Package | Description |
---|---|
owltools.gfx |
GFX - OWL Graphics and Visualization
|
owltools.graph |
OWLGraph -- OBO-like Graph Wrapper for OWL Ontologies
|
owltools.io |
IO - Input/Output
|
Modifier and Type | Method and Description |
---|---|
void |
OWLGraphLayoutRenderer.addEdge(OWLGraphEdge e)
Adds an edge to the graph.
|
static RelationType |
OWLGraphStrokeEdge.getRelationType(OWLGraphEdge owlGraphEdge,
OWLGraphWrapper graph)
Sets the value of relType based on OWLGraphEdge properties
TODO : this is too hacky.
|
OWLGraphStrokeEdge |
OWLGraphLayoutRenderer.makeEdge(OWLGraphEdge e)
Make a layout edge from a OWLGraphEdge
make private?
|
Constructor and Description |
---|
OWLGraphStrokeEdge(OWLGraphLayoutNode parent,
OWLGraphLayoutNode child,
OWLGraphEdge oge,
OWLGraphWrapper graph) |
Modifier and Type | Field and Description |
---|---|
Map<org.semanticweb.owlapi.model.OWLObject,Set<OWLGraphEdge>> |
OWLGraphWrapperEdges.inferredEdgeBySource |
Modifier and Type | Method and Description |
---|---|
OWLGraphEdge |
OWLGraphWrapperEdges.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
|
OWLGraphEdge |
OWLGraphWrapperEdgesExtended.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 |
OWLGraphWrapperEdgesExtended.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. |
OWLGraphEdge |
OWLGraphEdge.merge(OWLGraphEdge edge)
Merges this
OWLGraphEdge and edge into a new one, containing
the union of their underlying OWLAxiom s, as returned by getAxioms() . |
Modifier and Type | Method and Description |
---|---|
static Set<OWLGraphEdge> |
OWLGraphUtil.findCommonSubsumersAsEdges(OWLGraphWrapper g,
org.semanticweb.owlapi.model.OWLObject x,
org.semanticweb.owlapi.model.OWLObject y) |
static Set<OWLGraphEdge> |
OWLGraphUtil.findLeastCommonSubsumersAsEdges(OWLGraphWrapper g,
org.semanticweb.owlapi.model.OWLObject x,
org.semanticweb.owlapi.model.OWLObject y) |
Set<OWLGraphEdge> |
OWLGraphWrapperEdges.getCompleteEdgesBetween(org.semanticweb.owlapi.model.OWLObject s,
org.semanticweb.owlapi.model.OWLObject t) |
Set<OWLGraphEdge> |
OWLGraphWrapperEdges.getCompleteOutgoingEdgesClosure(org.semanticweb.owlapi.model.OWLObject s)
|
Set<OWLGraphEdge> |
OWLGraphWrapperEdges.getEdgesBetween(org.semanticweb.owlapi.model.OWLObject s,
org.semanticweb.owlapi.model.OWLObject t) |
Set<OWLGraphEdge> |
OWLGraphWrapperEdgesExtended.getGCIIncomingEdges(org.semanticweb.owlapi.model.OWLClass t)
Retrieve OBO GCI relations incoming to
t as a Set of OWLGraphEdge s. |
Set<OWLGraphEdge> |
OWLGraphWrapperEdgesExtended.getGCIOutgoingEdges(org.semanticweb.owlapi.model.OWLClass s)
Retrieve OBO GCI relations outgoing from
s as a Set of OWLGraphEdge s. |
Set<OWLGraphEdge> |
OWLGraphWrapperEdgesExtended.getGCIOutgoingEdges(org.semanticweb.owlapi.model.OWLClass s,
Set<org.semanticweb.owlapi.model.OWLPropertyExpression> overProps)
Same as
OWLGraphWrapperEdgesExtended.getGCIOutgoingEdges(OWLClass) , but with a Set of
OWLPropertyExpression allowing to filter the relations retrieved. |
Set<OWLGraphEdge> |
OWLGraphWrapperEdges.getIncomingEdges(org.semanticweb.owlapi.model.OWLObject t) |
Set<OWLGraphEdge> |
OWLGraphWrapperEdges.getIncomingEdgesClosure(org.semanticweb.owlapi.model.OWLObject t)
gets all inferred edges coming in to the target edge
|
Set<OWLGraphEdge> |
OWLGraphWrapperEdges.getIncomingEdgesClosure(org.semanticweb.owlapi.model.OWLObject t,
boolean isComplete)
As
OWLGraphWrapperEdges.getIncomingEdgesClosure(OWLObject t) , but allows the option of including
'complete' edge list. |
Set<OWLGraphEdge> |
OWLGraphWrapperEdgesExtended.getIncomingEdgesWithGCI(org.semanticweb.owlapi.model.OWLObject t)
Similar to
OWLGraphWrapperEdges.getIncomingEdges(OWLObject) , but the returned
Set also includes OBO GCI incoming edges (see
OWLGraphWrapperEdgesExtended.getGCIIncomingEdges(OWLClass) ). |
Set<OWLGraphEdge> |
OWLGraphWrapperEdges.getInstanceChainsFromClosure(org.semanticweb.owlapi.model.OWLClass c)
Finds all edges between an instance i and he given class c.
|
Set<OWLGraphEdge> |
OWLGraphWrapperEdges.getOutgoingEdges(org.semanticweb.owlapi.model.OWLObject cls)
retrieves direct edges from a source
to the direct **named** target
e.g.
|
Set<OWLGraphEdge> |
OWLGraphWrapperEdges.getOutgoingEdges(org.semanticweb.owlapi.model.OWLObject obj,
boolean isClosure,
boolean isReflexive) |
Set<OWLGraphEdge> |
OWLGraphWrapperEdges.getOutgoingEdges(org.semanticweb.owlapi.model.OWLObject cls,
Set<? extends org.semanticweb.owlapi.model.OWLPropertyExpression> props)
retrieves direct edges from a source
to the direct **named** target for a given set of properties
e.g.
|
Set<OWLGraphEdge> |
OWLGraphWrapperEdges.getOutgoingEdgesClosure(org.semanticweb.owlapi.model.OWLObject s)
Retrieves the graph closure originating from source.
|
Set<OWLGraphEdge> |
OWLGraphWrapperEdges.getOutgoingEdgesClosure(org.semanticweb.owlapi.model.OWLObject s,
boolean isComplete)
|
Set<OWLGraphEdge> |
OWLGraphWrapperEdges.getOutgoingEdgesClosure(org.semanticweb.owlapi.model.OWLObject s,
Set<? extends org.semanticweb.owlapi.model.OWLPropertyExpression> overProperties)
As
OWLGraphWrapperEdges.getOutgoingEdgesClosure(OWLObject s) , but only consider the specified
set of properties when walking the graph. |
Set<OWLGraphEdge> |
OWLGraphWrapperEdges.getOutgoingEdgesClosureReflexive(org.semanticweb.owlapi.model.OWLObject s)
as
OWLGraphWrapperEdges.getOutgoingEdgesClosure(OWLObject) , but also includes an identity edge |
Set<OWLGraphEdge> |
OWLGraphWrapperEdges.getOutgoingEdgesClosureReflexive(org.semanticweb.owlapi.model.OWLObject s,
Set<? extends org.semanticweb.owlapi.model.OWLPropertyExpression> props)
as
OWLGraphWrapperEdges.getOutgoingEdgesClosure(OWLObject, Set) , but also include an identify edge |
Set<OWLGraphEdge> |
OWLGraphWrapperEdgesExtended.getOutgoingEdgesClosureWithGCI(org.semanticweb.owlapi.model.OWLObject s)
Similar to
OWLGraphWrapperEdges.getOutgoingEdgesClosure(OWLObject) , but also considering
OBO GCI relations. |
Set<OWLGraphEdge> |
OWLGraphWrapperEdgesExtended.getOutgoingEdgesNamedClosureOverSupProps(org.semanticweb.owlapi.model.OWLObject s)
Same method as
OWLGraphWrapperEdges.getOutgoingEdgesClosure(OWLObject) ,
except that only the OWLGraphEdge s 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> |
OWLGraphWrapperEdgesExtended.getOutgoingEdgesNamedClosureOverSupPropsWithGCI(org.semanticweb.owlapi.model.OWLObject s)
Similar to
OWLGraphWrapperEdgesExtended.getOutgoingEdgesNamedClosureOverSupProps(OWLObject) but with
the OBO GCI relations also taken into account. |
Set<OWLGraphEdge> |
OWLGraphWrapperEdgesExtended.getOutgoingEdgesWithGCI(org.semanticweb.owlapi.model.OWLObject s)
Similar to
OWLGraphWrapperEdges.getOutgoingEdges(OWLObject) , but the returned
Set also includes OBO GCI outgoing edges (see
OWLGraphWrapperEdgesExtended.getGCIOutgoingEdges(OWLClass) ). |
Set<OWLGraphEdge> |
OWLGraphWrapperEdgesExtended.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
OWLGraphWrapperEdgesExtended.getGCIOutgoingEdges(OWLClass) ). |
LinkedHashSet<OWLGraphEdge> |
OWLGraphWrapperEdgesExtended.getOWLGraphEdgeSubRelsReflexive(OWLGraphEdge edge)
Get the sub-relations of
edge . |
Set<OWLGraphEdge> |
OWLGraphWrapperEdges.getOWLGraphEdgeSubsumers(OWLGraphEdge e)
generalizes over quantified properties
|
Set<OWLGraphEdge> |
OWLGraphWrapperEdges.getOWLGraphEdgeSubsumers(OWLGraphEdge e,
int i) |
Set<OWLGraphEdge> |
OWLGraphWrapperEdges.getPrimitiveIncomingEdges(org.semanticweb.owlapi.model.OWLObject t) |
Set<OWLGraphEdge> |
OWLGraphWrapperEdges.getPrimitiveOutgoingEdges(org.semanticweb.owlapi.model.OWLObject s)
primitive edges connect any combination of named objects and expressions
|
Set<OWLGraphEdge> |
OWLGraphWrapperEdges.getPrimitiveOutgoingEdges(org.semanticweb.owlapi.model.OWLObject s,
Set<? extends org.semanticweb.owlapi.model.OWLPropertyExpression> overProperties) |
protected Set<OWLGraphEdge> |
OWLGraphWrapperEdges.primitiveEdgeToFullEdges(OWLGraphEdge e) |
Modifier and Type | Method and Description |
---|---|
boolean |
OWLGraphEdge.OWLGraphEdgeSet.add(OWLGraphEdge edge)
Try to add
edge to this OWLGraphEdgeSet , or, if it already
contains an equal OWLGraphEdge , merges their underlying OWLAxiom s
(as returned by their getOWLAxioms methods). |
boolean |
OWLGraphManipulator.addEdge(OWLGraphEdge edge)
Add
edge to its related ontology. |
String |
OWLGraphWrapperEdgesAdvanced.classifyRelationship(OWLGraphEdge owlGraphEdge,
org.semanticweb.owlapi.model.OWLObject edgeDirector,
Set<? extends org.semanticweb.owlapi.model.OWLPropertyExpression> props)
Classify the an edge and target as a human readable string for further processing.
|
protected boolean |
OWLGraphWrapperEdges.combineEdgePair(OWLGraphEdge mergedEdge,
List<OWLQuantifiedProperty> neQp,
List<OWLQuantifiedProperty> extEdgeQp,
int nextDist)
Combine the
OWLQuantifiedProperty List s neQp and
extEdgeQp and assigned the resulting OWLQuantifiedProperty s
to mergedEdge . |
OWLGraphEdge |
OWLGraphWrapperEdges.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
|
OWLGraphEdge |
OWLGraphWrapperEdgesExtended.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 |
OWLGraphWrapperEdgesExtended.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 |
OWLGraphWrapperEdgesExtended.edgeToSourceExpression(OWLGraphEdge e)
Translates the source of an
OWLGraphEdge into an OWLClassExpression
(but, as the method getSource() returns an OWLObject ,
this method also returns an OWLObject ). |
org.semanticweb.owlapi.model.OWLObject |
OWLGraphWrapperEdges.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.
|
boolean |
OWLGraphEdge.equalsGCI(OWLGraphEdge e)
Checks that the
gciFiller and gciRelation of this OWLGraphEdge
an of e are equals. |
String |
OWLGraphWrapperEdges.getEdgeLabel(OWLGraphEdge e)
Get the human readable label for an edge.
|
LinkedHashSet<OWLGraphEdge> |
OWLGraphWrapperEdgesExtended.getOWLGraphEdgeSubRelsReflexive(OWLGraphEdge edge)
Get the sub-relations of
edge . |
Set<OWLGraphEdge> |
OWLGraphWrapperEdges.getOWLGraphEdgeSubsumers(OWLGraphEdge e)
generalizes over quantified properties
|
Set<OWLGraphEdge> |
OWLGraphWrapperEdges.getOWLGraphEdgeSubsumers(OWLGraphEdge e,
int i) |
boolean |
OWLGraphWrapperEdgesExtended.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 |
OWLGraphManipulator.isAPartOfEdge(OWLGraphEdge edge)
Determine if
edge represents a part_of relation or one of its sub-relations
(e.g., "deep_part_of"). |
boolean |
OWLGraphManipulator.isASubClassOfEdge(OWLGraphEdge edge)
Determine if
edge represents an is_a relation. |
boolean |
OWLGraphWrapperEdges.isExcludeEdge(OWLGraphEdge edge) |
OWLGraphEdge |
OWLGraphEdge.merge(OWLGraphEdge edge)
Merges this
OWLGraphEdge and edge into a new one, containing
the union of their underlying OWLAxiom s, as returned by getAxioms() . |
protected Set<OWLGraphEdge> |
OWLGraphWrapperEdges.primitiveEdgeToFullEdges(OWLGraphEdge e) |
Set<org.semanticweb.owlapi.model.OWLObject> |
OWLGraphWrapperEdges.queryDescendants(OWLGraphEdge e)
Treats an edge as a path and performs a query.
|
boolean |
OWLGraphManipulator.removeEdge(OWLGraphEdge edge)
Remove
edge from its ontology. |
Modifier and Type | Method and Description |
---|---|
boolean |
OWLGraphEdge.OWLGraphEdgeSet.addAll(Collection<? extends OWLGraphEdge> edges)
Try to add or merge each element of
edges into this OWLGraphEdgeSet ,
as performed by the method OWLGraphEdge.OWLGraphEdgeSet.add(OWLGraphEdge) . |
int |
OWLGraphManipulator.addEdges(Set<OWLGraphEdge> edges)
Add
edges to their related ontology. |
protected void |
OWLGraphWrapperEdges.filterEdges(Set<OWLGraphEdge> edges,
Set<? extends org.semanticweb.owlapi.model.OWLPropertyExpression> overProperties) |
int |
OWLGraphManipulator.removeEdges(Collection<OWLGraphEdge> edges)
Remove
edges from their related ontology. |
Constructor and Description |
---|
OWLGraphEdge(OWLGraphEdge edge)
Copy constructor.
|
Constructor and Description |
---|
OWLGraphEdgeSet(Set<OWLGraphEdge> edges) |
Modifier and Type | Method and Description |
---|---|
Object |
OWLGsonRenderer.convert(OWLGraphEdge edge) |
Object |
OWLGsonParser.convert(OWLGraphEdge edge) |
String |
OWLPrettyPrinter.render(OWLGraphEdge edge) |
void |
OWLGsonRenderer.render(OWLGraphEdge a) |
void |
OWLGsonParser.render(OWLGraphEdge a) |
void |
GraphClosureRenderer.render(OWLGraphEdge e) |
void |
CompactGraphClosureRenderer.render(OWLGraphEdge e) |
void |
ClassExpressionGraphClosureRenderer.render(OWLGraphEdge e) |
void |
ChadoGraphClosureRenderer.render(OWLGraphEdge e) |
abstract void |
AbstractClosureRenderer.render(OWLGraphEdge e) |
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