- c1 - Variable in class owltools.util.ClassExpressionPair
-
- c2 - Variable in class owltools.util.ClassExpressionPair
-
- cacheEdges() - Method in class owltools.graph.OWLGraphWrapperEdges
-
caches full outgoing and incoming edges
- calculate_overlap(Pheno, Pheno, HashMap<String, IndividualPair>) - Static method in class owltools.phenolog.Main
-
- CardinalityContraintsTools - Class in owltools.graph
-
Tools to handle cardinality constraints in OWL.
- CardinalityContraintsTools() - Constructor for class owltools.graph.CardinalityContraintsTools
-
- CardinalityContraintsTools.CardinalityReporter - Class in owltools.graph
-
- CatalogXmlIRIMapper - Class in owltools.io
-
OWLOntologyIRIMapper
using the mappings from a catalog.xml file.
- CatalogXmlIRIMapper(String) - Constructor for class owltools.io.CatalogXmlIRIMapper
-
Create an CatalogXmlIRIMapper from the given catalog.xml file.
- CatalogXmlIRIMapper(File) - Constructor for class owltools.io.CatalogXmlIRIMapper
-
Create an CatalogXmlIRIMapper from the given catalog.xml file.
- CatalogXmlIRIMapper(File, File) - Constructor for class owltools.io.CatalogXmlIRIMapper
-
Create an CatalogXmlIRIMapper from the given catalog.xml file.
- CatalogXmlIRIMapper(URL) - Constructor for class owltools.io.CatalogXmlIRIMapper
-
Create an CatalogXmlIRIMapper from the given catalog URL.
- CatalogXmlIRIMapper(URL, File) - Constructor for class owltools.io.CatalogXmlIRIMapper
-
Create an CatalogXmlIRIMapper from the given catalog URL.
- categorizeNamespace(OWLObject, Map<String, Object>) - Method in class owltools.graph.OWLGraphWrapperEdgesAdvanced
-
- categorizeObject(OWLNamedObject, Map<String, String>, Set<String>, boolean) - Method in class owltools.graph.OWLGraphWrapperEdgesAdvanced
-
Create a category for a given named object.
- ChadoGraphClosureRenderer - Class in owltools.io
-
implements a graph closure writer suitable for imports into Chado; in particular:
all identifiers are translated to OBO IDs
relationship chains of length > 1 are ignored
SUBCLASS is written as is_a, and only existential restrictions are emitted
- ChadoGraphClosureRenderer(PrintStream) - Constructor for class owltools.io.ChadoGraphClosureRenderer
-
- ChadoGraphClosureRenderer(String) - Constructor for class owltools.io.ChadoGraphClosureRenderer
-
- changeAxiomAnnotations(OWLAxiom, Set<OWLAnnotation>, OWLOntology) - Static method in class owltools.graph.AxiomAnnotationTools
-
Update the given axiom to a new set of axiom annotation.
Side effect: This removes the old axiom and adds the new axiom to
the given ontology.
- changeAxiomAnnotations(OWLAxiom, Set<OWLAnnotation>, OWLDataFactory) - Static method in class owltools.graph.AxiomAnnotationTools
-
Update the given axiom to the new set of axiom annotation.
- checkPotentialRedundantSubClassAxioms(Collection<? extends OWLAxiom>) - Method in class owltools.InferenceBuilder
-
Check the list of axioms for potential redundant subClass axioms of type:
- checkPotentialRedundantSubClassAxioms() - Method in class owltools.InferenceBuilder
-
Check all classes for potential redundant subClass axioms of type:
- childArrowShape - Variable in class owltools.gfx.GraphicsConfig.RelationConfig
-
- ClassExpression - Interface in owltools.frame
-
- ClassExpressionGraphClosureRenderer - Class in owltools.io
-
Writes graph closure as class expressions
- ClassExpressionGraphClosureRenderer(PrintStream) - Constructor for class owltools.io.ClassExpressionGraphClosureRenderer
-
- ClassExpressionGraphClosureRenderer(String) - Constructor for class owltools.io.ClassExpressionGraphClosureRenderer
-
- ClassExpressionLD - Class in owltools.frame.jsonld
-
- ClassExpressionLD() - Constructor for class owltools.frame.jsonld.ClassExpressionLD
-
- ClassExpressionPair - Class in owltools.util
-
- ClassExpressionPair(OWLClassExpression, OWLClassExpression) - Constructor for class owltools.util.ClassExpressionPair
-
- ClassFrame - Interface in owltools.frame
-
- ClassFrameLD - Class in owltools.frame.jsonld
-
- ClassFrameLD() - Constructor for class owltools.frame.jsonld.ClassFrameLD
-
- classifyRelationship(OWLGraphEdge, OWLObject, Set<? extends OWLPropertyExpression>) - Method in class owltools.graph.OWLGraphWrapperEdgesAdvanced
-
Classify the an edge and target as a human readable string for further processing.
- classMap - Variable in class owltools.io.TableToAxiomConverter.Config
-
- ClassStub - Interface in owltools.frame
-
- ClassStubLD - Class in owltools.frame.jsonld
-
- ClassStubLD() - Constructor for class owltools.frame.jsonld.ClassStubLD
-
- ClassStubLD(String, String) - Constructor for class owltools.frame.jsonld.ClassStubLD
-
- clear() - Method in class owltools.util.BloomFilter
-
Sets all bits to false in the Bloom filter.
- clearCachedEdges() - Method in class owltools.graph.OWLGraphWrapperEdges
-
Clear the current edge cache.
- clearCachedEdges() - Method in class owltools.graph.OWLGraphWrapperEdgesExtended
-
- clearFilters() - Method in class owltools.InferenceBuilder
-
- close() - Method in class owltools.graph.OWLGraphWrapperEdgesAdvanced
-
- close() - Method in class owltools.mooncat.ontologymetadata.ImportChainDotWriter
-
- code - Variable in enum owltools.gfx.RelationType
-
- COL_SUBSET - Variable in class owltools.idmap.IDMappingPIRParser
-
- colIxSubset - Variable in class owltools.idmap.IDMappingPIRParser
-
- color - Variable in class owltools.gfx.GraphicsConfig.RelationConfig
-
- color - Variable in enum owltools.gfx.RelationType
-
- colour - Variable in class owltools.gfx.OWLGraphStrokeEdge.SVGEdge
-
- COLS - Static variable in class owltools.idmap.IDMappingPIRParser
-
- combinedQuantifiedPropertyPair(OWLQuantifiedProperty, OWLQuantifiedProperty) - Method in class owltools.graph.OWLGraphWrapperEdges
-
Edge composition rules
TODO - property chains of length > 2
- combineEdgePair(OWLObject, OWLGraphEdge, OWLGraphEdge, int) - Method in class owltools.graph.OWLGraphWrapperEdges
-
Composes two graph edges into a new edge, using axioms in the ontology to determine the correct composition
- combineEdgePair(OWLGraphEdge, List<OWLQuantifiedProperty>, List<OWLQuantifiedProperty>, int) - Method in class owltools.graph.OWLGraphWrapperEdges
-
Combine the OWLQuantifiedProperty
List
s neQp
and
extEdgeQp
and assigned the resulting OWLQuantifiedProperty
s
to mergedEdge
.
- combineEdgePairWithGCI(OWLObject, OWLGraphEdge, OWLGraphEdge, int) - Method in class owltools.graph.OWLGraphWrapperEdgesExtended
-
- combineEdgePairWithSuperPropsAndGCI(OWLGraphEdge, OWLGraphEdge) - Method in class owltools.graph.OWLGraphWrapperEdgesExtended
-
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.
- Combo(Set<String>, String) - Constructor for class owltools.mooncat.BridgeExtractor.Combo
-
- COMMON - Static variable in class owltools.graph.RelationSets
-
- CompactGraphClosureReader - Class in owltools.io
-
Note that the ontology must be loaded prior to restored a closure table
- CompactGraphClosureReader(OWLGraphWrapper) - Constructor for class owltools.io.CompactGraphClosureReader
-
- CompactGraphClosureRenderer - Class in owltools.io
-
Similar to GraphClosureRenderer, writes in a more compact format
- CompactGraphClosureRenderer(PrintStream) - Constructor for class owltools.io.CompactGraphClosureRenderer
-
- CompactGraphClosureRenderer(String) - Constructor for class owltools.io.CompactGraphClosureRenderer
-
- compareTo(GenePheno) - Method in class owltools.phenolog.GenePheno
-
- compareTo(Individual) - Method in class owltools.phenolog.Individual
-
- compareTo(IndividualPair) - Method in class owltools.phenolog.IndividualPair
-
- compareTo(Pheno) - Method in class owltools.phenolog.Pheno
-
- Config() - Constructor for class owltools.graph.OWLGraphWrapperEdges.Config
-
- config - Variable in class owltools.io.StanzaToOWLConverter
-
- Config() - Constructor for class owltools.io.StanzaToOWLConverter.Config
-
- config - Variable in class owltools.io.TableToAxiomConverter
-
- Config() - Constructor for class owltools.io.TableToAxiomConverter.Config
-
- contains(E) - Method in class owltools.util.BloomFilter
-
Returns true if the element could have been inserted into the Bloom filter.
- containsAll(Collection<? extends E>) - Method in class owltools.util.BloomFilter
-
Returns true if all the elements of a Collection could have been inserted
into the Bloom filter.
- convert() - Method in class owltools.io.OWLGsonParser
-
- convert(OWLObject) - Method in class owltools.io.OWLGsonParser
-
- convert(OWLOntology) - Method in class owltools.io.OWLGsonParser
-
- convert(OWLAxiom) - Method in class owltools.io.OWLGsonParser
-
- convert(OWLGraphEdge) - Method in class owltools.io.OWLGsonParser
-
- convert(OWLImportsDeclaration) - Method in class owltools.io.OWLGsonRenderer
-
- convert(OWLObject) - Method in class owltools.io.OWLGsonRenderer
-
- convert(OWLOntology) - Method in class owltools.io.OWLGsonRenderer
-
- convert(OWLAxiom) - Method in class owltools.io.OWLGsonRenderer
-
- convert(OWLGraphEdge) - Method in class owltools.io.OWLGsonRenderer
-
- convertAxiom(Map) - Method in class owltools.io.OWLGsonParser
-
- convertAxioms(Object[]) - Method in class owltools.io.OWLGsonParser
-
- convertOntology(Map<Object, Object>) - Method in class owltools.io.OWLGsonParser
-
- count() - Method in class owltools.util.BloomFilter
-
Returns the number of elements added to the Bloom filter after it
was constructed or after clear() was called.
- createHash(String, Charset) - Static method in class owltools.util.BloomFilter
-
Generates a digest based on the contents of a String.
- createHash(String) - Static method in class owltools.util.BloomFilter
-
Generates a digest based on the contents of a String.
- createHash(byte[]) - Static method in class owltools.util.BloomFilter
-
Generates a digest based on the contents of an array of bytes.
- createManchesterSyntaxPrettyPrinter(OWLGraphWrapperExtended) - Static method in class owltools.io.OWLPrettyPrinter
-
- createMap() - Method in class owltools.mooncat.SpeciesMergeUtil
-
builds ecmap, a map between species-classes to generic-classes
also populates ssClasses
- createNonBufferingReasoner(OWLOntology) - Method in class owltools.reasoner.GraphReasonerFactory
-
- createNonBufferingReasoner(OWLOntology, OWLReasonerConfiguration) - Method in class owltools.reasoner.GraphReasonerFactory
-
- createNonBufferingReasoner(OWLOntology) - Method in class owltools.reasoner.LazyExpressionMaterializingReasonerFactory
-
Deprecated.
- createNonBufferingReasoner(OWLOntology, OWLReasonerConfiguration) - Method in class owltools.reasoner.LazyExpressionMaterializingReasonerFactory
-
Deprecated.
- createObjectPropertyView(OWLOntology, OWLOntology, OWLObjectProperty, Map<OWLClass, OWLClass>, boolean) - Static method in class owltools.mooncat.TransformationUtils
-
- createReasoner(OWLOntology) - Method in class owltools.reasoner.GraphReasonerFactory
-
- createReasoner(OWLOntology, OWLReasonerConfiguration) - Method in class owltools.reasoner.GraphReasonerFactory
-
- createReasoner(OWLOntology) - Method in class owltools.reasoner.LazyExpressionMaterializingReasonerFactory
-
Deprecated.
- createReasoner(OWLOntology, OWLReasonerConfiguration) - Method in class owltools.reasoner.LazyExpressionMaterializingReasonerFactory
-
Deprecated.
- createReasonerDiff(OWLGraphWrapper, OWLGraphWrapper, String) - Static method in class owltools.diff.ReasonerDiff
-
- createShuntGraph(OWLGraphWrapper, OWLObject, Set<OWLPropertyExpression>, boolean) - Static method in class owltools.util.ShuntGraphUtils
-
Generate a shunt graph G = (V,E) which is a subset of the ontology
GO = (VO,EO)
from a focus object X and relationset R
such that:
V contains every node reachable from X over some relations r1,t2,...
- createShuntGraphPair(OWLGraphWrapper, OWLObject, Set<OWLPropertyExpression>, boolean) - Static method in class owltools.util.ShuntGraphUtils
-
Generate two shunt graphs, one based on the topology and the other based
on the inferred graph.
- createSubOntologyFromDLQuery(String, OWLGraphWrapper, OWLGraphWrapper, OWLReasonerFactory, Set<OWLOntology>) - Method in class owltools.mooncat.QuerySubsetGenerator
-
Create a new sub ontology from a given DL query and source ontology.
- createSubOntologyFromDLQuery(OWLClass, OWLGraphWrapper, OWLGraphWrapper, OWLReasonerFactory, Set<OWLOntology>) - Method in class owltools.mooncat.QuerySubsetGenerator
-
Create a new sub ontology from a given DL query and source ontology.
- createSubSet(OWLGraphWrapper, Set<OWLClass>, Set<OWLOntology>) - Method in class owltools.mooncat.QuerySubsetGenerator
-
Given a collection of classes (such as those generated from a reasoner getSubClasses call), create a
subset ontology and place it in targetGraph.
- createSubSet(OWLGraphWrapper, Set<OWLClass>, Set<OWLOntology>, boolean, boolean) - Method in class owltools.mooncat.QuerySubsetGenerator
-
- createSubsetMap(String) - Method in class owltools.mooncat.Mooncat
-
- createSubsetMap(Set<OWLObject>) - Method in class owltools.mooncat.Mooncat
-
Note: this assumes you have already filtered any relations not to be
propagated over from the graph
- crender(OWLObject) - Method in class owltools.io.CompactGraphClosureRenderer
-
- currentCols - Variable in class owltools.idmap.AbstractMappingParser
-
- currentRow - Variable in class owltools.idmap.AbstractMappingParser
-
- g - Variable in class owltools.gfx.OWLGraphLayoutRenderer
-
- GCIUtil - Class in owltools.reasoner
-
Utility for rendering inferred axioms from GCIs
- GCIUtil() - Constructor for class owltools.reasoner.GCIUtil
-
- GenePheno - Class in owltools.phenolog
-
Represents a characteristic of an individual.
- GenePheno(String, String, String, String) - Constructor for class owltools.phenolog.GenePheno
-
- GenePheno(String, String) - Constructor for class owltools.phenolog.GenePheno
-
- GenePhenoTsvParser - Class in owltools.phenolog
-
- GenePhenoTsvParser() - Constructor for class owltools.phenolog.GenePhenoTsvParser
-
- generalGson - Static variable in class owltools.io.GeneralObjectDeserializer
-
generalGson
is a Gson instance which provides
for general deserializing.
- GeneralObjectDeserializer - Class in owltools.io
-
Use this class to create a general object-tree using the Gson
parser
(see http://code.google.com/p/google-gson/).
- GeneralObjectDeserializer() - Constructor for class owltools.io.GeneralObjectDeserializer
-
- getAdded() - Method in class owltools.graph.CardinalityContraintsTools.CardinalityReporter
-
- getAdjacent(T) - Method in interface owltools.util.Adjacency
-
- getAllOntologies() - Method in class owltools.graph.OWLGraphWrapperBasic
-
in general application code need not call this - it is mostly used internally
- getAllOntologies() - Method in class owltools.mooncat.Mooncat
-
- getAllOWLClasses() - Method in class owltools.graph.OWLGraphWrapperBasic
-
Fetch all OWLClass
objects from all ontologies.
- getAllOWLClasses() - Method in class owltools.graph.OWLGraphWrapperEdgesExtended
-
- getAllOWLClassesFromSource() - Method in class owltools.graph.OWLGraphWrapperEdgesExtended
-
- getAllOWLObjects() - Method in class owltools.graph.OWLGraphWrapperBasic
-
fetches all classes, individuals and object properties in all ontologies.
- getAllOWLObjectsByAltId() - Method in class owltools.graph.OWLGraphWrapperExtended
-
Find all corresponding OWLObject
s with an OBO-style alternate identifier.
- getAllOWLSubClassOfAxiomsForSubClass(OWLClass) - Method in class owltools.graph.OWLGraphWrapperBasic
-
Fetch all OWLSubClassOfAxiom
axioms for a given subClass
(OWLClass
) from all ontologies.
- getAllOWLSubClassOfAxiomsForSuperClass(OWLClass) - Method in class owltools.graph.OWLGraphWrapperBasic
-
Fetch all OWLSubClassOfAxiom
axioms for a given superClass
(OWLClass
) from all ontologies.
- getAllUsedSubsets() - Method in class owltools.graph.OWLGraphWrapperExtended
-
fetches all subset names that are used
- getAltIds(OWLObject) - Method in class owltools.graph.OWLGraphWrapperExtended
-
It returns the values of the alt_id tag
- getAncestors(OWLObject) - Method in class owltools.graph.OWLGraphWrapperEdges
-
returns all ancestors of an object.
- getAncestors(OWLObject, Set<OWLPropertyExpression>) - Method in class owltools.graph.OWLGraphWrapperEdges
-
returns all ancestors that can be reached over subclass or
the specified set of relations
- getAncestors(OWLObject, Set<OWLPropertyExpression>, boolean) - Method in class owltools.graph.OWLGraphWrapperEdges
-
As overProps
,
but if isStrict is true, then only consider paths that include at least one edge
with a property in the specified set.
- getancestors() - Method in class owltools.phenolog.Pheno
-
- getAncestorsReflexive(OWLObject) - Method in class owltools.graph.OWLGraphWrapperEdges
-
- getAncestorsReflexive(OWLObject, Set<OWLPropertyExpression>) - Method in class owltools.graph.OWLGraphWrapperEdges
-
- getAncestorsThroughIsA(OWLObject) - Method in class owltools.graph.OWLGraphWrapperEdgesExtended
-
Retrieve OWLClass
ancestors of x
only using "is_a" relations
(SubClassOf
).
- getAnnotationProperty(String) - Method in class owltools.graph.OWLGraphWrapperExtended
-
It translates a oboformat tag into an OWL annotation property
- getAnnotationPropertyValue(OWLObject, String) - Method in class owltools.graph.OWLGraphWrapperExtended
-
Get the annotation property value for a tag.
- getAnnotationPropertyValue(OWLObject, List<String>) - Method in class owltools.graph.OWLGraphWrapperExtended
-
Get the annotation property value for a tag.
- getAnnotationPropertyValues(OWLObject, String) - Method in class owltools.graph.OWLGraphWrapperExtended
-
Get the annotation property values for a tag.
- getAnnotationPropertyValues(OWLObject, List<String>) - Method in class owltools.graph.OWLGraphWrapperExtended
-
Get the annotation property values for a tag.
- getAnnotations(OWLEntity, OWLAnnotationProperty, OWLOntology) - Static method in class owltools.util.OwlHelper
-
- getAnnotations(OWLEntity, OWLOntology) - Static method in class owltools.util.OwlHelper
-
- getAnnotations(OWLEntity, Set<OWLOntology>) - Static method in class owltools.util.OwlHelper
-
- getAnnotationValue(OWLObject, OWLAnnotationProperty) - Method in class owltools.graph.OWLGraphWrapperExtended
-
fetches the value of a single-valued annotation property for an OWLObject
- getAnnotationValues(OWLObject, OWLAnnotationProperty) - Method in class owltools.graph.OWLGraphWrapperExtended
-
gets the values of all annotation assertions to an OWLObject for a particular annotation property
- getAssertedViewOntology() - Method in class owltools.mooncat.PropertyViewOntologyBuilder
-
Automatically generated Property View Ontology O(P)
containing axioms C' == P some C, for each C in source ontology
- getAttributes() - Method in class owltools.phenolog.Individual
-
- getAxiom() - Method in class owltools.RedundantInferences.RedundantAxiom
-
- getAxiomAnnotationValues(IRI, OWLAxiom) - Static method in class owltools.graph.AxiomAnnotationTools
-
Retrieve the literal values for the axiom annotations with the given
annotation property IRI.
- getAxiomOne() - Method in class owltools.InferenceBuilder.PotentialRedundant
-
- getAxioms() - Method in class owltools.graph.OWLGraphEdge
-
Returns A Set
containing the underlying OWLAxiom
s that allowed
to produce this OWLGraphEdge
.
- getAxiomsForSubset(Set<OWLObject>) - Method in class owltools.mooncat.Mooncat
-
Given a set of objects (e.g.
- getAxiomTwo() - Method in class owltools.InferenceBuilder.PotentialRedundant
-
- getBit(int) - Method in class owltools.util.BloomFilter
-
Read a single bit from the Bloom filter.
- getBitSet() - Method in class owltools.util.BloomFilter
-
Return the bit set used to store the Bloom filter.
- getBitsPerElement() - Method in class owltools.util.BloomFilter
-
Get actual number of bits per element based on the number of elements that have currently been inserted and the length
of the Bloom filter.
- getBottomClassNode() - Method in class owltools.reasoner.GraphReasoner
-
- getBottomClassNode() - Method in class owltools.reasoner.LazyExpressionMaterializingReasoner
-
Deprecated.
- getBottomDataPropertyNode() - Method in class owltools.reasoner.GraphReasoner
-
- getBottomDataPropertyNode() - Method in class owltools.reasoner.LazyExpressionMaterializingReasoner
-
Deprecated.
- getBottomObjectPropertyNode() - Method in class owltools.reasoner.GraphReasoner
-
- getBottomObjectPropertyNode() - Method in class owltools.reasoner.LazyExpressionMaterializingReasoner
-
Deprecated.
- getBufferingMode() - Method in class owltools.reasoner.LazyExpressionMaterializingReasoner
-
Deprecated.
- getBuiltin(OWLObject) - Method in class owltools.graph.OWLGraphWrapperExtended
-
Deprecated.
- getCategory() - Method in interface owltools.graph.OWLGraphWrapper.ISynonym
-
- getCategory() - Method in class owltools.graph.OWLGraphWrapper.Synonym
-
- getChildren(String) - Method in class owltools.graph.shunt.OWLShuntGraph
-
Return the set of children of a node as IDs.
- getClassA() - Method in class owltools.InferenceBuilder.PotentialRedundant
-
- getClassB() - Method in class owltools.InferenceBuilder.PotentialRedundant
-
- getClosest() - Method in class owltools.phenolog.Pheno
-
- getClosestDistance() - Method in class owltools.phenolog.Pheno
-
- getClosestOverlap() - Method in class owltools.phenolog.Pheno
-
- getClosestOverlapPairs() - Method in class owltools.phenolog.Pheno
-
- getClosureAxiomsOfExternalReferencedEntities() - Method in class owltools.mooncat.Mooncat
-
find all axioms in closure of external referenced entities.
- getClosureOfExternalReferencedEntities() - Method in class owltools.mooncat.Mooncat
-
finds the full closure of all external referenced entities.
- getComment(OWLObject) - Method in class owltools.graph.OWLGraphWrapperExtended
-
gets the value of rdfs:comment for an OWLObject
- getComment(OWLObject, List<String>) - Method in class owltools.graph.OWLGraphWrapperExtended
-
gets the value of rdfs:comment for an OWLObject
- getComments(OWLObject) - Method in class owltools.graph.OWLGraphWrapperExtended
-
gets all values of rdfs:comment for an OWLObject
- getComments(OWLObject, List<String>) - Method in class owltools.graph.OWLGraphWrapperExtended
-
gets all values of rdfs:comment for an OWLObject
- getCompleteEdgesBetween(OWLObject, OWLObject) - Method in class owltools.graph.OWLGraphWrapperEdges
-
- getCompleteOutgoingEdgesClosure(OWLObject) - Method in class owltools.graph.OWLGraphWrapperEdges
-
- getConfig() - Method in class owltools.graph.OWLGraphWrapperEdges
-
- getConsider(OWLObject) - Method in class owltools.graph.OWLGraphWrapperExtended
-
It returns the values of the consider tag.
- getCreatedBy(OWLObject) - Method in class owltools.graph.OWLGraphWrapperExtended
-
It returns the value of the created_by tag
- getCurrentEdgesAdvancedCacheSize() - Method in class owltools.graph.OWLGraphWrapperEdgesAdvanced
-
- getDanglingAxioms(OWLOntology) - Method in class owltools.mooncat.Mooncat
-
- getDanglingClasses() - Method in class owltools.mooncat.Mooncat
-
- getDanglingClasses(OWLOntology) - Method in class owltools.mooncat.Mooncat
-
- getDataFactory() - Method in class owltools.graph.OWLGraphWrapperBasic
-
- getDataPropertyDomains(OWLDataProperty, boolean) - Method in class owltools.reasoner.GraphReasoner
-
- getDataPropertyDomains(OWLDataProperty, boolean) - Method in class owltools.reasoner.LazyExpressionMaterializingReasoner
-
Deprecated.
- getDataPropertyValues(OWLNamedIndividual, OWLDataProperty) - Method in class owltools.reasoner.GraphReasoner
-
- getDataPropertyValues(OWLNamedIndividual, OWLDataProperty) - Method in class owltools.reasoner.LazyExpressionMaterializingReasoner
-
Deprecated.
- getDef(OWLObject) - Method in class owltools.graph.OWLGraphWrapperExtended
-
Gets the textual definition of an OWLObject
- getDef(OWLObject, List<String>) - Method in class owltools.graph.OWLGraphWrapperExtended
-
Gets the textual definition of an OWLObject
- getDefaultOboNamespace() - Method in class owltools.io.ParserWrapper.OWLGraphWrapperNameProvider
-
- getDefXref(OWLObject) - Method in class owltools.graph.OWLGraphWrapperExtended
-
Get the definition xrefs (IAO_0000115)
- getDefXref(OWLObject, List<String>) - Method in class owltools.graph.OWLGraphWrapperExtended
-
Get the definition xrefs (IAO_0000115)
- getDescendants(OWLObject) - Method in class owltools.graph.OWLGraphWrapperEdges
-
gets all descendants d of x, where d is reachable by any path.
- getDescendantsReflexive(OWLObject) - Method in class owltools.graph.OWLGraphWrapperEdges
-
gets all reflexive descendants d of x, where d is reachable by any path.
- getDescendantsThroughIsA(OWLObject) - Method in class owltools.graph.OWLGraphWrapperEdgesExtended
-
Retrieve OWLClass
descendants of x
only using "is_a" relations
(SubClassOf
).
- getDifferentiaRelation() - Method in class owltools.tr.LinkMaker.LinkPattern
-
- getDifferentIndividuals(OWLNamedIndividual) - Method in class owltools.reasoner.GraphReasoner
-
- getDifferentIndividuals(OWLNamedIndividual) - Method in class owltools.reasoner.LazyExpressionMaterializingReasoner
-
Deprecated.
- getDisjointClasses(OWLClassExpression) - Method in class owltools.reasoner.GraphReasoner
-
- getDisjointClasses(OWLClassExpression) - Method in class owltools.reasoner.LazyExpressionMaterializingReasoner
-
Deprecated.
- getDisjointDataProperties(OWLDataPropertyExpression) - Method in class owltools.reasoner.GraphReasoner
-
- getDisjointDataProperties(OWLDataPropertyExpression) - Method in class owltools.reasoner.LazyExpressionMaterializingReasoner
-
Deprecated.
- getDisjointObjectProperties(OWLObjectPropertyExpression) - Method in class owltools.reasoner.GraphReasoner
-
- getDisjointObjectProperties(OWLObjectPropertyExpression) - Method in class owltools.reasoner.LazyExpressionMaterializingReasoner
-
Deprecated.
- getDistance() - Method in class owltools.graph.OWLGraphEdge
-
- getDocumentIRI(IRI) - Method in class owltools.io.CatalogXmlIRIMapper
-
- getDocumentIRI(IRI) - Method in class owltools.io.LocalMirrorIRIMapper
-
- getDomain(OWLObjectProperty) - Method in class owltools.graph.OWLGraphWrapperExtended
-
It returns the (first) value of the domain tag
- getDummyString(OWLObject, List<String>) - Method in class owltools.graph.OWLGraphWrapperEdgesAdvanced
-
Helper function for flex loader for un-used single string fields
- getDummyStrings(OWLObject, List<String>) - Method in class owltools.graph.OWLGraphWrapperEdgesAdvanced
-
Helper function for flex loader for un-used single List of string fields
- getEdgeLabel(OWLGraphEdge) - Method in class owltools.graph.OWLGraphWrapperEdges
-
Get the human readable label for an edge.
- getEdges() - Method in class owltools.mooncat.ProvenanceReasonerWrapper
-
- getEdgesBetween(OWLObject, OWLObject) - Method in class owltools.graph.OWLGraphWrapperEdges
-
- getElementsOntology() - Method in class owltools.mooncat.PropertyViewOntologyBuilder
-
- getEquivalentClasses(OWLClassExpression) - Method in class owltools.reasoner.GraphReasoner
-
- getEquivalentClasses(OWLClassExpression) - Method in class owltools.reasoner.LazyExpressionMaterializingReasoner
-
Deprecated.
- getEquivalentClasses(OWLClass, OWLOntology) - Static method in class owltools.util.OwlHelper
-
- getEquivalentClasses(OWLClass, Set<OWLOntology>) - Static method in class owltools.util.OwlHelper
-
- getEquivalentDataProperties(OWLDataProperty) - Method in class owltools.reasoner.GraphReasoner
-
- getEquivalentDataProperties(OWLDataProperty) - Method in class owltools.reasoner.LazyExpressionMaterializingReasoner
-
Deprecated.
- getEquivalentNamedClassPairs() - Method in class owltools.InferenceBuilder
-
- getEquivalentObjectProperties(OWLObjectPropertyExpression) - Method in class owltools.reasoner.GraphReasoner
-
- getEquivalentObjectProperties(OWLObjectPropertyExpression) - Method in class owltools.reasoner.LazyExpressionMaterializingReasoner
-
Deprecated.
- getExcludedClasses() - Method in class owltools.mooncat.PropertyViewOntologyBuilder
-
- getExisiting() - Method in class owltools.tr.LinkMaker.LinkMakerResult
-
- getExistsEntailed() - Method in class owltools.JustifyAssertionsTool.JustifyResult
-
- getExistsNotEntailed() - Method in class owltools.JustifyAssertionsTool.JustifyResult
-
- getExistsRedundant() - Method in class owltools.JustifyAssertionsTool.JustifyResult
-
- getExpectedBitsPerElement() - Method in class owltools.util.BloomFilter
-
Get expected number of bits per element when the Bloom filter is full.
- getExpectedNumberOfElements() - Method in class owltools.util.BloomFilter
-
Returns the expected number of elements to be inserted into the filter.
- getExplaination(String, String, OWLQuantifiedProperty.Quantifier) - Method in class owltools.InferenceBuilder
-
- getExternalReferencedEntities() - Method in class owltools.mooncat.Mooncat
-
returns set of entities that belong to a referenced ontology that are referenced in the source ontology.
- getFactory(String) - Static method in class owltools.InferenceBuilder
-
- getFalsePositiveProbability(double) - Method in class owltools.util.BloomFilter
-
Calculate the probability of a false positive given the specified
number of inserted elements.
- getFalsePositiveProbability() - Method in class owltools.util.BloomFilter
-
Get the current probability of a false positive.
- getFiller() - Method in class owltools.frame.jsonld.RestrictionLD
-
- getFiller() - Method in class owltools.frame.jsonld.SomeValuesFromLD
-
- getFiller() - Method in interface owltools.frame.Restriction
-
- getFinalQuantifiedProperty() - Method in class owltools.graph.OWLGraphEdge
-
- getFirstQuantifiedProperty() - Method in class owltools.graph.OWLGraphEdge
-
- getFragmentID(OWLObject) - Static method in class owltools.mooncat.TransformationUtils
-
- getFreshEntityPolicy() - Method in class owltools.reasoner.LazyExpressionMaterializingReasoner
-
Deprecated.
- getGCIFiller() - Method in class owltools.graph.OWLGraphEdge
-
Returns the OWLClass
that is the OBO gci_filler
of this OWLGraphEdge
.
- getGciFillers() - Method in class owltools.io.InferredParentRenderer
-
- getGCIIncomingEdges(OWLClass) - Method in class owltools.graph.OWLGraphWrapperEdgesExtended
-
Retrieve OBO GCI relations incoming to t
as a Set
of OWLGraphEdge
s.
- getGCIOutgoingEdges(OWLClass) - Method in class owltools.graph.OWLGraphWrapperEdgesExtended
-
Retrieve OBO GCI relations outgoing from s
as a Set
of OWLGraphEdge
s.
- getGCIOutgoingEdges(OWLClass, Set<OWLPropertyExpression>) - Method in class owltools.graph.OWLGraphWrapperEdgesExtended
-
- getGciProperty() - Method in class owltools.io.InferredParentRenderer
-
- getGCIRelation() - Method in class owltools.graph.OWLGraphEdge
-
Returns the OWLObjectPropertyExpression
that is the OBO gci_relation
of this OWLGraphEdge
.
- getGraph() - Method in class owltools.mooncat.Mooncat
-
- getHeight() - Method in class owltools.gfx.OWLGraphLayoutNode
-
- gethmp() - Method in class owltools.phenolog.PhenoTransitiveClosure
-
- gethmpair() - Method in class owltools.phenolog.PhenoTransitiveClosure
-
- gethsp() - Method in class owltools.phenolog.PhenoTransitiveClosure
-
- getId() - Method in class owltools.graph.shunt.OWLShuntNode
-
- getId() - Method in class owltools.phenolog.Attribute
-
- getid() - Method in class owltools.phenolog.GenePheno
-
- getId() - Method in class owltools.phenolog.Individual
-
- getId() - Method in class owltools.phenolog.Pheno
-
- getIdentifier(OWLObject) - Method in class owltools.graph.OWLGraphWrapperExtended
-
gets the OBO-style ID of the specified object.
- getIdentifier(OWLObject, boolean) - Method in class owltools.graph.OWLGraphWrapperExtended
-
Gets the OBO-style ID of the specified object.
- getIdentifier(OWLObject, List<String>) - Method in class owltools.graph.OWLGraphWrapperExtended
-
- getIdentifier(IRI) - Method in class owltools.graph.OWLGraphWrapperExtended
-
gets the OBO-style ID of the specified object.
- getIncomingEdges(OWLObject) - Method in class owltools.graph.OWLGraphWrapperEdges
-
- getIncomingEdgesClosure(OWLObject, boolean) - Method in class owltools.graph.OWLGraphWrapperEdges
-
- getIncomingEdgesClosure(OWLObject) - Method in class owltools.graph.OWLGraphWrapperEdges
-
gets all inferred edges coming in to the target edge
- getIncomingEdgesWithGCI(OWLObject) - Method in class owltools.graph.OWLGraphWrapperEdgesExtended
-
- getIndex(NODE) - Method in class owltools.util.AbstractTarjan
-
- getIndex(T) - Method in class owltools.util.MappingTarjan
-
- getIndividualDescendants(OWLObject) - Method in class owltools.graph.OWLGraphWrapperEdges
-
return all individuals i where x is reachable from i
- getIndividualNodeSetPolicy() - Method in class owltools.reasoner.LazyExpressionMaterializingReasoner
-
Deprecated.
- getIndividualPairs() - Method in class owltools.phenolog.PhenologEngine
-
- getIndividuals() - Method in class owltools.phenolog.Pheno
-
- getInferredGraph() - Method in class owltools.util.ShuntGraphUtils.ShuntGraphPair
-
- getInferredViewOntology() - Method in class owltools.mooncat.PropertyViewOntologyBuilder
-
- getInstanceChainsFromClosure(OWLClass) - Method in class owltools.graph.OWLGraphWrapperEdges
-
Finds all edges between an instance i and he given class c.
- getInstances(OWLClassExpression, boolean) - Method in class owltools.reasoner.GraphReasoner
-
- getInstances(OWLClassExpression, boolean) - Method in class owltools.reasoner.LazyExpressionMaterializingReasoner
-
Deprecated.
- getInstancesFromClosure(OWLClass) - Method in class owltools.graph.OWLGraphWrapperEdges
-
Find all edges of the form [i INST c] in the graph closure.
- getInverseObjectProperties(OWLObjectPropertyExpression) - Method in class owltools.reasoner.GraphReasoner
-
- getInverseObjectProperties(OWLObjectPropertyExpression) - Method in class owltools.reasoner.LazyExpressionMaterializingReasoner
-
Deprecated.
- getIRI() - Method in enum owltools.vocab.OBOUpperVocabulary
-
- getIRIByIdentifier(String) - Method in class owltools.graph.OWLGraphWrapperExtended
-
- getIRIByIdentifier(String, boolean) - Method in class owltools.graph.OWLGraphWrapperExtended
-
- getIRIByLabel(String) - Method in class owltools.graph.OWLGraphWrapperExtended
-
fetches an OWL IRI by rdfs:label
- getIRIByLabel(String, boolean) - Method in class owltools.graph.OWLGraphWrapperExtended
-
fetches an OWL IRI by rdfs:label, optionally testing for uniqueness
- getIRIMappers() - Method in class owltools.io.ParserWrapper
-
- getIsAnonymous(OWLObject) - Method in class owltools.graph.OWLGraphWrapperExtended
-
Deprecated.
- getIsAntiSymmetric(OWLObject) - Method in class owltools.graph.OWLGraphWrapperExtended
-
It returns the value of the is_anti_symmetric tag or IAO_0000427 annotation
- getIsaPartofClosureMap(OWLObject) - Method in class owltools.graph.OWLGraphWrapperEdgesAdvanced
-
Deprecated.
- getIsaPartofIDClosure(OWLObject) - Method in class owltools.graph.OWLGraphWrapperEdgesAdvanced
-
Deprecated.
- getIsaPartofIDClosure(OWLObject, List<String>) - Method in class owltools.graph.OWLGraphWrapperEdgesAdvanced
-
Deprecated.
- getIsaPartofLabelClosure(OWLObject) - Method in class owltools.graph.OWLGraphWrapperEdgesAdvanced
-
Deprecated.
- getIsaPartofLabelClosure(OWLObject, List<String>) - Method in class owltools.graph.OWLGraphWrapperEdgesAdvanced
-
Deprecated.
- getIsCyclic(OWLObject) - Method in class owltools.graph.OWLGraphWrapperExtended
-
It returns the value of the is_cyclic tag
- getisFromTC() - Method in class owltools.phenolog.Pheno
-
- getIsFunctional(OWLObjectProperty) - Method in class owltools.graph.OWLGraphWrapperExtended
-
true if c is functional in the graph
- getIsInverseFunctional(OWLObjectProperty) - Method in class owltools.graph.OWLGraphWrapperExtended
-
true if c is inverse functional in the graph
- getIsMetaTag(OWLObject) - Method in class owltools.graph.OWLGraphWrapperExtended
-
It returns the value of the is_metadata_tag tag.
- getIsObsolete(OWLObject) - Method in class owltools.graph.OWLGraphWrapperExtended
-
It returns the value of the is-obsolete tag.
- getIsObsoleteBinaryString(OWLObject, List<String>) - Method in class owltools.graph.OWLGraphWrapperExtended
-
It returns the value of the is-obsolete tag.
- getIsReflexive(OWLObjectProperty) - Method in class owltools.graph.OWLGraphWrapperExtended
-
true if c is reflexive in the graph
- getIsSymmetric(OWLObjectProperty) - Method in class owltools.graph.OWLGraphWrapperExtended
-
true if c is symmetric in the graph
- getIsTransitive(OWLObjectProperty) - Method in class owltools.graph.OWLGraphWrapperExtended
-
true if c is transitive in the graph
- getK() - Method in class owltools.util.BloomFilter
-
Returns the value chosen for K.
K is the optimal number of hash functions based on the size
of the Bloom filter and the expected number of inserted elements.
- getKey() - Method in class owltools.io.OWLJSONFormat
-
- getLabel() - Method in interface owltools.graph.OWLGraphWrapper.ISynonym
-
- getLabel() - Method in class owltools.graph.OWLGraphWrapper.Synonym
-
- getLabel(OWLObject) - Method in class owltools.graph.OWLGraphWrapperExtended
-
fetches the rdfs:label for an OWLObject
- getLabel(OWLObject, List<String>) - Method in class owltools.graph.OWLGraphWrapperExtended
-
fetches the rdfs:label for an OWLObject
- getLabel() - Method in class owltools.graph.shunt.OWLShuntNode
-
- getLabel(OWLEntity, OWLOntology) - Method in class owltools.mooncat.PropertyViewOntologyBuilder
-
- getLabel() - Method in class owltools.phenolog.Attribute
-
- getlabel() - Method in class owltools.phenolog.GenePheno
-
- getLabel() - Method in class owltools.phenolog.Individual
-
- getLabel() - Method in class owltools.phenolog.Pheno
-
- getLabelOrDisplayId(OWLObject) - Method in class owltools.graph.OWLGraphWrapperExtended
-
- getLabelOrId(OWLEntity) - Method in class owltools.io.OWLPrettyPrinter.LabelProvider
-
- getLastQuantifiedProperty() - Method in class owltools.graph.OWLGraphEdge
-
- getLeafClasses() - Method in class owltools.mooncat.PropertyViewOntologyBuilder
-
- getLeaves() - Method in class owltools.graph.shunt.OWLShuntGraph
-
Return the set of graph leaves (no children) as IDs.
- getLineageShuntGraph(OWLObject, List<String>) - Method in class owltools.graph.OWLGraphWrapperEdgesAdvanced
-
Gets all ancestors that are OWLNamedObjects.
- getLineageShuntGraphJSON(OWLObject, List<String>) - Method in class owltools.graph.OWLGraphWrapperEdgesAdvanced
-
Return a JSONized version of the output of getLineageShuntGraph
- getLowlink(NODE) - Method in class owltools.util.AbstractTarjan
-
- getLowlink(T) - Method in class owltools.util.MappingTarjan
-
- getManager() - Method in class owltools.graph.OWLGraphWrapperBasic
-
- getManager() - Method in class owltools.io.ParserWrapper
-
- getManager() - Method in class owltools.mooncat.Mooncat
-
- getManager() - Method in class owltools.mooncat.ProvenanceReasonerWrapper
-
- getManifestVersion(String) - Static method in class owltools.version.VersionInfo
-
Try to retrieve the value for the given key from a manifest file.
- getMappings() - Method in class owltools.io.CatalogXmlIRIMapper
-
- getMappings() - Method in class owltools.tr.TemplatedTransformer
-
- getMaxCardinality() - Method in class owltools.graph.OWLQuantifiedProperty
-
- getMember1() - Method in class owltools.phenolog.IndividualPair
-
- getMember2() - Method in class owltools.phenolog.IndividualPair
-
- getMetadata() - Method in class owltools.graph.shunt.OWLShuntEdge
-
- getMetadata() - Method in class owltools.graph.shunt.OWLShuntNode
-
- getMinCardinality() - Method in class owltools.graph.OWLQuantifiedProperty
-
- getModified() - Method in class owltools.tr.LinkMaker.LinkMakerResult
-
- getMoreSpecific() - Method in class owltools.RedundantInferences.RedundantAxiom
-
- getName(String) - Method in class owltools.io.ParserWrapper.OboAndOwlNameProvider
-
- getName(String) - Method in class owltools.io.ParserWrapper.OWLGraphWrapperNameProvider
-
- getNamedAncestors(OWLObject) - Method in class owltools.graph.OWLGraphWrapperEdges
-
Gets all ancestors that are OWLNamedObjects
- getNamedAncestorsReflexive(OWLObject) - Method in class owltools.graph.OWLGraphWrapperEdges
-
- getNamedAncestorsWithGCI(OWLObject) - Method in class owltools.graph.OWLGraphWrapperEdgesExtended
-
- getNamedAncestorsWithGCI(OWLObject, Set<OWLPropertyExpression>) - Method in class owltools.graph.OWLGraphWrapperEdgesExtended
-
- getNamespace(OWLObject) - Method in class owltools.graph.OWLGraphWrapperExtended
-
It returns the value of the OBO-namespace tag
- getNamespace(OWLObject, List<String>) - Method in class owltools.graph.OWLGraphWrapperExtended
-
It returns the value of the OBO-namespace tag.
- getNewAxioms() - Method in class owltools.diff.ReasonerDiff
-
- getNewInferred() - Method in class owltools.JustifyAssertionsTool.JustifyResult
-
- getNewRelation() - Method in class owltools.tr.LinkMaker.LinkPattern
-
- getNode(OWLObject) - Method in class owltools.gfx.OWLGraphLayoutRenderer
-
fetch a layout node via the cognate OWLObject
make private?
- getNonTCIndividualSize() - Method in class owltools.phenolog.Pheno
-
- getObjectByAltId(String) - Method in class owltools.graph.OWLGraphWrapperExtended
-
- getObjectProperty(OWLDataFactory) - Method in enum owltools.vocab.OBOUpperVocabulary
-
- getObjectProperty(OWLOntology) - Method in enum owltools.vocab.OBOUpperVocabulary
-
- getObjectPropertyDomains(OWLObjectPropertyExpression, boolean) - Method in class owltools.reasoner.GraphReasoner
-
- getObjectPropertyDomains(OWLObjectPropertyExpression, boolean) - Method in class owltools.reasoner.LazyExpressionMaterializingReasoner
-
Deprecated.
- getObjectPropertyRanges(OWLObjectPropertyExpression, boolean) - Method in class owltools.reasoner.GraphReasoner
-
- getObjectPropertyRanges(OWLObjectPropertyExpression, boolean) - Method in class owltools.reasoner.LazyExpressionMaterializingReasoner
-
Deprecated.
- getObjectPropertyValues(OWLNamedIndividual, OWLObjectPropertyExpression) - Method in class owltools.reasoner.GraphReasoner
-
- getObjectPropertyValues(OWLNamedIndividual, OWLObjectPropertyExpression) - Method in class owltools.reasoner.LazyExpressionMaterializingReasoner
-
Deprecated.
- getObjectPropertyValues(OWLIndividual, OWLOntology) - Static method in class owltools.util.OwlHelper
-
- getOBOdoc() - Method in class owltools.io.ParserWrapper
-
- getobolink() - Method in class owltools.phenolog.PhenoTransitiveClosure
-
- getOBOSynonyms(OWLObject) - Method in class owltools.graph.OWLGraphWrapper
-
It returns list of synonyms as encoded by OBO2OWL.
- getOBOSynonymStrings(OWLObject, List<String>) - Method in class owltools.graph.OWLGraphWrapper
-
It returns String Listof synonyms.
- getOnlyInTaxon(OWLObject, List<String>) - Method in class owltools.graph.OWLGraphWrapperEdgesAdvanced
-
- getOnlyInTaxonClosure(OWLObject, List<String>) - Method in class owltools.graph.OWLGraphWrapperEdgesAdvanced
-
- getOnlyInTaxonClosureLabels(OWLObject, List<String>) - Method in class owltools.graph.OWLGraphWrapperEdgesAdvanced
-
- getOnlyInTaxonLabelMap(OWLObject, List<String>) - Method in class owltools.graph.OWLGraphWrapperEdgesAdvanced
-
- getOnlyInTaxonLabels(OWLObject, List<String>) - Method in class owltools.graph.OWLGraphWrapperEdgesAdvanced
-
- getOntology() - Method in class owltools.graph.OWLGraphEdge
-
- getOntology() - Method in class owltools.graph.OWLGraphWrapper
-
Deprecated.
- getOntology() - Method in class owltools.mooncat.Mooncat
-
- getOntologyId() - Method in class owltools.graph.OWLGraphWrapperExtended
-
gets the OBO-style ID of the source ontology IRI.
- getOntologyLeaves() - Method in class owltools.graph.OWLGraphWrapperEdgesExtended
-
Return the
OWLClass
es leaves of any ontology
(
OWLClass
es 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)
- getOntologyRoots() - Method in class owltools.graph.OWLGraphWrapperEdgesExtended
-
Return the
OWLClass
es root of any ontology
(
OWLClass
es with no outgoing edges as returned by
{OWLGraphWrapperEdges#getOutgoingEdgesWithGCI(OWLObject)}), and not deprecated
(
OWLGraphWrapperExtended.isObsolete(OWLObject)
returns
false
)).
- getOntologyRoots(Set<OWLPropertyExpression>) - Method in class owltools.graph.OWLGraphWrapperEdgesExtended
-
Return the
OWLClass
es root of any ontology over the specified
OWLPropertyExpression
s (
OWLClass
es 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).
- getOriginalClassForViewClass(OWLClass) - Method in class owltools.mooncat.PropertyViewOntologyBuilder
-
- getOrthologs() - Method in class owltools.phenolog.Individual
-
- getOutgoingEdges(OWLObject) - Method in class owltools.graph.OWLGraphWrapperEdges
-
retrieves direct edges from a source
to the direct **named** target
e.g.
- getOutgoingEdges(OWLObject, Set<? extends OWLPropertyExpression>) - Method in class owltools.graph.OWLGraphWrapperEdges
-
retrieves direct edges from a source
to the direct **named** target for a given set of properties
e.g.
- getOutgoingEdges(OWLObject, boolean, boolean) - Method in class owltools.graph.OWLGraphWrapperEdges
-
- getOutgoingEdgesClosure(OWLObject) - Method in class owltools.graph.OWLGraphWrapperEdges
-
Retrieves the graph closure originating from source.
- getOutgoingEdgesClosure(OWLObject, Set<? extends OWLPropertyExpression>) - Method in class owltools.graph.OWLGraphWrapperEdges
-
- getOutgoingEdgesClosure(OWLObject, boolean) - Method in class owltools.graph.OWLGraphWrapperEdges
-
- getOutgoingEdgesClosureReflexive(OWLObject) - Method in class owltools.graph.OWLGraphWrapperEdges
-
- getOutgoingEdgesClosureReflexive(OWLObject, Set<? extends OWLPropertyExpression>) - Method in class owltools.graph.OWLGraphWrapperEdges
-
- getOutgoingEdgesClosureWithGCI(OWLObject) - Method in class owltools.graph.OWLGraphWrapperEdgesExtended
-
- getOutgoingEdgesNamedClosureOverSupProps(OWLObject) - Method in class owltools.graph.OWLGraphWrapperEdgesExtended
-
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
).
- getOutgoingEdgesNamedClosureOverSupPropsWithGCI(OWLObject) - Method in class owltools.graph.OWLGraphWrapperEdgesExtended
-
- getOutgoingEdgesWithGCI(OWLObject) - Method in class owltools.graph.OWLGraphWrapperEdgesExtended
-
- getOutgoingEdgesWithGCI(OWLObject, Set<OWLPropertyExpression>) - Method in class owltools.graph.OWLGraphWrapperEdgesExtended
-
- getOWLAnnotationProperty(IRI) - Method in class owltools.graph.OWLGraphWrapperExtended
-
- getOWLClass(String) - Method in class owltools.graph.OWLGraphWrapperExtended
-
Returns an OWLClass given an IRI string
- getOWLClass(IRI) - Method in class owltools.graph.OWLGraphWrapperExtended
-
Returns an OWLClass given an IRI
- getOWLClass(OWLObject) - Method in class owltools.graph.OWLGraphWrapperExtended
-
- getOWLClass(OWLDataFactory) - Method in enum owltools.vocab.OBOUpperVocabulary
-
- getOWLClass(OWLOntology) - Method in enum owltools.vocab.OBOUpperVocabulary
-
- getOWLClassAncestors(OWLClass) - Method in class owltools.graph.OWLGraphWrapperEdgesExtended
-
Return the OWLClass
es ancestor of sourceClass
.
- getOWLClassAncestorsWithGCI(OWLObject) - Method in class owltools.graph.OWLGraphWrapperEdgesExtended
-
- getOWLClassByIdentifier(String) - Method in class owltools.graph.OWLGraphWrapperExtended
-
Given an OBO-style ID, return the corresponding OWLClass, if it is declared - otherwise null
- getOWLClassByIdentifier(String, boolean) - Method in class owltools.graph.OWLGraphWrapperExtended
-
- getOWLClassByIdentifierNoAltIds(String) - Method in class owltools.graph.OWLGraphWrapperExtended
-
Given an OBO-style ID, return the corresponding OWLClass, if it is declared and not an alt_id - otherwise null
- getOWLClassDescendants(OWLClass) - Method in class owltools.graph.OWLGraphWrapperEdgesExtended
-
Return the OWLClass
es descendant of parentClass
.
- getOWLClassDescendantsWithGCI(OWLClass) - Method in class owltools.graph.OWLGraphWrapperEdgesExtended
-
- getOWLClassDescendantsWithGCI(OWLClass, Set<OWLPropertyExpression>) - Method in class owltools.graph.OWLGraphWrapperEdgesExtended
-
Similar to #getOWLClassDescendantsWithGCI(OWLObject)
but allowing to filter
the relations considered.
- getOWLClassDirectAncestors(OWLClass) - Method in class owltools.graph.OWLGraphWrapperEdgesExtended
-
Return the OWLClass
es that are direct parent of subClass
.
- getOWLClassDirectDescendants(OWLClass) - Method in class owltools.graph.OWLGraphWrapperEdgesExtended
-
Return the OWLClass
es directly descendant of parentClass
.
- getOWLClassDirectDescendantsWithGCI(OWLClass) - Method in class owltools.graph.OWLGraphWrapperEdgesExtended
-
- getOWLClassesInSubset(String) - Method in class owltools.graph.OWLGraphWrapperExtended
-
given a subset name, find all OWLClasses assigned to that subset
- getOWLGraphEdgeSubRelsReflexive(OWLGraphEdge) - Method in class owltools.graph.OWLGraphWrapperEdgesExtended
-
Get the sub-relations of edge
.
- getOWLGraphEdgeSubsumers(OWLGraphEdge) - Method in class owltools.graph.OWLGraphWrapperEdges
-
generalizes over quantified properties
- getOWLGraphEdgeSubsumers(OWLGraphEdge, int) - Method in class owltools.graph.OWLGraphWrapperEdges
-
- getOwlGraphWrapper() - Method in class owltools.graph.OWLGraphManipulator
-
Get the OWLGraphWrapper
on which modifications
are performed.
- getOWLGraphWrapper() - Method in class owltools.InferenceBuilder
-
- getOWLIndividual(IRI) - Method in class owltools.graph.OWLGraphWrapperExtended
-
Returns an OWLNamedIndividual with this IRI if it has been declared
in the source or support ontologies.
- getOWLIndividual(String) - Method in class owltools.graph.OWLGraphWrapperExtended
-
- getOWLIndividualByIdentifier(String) - Method in class owltools.graph.OWLGraphWrapperExtended
-
Given an OBO-style ID, return the corresponding OWLNamedIndividual, if it is declared - otherwise null
- getOwlObject() - Method in class owltools.gfx.OWLGraphLayoutNode
-
- getOWLObject(String) - Method in class owltools.graph.OWLGraphWrapperExtended
-
Returns the OWLObject with this IRI
(where IRI is specified as a string - e.g http://purl.obolibrary.org/obo/GO_0008150)
- getOWLObject(IRI) - Method in class owltools.graph.OWLGraphWrapperExtended
-
Returns the OWLObject with this IRI
- getOWLObjectByAltId(String) - Method in class owltools.graph.OWLGraphWrapperExtended
-
Find the corresponding OWLObject
for a given OBO-style alternate identifier.
- getOWLObjectByIdentifier(String) - Method in class owltools.graph.OWLGraphWrapperExtended
-
Given an OBO-style ID, return the corresponding OWLObject, if it is declared - otherwise null
- getOWLObjectByLabel(String) - Method in class owltools.graph.OWLGraphWrapperExtended
-
fetches an OWL Object by rdfs:label
- getOWLObjectProperty(String) - Method in class owltools.graph.OWLGraphWrapperExtended
-
Returns the OWLObjectProperty with this IRI
- getOWLObjectProperty(IRI) - Method in class owltools.graph.OWLGraphWrapperExtended
-
- getOWLObjectPropertyByIdentifier(String) - Method in class owltools.graph.OWLGraphWrapperExtended
-
Given an OBO-style ID, return the corresponding OWLObjectProperty, if it is declared - otherwise null
- getOWLObjectsByAltId(Set<String>) - Method in class owltools.graph.OWLGraphWrapperExtended
-
Find the corresponding OWLObject
s for a given set of OBO-style alternate identifiers.
- getOWLObjectsInSubset(String) - Method in class owltools.graph.OWLGraphWrapperExtended
-
given a subset name, find all OWLObjects (typically OWLClasses) assigned to that subset
- getParents(String) - Method in class owltools.graph.shunt.OWLShuntGraph
-
Return the set of parents of a node as IDs.
- getPendingAxiomAdditions() - Method in class owltools.reasoner.LazyExpressionMaterializingReasoner
-
Deprecated.
- getPendingAxiomRemovals() - Method in class owltools.reasoner.LazyExpressionMaterializingReasoner
-
Deprecated.
- getPendingChanges() - Method in class owltools.reasoner.LazyExpressionMaterializingReasoner
-
Deprecated.
- getpermutedgenes(int, int, ArrayList<Individual>) - Static method in class owltools.phenolog.Main
-
- getphenoid() - Method in class owltools.phenolog.GenePheno
-
- getphenolabel() - Method in class owltools.phenolog.GenePheno
-
- getPrecomputableInferenceTypes() - Method in class owltools.reasoner.GraphReasoner
-
- getPrecomputableInferenceTypes() - Method in class owltools.reasoner.LazyExpressionMaterializingReasoner
-
Deprecated.
- getPredictions() - Method in class owltools.tr.LinkMaker.LinkMakerResult
-
- getprefix() - Method in class owltools.phenolog.PhenoTransitiveClosure
-
- getPrimitiveIncomingEdges(OWLObject) - Method in class owltools.graph.OWLGraphWrapperEdges
-
- getPrimitiveOutgoingEdges(OWLObject) - Method in class owltools.graph.OWLGraphWrapperEdges
-
primitive edges connect any combination of named objects and expressions
- getPrimitiveOutgoingEdges(OWLObject, Set<? extends OWLPropertyExpression>) - Method in class owltools.graph.OWLGraphWrapperEdges
-
- getProfiler() - Method in class owltools.graph.OWLGraphWrapperEdges
-
- getProperties() - Method in class owltools.io.InferredParentRenderer
-
- getProperty() - Method in class owltools.graph.OWLQuantifiedProperty
-
- getProperty() - Method in class owltools.InferenceBuilder.PotentialRedundant
-
- getPropertyChains(OWLObjectProperty) - Method in class owltools.mooncat.PropertyViewOntologyBuilder
-
- getPropertyId() - Method in class owltools.graph.OWLQuantifiedProperty
-
- getQuantifiedPropertyList() - Method in class owltools.graph.OWLGraphEdge
-
- getQuantifier() - Method in class owltools.graph.OWLQuantifiedProperty
-
- getRange(OWLObjectProperty) - Method in class owltools.graph.OWLGraphWrapperExtended
-
It returns the (first) value of the range tag
- getReasoner() - Method in class owltools.graph.OWLGraphWrapperEdges
-
- getReasoner(OWLOntology) - Method in class owltools.InferenceBuilder
-
- getReasoner() - Method in class owltools.io.InferredParentRenderer
-
- getReasonerName() - Method in class owltools.reasoner.GraphReasoner
-
- getReasonerName() - Method in class owltools.reasoner.GraphReasonerFactory
-
- getReasonerName() - Method in class owltools.reasoner.LazyExpressionMaterializingReasoner
-
Deprecated.
- getReasonerName() - Method in class owltools.reasoner.LazyExpressionMaterializingReasonerFactory
-
Deprecated.
- getReasonerVersion() - Method in class owltools.reasoner.GraphReasoner
-
- getReasonerVersion() - Method in class owltools.reasoner.LazyExpressionMaterializingReasoner
-
Deprecated.
- getRedundantAxioms() - Method in class owltools.InferenceBuilder
-
- getRedundantAxioms(OWLOntology, OWLReasoner, OWLDataFactory) - Method in class owltools.InferenceBuilder
-
Search for redundant axioms.
- getReferencedOntologies() - Method in class owltools.mooncat.Mooncat
-
delegates to OWLGraphWrapper support ontologies
- getRelationClosureMap(OWLObject, List<String>) - Method in class owltools.graph.OWLGraphWrapperEdgesAdvanced
-
Return a map of id to label for the closure of the ontology using the supplied relation id list and .isSubClassOf().
- getRelationClosureMapEngine(OWLObject, List<String>) - Method in class owltools.graph.OWLGraphWrapperEdgesAdvanced
-
- getRelationIDClosure(OWLObject, List<String>) - Method in class owltools.graph.OWLGraphWrapperEdgesAdvanced
-
Return a overlaps with getIsaPartofLabelClosure and stuff in GafSolrDocumentLoader.
- getRelationLabelClosure(OWLObject, List<String>) - Method in class owltools.graph.OWLGraphWrapperEdgesAdvanced
-
Return a overlaps with getIsaPartofIDClosure and stuff in GafSolrDocumentLoader.
- getRelationOrChain(String) - Method in class owltools.graph.OWLGraphWrapperEdges
-
If available, return the elements of the equivalent property chain.
- getRelationSet(String) - Static method in class owltools.graph.RelationSets
-
- getRelationType(OWLGraphEdge, OWLGraphWrapper) - Static method in class owltools.gfx.OWLGraphStrokeEdge
-
Sets the value of relType based on OWLGraphEdge properties
TODO : this is too hacky.
- getRemoved() - Method in class owltools.graph.CardinalityContraintsTools.CardinalityReporter
-
- getRemovedInferredAxioms() - Method in class owltools.diff.ReasonerDiff
-
- getReplacedBy(OWLObject) - Method in class owltools.graph.OWLGraphWrapperExtended
-
It returns the values of the replaced_by tag or IAO_0100001 annotation.
- getRootOntology() - Method in class owltools.reasoner.LazyExpressionMaterializingReasoner
-
Deprecated.
- getRoots() - Method in class owltools.graph.shunt.OWLShuntGraph
-
Return the set of graph roots (no parents) as IDs.
- getSameIndividuals(OWLNamedIndividual) - Method in class owltools.reasoner.GraphReasoner
-
- getSameIndividuals(OWLNamedIndividual) - Method in class owltools.reasoner.LazyExpressionMaterializingReasoner
-
Deprecated.
- getScope() - Method in interface owltools.graph.OWLGraphWrapper.ISynonym
-
- getScope() - Method in class owltools.graph.OWLGraphWrapper.Synonym
-
- getSegmentShuntGraph(OWLObject, List<String>) - Method in class owltools.graph.OWLGraphWrapperEdgesAdvanced
-
Gets all ancestors and direct descendants (distance == 1) that are OWLNamedObjects.
- getSegmentShuntGraphJSON(OWLObject, List<String>) - Method in class owltools.graph.OWLGraphWrapperEdgesAdvanced
-
Return a JSONized version of the output of getSegmentShuntGraph
Defaults to is_a/part_of and regulates.
- getShortForm(OWLEntity) - Method in class owltools.io.OWLPrettyPrinter.LabelProvider
-
- getSingleQuantifiedProperty() - Method in class owltools.graph.OWLGraphEdge
-
- getSkolemIRI(OWLEntity...) - Static method in class owltools.mooncat.TransformationUtils
-
- getSkolemIRI(List<OWLEntity>) - Static method in class owltools.mooncat.TransformationUtils
-
- getSource() - Method in class owltools.graph.OWLGraphEdge
-
- getSourceId() - Method in class owltools.graph.OWLGraphEdge
-
- getSourceOntology() - Method in class owltools.graph.OWLGraphWrapperBasic
-
Every OWLGraphWrapper objects wraps zero or one source ontologies.
- getSourceOntologyPrefixes() - Method in class owltools.mooncat.Mooncat
-
E.g.
- getSources() - Method in interface owltools.util.Adjacency
-
- getStream() - Method in class owltools.io.AbstractClosureReader
-
- getStream() - Method in class owltools.io.AbstractRenderer
-
- getSubAnnotationPropertiesOf(OWLAnnotationProperty) - Method in class owltools.graph.OWLGraphWrapperEdgesExtended
-
Returns the direct child properties of prop
in all ontologies.
- getSubAnnotationPropertyClosureOf(OWLAnnotationProperty) - Method in class owltools.graph.OWLGraphWrapperEdgesExtended
-
Returns all child properties of prop
in all ontologies,
ordered from the more general (closer from prop
) to the more precise.
- getSubAnnotationPropertyReflexiveClosureOf(OWLAnnotationProperty) - Method in class owltools.graph.OWLGraphWrapperEdgesExtended
-
Returns all sub-properties of prop
in all ontologies,
and prop
itself as the first element (reflexive).
- getSubClasses(OWLClassExpression, boolean) - Method in class owltools.reasoner.GraphReasoner
-
- getSubClasses(OWLClassExpression, boolean) - Method in class owltools.reasoner.LazyExpressionMaterializingReasoner
-
Deprecated.
- getSubClasses(OWLClass, OWLOntology) - Static method in class owltools.util.OwlHelper
-
- getSubClasses(OWLClass, Set<OWLOntology>) - Static method in class owltools.util.OwlHelper
-
- getSubClassesNames(OWLClass) - Method in class owltools.graph.OWLGraphWrapperEdgesAdvanced
-
Deprecated.
- getSubClassOfAxioms() - Method in class owltools.graph.OWLGraphEdge
-
- getSubClassOfSomeValuesFromAxioms(OWLReasoner) - Static method in class owltools.reasoner.GCIUtil
-
- getSubClassOfSomeValuesFromAxioms(OWLOntology, OWLReasoner) - Static method in class owltools.reasoner.GCIUtil
-
Generates trivial SVF axioms from existing GCIs
- getSubDataProperties(OWLDataProperty, boolean) - Method in class owltools.reasoner.GraphReasoner
-
- getSubDataProperties(OWLDataProperty, boolean) - Method in class owltools.reasoner.LazyExpressionMaterializingReasoner
-
Deprecated.
- getSubGenus() - Method in class owltools.tr.LinkMaker.LinkPattern
-
- getSubObjectProperties(OWLObjectPropertyExpression, boolean) - Method in class owltools.reasoner.GraphReasoner
-
- getSubObjectProperties(OWLObjectPropertyExpression, boolean) - Method in class owltools.reasoner.LazyExpressionMaterializingReasoner
-
Deprecated.
- getSubProperties(OWLAnnotationProperty, OWLOntology) - Static method in class owltools.util.OwlHelper
-
- getSubProperties(OWLAnnotationProperty, Set<OWLOntology>) - Static method in class owltools.util.OwlHelper
-
- getSubProperties(OWLObjectPropertyExpression, OWLOntology) - Static method in class owltools.util.OwlHelper
-
- getSubPropertiesOf(OWLObjectPropertyExpression) - Method in class owltools.graph.OWLGraphWrapperEdgesExtended
-
Returns the direct child properties of prop
in all ontologies.
- getSubPropertyClosureOf(OWLObjectPropertyExpression) - Method in class owltools.graph.OWLGraphWrapperEdgesExtended
-
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").
- getSubPropertyReflexiveClosureOf(OWLObjectPropertyExpression) - Method in class owltools.graph.OWLGraphWrapperEdgesExtended
-
Returns all sub-properties of prop
in all ontologies,
and prop
itself as the first element (reflexive).
- getSubsets(OWLObject) - Method in class owltools.graph.OWLGraphWrapperExtended
-
Returns the values of the subset tag for a given OWLObject
- getSubsets(OWLObject, List<String>) - Method in class owltools.graph.OWLGraphWrapperExtended
-
It returns the value of the subset tag.
- getSubsumersFromClosure(OWLObject) - Method in class owltools.graph.OWLGraphWrapperEdges
-
find the set of classes or class expressions subsuming source, using the graph closure.
- getSuperClasses(OWLClassExpression, boolean) - Method in class owltools.reasoner.GraphReasoner
-
- getSuperClasses(OWLClassExpression, boolean) - Method in class owltools.reasoner.LazyExpressionMaterializingReasoner
-
Deprecated.
- getSuperClasses(OWLClass, OWLOntology) - Static method in class owltools.util.OwlHelper
-
- getSuperClasses(OWLClass, Set<OWLOntology>) - Static method in class owltools.util.OwlHelper
-
- getSuperClassesOver(OWLClassExpression, OWLObjectProperty, boolean) - Method in class owltools.reasoner.GraphReasoner
-
- getSuperClassExpressions(OWLClassExpression, boolean) - Method in class owltools.reasoner.GraphReasoner
-
note that this is not a standard reasoner method
- getSuperDataProperties(OWLDataProperty, boolean) - Method in class owltools.reasoner.GraphReasoner
-
- getSuperDataProperties(OWLDataProperty, boolean) - Method in class owltools.reasoner.LazyExpressionMaterializingReasoner
-
Deprecated.
- getSuperGenus() - Method in class owltools.tr.LinkMaker.LinkPattern
-
- getSuperObjectProperties(OWLObjectPropertyExpression, boolean) - Method in class owltools.reasoner.GraphReasoner
-
- getSuperObjectProperties(OWLObjectPropertyExpression, boolean) - Method in class owltools.reasoner.LazyExpressionMaterializingReasoner
-
Deprecated.
- getSuperProperties(OWLAnnotationProperty, OWLOntology) - Static method in class owltools.util.OwlHelper
-
- getSuperProperties(OWLAnnotationProperty, Set<OWLOntology>) - Static method in class owltools.util.OwlHelper
-
- getSuperProperties(OWLObjectPropertyExpression, OWLOntology) - Static method in class owltools.util.OwlHelper
-
- getSuperPropertiesOf(OWLObjectPropertyExpression) - Method in class owltools.graph.OWLGraphWrapperEdges
-
returns parent properties of p in all ontologies
- getSuperPropertyClosureOf(OWLObjectPropertyExpression) - Method in class owltools.graph.OWLGraphWrapperEdges
-
- getSuperPropertyReflexiveClosureOf(OWLObjectPropertyExpression) - Method in class owltools.graph.OWLGraphWrapperEdges
-
- getSuperPropertyReflexiveClosureOf(OWLObjectPropertyExpression) - Method in class owltools.graph.OWLGraphWrapperEdgesExtended
-
Returns all parent properties of prop
in all ontologies,
and prop
itself as the first element (reflexive).
- getSupportOntologySet() - Method in class owltools.graph.OWLGraphWrapperBasic
-
all operations are over a set of ontologies - the source ontology plus
any number of supporting ontologies.
- getSynonymStrings(OWLObject) - Method in class owltools.graph.OWLGraphWrapper
-
Deprecated.
- getTarget() - Method in class owltools.graph.OWLGraphEdge
-
- getTargetId() - Method in class owltools.graph.OWLGraphEdge
-
- getTimeOut() - Method in class owltools.reasoner.LazyExpressionMaterializingReasoner
-
Deprecated.
- getTopClassNode() - Method in class owltools.reasoner.GraphReasoner
-
- getTopClassNode() - Method in class owltools.reasoner.LazyExpressionMaterializingReasoner
-
Deprecated.
- getTopDataPropertyNode() - Method in class owltools.reasoner.GraphReasoner
-
- getTopDataPropertyNode() - Method in class owltools.reasoner.LazyExpressionMaterializingReasoner
-
Deprecated.
- getTopObjectPropertyNode() - Method in class owltools.reasoner.GraphReasoner
-
- getTopObjectPropertyNode() - Method in class owltools.reasoner.LazyExpressionMaterializingReasoner
-
Deprecated.
- getTopologyGraph() - Method in class owltools.util.ShuntGraphUtils.ShuntGraphPair
-
- getTruncatedId(OWLEntity) - Method in class owltools.io.OWLPrettyPrinter.LabelProvider
-
- getType() - Method in class owltools.frame.jsonld.BaseLD
-
- getType() - Method in class owltools.frame.jsonld.ClassExpressionLD
-
- getType() - Method in class owltools.frame.jsonld.ClassFrameLD
-
- getType() - Method in class owltools.frame.jsonld.ClassStubLD
-
- getType() - Method in class owltools.frame.jsonld.PropertyStubLD
-
- getType() - Method in class owltools.frame.jsonld.RestrictionLD
-
- getType() - Method in class owltools.graph.shunt.OWLShuntNode
-
- getTypes(OWLNamedIndividual, boolean) - Method in class owltools.reasoner.GraphReasoner
-
- getTypes(OWLNamedIndividual, boolean) - Method in class owltools.reasoner.LazyExpressionMaterializingReasoner
-
Deprecated.
- getTypes(OWLIndividual, OWLOntology) - Static method in class owltools.util.OwlHelper
-
- getTypes(OWLNamedIndividual, OWLOntology) - Static method in class owltools.util.OwlHelper
-
- getTypes(OWLNamedIndividual, Set<OWLOntology>) - Static method in class owltools.util.OwlHelper
-
- getUnsatisfiableClasses() - Method in class owltools.reasoner.GraphReasoner
-
- getUnsatisfiableClasses() - Method in class owltools.reasoner.LazyExpressionMaterializingReasoner
-
Deprecated.
- getVersions() - Method in class owltools.graph.OWLGraphWrapperExtended
-
Retrieve the version information of all ontologies.
- getViewEntities() - Method in class owltools.mooncat.PropertyViewOntologyBuilder
-
- getViewLabelPrefix() - Method in class owltools.mooncat.PropertyViewOntologyBuilder
-
- getViewLabelSuffix() - Method in class owltools.mooncat.PropertyViewOntologyBuilder
-
- getViewRootClass() - Method in class owltools.mooncat.PropertyViewOntologyBuilder
-
As the we treat Thing as belonging to O, O(P) will contain "P some Thing", and this
will be the root of O(P)
- getWidth() - Method in class owltools.gfx.OWLGraphLayoutNode
-
- getWrappedReasoner() - Method in class owltools.reasoner.LazyExpressionMaterializingReasoner
-
Deprecated.
- getWrappedReasonerFactory() - Method in class owltools.reasoner.LazyExpressionMaterializingReasoner
-
Deprecated.
- getXref(OWLObject) - Method in class owltools.graph.OWLGraphWrapperExtended
-
get the values of of the obo xref tag
- getXref(OWLObject, List<String>) - Method in class owltools.graph.OWLGraphWrapperExtended
-
get the values of of the obo xref tag
- getXrefs() - Method in interface owltools.graph.OWLGraphWrapper.ISynonym
-
- getXrefs() - Method in class owltools.graph.OWLGraphWrapper.Synonym
-
- GMTParser - Class in owltools.io
-
reads in a table (e.g.
- GMTParser(OWLGraphWrapper) - Constructor for class owltools.io.GMTParser
-
- graph - Variable in class owltools.io.AbstractRenderer
-
- graph - Variable in class owltools.io.StanzaToOWLConverter
-
- graph - Variable in class owltools.io.TableToAxiomConverter
-
- GraphClosureRenderer - Class in owltools.io
-
- GraphClosureRenderer(PrintStream) - Constructor for class owltools.io.GraphClosureRenderer
-
- GraphClosureRenderer(String) - Constructor for class owltools.io.GraphClosureRenderer
-
- graphEdgeExcludeSet - Variable in class owltools.graph.OWLGraphWrapperEdges.Config
-
- graphEdgeIncludeSet - Variable in class owltools.graph.OWLGraphWrapperEdges.Config
-
- GraphicsConfig - Class in owltools.gfx
-
- GraphicsConfig() - Constructor for class owltools.gfx.GraphicsConfig
-
- graphicsConfig - Variable in class owltools.gfx.OWLGraphLayoutRenderer
-
- GraphicsConfig.RelationConfig - Class in owltools.gfx
-
- GraphReader - Interface in owltools.io
-
- GraphReasoner - Class in owltools.reasoner
-
incomplete.
- GraphReasoner(OWLOntology, OWLReasonerConfiguration, BufferingMode) - Constructor for class owltools.reasoner.GraphReasoner
-
- GraphReasonerFactory - Class in owltools.reasoner
-
- GraphReasonerFactory() - Constructor for class owltools.reasoner.GraphReasonerFactory
-
- GraphRenderer - Interface in owltools.io
-
- GraphStyle - Class in owltools.gfx
-
hacked crudely from QuickGO
- GraphStyle() - Constructor for class owltools.gfx.GraphStyle
-
Create default style.
- GraphStyle(Map<String, String>) - Constructor for class owltools.gfx.GraphStyle
-
Create a custom style
TODO implement configuration options.
- read(String) - Method in class owltools.io.AbstractClosureReader
-
- read() - Method in class owltools.io.AbstractClosureReader
-
- read() - Method in class owltools.io.CompactGraphClosureReader
-
- read() - Method in interface owltools.io.GraphReader
-
- read(String) - Method in interface owltools.io.GraphReader
-
- reader - Variable in class owltools.idmap.AbstractMappingParser
-
- reason() - Method in class owltools.mooncat.ProvenanceReasonerWrapper
-
- reasoner - Variable in class owltools.mooncat.EquivalenceSetMergeUtil
-
- reasoner - Variable in class owltools.mooncat.SpeciesMergeUtil
-
- reasoner - Variable in class owltools.mooncat.SpeciesSubsetterUtil
-
- REASONER_ELK - Static variable in class owltools.InferenceBuilder
-
- REASONER_HERMIT - Static variable in class owltools.InferenceBuilder
-
- ReasonerDiff - Class in owltools.diff
-
- ReasonerDiff(List<OWLAxiom>, List<OWLAxiom>) - Constructor for class owltools.diff.ReasonerDiff
-
- reasonLeavingOneOut(OWLOntology) - Method in class owltools.mooncat.ProvenanceReasonerWrapper
-
- reduce(List<String>) - Method in class owltools.mooncat.BridgeExtractor.Combo
-
if srcOntIds is a subset of xOntIds, then replace that subset
with tgtOntId
- reduceAxiomAnnotationsToOboBasic(OWLOntology) - Static method in class owltools.graph.AxiomAnnotationTools
-
Remove axiom annotations, which do not comply with the OBO-Basic level,
i.e.
- reduceAxiomAnnotationsToOboBasic(OWLAxiom, OWLOntology) - Static method in class owltools.graph.AxiomAnnotationTools
-
Remove axiom annotations, which do not comply with the OBO-Basic level,
i.e.
- reducePartOfIsARelations() - Method in class owltools.graph.OWLGraphManipulator
-
Remove redundant relations by considering is_a (SubClassOf)
and part_of relations equivalent.
- reduceRelations() - Method in class owltools.graph.OWLGraphManipulator
-
Remove redundant relations.
- RedundantAxiom(OWLSubClassOfAxiom, Set<OWLClass>) - Constructor for class owltools.RedundantInferences.RedundantAxiom
-
- RedundantInferences - Class in owltools
-
- RedundantInferences.RedundantAxiom - Class in owltools
-
- REGULATES - Static variable in class owltools.graph.RelationSets
-
- RelationConfig() - Constructor for class owltools.gfx.GraphicsConfig.RelationConfig
-
- relationConfigMap - Variable in class owltools.gfx.GraphicsConfig
-
- relations - Variable in class owltools.gfx.HierarchyImage
-
- RelationSets - Class in owltools.graph
-
- RelationSets() - Constructor for class owltools.graph.RelationSets
-
- relationshipIDsToPropertySet(List<String>) - Method in class owltools.graph.OWLGraphWrapperEdgesAdvanced
-
Convert a list of relationship IDs to a hash set of OWLObjectProperties.
- RelationType - Enum in owltools.gfx
-
hacked crudely from QuickGO
TODO: use config object to map relationship types to colors
- RelationType.Polarity - Enum in owltools.gfx
-
- remakeOntologiesFromImportsClosure() - Method in class owltools.graph.OWLGraphWrapperBasic
-
- remakeOntologiesFromImportsClosure(IRI) - Method in class owltools.graph.OWLGraphWrapperBasic
-
- remove(OWLOntology, OWLAxiom) - Method in class owltools.graph.CardinalityContraintsTools.CardinalityReporter
-
- remove() - Method in class owltools.graph.shunt.OWLShuntGraphDFIterator
-
- removeCardinalityConstraints(OWLOntology) - Static method in class owltools.graph.CardinalityContraintsTools
-
Remove the cardinality constraints, by removing the axioms and replacing
them with the weaker axioms without the constraints.
- removeClass(OWLClass) - Method in class owltools.graph.OWLGraphManipulator
-
Remove from all ontologies the OWLClass
classToDel
,
and then update the OWLGraphWrapper
container.
- removeClassAndPropagateEdges(String) - Method in class owltools.graph.OWLGraphManipulator
-
Remove the OWLClass
with the OBO-style ID classToRemoveId
from the ontology, and propagate its incoming edges to the targets
of its outgoing edges.
- removeClasses(Set<OWLClass>) - Method in class owltools.graph.OWLGraphManipulator
-
Remove from all ontologies all OWLClass
es
present in classesToDel
,
and then update the OWLGraphWrapper
container.
- removeClassesNotInIDSpace(String, boolean) - Method in class owltools.mooncat.Mooncat
-
- removeDanglingAxioms(OWLOntology) - Method in class owltools.mooncat.Mooncat
-
Removes any axiom from ont if that axiom contains a dangling
reference - i.e.
- removeDanglingAxioms() - Method in class owltools.mooncat.Mooncat
-
- removeDirectEdgesBetween(String, String) - Method in class owltools.graph.OWLGraphManipulator
-
Remove direct edges between the OWLObject
s with the OBO-like IDs
sourceId
and targetId
.
- removeEdge(OWLGraphEdge) - Method in class owltools.graph.OWLGraphManipulator
-
Remove edge
from its ontology.
- removeEdges(Collection<OWLGraphEdge>) - Method in class owltools.graph.OWLGraphManipulator
-
Remove edges
from their related ontology.
- removeExternalEntities() - Method in class owltools.mooncat.Mooncat
-
- removeExternalEntities(OWLOntology) - Method in class owltools.mooncat.Mooncat
-
Removes all classes, individuals and object properties that are marked with
IAO_0000412
- removeExternalEntities(boolean, OWLOntology) - Method in class owltools.mooncat.Mooncat
-
removes external entities:
- anything marked with IAO_0000412 is removed
- if isMain is true then anything that is also present in an external ontology is removed
- removeExternalOntologyClasses(boolean) - Method in class owltools.mooncat.Mooncat
-
Removes all classes that have IAO_0000412 'imported from' set to another ontology.
- removeFilter(InferenceBuilder.OWLClassFilter) - Method in class owltools.InferenceBuilder
-
- removeIRIMapper(OWLOntologyIRIMapper) - Method in class owltools.io.ParserWrapper
-
- removeMarkAsInferredAxiom(OWLAxiom, OWLOntology) - Static method in class owltools.graph.AxiomAnnotationTools
-
Remove the inferred mark from the axiom.
Side effect: Removes the axiom in the given ontology and creates a
new axiom with the changed annotations.
- removeOtherSpecies() - Method in class owltools.mooncat.SpeciesSubsetterUtil
-
- removeRedundant(Set<OWLObject>) - Method in class owltools.mooncat.Mooncat
-
- removeRedundantSubClassAxioms(OWLOntology, OWLReasoner) - Static method in class owltools.RedundantInferences
-
Remove the redundant and marked as inferred super class assertions for
each class in the ontology signature.
- removeRelations(Collection<String>, boolean) - Method in class owltools.graph.OWLGraphManipulator
-
Remove the OWLAxiom
s in the ontologies
corresponding to the OWLObjectProperty
s listed in forbiddenRels
,
as OBO-style IDs.
- removeRelsToSubsets(Collection<String>) - Method in class owltools.graph.OWLGraphManipulator
-
- removeRelsToSubsets(Collection<String>, Collection<String>) - Method in class owltools.graph.OWLGraphManipulator
-
Remove is_a and part_of incoming edges to OWLClass
es
in subsets
, only if the source of the incoming edge
will not be left orphan of other is_a/part_of relations to OWLClass
es
not in subsets
.
- removeSpecies() - Method in class owltools.mooncat.SpeciesSubsetterUtil
-
- removeSubgraphs(Collection<String>, boolean) - Method in class owltools.graph.OWLGraphManipulator
-
- removeSubgraphs(Collection<String>, boolean, Collection<String>) - Method in class owltools.graph.OWLGraphManipulator
-
Remove from the ontology the subgraphs starting
from the OWLClass
es with their ID in subgraphRootIds
.
- removeSubsetClasses(Set<OWLClass>, boolean) - Method in class owltools.mooncat.Mooncat
-
Remove a set of classes from the ontology
- removeSubsetComplementClasses(Set<OWLClass>, boolean) - Method in class owltools.mooncat.Mooncat
-
Remove all classes *not* in subset.
- removeSupportOntology(OWLOntology) - Method in class owltools.graph.OWLGraphWrapperBasic
-
- removeUnrelatedRelations(Collection<String>) - Method in class owltools.graph.OWLGraphManipulator
-
Remove from all OWLOntologies
wrapped by this object
the OWLObjectProperty
s not related to the provided allowedRels
.
- render(Graphics2D) - Method in class owltools.gfx.HierarchyImage
-
- render() - Method in class owltools.gfx.ImageRender
-
- render(Graphics2D) - Method in class owltools.gfx.ImageRender
-
- render(Graphics2D) - Method in class owltools.gfx.OWLGraphLayoutNode
-
- render(OWLGraphWrapper) - Method in class owltools.io.AbstractClosureRenderer
-
- render(OWLGraphEdge) - Method in class owltools.io.AbstractClosureRenderer
-
- render(OWLGraphEdge) - Method in class owltools.io.ChadoGraphClosureRenderer
-
- render(OWLGraphEdge) - Method in class owltools.io.ClassExpressionGraphClosureRenderer
-
- render(OWLGraphEdge) - Method in class owltools.io.CompactGraphClosureRenderer
-
- render(OWLGraphWrapper) - Method in class owltools.io.EdgeTableRenderer
-
- render(OWLGraphEdge) - Method in class owltools.io.GraphClosureRenderer
-
- render(OWLGraphWrapper) - Method in interface owltools.io.GraphRenderer
-
- render(OWLGraphWrapper) - Method in class owltools.io.InferredParentRenderer
-
- render(OWLAxiom) - Method in class owltools.io.OWLGsonParser
-
- render(OWLGraphEdge) - Method in class owltools.io.OWLGsonParser
-
- render(OWLOntology) - Method in class owltools.io.OWLGsonParser
-
- render(Set) - Method in class owltools.io.OWLGsonParser
-
- render(OWLAxiom) - Method in class owltools.io.OWLGsonRenderer
-
- render(OWLGraphEdge) - Method in class owltools.io.OWLGsonRenderer
-
- render(OWLOntology) - Method in class owltools.io.OWLGsonRenderer
-
- render(Set) - Method in class owltools.io.OWLGsonRenderer
-
- render(OWLObject) - Method in class owltools.io.OWLPrettyPrinter
-
- render(OWLAxiom) - Method in class owltools.io.OWLPrettyPrinter
-
- render(OWLGraphEdge) - Method in class owltools.io.OWLPrettyPrinter
-
- render(OWLGraphWrapper) - Method in class owltools.io.TableRenderer
-
- renderDot() - Method in class owltools.gfx.OWLGraphvizRenderer
-
- renderDot(OWLOntology, String, String, boolean) - Method in class owltools.mooncat.ontologymetadata.ImportChainDotWriter
-
- renderDot(Collection<OWLOntology>, String, String, boolean) - Method in class owltools.mooncat.ontologymetadata.ImportChainDotWriter
-
- renderDot(OWLOntology, Collection<OWLOntology>, String, String, boolean) - Method in class owltools.mooncat.ontologymetadata.ImportChainDotWriter
-
Render a dot file for the given ontologies (aka set of annotations).
- renderHTML(File) - Method in class owltools.gfx.OWLGraphLayoutRenderer
-
generates both HTML and a PNG
- renderID(Graphics2D) - Method in class owltools.gfx.OWLGraphLayoutNode
-
- renderId(String) - Method in class owltools.io.OWLPrettyPrinter
-
- renderImage(String, OutputStream) - Method in class owltools.gfx.OWLGraphLayoutRenderer
-
renders the graph in the specified format
- renderImage(String, OutputStream) - Method in class owltools.gfx.OWLGraphvizRenderer
-
- renderIRI(String) - Method in class owltools.io.OWLPrettyPrinter
-
- renderMarkdown(OWLGraphWrapper, String, boolean) - Static method in class owltools.mooncat.ontologymetadata.OntologyMetadataMarkdownWriter
-
- report() - Method in class owltools.profile.Profiler
-
- ResonerDiffCommandLine - Class in owltools.diff
-
- ResonerDiffCommandLine() - Constructor for class owltools.diff.ResonerDiffCommandLine
-
- Restriction - Interface in owltools.frame
-
- RestrictionLD - Class in owltools.frame.jsonld
-
- RestrictionLD() - Constructor for class owltools.frame.jsonld.RestrictionLD
-
- retainAxiomsInPropertySubset(Set<OWLObjectProperty>) - Method in class owltools.mooncat.Mooncat
-
- retainAxiomsInPropertySubset(OWLOntology, Set<OWLObjectProperty>) - Static method in class owltools.mooncat.Mooncat
-
- retainAxiomsInPropertySubset(OWLOntology, Set<OWLObjectProperty>, OWLReasoner) - Static method in class owltools.mooncat.Mooncat
-
given an ontology *ont* and a set of object properties *filterProps*, remove all axioms from ontology that
have an object property P in their signature where P is not in *filterProps*
- right() - Method in class owltools.gfx.OWLGraphLayoutNode
-
- right - Variable in class owltools.gfx.OWLGraphLayoutNode.SVGRectangle
-
- rightMargin - Static variable in class owltools.gfx.HierarchyImage
-
- rootClass - Variable in class owltools.mooncat.SpeciesSubsetterUtil
-
- rowToAxioms(String[]) - Method in class owltools.io.TableToAxiomConverter
-