLGraphEdge> |
getPrimitiveOutgoingEdges(org.semanticweb.owlapi.model.OWLObject s)
primitive edges connect any combination of named objects and expressions e.g. |
Profiler |
getProfiler()
|
String |
getRange(org.semanticweb.owlapi.model.OWLObjectProperty prop)
It returns the value of the range tag |
org.semanticweb.owlapi.reasoner.OWLReasoner |
getReasoner()
|
List<String> |
getReplacedBy(org.semanticweb.owlapi.model.OWLObject c)
It returns the values of the replaced_by tag or IAO_0100001 annotation. |
OWLShuntGraph |
getSegmentShuntGraph(org.semanticweb.owlapi.model.OWLObject x)
Gets all ancestors and direct descendents (distance == 1) that are OWLNamedObjects. |
String |
getSegmentShuntGraphJSON(org.semanticweb.owlapi.model.OWLObject x)
Return a JSONized version of the output of getSegmentShuntGraph |
org.semanticweb.owlapi.model.OWLOntology |
getSourceOntology()
Every OWLGraphWrapper objects wraps zero or one source ontologies. |
String[] |
getSubClassesNames(org.semanticweb.owlapi.model.OWLClass cls)
Deprecated. |
List<String> |
getSubsets(org.semanticweb.owlapi.model.OWLObject c)
It returns the value of the subset tag. |
Set<org.semanticweb.owlapi.model.OWLObject> |
getSubsumersFromClosure(org.semanticweb.owlapi.model.OWLObject s)
find the set of classes or class expressions subsuming source, using the graph closure. |
Set<org.semanticweb.owlapi.model.OWLObjectPropertyExpression> |
getSuperPropertiesOf(org.semanticweb.owlapi.model.OWLObjectPropertyExpression p)
returns parent properties of p in all ontologies |
Set<org.semanticweb.owlapi.model.OWLObjectPropertyExpression> |
getSuperPropertyClosureOf(org.semanticweb.owlapi.model.OWLObjectPropertyExpression p)
|
Set<org.semanticweb.owlapi.model.OWLObjectPropertyExpression> |
getSuperPropertyReflexiveClosureOf(org.semanticweb.owlapi.model.OWLObjectPropertyExpression p)
|
Set<org.semanticweb.owlapi.model.OWLOntology> |
getSupportOntologySet()
all operations are over a set of ontologies - the source ontology plus any number of supporting ontologies. |
String[] |
getSynonymStrings(org.semanticweb.owlapi.model.OWLObject c)
Deprecated. |
List<String> |
getXref(org.semanticweb.owlapi.model.OWLObject c)
get the values of of the obo xref tag |
boolean |
isExcludeEdge(OWLGraphEdge edge)
|
boolean |
isObsolete(org.semanticweb.owlapi.model.OWLObject c)
tests if an OWLObject has been declared obsolete in the source ontology |
void |
mergeImportClosure()
note: may move to mooncat |
void |
mergeImportClosure(boolean isRemovedImportsDeclarations)
|
void |
mergeOntology(org.semanticweb.owlapi.model.OWLOntology extOnt)
Adds all axioms from extOnt into source ontology |
void |
mergeOntology(org.semanticweb.owlapi.model.OWLOntology extOnt,
boolean isRemoveFromSupportList)
|
void |
mergeSupportOntology(String ontologyIRI)
|
void |
mergeSupportOntology(String ontologyIRI,
boolean isRemoveFromSupportList)
|
Set<org.semanticweb.owlapi.model.OWLObject> |
queryDescendants(org.semanticweb.owlapi.model.OWLClassExpression t)
Performs a closed-world query using a DL expression as a set of boolean database-style constraints. |
Set<org.semanticweb.owlapi.model.OWLObject> |
queryDescendants(org.semanticweb.owlapi.model.OWLClassExpression t,
boolean isInstances,
boolean isClasses)
|
Set<org.semanticweb.owlapi.model.OWLObject> |
queryDescendants(OWLGraphEdge e)
Treats an edge as a path and performs a query. |
void |
remakeOntologiesFromImportsClosure()
|
void |
remakeOntologiesFromImportsClosure(org.semanticweb.owlapi.model.IRI ontologyIRI)
|
void |
removeSupportOntology(org.semanticweb.owlapi.model.OWLOntology o)
|
void |
setConfig(OWLGraphWrapper.Config config)
|
void |
setOntology(org.semanticweb.owlapi.model.OWLOntology ontology)
Deprecated. |
void |
setProfiler(Profiler profiler)
|
void |
setReasoner(org.semanticweb.owlapi.reasoner.OWLReasoner reasoner)
|
void |
setSourceOntology(org.semanticweb.owlapi.model.OWLOntology sourceOntology)
|
void |
setSupportOntologySet(Set<org.semanticweb.owlapi.model.OWLOntology> supportOntologySet)
|
void |
useImportClosureForQueries()
Deprecated. |
Methods inherited from class java.lang.Object |
---|
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Field Detail |
---|
public static final String DEFAULT_IRI_PREFIX
public Map<org.semanticweb.owlapi.model.OWLObject,Set<OWLGraphEdge>> inferredEdgeBySource
Constructor Detail |
---|
public OWLGraphWrapper(org.semanticweb.owlapi.model.OWLOntology ontology) throws org.semanticweb.owlapi.model.UnknownOWLOntologyException, org.semanticweb.owlapi.model.OWLOntologyCreationException
ontology
-
org.semanticweb.owlapi.model.OWLOntologyCreationException
org.semanticweb.owlapi.model.UnknownOWLOntologyException
@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 ontology
iri
-
org.semanticweb.owlapi.model.OWLOntologyCreationException
Method Detail |
---|
public void addImport(org.semanticweb.owlapi.model.OWLOntology extOnt)
extOnt
- @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
public void mergeOntology(org.semanticweb.owlapi.model.OWLOntology extOnt) throws org.semanticweb.owlapi.model.OWLOntologyCreationException
extOnt
-
org.semanticweb.owlapi.model.OWLOntologyCreationException
public void mergeOntology(org.semanticweb.owlapi.model.OWLOntology extOnt, boolean isRemoveFromSupportList) throws org.semanticweb.owlapi.model.OWLOntologyCreationException
org.semanticweb.owlapi.model.OWLOntologyCreationException
public void mergeSupportOntology(String ontologyIRI, boolean isRemoveFromSupportList) throws org.semanticweb.owlapi.model.OWLOntologyCreationException
org.semanticweb.owlapi.model.OWLOntologyCreationException
public void mergeSupportOntology(String ontologyIRI) 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)
public org.semanticweb.owlapi.model.OWLOntology getSourceOntology()
public void setSourceOntology(org.semanticweb.owlapi.model.OWLOntology sourceOntology)
public Profiler getProfiler()
public void setProfiler(Profiler profiler)
public org.semanticweb.owlapi.reasoner.OWLReasoner getReasoner()
public void setReasoner(org.semanticweb.owlapi.reasoner.OWLReasoner reasoner)
reasoner
- public Set<org.semanticweb.owlapi.model.OWLOntology> getSupportOntologySet()
public void setSupportOntologySet(Set<org.semanticweb.owlapi.model.OWLOntology> supportOntologySet)
public void addSupportOntology(org.semanticweb.owlapi.model.OWLOntology o)
public void removeSupportOntology(org.semanticweb.owlapi.model.OWLOntology o)
public void addSupportOntologiesFromImportsClosure()
public void addSupportOntologiesFromImportsClosure(boolean doForAllSupportOntologies)
doForAllSupportOntologies
- public void addImportsFromSupportOntologies()
public void remakeOntologiesFromImportsClosure() throws org.semanticweb.owlapi.model.OWLOntologyCreationException
org.semanticweb.owlapi.model.OWLOntologyCreationException
public void remakeOntologiesFromImportsClosure(org.semanticweb.owlapi.model.IRI ontologyIRI) throws org.semanticweb.owlapi.model.OWLOntologyCreationException
org.semanticweb.owlapi.model.OWLOntologyCreationException
public void mergeImportClosure() throws org.semanticweb.owlapi.model.OWLOntologyCreationException
org.semanticweb.owlapi.model.OWLOntologyCreationException
public void mergeImportClosure(boolean isRemovedImportsDeclarations) throws org.semanticweb.owlapi.model.OWLOntologyCreationException
org.semanticweb.owlapi.model.OWLOntologyCreationException
public Set<org.semanticweb.owlapi.model.OWLOntology> getAllOntologies()
public org.semanticweb.owlapi.model.OWLDataFactory getDataFactory()
public org.semanticweb.owlapi.model.OWLOntologyManager getManager()
public OWLGraphWrapper.Config getConfig()
public void setConfig(OWLGraphWrapper.Config config)
public Set<OWLGraphEdge> getOutgoingEdges(org.semanticweb.owlapi.model.OWLObject cls)
cls
- source
public Set<OWLGraphEdge> getOutgoingEdges(org.semanticweb.owlapi.model.OWLObject obj, boolean isClosure, boolean isReflexive)
public Set<OWLGraphEdge> getPrimitiveOutgoingEdges(org.semanticweb.owlapi.model.OWLObject s)
s
- source
OWLGraphEdge
public boolean isExcludeEdge(OWLGraphEdge edge)
public void cacheEdges()
public Set<OWLGraphEdge> getIncomingEdges(org.semanticweb.owlapi.model.OWLObject t)
t
-
public Set<OWLGraphEdge> getPrimitiveIncomingEdges(org.semanticweb.owlapi.model.OWLObject t)
public org.semanticweb.owlapi.model.OWLObject edgeToTargetExpression(OWLGraphEdge e)
e
- edge
public Set<OWLGraphEdge> getOutgoingEdgesClosure(org.semanticweb.owlapi.model.OWLObject s)
s
- source
public Set<OWLGraphEdge> getOutgoingEdgesClosureReflexive(org.semanticweb.owlapi.model.OWLObject s)
s
-
OWLGraphEdge
public Set<org.semanticweb.owlapi.model.OWLObject> getSubsumersFromClosure(org.semanticweb.owlapi.model.OWLObject s)
s
- source
OWLObject
public Set<OWLGraphEdge> getOutgoingEdgesClosure(org.semanticweb.owlapi.model.OWLObject s, boolean isComplete)
getIncomingEdgesClosure(OWLObject s, boolean isComplete)
s
- isComplete
-
public Set<OWLGraphEdge> getCompleteOutgoingEdgesClosure(org.semanticweb.owlapi.model.OWLObject s)
getIncomingEdgesClosure(OWLObject s, boolean isComplete)
s
-
public Set<org.semanticweb.owlapi.model.OWLObject> queryDescendants(OWLGraphEdge e)
e
-
OWLObject
, never nullpublic Set<org.semanticweb.owlapi.model.OWLObject> queryDescendants(org.semanticweb.owlapi.model.OWLClassExpression t)
t
- classExpression
public Set<org.semanticweb.owlapi.model.OWLObject> queryDescendants(org.semanticweb.owlapi.model.OWLClassExpression t, boolean isInstances, boolean isClasses)
public Set<OWLGraphEdge> getEdgesBetween(org.semanticweb.owlapi.model.OWLObject s, org.semanticweb.owlapi.model.OWLObject t)
s
- sourcet
- target
public Set<OWLGraphEdge> getCompleteEdgesBetween(org.semanticweb.owlapi.model.OWLObject s, org.semanticweb.owlapi.model.OWLObject t)
public Set<org.semanticweb.owlapi.model.OWLObject> getAncestors(org.semanticweb.owlapi.model.OWLObject x)
x
- source
public Set<org.semanticweb.owlapi.model.OWLObject> getAncestors(org.semanticweb.owlapi.model.OWLObject x, Set<org.semanticweb.owlapi.model.OWLPropertyExpression> overProps)
x
- the sourceObjectoverProps
-
public Set<org.semanticweb.owlapi.model.OWLObject> getAncestorsReflexive(org.semanticweb.owlapi.model.OWLObject x)
public Set<org.semanticweb.owlapi.model.OWLObject> getAncestorsReflexive(org.semanticweb.owlapi.model.OWLObject x, Set<org.semanticweb.owlapi.model.OWLPropertyExpression> overProps)
public Set<org.semanticweb.owlapi.model.OWLObject> getNamedAncestors(org.semanticweb.owlapi.model.OWLObject x)
x
-
public Set<org.semanticweb.owlapi.model.OWLObject> getNamedAncestorsReflexive(org.semanticweb.owlapi.model.OWLObject x)
public String getEdgeLabel(OWLGraphEdge e)
e
-
public OWLShuntGraph addAncestorsToShuntGraph(org.semanticweb.owlapi.model.OWLObject x, OWLShuntGraph g)
s
- x
- g
-
public OWLShuntGraph addDirectDescendentsToShuntGraph(org.semanticweb.owlapi.model.OWLObject x, OWLShuntGraph g)
s
- x
- g
-
public OWLShuntGraph getSegmentShuntGraph(org.semanticweb.owlapi.model.OWLObject x)
x
-
public String getSegmentShuntGraphJSON(org.semanticweb.owlapi.model.OWLObject x)
x
-
public Set<org.semanticweb.owlapi.model.OWLObject> getDescendants(org.semanticweb.owlapi.model.OWLObject x)
x
-
getAncestors(org.semanticweb.owlapi.model.OWLObject)
,
owltools.graph
public Set<org.semanticweb.owlapi.model.OWLObject> getDescendantsReflexive(org.semanticweb.owlapi.model.OWLObject x)
x
-
getAncestors(org.semanticweb.owlapi.model.OWLObject)
,
owltools.graph
public Set<org.semanticweb.owlapi.model.OWLObject> getIndividualDescendants(org.semanticweb.owlapi.model.OWLObject x)
x
-
OWLObject
spublic Set<OWLGraphEdge> getIncomingEdgesClosure(org.semanticweb.owlapi.model.OWLObject t, boolean isComplete)
getIncomingEdgesClosure(OWLObject t)
, but allows the option of including
'complete' edge list. A complete edge list also includes redundant subsuming paths. E.g
if there is a path
t
- isComplete
-
public Set<OWLGraphEdge> getIncomingEdgesClosure(org.semanticweb.owlapi.model.OWLObject t)
t
- target
getOutgoingEdgesClosure(org.semanticweb.owlapi.model.OWLObject)
public OWLGraphEdge combineEdgePair(org.semanticweb.owlapi.model.OWLObject s, OWLGraphEdge ne, OWLGraphEdge extEdge, int nextDist)
s
- - source nodene
- - edge 1extEdge
- - edge 2nextDist
- - new distance
public Set<org.semanticweb.owlapi.model.OWLIndividual> getInstancesFromClosure(org.semanticweb.owlapi.model.OWLClass c)
c
- owlClass
public Set<OWLGraphEdge> getInstanceChainsFromClosure(org.semanticweb.owlapi.model.OWLClass c)
c
- owlClass
public Set<org.semanticweb.owlapi.model.OWLObject> getAllOWLObjects()
public String getLabel(org.semanticweb.owlapi.model.OWLObject c)
c
-
public String getLabelOrDisplayId(org.semanticweb.owlapi.model.OWLObject c)
public boolean isObsolete(org.semanticweb.owlapi.model.OWLObject c)
c
-
public String getComment(org.semanticweb.owlapi.model.OWLObject c)
c
-
public String getAnnotationValue(org.semanticweb.owlapi.model.OWLObject c, org.semanticweb.owlapi.model.OWLAnnotationProperty lap)
c
- lap
-
public List<String> getAnnotationValues(org.semanticweb.owlapi.model.OWLObject c, org.semanticweb.owlapi.model.OWLAnnotationProperty lap)
c
- lap
-
public String getDef(org.semanticweb.owlapi.model.OWLObject c)
c
-
public boolean getIsMetaTag(org.semanticweb.owlapi.model.OWLObject c)
c
- could OWLClass or OWLObjectProperty
public List<String> getSubsets(org.semanticweb.owlapi.model.OWLObject c)
c
- could OWLClass or OWLObjectProperty
public Set<String> getAllUsedSubsets()
public Set<org.semanticweb.owlapi.model.OWLObject> getOWLObjectsInSubset(String subset)
subset
-
OWLObject
public Set<org.semanticweb.owlapi.model.OWLClass> getOWLClassesInSubset(String subset)
subset
-
OWLClass
public String getDomain(org.semanticweb.owlapi.model.OWLObjectProperty prop)
prop
-
public String getRange(org.semanticweb.owlapi.model.OWLObjectProperty prop)
prop
-
public List<String> getReplacedBy(org.semanticweb.owlapi.model.OWLObject c)
c
- could OWLClass or OWLObjectProperty
public List<String> getConsider(org.semanticweb.owlapi.model.OWLObject c)
c
- could OWLClass or OWLObjectProperty
public boolean getIsObsolete(org.semanticweb.owlapi.model.OWLObject c)
c
- could OWLClass or OWLObjectProperty
public String getIsObsoleteBinaryString(org.semanticweb.owlapi.model.OWLObject c)
c
- could OWLClass or OWLObjectProperty
public List<String> getAltIds(org.semanticweb.owlapi.model.OWLObject c)
c
-
@Deprecated public boolean getBuiltin(org.semanticweb.owlapi.model.OWLObject c)
c
-
@Deprecated public boolean getIsAnonymous(org.semanticweb.owlapi.model.OWLObject c)
c
-
public org.semanticweb.owlapi.model.OWLAnnotationProperty getAnnotationProperty(String tag)
tag
-
OWLAnnotationProperty
public String getNamespace(org.semanticweb.owlapi.model.OWLObject c)
c
-
public String getCreatedBy(org.semanticweb.owlapi.model.OWLObject c)
c
-
public boolean getIsAntiSymmetric(org.semanticweb.owlapi.model.OWLObject c)
c
-
public boolean getIsCyclic(org.semanticweb.owlapi.model.OWLObject c)
c
-
public boolean getIsTransitive(org.semanticweb.owlapi.model.OWLObjectProperty c)
c
-
public boolean getIsFunctional(org.semanticweb.owlapi.model.OWLObjectProperty c)
c
-
public boolean getIsInverseFunctional(org.semanticweb.owlapi.model.OWLObjectProperty c)
public boolean getIsReflexive(org.semanticweb.owlapi.model.OWLObjectProperty c)
public boolean getIsSymmetric(org.semanticweb.owlapi.model.OWLObjectProperty c)
public Set<org.semanticweb.owlapi.model.OWLObjectPropertyExpression> getSuperPropertiesOf(org.semanticweb.owlapi.model.OWLObjectPropertyExpression p)
p
-
public Set<org.semanticweb.owlapi.model.OWLObjectPropertyExpression> getSuperPropertyClosureOf(org.semanticweb.owlapi.model.OWLObjectPropertyExpression p)
public Set<org.semanticweb.owlapi.model.OWLObjectPropertyExpression> getSuperPropertyReflexiveClosureOf(org.semanticweb.owlapi.model.OWLObjectPropertyExpression p)
public Set<OWLGraphEdge> getOWLGraphEdgeSubsumers(OWLGraphEdge e)
e
-
public Set<OWLGraphEdge> getOWLGraphEdgeSubsumers(OWLGraphEdge e, int i)
public List<String> getXref(org.semanticweb.owlapi.model.OWLObject c)
c
-
public List<String> getDefXref(org.semanticweb.owlapi.model.OWLObject c)
c
-
public Map<String,String> getIsaPartofClosureMap(org.semanticweb.owlapi.model.OWLObject c)
c
-
public List<String> getIsaPartofIDClosure(org.semanticweb.owlapi.model.OWLObject c)
c
-
public List<String> getIsaPartofLabelClosure(org.semanticweb.owlapi.model.OWLObject c)
c
-
@Deprecated public String[] getSubClassesNames(org.semanticweb.owlapi.model.OWLClass cls)
cls
-
@Deprecated public String[] getSynonymStrings(org.semanticweb.owlapi.model.OWLObject c)
c
-
public List<OWLGraphWrapper.ISynonym> getOBOSynonyms(org.semanticweb.owlapi.model.OWLObject c)
c
-
public List<String> getOBOSynonymStrings(org.semanticweb.owlapi.model.OWLObject c)
c
-
public String getOntologyId()
public String getIdentifier(org.semanticweb.owlapi.model.OWLObject owlObject)
owlObject
-
public String getIdentifier(org.semanticweb.owlapi.model.IRI iriId)
iriId
-
public org.semanticweb.owlapi.model.IRI getIRIByIdentifier(String id)
public org.semanticweb.owlapi.model.OWLObject getOWLObjectByIdentifier(String id)
id
- - e.g. GO:0008150
public org.semanticweb.owlapi.model.OWLObjectProperty getOWLObjectPropertyByIdentifier(String id)
id
- - e.g. GO:0008150
public org.semanticweb.owlapi.model.OWLNamedIndividual getOWLIndividualByIdentifier(String id)
id
- - e.g. GO:0008150
public org.semanticweb.owlapi.model.OWLClass getOWLClassByIdentifier(String id)
id
- - e.g. GO:0008150
public org.semanticweb.owlapi.model.OWLObject getOWLObjectByLabel(String label)
label
-
public org.semanticweb.owlapi.model.IRI getIRIByLabel(String label)
label
-
public org.semanticweb.owlapi.model.IRI getIRIByLabel(String label, boolean isEnforceUnivocal) throws SharedLabelException
label
- isEnforceUnivocal
-
SharedLabelException
- if >1 IRI shares input labelpublic org.semanticweb.owlapi.model.OWLClass getOWLClass(String s)
s
- IRI string
OWLClass
public org.semanticweb.owlapi.model.OWLClass getOWLClass(org.semanticweb.owlapi.model.IRI iri)
iri
-
OWLClass
public org.semanticweb.owlapi.model.OWLClass getOWLClass(org.semanticweb.owlapi.model.OWLObject x)
x
-
OWLClass
public org.semanticweb.owlapi.model.OWLNamedIndividual getOWLIndividual(org.semanticweb.owlapi.model.IRI iri)
iri
-
OWLNamedIndividual
public org.semanticweb.owlapi.model.OWLNamedIndividual getOWLIndividual(String s)
s
-
OWLNamedIndividual
getOWLIndividual(IRI)
public org.semanticweb.owlapi.model.OWLObjectProperty getOWLObjectProperty(String iri)
iri
-
OWLObjectProperty
public org.semanticweb.owlapi.model.OWLObjectProperty getOWLObjectProperty(org.semanticweb.owlapi.model.IRI iri)
public org.semanticweb.owlapi.model.OWLAnnotationProperty getOWLAnnotationProperty(org.semanticweb.owlapi.model.IRI iri)
public org.semanticweb.owlapi.model.OWLObject getOWLObject(String s)
s
- IRI string
OWLObject
getOWLObject(IRI iri)
public org.semanticweb.owlapi.model.OWLObject getOWLObject(org.semanticweb.owlapi.model.IRI s)
s
- entity IRI
OWLObject
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