public class OWLGraphWrapperEdgesAdvanced extends OWLGraphWrapperEdgesExtended implements Closeable
OWLGraphWrapper
,
OWLGraphWrapperEdges
OWLGraphWrapperEdges.Config
inferredEdgeBySource, profiler
sourceOntology, supportOntologySet
Modifier | Constructor and Description |
---|---|
protected |
OWLGraphWrapperEdgesAdvanced(org.semanticweb.owlapi.model.OWLOntology ontology) |
protected |
OWLGraphWrapperEdgesAdvanced(String iri) |
Modifier and Type | Method and Description |
---|---|
OWLShuntGraph |
addDirectDescendentsToShuntGraph(org.semanticweb.owlapi.model.OWLObject x,
OWLShuntGraph g,
List<String> rel_ids)
Add a set of edges, as descendants to x in OWLShuntGraph g.
|
void |
addPropertiesForMaterialization(Iterable<org.semanticweb.owlapi.model.OWLObjectProperty> properties) |
void |
addPropertyForMaterialization(org.semanticweb.owlapi.model.OWLObjectProperty p) |
void |
addPropertyIdsForMaterialization(Iterable<String> propertyIds) |
OWLShuntGraph |
addStepwiseAncestorsToShuntGraph(org.semanticweb.owlapi.model.OWLObject x,
OWLShuntGraph g,
List<String> rel_ids)
Add a set of edges, as ancestors to x in OWLShuntGraph g.
|
OWLShuntGraph |
addTransitiveAncestorsToShuntGraph(org.semanticweb.owlapi.model.OWLObject x,
OWLShuntGraph g,
List<String> rel_ids)
Add a set of edges, as ancestors to x in OWLShuntGraph g.
|
String |
categorizeNamespace(org.semanticweb.owlapi.model.OWLObject c,
Map<String,Object> configuration) |
String |
categorizeObject(org.semanticweb.owlapi.model.OWLNamedObject named,
Map<String,String> idspaceMappings,
Set<String> useNamespace,
boolean useFallback)
Create a category for a given named object.
|
String |
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.
|
void |
close() |
long |
getCurrentEdgesAdvancedCacheSize() |
String |
getDummyString(org.semanticweb.owlapi.model.OWLObject c,
List<String> sargs)
Helper function for flex loader for un-used single string fields
|
List<String> |
getDummyStrings(org.semanticweb.owlapi.model.OWLObject c,
List<String> sargs)
Helper function for flex loader for un-used single List of string fields
|
Map<String,String> |
getIsaPartofClosureMap(org.semanticweb.owlapi.model.OWLObject c)
Deprecated.
|
List<String> |
getIsaPartofIDClosure(org.semanticweb.owlapi.model.OWLObject c)
Deprecated.
|
List<String> |
getIsaPartofIDClosure(org.semanticweb.owlapi.model.OWLObject c,
List<String> sargs)
Deprecated.
|
List<String> |
getIsaPartofLabelClosure(org.semanticweb.owlapi.model.OWLObject c)
Deprecated.
|
List<String> |
getIsaPartofLabelClosure(org.semanticweb.owlapi.model.OWLObject c,
List<String> sargs)
Deprecated.
|
OWLShuntGraph |
getLineageShuntGraph(org.semanticweb.owlapi.model.OWLObject x,
List<String> rel_ids)
Gets all ancestors that are OWLNamedObjects.
|
String |
getLineageShuntGraphJSON(org.semanticweb.owlapi.model.OWLObject x,
List<String> sargs)
Return a JSONized version of the output of getLineageShuntGraph
|
OWLShuntGraph |
getNeighbors(org.semanticweb.owlapi.model.OWLObject x)
Retrieve direct neighbors of x in a shunt graph.
|
OWLShuntGraph |
getNeighbors(org.semanticweb.owlapi.model.OWLObject x,
List<String> sargs)
Retrieve direct neighbors of x in a shunt graph.
|
String |
getNeighborsJSON(org.semanticweb.owlapi.model.OWLObject x,
List<String> sargs)
Retrieve direct neighbors of x in a shunt graph JSON string.
|
OWLShuntGraph |
getNeighborsLimited(org.semanticweb.owlapi.model.OWLObject x,
int edgeLimit) |
String |
getNeighborsLimitedJSON(org.semanticweb.owlapi.model.OWLObject x,
List<String> sargs)
Retrieve direct neighbors of x in a shunt graph JSON string.
|
Set<String> |
getOnlyInTaxon(org.semanticweb.owlapi.model.OWLObject x,
List<String> sargs) |
Set<String> |
getOnlyInTaxonClosure(org.semanticweb.owlapi.model.OWLObject x,
List<String> relation_ids) |
Set<String> |
getOnlyInTaxonClosureLabels(org.semanticweb.owlapi.model.OWLObject x,
List<String> relation_ids) |
Map<String,String> |
getOnlyInTaxonLabelMap(org.semanticweb.owlapi.model.OWLObject x,
List<String> sargs) |
Set<String> |
getOnlyInTaxonLabels(org.semanticweb.owlapi.model.OWLObject x,
List<String> sargs) |
Map<String,String> |
getRelationClosureMap(org.semanticweb.owlapi.model.OWLObject c,
List<String> relation_ids)
Return a map of id to label for the closure of the ontology using the supplied relation id list and .isSubClassOf().
|
Map<String,String> |
getRelationClosureMapEngine(org.semanticweb.owlapi.model.OWLObject obj,
List<String> relation_ids)
Generator for the cache in
getRelationClosureMap(OWLObject, List) . |
List<String> |
getRelationIDClosure(org.semanticweb.owlapi.model.OWLObject c,
List<String> relation_ids)
Return a overlaps with getIsaPartofLabelClosure and stuff in GafSolrDocumentLoader.
|
List<String> |
getRelationLabelClosure(org.semanticweb.owlapi.model.OWLObject c,
List<String> relation_ids)
Return a overlaps with getIsaPartofIDClosure and stuff in GafSolrDocumentLoader.
|
OWLShuntGraph |
getSegmentShuntGraph(org.semanticweb.owlapi.model.OWLObject x,
List<String> rel_ids)
Gets all ancestors and direct descendants (distance == 1) that are OWLNamedObjects.
|
String |
getSegmentShuntGraphJSON(org.semanticweb.owlapi.model.OWLObject x,
List<String> sargs)
Return a JSONized version of the output of getSegmentShuntGraph
Defaults to is_a/part_of and regulates.
|
String[] |
getSubClassesNames(org.semanticweb.owlapi.model.OWLClass cls)
Deprecated.
|
Set<org.semanticweb.owlapi.model.OWLObjectProperty> |
relationshipIDsToPropertySet(List<String> relation_ids)
Convert a list of relationship IDs to a hash set of OWLObjectProperties.
|
void |
setEdgesAdvancedCacheSize(int size) |
clearCachedEdges, combineEdgePairWithGCI, combineEdgePairWithSuperPropsAndGCI, edgeToSourceExpression, getAllOWLClasses, getAllOWLClassesFromSource, getAncestorsThroughIsA, getDescendantsThroughIsA, getGCIIncomingEdges, getGCIOutgoingEdges, getGCIOutgoingEdges, getIncomingEdgesWithGCI, getNamedAncestorsWithGCI, getNamedAncestorsWithGCI, getOntologyLeaves, getOntologyRoots, getOntologyRoots, getOutgoingEdgesClosureWithGCI, getOutgoingEdgesNamedClosureOverSupProps, getOutgoingEdgesNamedClosureOverSupPropsWithGCI, getOutgoingEdgesWithGCI, getOutgoingEdgesWithGCI, getOWLClassAncestors, getOWLClassAncestorsWithGCI, getOWLClassDescendants, getOWLClassDescendantsWithGCI, getOWLClassDescendantsWithGCI, getOWLClassDirectAncestors, getOWLClassDirectDescendants, getOWLClassDirectDescendantsWithGCI, getOWLGraphEdgeSubRelsReflexive, getSubAnnotationPropertiesOf, getSubAnnotationPropertyClosureOf, getSubAnnotationPropertyReflexiveClosureOf, getSubPropertiesOf, getSubPropertyClosureOf, getSubPropertyReflexiveClosureOf, getSuperPropertyReflexiveClosureOf, hasFirstEdgeMoreGeneralGCIParams, isOWLObjectInSubsets, isRealClass
cacheEdges, combinedQuantifiedPropertyPair, combineEdgePair, combineEdgePair, edgeToTargetExpression, expandRelationChain, filterEdges, getAncestors, getAncestors, getAncestors, getAncestorsReflexive, getAncestorsReflexive, getCompleteEdgesBetween, getCompleteOutgoingEdgesClosure, getConfig, getDescendants, getDescendantsReflexive, getEdgeLabel, getEdgesBetween, getIncomingEdges, getIncomingEdgesClosure, getIncomingEdgesClosure, getIndividualDescendants, getInstanceChainsFromClosure, getInstancesFromClosure, getNamedAncestors, getNamedAncestorsReflexive, getOutgoingEdges, getOutgoingEdges, getOutgoingEdges, getOutgoingEdgesClosure, getOutgoingEdgesClosure, getOutgoingEdgesClosure, getOutgoingEdgesClosureReflexive, getOutgoingEdgesClosureReflexive, getOWLGraphEdgeSubsumers, getOWLGraphEdgeSubsumers, getPrimitiveIncomingEdges, getPrimitiveOutgoingEdges, getPrimitiveOutgoingEdges, getProfiler, getReasoner, getRelationOrChain, getSubsumersFromClosure, getSuperPropertiesOf, getSuperPropertyClosureOf, isExcluded, isExcludeEdge, primitiveEdgeToFullEdges, queryDescendants, queryDescendants, queryDescendants, setConfig, setProfiler, setReasoner
getAllOWLObjectsByAltId, getAllUsedSubsets, getAltIds, getAnnotationProperty, getAnnotationPropertyValue, getAnnotationPropertyValue, getAnnotationPropertyValues, getAnnotationPropertyValues, getAnnotationValue, getAnnotationValues, getBuiltin, getComment, getComment, getComments, getComments, getConsider, getCreatedBy, getDef, getDef, getDefXref, getDefXref, getDomain, getIdentifier, getIdentifier, getIdentifier, getIdentifier, getIdSpace, getIdSpace, getIRIByIdentifier, getIRIByIdentifier, getIRIByLabel, getIRIByLabel, getIsAnonymous, getIsAntiSymmetric, getIsCyclic, getIsFunctional, getIsInverseFunctional, getIsMetaTag, getIsObsolete, getIsObsoleteBinaryString, getIsReflexive, getIsSymmetric, getIsTransitive, getLabel, getLabel, getLabelOrDisplayId, getNamespace, getNamespace, getObjectByAltId, getOntologyId, getOWLAnnotationProperty, getOWLClass, getOWLClass, getOWLClass, getOWLClassByIdentifier, getOWLClassByIdentifier, getOWLClassByIdentifierNoAltIds, getOWLClassesInSubset, getOWLIndividual, getOWLIndividual, getOWLIndividualByIdentifier, getOWLObject, getOWLObject, getOWLObjectByAltId, getOWLObjectByIdentifier, getOWLObjectByLabel, getOWLObjectProperty, getOWLObjectProperty, getOWLObjectPropertyByIdentifier, getOWLObjectsByAltId, getOWLObjectsInSubset, getRange, getReplacedBy, getSubsets, getSubsets, getVersions, getXref, getXref, isObsolete
addImport, addImportsFromSupportOntologies, addSupportOntologiesFromImportsClosure, addSupportOntologiesFromImportsClosure, addSupportOntology, getAllOntologies, getAllOWLObjects, getAllOWLSubClassOfAxiomsForSubClass, getAllOWLSubClassOfAxiomsForSuperClass, getDataFactory, getManager, getSourceOntology, getSupportOntologySet, mergeImportClosure, mergeImportClosure, mergeOntology, mergeOntology, mergeSpecificImport, mergeSupportOntology, mergeSupportOntology, mergeSupportOntology, mergeSupportOntology, remakeOntologiesFromImportsClosure, remakeOntologiesFromImportsClosure, removeSupportOntology, setSourceOntology, setSupportOntologySet
protected OWLGraphWrapperEdgesAdvanced(org.semanticweb.owlapi.model.OWLOntology ontology)
protected OWLGraphWrapperEdgesAdvanced(String iri) throws org.semanticweb.owlapi.model.OWLOntologyCreationException
org.semanticweb.owlapi.model.OWLOntologyCreationException
public void setEdgesAdvancedCacheSize(int size)
public long getCurrentEdgesAdvancedCacheSize()
public void addPropertyForMaterialization(org.semanticweb.owlapi.model.OWLObjectProperty p)
public void addPropertiesForMaterialization(Iterable<org.semanticweb.owlapi.model.OWLObjectProperty> properties)
public void addPropertyIdsForMaterialization(Iterable<String> propertyIds)
public void close() throws IOException
close
in interface Closeable
close
in interface AutoCloseable
IOException
public Set<org.semanticweb.owlapi.model.OWLObjectProperty> relationshipIDsToPropertySet(List<String> relation_ids)
relation_ids
- getRelationClosureMapEngine(OWLObject, List)
public String classifyRelationship(OWLGraphEdge owlGraphEdge, org.semanticweb.owlapi.model.OWLObject edgeDirector, Set<? extends org.semanticweb.owlapi.model.OWLPropertyExpression> props)
owlGraphEdge
- edge under considerationedgeDirector
- props
- properties setaddDirectDescendentsToShuntGraph(org.semanticweb.owlapi.model.OWLObject, owltools.graph.shunt.OWLShuntGraph, java.util.List<java.lang.String>)
,
addStepwiseAncestorsToShuntGraph(org.semanticweb.owlapi.model.OWLObject, owltools.graph.shunt.OWLShuntGraph, java.util.List<java.lang.String>)
public OWLShuntGraph addStepwiseAncestorsToShuntGraph(org.semanticweb.owlapi.model.OWLObject x, OWLShuntGraph g, List<String> rel_ids)
x
- g
- rel_ids
- public OWLShuntGraph addTransitiveAncestorsToShuntGraph(org.semanticweb.owlapi.model.OWLObject x, OWLShuntGraph g, List<String> rel_ids)
x
- g
- rel_ids
- public OWLShuntGraph addDirectDescendentsToShuntGraph(org.semanticweb.owlapi.model.OWLObject x, OWLShuntGraph g, List<String> rel_ids)
x
- g
- rel_ids
- public OWLShuntGraph getSegmentShuntGraph(org.semanticweb.owlapi.model.OWLObject x, List<String> rel_ids)
TODO: we're current just doing distance == 1 up; we'll want to have a more full graph in the future
TODO: a work in progress
x
- rel_ids
- public OWLShuntGraph getLineageShuntGraph(org.semanticweb.owlapi.model.OWLObject x, List<String> rel_ids)
This graph information is concerned almost exclusively with the arguments transitive relations with all of its ancestors.
x
- rel_ids
- public String getSegmentShuntGraphJSON(org.semanticweb.owlapi.model.OWLObject x, List<String> sargs)
x
- sargs
- public String getLineageShuntGraphJSON(org.semanticweb.owlapi.model.OWLObject x, List<String> sargs)
x
- sargs
- public Map<String,String> getRelationClosureMap(org.semanticweb.owlapi.model.OWLObject c, List<String> relation_ids)
Intended for GOlr loading.
c
- relation_ids
- getRelationClosureMapEngine(OWLObject, List)
public Map<String,String> getRelationClosureMapEngine(org.semanticweb.owlapi.model.OWLObject obj, List<String> relation_ids)
getRelationClosureMap(OWLObject, List)
.obj
- relation_ids
- getRelationClosureMap(OWLObject, List)
@Deprecated public Map<String,String> getIsaPartofClosureMap(org.semanticweb.owlapi.model.OWLObject c)
Intended for GOlr loading.
c
- @Deprecated public List<String> getIsaPartofIDClosure(org.semanticweb.owlapi.model.OWLObject c)
Intended for GOlr loading.
c
- @Deprecated public List<String> getIsaPartofIDClosure(org.semanticweb.owlapi.model.OWLObject c, List<String> sargs)
Intended for GOlr loading.
This is a curried FlexLoader s-expression version of getIsaPartofIDClosure(OWLObject)
.
c
- sargs
- getIsaPartofIDClosure(OWLObject)
public List<String> getRelationIDClosure(org.semanticweb.owlapi.model.OWLObject c, List<String> relation_ids)
Intended for GOlr loading.
c
- relation_ids
- @Deprecated public List<String> getIsaPartofLabelClosure(org.semanticweb.owlapi.model.OWLObject c)
Intended for GOlr loading.
c
- @Deprecated public List<String> getIsaPartofLabelClosure(org.semanticweb.owlapi.model.OWLObject c, List<String> sargs)
Intended for GOlr loading.
This is a curried FlexLoader s-expression version of getIsaPartofLabelClosure(OWLObject)
.
c
- sargs
- getIsaPartofLabelClosure(OWLObject)
public List<String> getRelationLabelClosure(org.semanticweb.owlapi.model.OWLObject c, List<String> relation_ids)
Intended for GOlr loading.
c
- relation_ids
- @Deprecated public String[] getSubClassesNames(org.semanticweb.owlapi.model.OWLClass cls)
cls
- public String categorizeNamespace(org.semanticweb.owlapi.model.OWLObject c, Map<String,Object> configuration)
public String categorizeObject(org.semanticweb.owlapi.model.OWLNamedObject named, Map<String,String> idspaceMappings, Set<String> useNamespace, boolean useFallback)
named
- idspaceMappings
- useNamespace
- useFallback
- if false ignore fall-backpublic String getDummyString(org.semanticweb.owlapi.model.OWLObject c, List<String> sargs)
c
- sargs
- public List<String> getDummyStrings(org.semanticweb.owlapi.model.OWLObject c, List<String> sargs)
c
- sargs
- public Set<String> getOnlyInTaxon(org.semanticweb.owlapi.model.OWLObject x, List<String> sargs)
public Set<String> getOnlyInTaxonLabels(org.semanticweb.owlapi.model.OWLObject x, List<String> sargs)
public Map<String,String> getOnlyInTaxonLabelMap(org.semanticweb.owlapi.model.OWLObject x, List<String> sargs)
public Set<String> getOnlyInTaxonClosure(org.semanticweb.owlapi.model.OWLObject x, List<String> relation_ids)
public Set<String> getOnlyInTaxonClosureLabels(org.semanticweb.owlapi.model.OWLObject x, List<String> relation_ids)
public OWLShuntGraph getNeighbors(org.semanticweb.owlapi.model.OWLObject x, List<String> sargs)
Intended for GOlr loading.
This is a curried FlexLoader s-expression version of getNeighbors(OWLObject)
.
x
- sargs
- public String getNeighborsJSON(org.semanticweb.owlapi.model.OWLObject x, List<String> sargs)
Intended for GOlr loading.
This is a curried FlexLoader s-expression version of
getNeighbors(OWLObject)
with a conversion of the graph to a JSON
string.
x
- sargs
- public String getNeighborsLimitedJSON(org.semanticweb.owlapi.model.OWLObject x, List<String> sargs)
getNeighborsLimited(OWLObject, int)
with a conversion of the graph to a JSON
string.x
- sargs
- public OWLShuntGraph getNeighborsLimited(org.semanticweb.owlapi.model.OWLObject x, int edgeLimit)
public OWLShuntGraph getNeighbors(org.semanticweb.owlapi.model.OWLObject x)
x
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