owltools.graph

Class OWLGraphWrapperEdgesExtended

java.lang.Object

owltools.graph.OWLGraphWrapperBasic

owltools.graph.OWLGraphWrapperExtended

owltools.graph.OWLGraphWrapperEdges

owltools.graph.OWLGraphWrapperEdgesExtended

Direct Known Subclasses:

OWLGraphWrapperEdgesAdvanced

public class OWLGraphWrapperEdgesExtended
extends OWLGraphWrapperEdges

This class groups methods that could be modified, or added to OWLGraphWrapper and parent classes.

Since:

November 2013

Version:

October 2014

Author:

Frederic Bastian

Nested Class Summary

Nested classes/interfaces inherited from class owltools.graph.OWLGraphWrapperEdges

OWLGraphWrapperEdges.Config

Field Summary

Fields inherited from class owltools.graph.OWLGraphWrapperEdges

inferredEdgeBySource, profiler

Fields inherited from class owltools.graph.OWLGraphWrapperBasic

sourceOntology, supportOntologySet

Constructor Summary

Constructors

Modifier	Constructor and Description
	OWLGraphWrapperEdgesExtended(org.semanticweb.owlapi.model.OWLOntology ontology) Default constructor.
protected	OWLGraphWrapperEdgesExtended(String iri)

Method Summary

Methods

Modifier and Type	Method and Description
void	clearCachedEdges() Clear the current edge cache.
OWLGraphEdge	combineEdgePairWithGCI(org.semanticweb.owlapi.model.OWLObject s, OWLGraphEdge ne, OWLGraphEdge extEdge, int nextDist) Same as OWLGraphWrapperEdges.combineEdgePair(OWLObject, OWLGraphEdge, OWLGraphEdge, int) except that the GCI filler an GCI relation of the edges are taken into account.
OWLGraphEdge	combineEdgePairWithSuperPropsAndGCI(OWLGraphEdge firstEdge, OWLGraphEdge secondEdge) Combines firstEdge and secondEdge to create a new edge from the source of firstEdge to the target of secondEdge, with properties combined in a regular way, and over super properties.
org.semanticweb.owlapi.model.OWLObject	edgeToSourceExpression(OWLGraphEdge e) Translates the source of an OWLGraphEdge into an OWLClassExpression (but, as the method OWLGraphEdge.getSource() returns an OWLObject, this method also returns an OWLObject).
Set<org.semanticweb.owlapi.model.OWLClass>	getAllOWLClasses() Get all OWLClasses from all ontologies, that are neither top entity (owl:thing), nor bottom entity (owl:nothing), nor deprecated (OWLGraphWrapperExtended.isObsolete(OWLObject) returns false).
Set<org.semanticweb.owlapi.model.OWLClass>	getAllOWLClassesFromSource() Get only the OWLClasses from the OWLOntology returned by OWLGraphWrapperBasic.getSourceOntology(), that are neither top entity (owl:thing), nor bottom entity (owl:nothing), nor deprecated (OWLGraphWrapperExtended.isObsolete(OWLObject) returns false).
Set<org.semanticweb.owlapi.model.OWLClass>	getAncestorsThroughIsA(org.semanticweb.owlapi.model.OWLObject x) Retrieve OWLClass ancestors of x only using "is_a" relations (SubClassOf).
Set<org.semanticweb.owlapi.model.OWLClass>	getDescendantsThroughIsA(org.semanticweb.owlapi.model.OWLObject x) Retrieve OWLClass descendants of x only using "is_a" relations (SubClassOf).
Set<OWLGraphEdge>	getGCIIncomingEdges(org.semanticweb.owlapi.model.OWLClass t) Retrieve OBO GCI relations incoming to t as a Set of OWLGraphEdges.
Set<OWLGraphEdge>	getGCIOutgoingEdges(org.semanticweb.owlapi.model.OWLClass s) Retrieve OBO GCI relations outgoing from s as a Set of OWLGraphEdges.
Set<OWLGraphEdge>	getGCIOutgoingEdges(org.semanticweb.owlapi.model.OWLClass s, Set<org.semanticweb.owlapi.model.OWLPropertyExpression> overProps) Same as getGCIOutgoingEdges(OWLClass), but with a Set of OWLPropertyExpression allowing to filter the relations retrieved.
Set<OWLGraphEdge>	getIncomingEdgesWithGCI(org.semanticweb.owlapi.model.OWLObject t) Similar to OWLGraphWrapperEdges.getIncomingEdges(OWLObject), but the returned Set also includes OBO GCI incoming edges (see getGCIIncomingEdges(OWLClass)).
Set<org.semanticweb.owlapi.model.OWLNamedObject>	getNamedAncestorsWithGCI(org.semanticweb.owlapi.model.OWLObject sourceObject) Similar to OWLGraphWrapperEdges.getNamedAncestors(OWLObject) but also considering GCI relations.
Set<org.semanticweb.owlapi.model.OWLNamedObject>	getNamedAncestorsWithGCI(org.semanticweb.owlapi.model.OWLObject sourceObject, Set<org.semanticweb.owlapi.model.OWLPropertyExpression> overProps) Similar to getNamedAncestorsWithGCI(OWLObject, Set) but allowing to filter the relations considered.
Set<org.semanticweb.owlapi.model.OWLClass>	getOntologyLeaves() Return the OWLClasses leaves of any ontology (OWLClasses with no incoming edges as returned by {OWLGraphWrapperEdges#getIncomingEdgesWithGCI(OWLObject)}), and not deprecated (OWLGraphWrapperExtended.isObsolete(OWLObject) returns false; edges incoming from an obsolete class are not considered)
Set<org.semanticweb.owlapi.model.OWLClass>	getOntologyRoots() Return the OWLClasses root of any ontology (OWLClasses with no outgoing edges as returned by {OWLGraphWrapperEdges#getOutgoingEdgesWithGCI(OWLObject)}), and not deprecated (OWLGraphWrapperExtended.isObsolete(OWLObject) returns false)).
Set<org.semanticweb.owlapi.model.OWLClass>	getOntologyRoots(Set<org.semanticweb.owlapi.model.OWLPropertyExpression> overProperties) Return the OWLClasses root of any ontology over the specified OWLPropertyExpressions (OWLClasses with no outgoing edges of the specified type, as returned by {OWLGraphWrapperEdges#getOutgoingEdgesWithGCI(OWLObject, Set)}), and not deprecated (OWLGraphWrapperExtended.isObsolete(OWLObject) returns false); edges going to obsolete classes are not taken into account).
Set<OWLGraphEdge>	getOutgoingEdgesClosureWithGCI(org.semanticweb.owlapi.model.OWLObject s) Similar to OWLGraphWrapperEdges.getOutgoingEdgesClosure(OWLObject), but also considering OBO GCI relations.
Set<OWLGraphEdge>	getOutgoingEdgesNamedClosureOverSupProps(org.semanticweb.owlapi.model.OWLObject s) Same method as OWLGraphWrapperEdges.getOutgoingEdgesClosure(OWLObject), except that only the OWLGraphEdges going to a named target are returned, and that the list of connecting edge properties are not only combined using the composition rules as usual, but also over super properties (see for instance #combineEdgePairWithSuperPropsAndGCI(OWLGraphEdge, OWLGraphEdge).
Set<OWLGraphEdge>	getOutgoingEdgesNamedClosureOverSupPropsWithGCI(org.semanticweb.owlapi.model.OWLObject s) Similar to getOutgoingEdgesNamedClosureOverSupProps(OWLObject) but with the OBO GCI relations also taken into account.
Set<OWLGraphEdge>	getOutgoingEdgesWithGCI(org.semanticweb.owlapi.model.OWLObject s) Similar to OWLGraphWrapperEdges.getOutgoingEdges(OWLObject), but the returned Set also includes OBO GCI outgoing edges (see getGCIOutgoingEdges(OWLClass)).
Set<OWLGraphEdge>	getOutgoingEdgesWithGCI(org.semanticweb.owlapi.model.OWLObject s, Set<org.semanticweb.owlapi.model.OWLPropertyExpression> overProperties) Similar to OWLGraphWrapperEdges.getOutgoingEdges(OWLObject, Set), but the returned Set also includes OBO GCI outgoing edges (see getGCIOutgoingEdges(OWLClass)).
Set<org.semanticweb.owlapi.model.OWLClass>	getOWLClassAncestors(org.semanticweb.owlapi.model.OWLClass sourceClass) Return the OWLClasses ancestor of sourceClass.
Set<org.semanticweb.owlapi.model.OWLClass>	getOWLClassAncestorsWithGCI(org.semanticweb.owlapi.model.OWLObject sourceObject) Similar to getNamedAncestorsWithGCI(OWLObject) but returning only OWLClasses.
Set<org.semanticweb.owlapi.model.OWLClass>	getOWLClassDescendants(org.semanticweb.owlapi.model.OWLClass parentClass) Return the OWLClasses descendant of parentClass.
Set<org.semanticweb.owlapi.model.OWLClass>	getOWLClassDescendantsWithGCI(org.semanticweb.owlapi.model.OWLClass parentClass) Similar to getOWLClassDescendants(OWLClass) but also considering GCI relations.
Set<org.semanticweb.owlapi.model.OWLClass>	getOWLClassDescendantsWithGCI(org.semanticweb.owlapi.model.OWLClass parentClass, Set<org.semanticweb.owlapi.model.OWLPropertyExpression> overProps) Similar to #getOWLClassDescendantsWithGCI(OWLObject) but allowing to filter the relations considered.
Set<org.semanticweb.owlapi.model.OWLClass>	getOWLClassDirectAncestors(org.semanticweb.owlapi.model.OWLClass subClass) Return the OWLClasses that are direct parent of subClass.
Set<org.semanticweb.owlapi.model.OWLClass>	getOWLClassDirectDescendants(org.semanticweb.owlapi.model.OWLClass parentClass) Return the OWLClasses directly descendant of parentClass.
Set<org.semanticweb.owlapi.model.OWLClass>	getOWLClassDirectDescendantsWithGCI(org.semanticweb.owlapi.model.OWLClass parentClass) Similar to getOWLClassDirectDescendants(OWLClass) but also considering GCI relations.
LinkedHashSet<OWLGraphEdge>	getOWLGraphEdgeSubRelsReflexive(OWLGraphEdge edge) Get the sub-relations of edge.
Set<org.semanticweb.owlapi.model.OWLAnnotationProperty>	getSubAnnotationPropertiesOf(org.semanticweb.owlapi.model.OWLAnnotationProperty prop) Returns the direct child properties of prop in all ontologies.
LinkedHashSet<org.semanticweb.owlapi.model.OWLAnnotationProperty>	getSubAnnotationPropertyClosureOf(org.semanticweb.owlapi.model.OWLAnnotationProperty prop) Returns all child properties of prop in all ontologies, ordered from the more general (closer from prop) to the more precise.
LinkedHashSet<org.semanticweb.owlapi.model.OWLAnnotationProperty>	getSubAnnotationPropertyReflexiveClosureOf(org.semanticweb.owlapi.model.OWLAnnotationProperty prop) Returns all sub-properties of prop in all ontologies, and prop itself as the first element (reflexive).
Set<org.semanticweb.owlapi.model.OWLObjectPropertyExpression>	getSubPropertiesOf(org.semanticweb.owlapi.model.OWLObjectPropertyExpression prop) Returns the direct child properties of prop in all ontologies.
LinkedHashSet<org.semanticweb.owlapi.model.OWLObjectPropertyExpression>	getSubPropertyClosureOf(org.semanticweb.owlapi.model.OWLObjectPropertyExpression prop) Returns all child properties of prop in all ontologies, ordered from the more general (closer from prop) to the more precise (e.g., for the "overlaps" property, return "part_of" then "in_deep_part_of").
LinkedHashSet<org.semanticweb.owlapi.model.OWLObjectPropertyExpression>	getSubPropertyReflexiveClosureOf(org.semanticweb.owlapi.model.OWLObjectPropertyExpression prop) Returns all sub-properties of prop in all ontologies, and prop itself as the first element (reflexive).
LinkedHashSet<org.semanticweb.owlapi.model.OWLObjectPropertyExpression>	getSuperPropertyReflexiveClosureOf(org.semanticweb.owlapi.model.OWLObjectPropertyExpression prop) Returns all parent properties of prop in all ontologies, and prop itself as the first element (reflexive).
boolean	hasFirstEdgeMoreGeneralGCIParams(OWLGraphEdge firstEdge, OWLGraphEdge otherEdge) Determines whether the GCI parameters of the GCI relation firstEdge are more general than the GCI parameters of the GCI relation otherEdge.
boolean	isOWLObjectInSubsets(org.semanticweb.owlapi.model.OWLObject testObject, Collection<String> subsets) Determine if testObject belongs to at least one of the subsets in subsets.
boolean	isRealClass(org.semanticweb.owlapi.model.OWLObject object) Determines that object is an OWLClass that is neither owl:thing, nor owl:nothing, and that it is not deprecated (OWLGraphWrapperExtended.isObsolete(OWLObject) returns false).

Methods inherited from class owltools.graph.OWLGraphWrapperEdges

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

Methods inherited from class owltools.graph.OWLGraphWrapperExtended

getAllOWLObjectsByAltId, getAllUsedSubsets, getAltIds, getAnnotationProperty, getAnnotationPropertyValue, getAnnotationPropertyValue, getAnnotationPropertyValues, getAnnotationPropertyValues, getAnnotationValue, getAnnotationValues, getBuiltin, getComment, getComment, 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, getOWLClassesInSubset, getOWLIndividual, getOWLIndividual, getOWLIndividualByIdentifier, getOWLObject, getOWLObject, getOWLObjectByAltId, getOWLObjectByIdentifier, getOWLObjectByLabel, getOWLObjectProperty, getOWLObjectProperty, getOWLObjectPropertyByIdentifier, getOWLObjectsByAltId, getOWLObjectsInSubset, getRange, getReplacedBy, getSubsets, getSubsets, getVersions, getXref, getXref, isObsolete

Methods inherited from class owltools.graph.OWLGraphWrapperBasic

addImport, addImportsFromSupportOntologies, addSupportOntologiesFromImportsClosure, addSupportOntologiesFromImportsClosure, addSupportOntology, getAllOntologies, getAllOWLObjects, getAllOWLSubClassOfAxiomsForSubClass, getAllOWLSubClassOfAxiomsForSuperClass, getDataFactory, getManager, getSourceOntology, getSupportOntologySet, mergeImportClosure, mergeImportClosure, mergeOntology, mergeOntology, mergeSupportOntology, mergeSupportOntology, remakeOntologiesFromImportsClosure, remakeOntologiesFromImportsClosure, removeSupportOntology, setSourceOntology, setSupportOntologySet

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

OWLGraphWrapperEdgesExtended

public OWLGraphWrapperEdgesExtended(org.semanticweb.owlapi.model.OWLOntology ontology)

Default constructor.

Parameters:

ontology - The OWLOntology that this object wraps.

OWLGraphWrapperEdgesExtended

protected OWLGraphWrapperEdgesExtended(String iri)
                                throws org.semanticweb.owlapi.model.UnknownOWLOntologyException,
                                       org.semanticweb.owlapi.model.OWLOntologyCreationException

Throws:

org.semanticweb.owlapi.model.UnknownOWLOntologyException

org.semanticweb.owlapi.model.OWLOntologyCreationException

Method Detail

isOWLObjectInSubsets

public boolean isOWLObjectInSubsets(org.semanticweb.owlapi.model.OWLObject testObject,
                           Collection<String> subsets)

Determine if testObject belongs to at least one of the subsets in subsets.

Parameters:

testObject - An OWLObject for which we want to know if it belongs to a subset in subsets.

subsets - A Collection of Strings that are the names of the subsets for which we want to check belonging of testObject.

Returns:

true if testObject belongs to a subset in subsets, false otherwise.

getSubAnnotationPropertiesOf

public Set<org.semanticweb.owlapi.model.OWLAnnotationProperty> getSubAnnotationPropertiesOf(org.semanticweb.owlapi.model.OWLAnnotationProperty prop)

Returns the direct child properties of prop in all ontologies.

Parameters:

prop - The OWLAnnotationProperty for which we want the direct sub-properties.

Returns:

A Set of OWLAnnotationPropertys that are the direct sub-properties of prop.

See Also:

getSubPropertyClosureOf(OWLObjectPropertyExpression), getSubPropertyReflexiveClosureOf(OWLObjectPropertyExpression)

getSubAnnotationPropertyClosureOf

public LinkedHashSet<org.semanticweb.owlapi.model.OWLAnnotationProperty> getSubAnnotationPropertyClosureOf(org.semanticweb.owlapi.model.OWLAnnotationProperty prop)

Returns all child properties of prop in all ontologies, ordered from the more general (closer from prop) to the more precise.

Parameters:

prop - the OWLAnnotationProperty for which we want the ordered sub-properties.

Returns:

A LinkedHashSet of OWLAnnotationPropertys ordered from the more general to the more precise.

See Also:

getSubAnnotationPropertiesOf(OWLAnnotationProperty), getSubAnnotationPropertyReflexiveClosureOf(OWLAnnotationProperty)

getSubAnnotationPropertyReflexiveClosureOf

public LinkedHashSet<org.semanticweb.owlapi.model.OWLAnnotationProperty> getSubAnnotationPropertyReflexiveClosureOf(org.semanticweb.owlapi.model.OWLAnnotationProperty prop)

Returns all sub-properties of prop in all ontologies, and prop itself as the first element (reflexive). The returned sub-properties are ordered from the more general (the closest from prop) to the more precise.

Parameters:

prop - the OWLAnnotationProperty for which we want the ordered sub-properties.

Returns:

A LinkedHashSet of OWLAnnotationPropertys ordered from the more general to the more precise, with prop as the first element.

See Also:

getSubAnnotationPropertiesOf(OWLAnnotationProperty), getSubAnnotationPropertyClosureOf(OWLAnnotationProperty)

getSubPropertiesOf

public Set<org.semanticweb.owlapi.model.OWLObjectPropertyExpression> getSubPropertiesOf(org.semanticweb.owlapi.model.OWLObjectPropertyExpression prop)

Returns the direct child properties of prop in all ontologies.

Parameters:

prop - The OWLObjectPropertyExpression for which we want the direct sub-properties.

Returns:

A Set of OWLObjectPropertyExpressions that are the direct sub-properties of prop.

See Also:

getSubPropertyClosureOf(OWLObjectPropertyExpression), getSubPropertyReflexiveClosureOf(OWLObjectPropertyExpression)

getSubPropertyClosureOf

public LinkedHashSet<org.semanticweb.owlapi.model.OWLObjectPropertyExpression> getSubPropertyClosureOf(org.semanticweb.owlapi.model.OWLObjectPropertyExpression prop)

Returns all child properties of prop in all ontologies, ordered from the more general (closer from prop) to the more precise (e.g., for the "overlaps" property, return "part_of" then "in_deep_part_of").

Parameters:

prop - the OWLObjectPropertyExpression for which we want the ordered sub-properties.

Returns:

A LinkedHashSet of OWLObjectPropertyExpressions ordered from the more general to the more precise.

See Also:

getSubPropertiesOf(OWLObjectPropertyExpression), getSubPropertyReflexiveClosureOf(OWLObjectPropertyExpression)

getSubPropertyReflexiveClosureOf

public LinkedHashSet<org.semanticweb.owlapi.model.OWLObjectPropertyExpression> getSubPropertyReflexiveClosureOf(org.semanticweb.owlapi.model.OWLObjectPropertyExpression prop)

Returns all sub-properties of prop in all ontologies, and prop itself as the first element (reflexive). The returned sub-properties are ordered from the more general (the closest from prop) to the more precise. For instance, if prop is "overlaps", the returned properties will be "overlaps", then "part_of", then "in_deep_part_of", ....

Parameters:

prop - the OWLObjectPropertyExpression for which we want the ordered sub-properties.

Returns:

A LinkedHashSet of OWLObjectPropertyExpressions ordered from the more general to the more precise, with prop as the first element.

See Also:

getSubPropertiesOf(OWLObjectPropertyExpression), getSubPropertyClosureOf(OWLObjectPropertyExpression)

getSuperPropertyReflexiveClosureOf

public LinkedHashSet<org.semanticweb.owlapi.model.OWLObjectPropertyExpression> getSuperPropertyReflexiveClosureOf(org.semanticweb.owlapi.model.OWLObjectPropertyExpression prop)

Returns all parent properties of prop in all ontologies, and prop itself as the first element (reflexive). Unlike the method owltools.graph.OWLGraphWrapperEdges.getSuperPropertyReflexiveClosureOf, the returned super properties here are ordered from the more precise to the more general (e.g., "in_deep_part_of", then "part_of", then "overlaps").

Overrides:

getSuperPropertyReflexiveClosureOf in class OWLGraphWrapperEdges

Parameters:

prop - the OWLObjectPropertyExpression for which we want the ordered super properties.

Returns:

A LinkedHashSet of OWLObjectPropertyExpressions ordered from the more precise to the more general, with prop as the first element.

getOWLGraphEdgeSubRelsReflexive

public LinkedHashSet<OWLGraphEdge> getOWLGraphEdgeSubRelsReflexive(OWLGraphEdge edge)

Get the sub-relations of edge. This method returns OWLGraphEdges with their OWLQuantifiedPropertys corresponding to the sub-properties of the properties of edge (even indirect sub-properties), ordered from the more general relations (the closest to edge) to the more precise relations. The first OWLGraphEdge in the returned Set is edge (reflexive method).

This is the opposite method of owltools.graph.OWLGraphWrapperEdges.getOWLGraphEdgeSubsumers(OWLGraphEdge), with reflexivity added.

Parameters:

edge - A OWLGraphEdge for which all sub-relations should be obtained.

Returns:

A Set of OWLGraphEdges representing the sub-relations of edge ordered from the more general to the more precise relation, with edge as the first element. An empty Set if the OWLQuantifiedPropertys of edge have no sub-properties.

combineEdgePairWithSuperPropsAndGCI

public OWLGraphEdge combineEdgePairWithSuperPropsAndGCI(OWLGraphEdge firstEdge,
                                               OWLGraphEdge secondEdge)

Combines firstEdge and secondEdge to create a new edge from the source of firstEdge to the target of secondEdge, with properties combined in a regular way, and over super properties.

This method is similar to owltools.graph.OWLGraphWrapperEdges#combineEdgePair(OWLObject, OWLGraphEdge, OWLGraphEdge, int), except it also tries to combine the OWLQuantifiedPropertys of the edges over super properties (see combinePropertyPairOverSuperProperties( OWLQuantifiedProperty, OWLQuantifiedProperty), currently combines over 2 properties only).

If one or both of the edges are GCI relations, and that their GCI fillers and/or GCI relations are related (see hasFirstEdgeMoreGeneralGCIParams(OWLGraphEdge, OWLGraphEdge)), the combined returned edge will have the most restrictive GCI filler and GCI relation. If they are not related, the edges will not be combined.

Parameters:

firstEdge - A OWLGraphEdge that is the first edge to combine, its source will be the source of the new edge

secondEdge - A OWLGraphEdge that is the second edge to combine, its target will be the target of the new edge

Returns:

A OWLGraphEdge resulting from the composition of firstEdge and secondEdge, with its OWLQuantifiedPropertys composed in a regular way, but also over super properties, and with the most restrictive GCI filler and GCI relation.

getOutgoingEdgesNamedClosureOverSupProps

public Set<OWLGraphEdge> getOutgoingEdgesNamedClosureOverSupProps(org.semanticweb.owlapi.model.OWLObject s)

Same method as OWLGraphWrapperEdges.getOutgoingEdgesClosure(OWLObject), except that only the OWLGraphEdges going to a named target are returned, and that the list of connecting edge properties are not only combined using the composition rules as usual, but also over super properties (see for instance #combineEdgePairWithSuperPropsAndGCI(OWLGraphEdge, OWLGraphEdge).

Also, redundant edges are filtered: if an edge is a sub-property of another one, only the most precise edge is returned.

Parameters:

s - The OWLObject which outgoing edges start from.

Returns:

A Set of OWLGraphEdges that represent the graph closure originating from s, with OWLQuantifiedPropertys combined using standard composition rules, but also over super-properties.

getOutgoingEdgesNamedClosureOverSupPropsWithGCI

public Set<OWLGraphEdge> getOutgoingEdgesNamedClosureOverSupPropsWithGCI(org.semanticweb.owlapi.model.OWLObject s)

Similar to getOutgoingEdgesNamedClosureOverSupProps(OWLObject) but with the OBO GCI relations also taken into account.

If both edges are GCI relations, and their GCI fillers and/or GCI relations are related (see hasFirstEdgeMoreGeneralGCIParams(OWLGraphEdge, OWLGraphEdge)), the combined returned edge will have the most restrictive GCI filler and GCI relation. If they are not related, the edges will not be combined. To retrieve all ancestors of an object, using also GCI relations, you should rather use getNamedAncestorsWithGCI(OWLObject).

Parameters:

s - See getOutgoingEdgesNamedClosureOverSupProps(OWLObject)

Returns:

See getOutgoingEdgesNamedClosureOverSupProps(OWLObject)

getOutgoingEdgesClosureWithGCI

public Set<OWLGraphEdge> getOutgoingEdgesClosureWithGCI(org.semanticweb.owlapi.model.OWLObject s)

Similar to OWLGraphWrapperEdges.getOutgoingEdgesClosure(OWLObject), but also considering OBO GCI relations.

Note that GCI relations are not combined when their gci_filler or gci_relation are different. The closure might then be incomplete.

Parameters:

s - See OWLGraphWrapperEdges.getOutgoingEdgesClosure(OWLObject)

Returns:

See OWLGraphWrapperEdges.getOutgoingEdgesClosure(OWLObject)

getGCIOutgoingEdges

public Set<OWLGraphEdge> getGCIOutgoingEdges(org.semanticweb.owlapi.model.OWLClass s)

Retrieve OBO GCI relations outgoing from s as a Set of OWLGraphEdges. This is similar to the method OWLGraphWrapperEdges.getOutgoingEdges(OWLObject), but returning GCI relations only. The OBO "gci_filler" and "gci_relation" could be retrieved by calling OWLGraphEdge.getGCIFiller() and OWLGraphEdge.getGCIRelation(), respectively.

More formally: OBO GCI relations are represented as SubClassOf axioms, where the sub-class is an ObjectIntersectionOf, with one operand being an OWLClass, and the other operand being an ObjectSomeValuesFrom(ObjectPropertyExpression OWLClass). The ObjectPropertyExpression will be retrieved by calling OWLGraphEdge.getGCIRelation(), the associated OWLClass in the ObjectSomeValuesFrom will be retrieved by calling OWLGraphEdge.getGCIFiller(). The OWLClass operand in the ObjectIntersectionOf will be considered as the source of the OWLGraphEdge. The target will be the super-class of the SubClassOf axiom, expanded to reach a named target (as usually with methods in OWLGraphWrapper). The current implementation assumes that OWLGraphEges representing OBO GCI relations always have OWLClasses as source and target.

Parameters:

s - An OWLClass for which we want to retrieve outgoing OBO GCI relations.

Returns:

A Set of OWLGraphEdges corresponding to GCI relations outgoing from s.

getGCIOutgoingEdges

public Set<OWLGraphEdge> getGCIOutgoingEdges(org.semanticweb.owlapi.model.OWLClass s,
                                    Set<org.semanticweb.owlapi.model.OWLPropertyExpression> overProps)

Same as getGCIOutgoingEdges(OWLClass), but with a Set of OWLPropertyExpression allowing to filter the relations retrieved.

Parameters:

s - See getGCIOutgoingEdges(OWLClass).

overProps - A Set of OWLPropertyExpression allowing to filter the OWLGraphEdges returned.

Returns:

See getGCIOutgoingEdges(OWLClass).

See Also:

getGCIOutgoingEdges(OWLClass)

getGCIIncomingEdges

public Set<OWLGraphEdge> getGCIIncomingEdges(org.semanticweb.owlapi.model.OWLClass t)

Retrieve OBO GCI relations incoming to t as a Set of OWLGraphEdges. See #getGCIOutgoingEdges(OWLObject) for details about OBO GCI relations, and about retrieving the associated "gci_filler" and "gci_relation".

Parameters:

t - An OWLClass for which we want to retrieve incoming OBO GCI relations.

Returns:

A Set of OWLGraphEdges corresponding to GCI relations incoming to t.

getOutgoingEdgesWithGCI

public Set<OWLGraphEdge> getOutgoingEdgesWithGCI(org.semanticweb.owlapi.model.OWLObject s)

Similar to OWLGraphWrapperEdges.getOutgoingEdges(OWLObject), but the returned Set also includes OBO GCI outgoing edges (see getGCIOutgoingEdges(OWLClass)).

Parameters:

s - An OWLObject for which we want to retrieve outgoing edges, including OBO GCI relations.

Returns:

A Set of OWLGraphEdges outgoing from s, including OBO GCI relations.

See Also:

getOutgoingEdgesWithGCI(OWLObject, Set), getGCIOutgoingEdges(OWLClass)

getOutgoingEdgesWithGCI

public Set<OWLGraphEdge> getOutgoingEdgesWithGCI(org.semanticweb.owlapi.model.OWLObject s,
                                        Set<org.semanticweb.owlapi.model.OWLPropertyExpression> overProperties)

Similar to OWLGraphWrapperEdges.getOutgoingEdges(OWLObject, Set), but the returned Set also includes OBO GCI outgoing edges (see getGCIOutgoingEdges(OWLClass)).

Parameters:

s - An OWLObject for which we want to retrieve outgoing edges, including OBO GCI relations.

overProps - A Set of OWLPropertyExpression allowing to filter the OWLGraphEdges returned.

Returns:

A Set of OWLGraphEdges outgoing from s, including OBO GCI relations.

See Also:

getGCIOutgoingEdges(OWLClass)

getIncomingEdgesWithGCI

public Set<OWLGraphEdge> getIncomingEdgesWithGCI(org.semanticweb.owlapi.model.OWLObject t)

Similar to OWLGraphWrapperEdges.getIncomingEdges(OWLObject), but the returned Set also includes OBO GCI incoming edges (see getGCIIncomingEdges(OWLClass)).

Parameters:

t - An OWLObject for which we want to retrieve incoming edges, including OBO GCI relations.

Returns:

A Set of OWLGraphEdges incoming to t, including OBO GCI relations.

See Also:

getGCIIncomingEdges(OWLClass)

getNamedAncestorsWithGCI

public Set<org.semanticweb.owlapi.model.OWLNamedObject> getNamedAncestorsWithGCI(org.semanticweb.owlapi.model.OWLObject sourceObject)

Similar to OWLGraphWrapperEdges.getNamedAncestors(OWLObject) but also considering GCI relations.

Parameters:

sourceObject - An OWLObject for which we want to retrieve ancestors through classical relations and through OBO GCI relations.

Returns:

A Set of OWLNamedObjects that are ancestors of sourceObject through classical relations and through OBO GCI relations.

See Also:

getNamedAncestorsWithGCI(OWLObject, Set), #getOWLClassAncestorsWithGCI(OWLObject, Set)

getNamedAncestorsWithGCI

public Set<org.semanticweb.owlapi.model.OWLNamedObject> getNamedAncestorsWithGCI(org.semanticweb.owlapi.model.OWLObject sourceObject,
                                                                        Set<org.semanticweb.owlapi.model.OWLPropertyExpression> overProps)

Similar to getNamedAncestorsWithGCI(OWLObject, Set) but allowing to filter the relations considered.

Parameters:

sourceObject - An OWLObject for which we want to retrieve ancestors through classical relations and through OBO GCI relations.

overProps - A Set of OWLPropertyExpression allowing to filter the relations considered to retrieve ancestors.

Returns:

A Set of OWLObjects that are ancestors of sourceObject through classical relations and through OBO GCI relations, filtered using overProps.

See Also:

getNamedAncestorsWithGCI(OWLObject), getOWLClassAncestorsWithGCI(OWLObject)

getOWLClassAncestorsWithGCI

public Set<org.semanticweb.owlapi.model.OWLClass> getOWLClassAncestorsWithGCI(org.semanticweb.owlapi.model.OWLObject sourceObject)

Similar to getNamedAncestorsWithGCI(OWLObject) but returning only OWLClasses.

Parameters:

sourceObject - An OWLObject for which we want to retrieve ancestors through classical relations and through OBO GCI relations.

Returns:

A Set of OWLClasss that are ancestors of sourceObject through classical relations and through OBO GCI relations.

getOWLClassDirectDescendantsWithGCI

public Set<org.semanticweb.owlapi.model.OWLClass> getOWLClassDirectDescendantsWithGCI(org.semanticweb.owlapi.model.OWLClass parentClass)

Similar to getOWLClassDirectDescendants(OWLClass) but also considering GCI relations.

Parameters:

parentClass - An OWLClass for which we want to retrieve direct descendants through classical relations and through OBO GCI relations.

Returns:

A Set of OWLClasss that are direct descendants of parentClass through classical relations and through OBO GCI relations.

getOWLClassDescendantsWithGCI

public Set<org.semanticweb.owlapi.model.OWLClass> getOWLClassDescendantsWithGCI(org.semanticweb.owlapi.model.OWLClass parentClass)

Similar to getOWLClassDescendants(OWLClass) but also considering GCI relations.

Parameters:

parentClass - An OWLClass for which we want to retrieve descendants through classical relations and through OBO GCI relations.

Returns:

A Set of OWLClasss that are descendants of parentClass through classical relations and through OBO GCI relations.

getOWLClassDescendantsWithGCI

public Set<org.semanticweb.owlapi.model.OWLClass> getOWLClassDescendantsWithGCI(org.semanticweb.owlapi.model.OWLClass parentClass,
                                                                       Set<org.semanticweb.owlapi.model.OWLPropertyExpression> overProps)

Similar to #getOWLClassDescendantsWithGCI(OWLObject) but allowing to filter the relations considered.

Parameters:

parentClass - An OWLClass for which we want to retrieve descendants through classical relations and through OBO GCI relations.

overProps - A Set of OWLPropertyExpression allowing to filter the relations considered to retrieve descendants.

Returns:

A Set of OWLClasss that are descendants of parentClass through classical relations and through OBO GCI relations, filtered using overProps.

combineEdgePairWithGCI

public OWLGraphEdge combineEdgePairWithGCI(org.semanticweb.owlapi.model.OWLObject s,
                                  OWLGraphEdge ne,
                                  OWLGraphEdge extEdge,
                                  int nextDist)

Same as OWLGraphWrapperEdges.combineEdgePair(OWLObject, OWLGraphEdge, OWLGraphEdge, int) except that the GCI filler an GCI relation of the edges are taken into account.

If both edges are GCI relations, and their GCI fillers and/or GCI relations are related (see hasFirstEdgeMoreGeneralGCIParams(OWLGraphEdge, OWLGraphEdge)), the combined returned edge will have the most restrictive GCI filler and GCI relation. If they are not related, the edges will not be combined.

Parameters:

s - See combineEdgePair method.

ne - See combineEdgePair method.

extEdge - See combineEdgePair method.

nextDist - See combineEdgePair method.

Returns:

See combineEdgePair method.

See Also:

OWLGraphWrapperEdges.combineEdgePair(OWLObject, OWLGraphEdge, OWLGraphEdge, int)

hasFirstEdgeMoreGeneralGCIParams

public boolean hasFirstEdgeMoreGeneralGCIParams(OWLGraphEdge firstEdge,
                                       OWLGraphEdge otherEdge)

Determines whether the GCI parameters of the GCI relation firstEdge are more general than the GCI parameters of the GCI relation otherEdge.

Note that if the GCI parameters (OWLGraphEdge.getGCIFiller() and OWLGraphEdge.getGCIRelation()) of firstEdge and of otherEdge are equal, this method will return false (use OWLGraphEdge.equalsGCI(OWLGraphEdge) instead). As a result, this method will also return false if none of the arguments are GCI relations.

For this method to return true, one of the parameters of firstEdge has to be more general than the same parameter of otherEdge, while the other parameter of firstEdge is equal or more general than the same parameter of otherEdge.

Note that the order of the parameters is important (if hasFirstEdgeMoreGeneralGCI(edge1, edge2) returns true, hasFirstEdgeMoreGeneralGCI(edge2, edge1) will return false).

Parameters:

firstEdge - An OWLGraphEdge for which we want to determine whether its GCI parameters are more general than those of otherEdge.

otherEdge - An OWLGraphEdge for which we want to determine GCI parameter inclusion into those of firstEdge.

Returns:

true if firstEdge has more general GCI parameters than those of otherEdge.

getAncestorsThroughIsA

public Set<org.semanticweb.owlapi.model.OWLClass> getAncestorsThroughIsA(org.semanticweb.owlapi.model.OWLObject x)

Retrieve OWLClass ancestors of x only using "is_a" relations (SubClassOf).

Parameters:

x - An OWLObject for which we want to retrieve OWLClass ancestors through "is_a" relations, even indirect.

Returns:

A Set of OWLClasses that are the ancestors of x through "is_a" relations.

See Also:

getDescendantsThroughIsA(OWLObject)

getDescendantsThroughIsA

public Set<org.semanticweb.owlapi.model.OWLClass> getDescendantsThroughIsA(org.semanticweb.owlapi.model.OWLObject x)

Retrieve OWLClass descendants of x only using "is_a" relations (SubClassOf).

Parameters:

x - An OWLObject for which we want to retrieve OWLClass descendants through "is_a" relations, even indirect.

Returns:

A Set of OWLClasses that are the descendants of x through "is_a" relations.

See Also:

getAncestorsThroughIsA(OWLObject)

clearCachedEdges

public void clearCachedEdges()

Description copied from class: OWLGraphWrapperEdges

Clear the current edge cache.

Overrides:

clearCachedEdges in class OWLGraphWrapperEdges

See Also:

OWLGraphWrapperEdges.cacheEdges()

edgeToSourceExpression

public org.semanticweb.owlapi.model.OWLObject edgeToSourceExpression(OWLGraphEdge e)

Translates the source of an OWLGraphEdge into an OWLClassExpression (but, as the method OWLGraphEdge.getSource() returns an OWLObject, this method also returns an OWLObject). This is the equivalent method to OWLGraphWrapperEdges.edgeToTargetExpression(OWLGraphEdge), but for the source.

This is useful when an OWLGraphEdge corresponds to an OBO gci_relation (OWLGraphEdge.isGCI() returns true). In that case, the returned value is an OWLObjectIntersectionOf. If it is not a GCI, the returned value is equal to OWLGraphEdge.getSource().

Parameters:

e - The OWLGraphEdge for which we want to translate the source into an OWLClassExpression.

Returns:

An OWLObject corresponding to the source of e.

getAllOWLClasses

public Set<org.semanticweb.owlapi.model.OWLClass> getAllOWLClasses()

Get all OWLClasses from all ontologies, that are neither top entity (owl:thing), nor bottom entity (owl:nothing), nor deprecated (OWLGraphWrapperExtended.isObsolete(OWLObject) returns false).

Overrides:

getAllOWLClasses in class OWLGraphWrapperBasic

Returns:

a Set containing all "real" OWLClasses from all ontologies.

getAllOWLClassesFromSource

public Set<org.semanticweb.owlapi.model.OWLClass> getAllOWLClassesFromSource()

Get only the OWLClasses from the OWLOntology returned by OWLGraphWrapperBasic.getSourceOntology(), that are neither top entity (owl:thing), nor bottom entity (owl:nothing), nor deprecated (OWLGraphWrapperExtended.isObsolete(OWLObject) returns false).

Returns:

a Set of OWLClasses from the source ontology, owl:thing, owl:nothing, deprecated classes excluded.

getOntologyRoots

public Set<org.semanticweb.owlapi.model.OWLClass> getOntologyRoots()

Return the OWLClasses root of any ontology (OWLClasses with no outgoing edges as returned by {OWLGraphWrapperEdges#getOutgoingEdgesWithGCI(OWLObject)}), and not deprecated (OWLGraphWrapperExtended.isObsolete(OWLObject) returns false)).

Returns:

A Set of OWLClasses that are the roots of any ontology.

getOntologyRoots

public Set<org.semanticweb.owlapi.model.OWLClass> getOntologyRoots(Set<org.semanticweb.owlapi.model.OWLPropertyExpression> overProperties)

Return the OWLClasses root of any ontology over the specified OWLPropertyExpressions (OWLClasses with no outgoing edges of the specified type, as returned by {OWLGraphWrapperEdges#getOutgoingEdgesWithGCI(OWLObject, Set)}), and not deprecated (OWLGraphWrapperExtended.isObsolete(OWLObject) returns false); edges going to obsolete classes are not taken into account).

Filtering roots using overProperties allow to ask question such as: what are the roots of the ontology according only to is_a and part_of relations.

Parameters:

overProps - A Set of OWLPropertyExpression allowing to filter the roots returned.

Returns:

A Set of OWLClasses that are the roots of any ontology over the provided OWLPropertyExpressions.

getOntologyLeaves

public Set<org.semanticweb.owlapi.model.OWLClass> getOntologyLeaves()

Return the OWLClasses leaves of any ontology (OWLClasses with no incoming edges as returned by {OWLGraphWrapperEdges#getIncomingEdgesWithGCI(OWLObject)}), and not deprecated (OWLGraphWrapperExtended.isObsolete(OWLObject) returns false; edges incoming from an obsolete class are not considered)

Returns:

A Set of OWLClasses that are the leaves of any ontology.

getOWLClassDescendants

public Set<org.semanticweb.owlapi.model.OWLClass> getOWLClassDescendants(org.semanticweb.owlapi.model.OWLClass parentClass)

Return the OWLClasses descendant of parentClass. This method is the same than owltools.graph.OWLGraphWrapperEdges.getDescendants(OWLObject), except it returns only OWLClasses.

Parameters:

parentClass -

Returns:

A Set of OWLClasses being the descendants of parentClass.

getOWLClassDirectDescendants

public Set<org.semanticweb.owlapi.model.OWLClass> getOWLClassDirectDescendants(org.semanticweb.owlapi.model.OWLClass parentClass)

Return the OWLClasses directly descendant of parentClass. This method returns all sources of all edges incoming to parentClass, that are OWLClasses.

Parameters:

parentClass - The OWLClass for which we want the direct descendant OWLClasses

Returns:

A Set of OWLClasses being the direct descendants of parentClass.

See Also:

OWLGraphWrapperEdges.getIncomingEdges(OWLObject)

getOWLClassDirectAncestors

public Set<org.semanticweb.owlapi.model.OWLClass> getOWLClassDirectAncestors(org.semanticweb.owlapi.model.OWLClass subClass)

Return the OWLClasses that are direct parent of subClass. This method returns all sources of all edges incoming to subClass, that are OWLClasses.

Parameters:

subClass -

Returns:

A Set of OWLClasses being the direct parents of subClass.

See Also:

OWLGraphWrapperEdges.getOutgoingEdges(OWLObject)

getOWLClassAncestors

public Set<org.semanticweb.owlapi.model.OWLClass> getOWLClassAncestors(org.semanticweb.owlapi.model.OWLClass sourceClass)

Return the OWLClasses ancestor of sourceClass. This method is the same than owltools.graph.OWLGraphWrapperEdges.getAncestors(OWLObject), except it returns only the ancestor that are OWLClasses.

Parameters:

sourceClass -

Returns:

A Set of OWLClasses being the ancestors of sourceClass.

isRealClass

public boolean isRealClass(org.semanticweb.owlapi.model.OWLObject object)

Determines that object is an OWLClass that is neither owl:thing, nor owl:nothing, and that it is not deprecated (OWLGraphWrapperExtended.isObsolete(OWLObject) returns false).

Parameters:

object - An OWLObject to be checked to be an OWLClass actually used.

Returns:

true if object is an OWLClass that is not owl:thing, nor owl:nothing, and is not deprecated.