Skip navigation links
A B C D E F G H I J K L M N O P Q R S T U V W X Y 

A

AbstractClosureReader - Class in owltools.io
 
AbstractClosureReader(InputStream) - Constructor for class owltools.io.AbstractClosureReader
 
AbstractClosureReader(String) - Constructor for class owltools.io.AbstractClosureReader
 
AbstractClosureReader(OWLGraphWrapper) - Constructor for class owltools.io.AbstractClosureReader
 
AbstractClosureRenderer - Class in owltools.io
Renders the graph closure - i.e.
AbstractClosureRenderer(PrintStream) - Constructor for class owltools.io.AbstractClosureRenderer
 
AbstractClosureRenderer(String) - Constructor for class owltools.io.AbstractClosureRenderer
 
AbstractMappingParser - Class in owltools.idmap
Parses the IDMapping file available here: ftp://ftp.pir.georgetown.edu/databases/idmapping/idmapping.tb.gz
AbstractMappingParser() - Constructor for class owltools.idmap.AbstractMappingParser
 
AbstractRenderer - Class in owltools.io
Renders the graph closure - i.e.
AbstractRenderer(PrintStream) - Constructor for class owltools.io.AbstractRenderer
 
AbstractRenderer(String) - Constructor for class owltools.io.AbstractRenderer
 
AbstractTarjan<NODE> - Class in owltools.util
Basic implementation for the Tarjan algorithm.
AbstractTarjan(boolean) - Constructor for class owltools.util.AbstractTarjan
 
add(OWLOntology, OWLAxiom) - Method in class owltools.graph.CardinalityContraintsTools.CardinalityReporter
 
add(OWLGraphEdge) - Method in class owltools.graph.OWLGraphEdge.OWLGraphEdgeSet
Try to add edge to this OWLGraphEdgeSet, or, if it already contains an equal OWLGraphEdge, merges their underlying OWLAxioms (as returned by their getOWLAxioms methods).
add(E) - Method in class owltools.util.BloomFilter
Adds an object to the Bloom filter.
addAll(Collection<? extends OWLGraphEdge>) - Method in class owltools.graph.OWLGraphEdge.OWLGraphEdgeSet
Try to add or merge each element of edges into this OWLGraphEdgeSet, as performed by the method OWLGraphEdge.OWLGraphEdgeSet.add(OWLGraphEdge).
addAll(Collection<? extends E>) - Method in class owltools.util.BloomFilter
Adds all elements from a Collection to the Bloom filter.
addAllClasses() - Method in class owltools.gfx.OWLGraphLayoutRenderer
Adds all classes from the OGW into the rendered graph CAUTION: do this only for small ontologies
addAllObjects() - Method in class owltools.gfx.OWLGraphLayoutRenderer
Adds all objects from the OGW into the rendered graph.
addAnnotation(PropertyStubLD, Object) - Method in interface owltools.frame.Frame
 
addAnnotation(PropertyStubLD, Object) - Method in class owltools.frame.jsonld.FrameLD
 
addClassFrame(ClassFrame) - Method in class owltools.frame.jsonld.OntologyFrameLD
 
addClassFrame(ClassFrame) - Method in interface owltools.frame.OntologyFrame
 
addCombo(String, Set<String>) - Method in class owltools.mooncat.BridgeExtractor
 
addDirectDescendentsToShuntGraph(OWLObject, OWLShuntGraph, List<String>) - Method in class owltools.graph.OWLGraphWrapperEdgesAdvanced
Add a set of edges, as descendants to x in OWLShuntGraph g.
addEdge(OWLGraphEdge) - Method in class owltools.gfx.OWLGraphLayoutRenderer
Adds an edge to the graph.
addEdge(OWLGraphEdge) - Method in class owltools.graph.OWLGraphManipulator
Add edge to its related ontology.
addEdge(OWLShuntEdge) - Method in class owltools.graph.shunt.OWLShuntGraph
Simply "add" an edge to the graph.
addEdges(Set<OWLGraphEdge>) - Method in class owltools.graph.OWLGraphManipulator
Add edges to their related ontology.
addFilter(InferenceBuilder.OWLClassFilter) - Method in class owltools.InferenceBuilder
 
addImport(OWLOntology) - Method in class owltools.graph.OWLGraphWrapperBasic
adds an imports declaration between the source ontology and extOnt
addImport(String) - Method in class owltools.mooncat.Mooncat
Deprecated.
addImportsFromSupportOntologies() - Method in class owltools.graph.OWLGraphWrapperBasic
 
addIRIMapper(OWLOntologyIRIMapper) - Method in class owltools.io.ParserWrapper
 
addIRIMappers(List<OWLOntologyIRIMapper>) - Method in class owltools.io.ParserWrapper
 
addNode(OWLShuntNode) - Method in class owltools.graph.shunt.OWLShuntGraph
Simply "add" a node to the graph.
addObject(OWLObject) - Method in class owltools.gfx.OWLGraphLayoutRenderer
Adds an object to the graph to be rendered This will also add all ancestors of the focusObj, and all direct edges from each ancestor
addObjects(Set<OWLObject>) - Method in class owltools.gfx.OWLGraphLayoutRenderer
 
addPropertiesForMaterialization(Iterable<OWLObjectProperty>) - Method in class owltools.graph.OWLGraphWrapperEdgesAdvanced
 
addPropertyForMaterialization(OWLObjectProperty) - Method in class owltools.graph.OWLGraphWrapperEdgesAdvanced
 
addPropertyIdsForMaterialization(Iterable<String>) - Method in class owltools.graph.OWLGraphWrapperEdgesAdvanced
 
addQueryOntology(OWLOntology) - Method in class owltools.graph.OWLGraphWrapper
Deprecated.
addReferencedOntology(OWLOntology) - Method in class owltools.mooncat.Mooncat
 
addRow(String[]) - Method in class owltools.io.TableToAxiomConverter
 
addRow(OWLOntology, String[]) - Method in class owltools.io.TableToAxiomConverter
 
addSourceOntologyPrefix(String) - Method in class owltools.mooncat.Mooncat
Add a source ontology prefix to the internal set.
addStepwiseAncestorsToShuntGraph(OWLObject, OWLShuntGraph, List<String>) - Method in class owltools.graph.OWLGraphWrapperEdgesAdvanced
Add a set of edges, as ancestors to x in OWLShuntGraph g.
addSupportOntologiesFromImportsClosure() - Method in class owltools.graph.OWLGraphWrapperBasic
Each ontology in the import closure of the source ontology is added to the list of support ontologies
addSupportOntologiesFromImportsClosure(boolean) - Method in class owltools.graph.OWLGraphWrapperBasic
Each ontology in the import closure of the source ontology (and the import closure of each existing support ontology, if doForAllSupportOntologies is true) is added to the list of support ontologies
addSupportOntology(OWLOntology) - Method in class owltools.graph.OWLGraphWrapperBasic
 
addTransitiveAncestorsToShuntGraph(OWLObject, OWLShuntGraph, List<String>) - Method in class owltools.graph.OWLGraphWrapperEdgesAdvanced
Add a set of edges, as ancestors to x in OWLShuntGraph g.
addViewEntities(Set<OWLEntity>) - Method in class owltools.mooncat.PropertyViewOntologyBuilder
 
Adjacency<T> - Interface in owltools.util
Representation of a graph (i.e.
alternativeCode - Variable in enum owltools.gfx.RelationType
 
Annotation - Interface in owltools.frame
 
ANNOTATION_IRI_IS_INFERRED - Static variable in class owltools.graph.AxiomAnnotationTools
IRI for the default annotation marking an axiom as inferred.
AnnotationLD - Class in owltools.frame.jsonld
 
AnnotationLD() - Constructor for class owltools.frame.jsonld.AnnotationLD
 
AnnotationLD(PropertyStubLD, Object) - Constructor for class owltools.frame.jsonld.AnnotationLD
 
appendLine(CharSequence) - Method in class owltools.mooncat.ontologymetadata.ImportChainDotWriter
 
asPrefixOWLOntologyFormat() - Method in class owltools.io.OWLJSONFormat
 
Attribute - Class in owltools.phenolog
Represents a characteristic of an individual.
Attribute(String, String) - Constructor for class owltools.phenolog.Attribute
 
Attribute(String) - Constructor for class owltools.phenolog.Attribute
 
AxiomAnnotationsChanger(Set<OWLAnnotation>, OWLDataFactory) - Constructor for class owltools.graph.AxiomAnnotationTools.AxiomAnnotationsChanger
 
AxiomAnnotationTools - Class in owltools.graph
These are helper methods to check and modify axiom annotations.
AxiomAnnotationTools() - Constructor for class owltools.graph.AxiomAnnotationTools
 
AxiomAnnotationTools.AxiomAnnotationsChanger - Class in owltools.graph
Visitor which returns a new axiom of the same type with the new annotations.
axiomType - Variable in class owltools.io.TableToAxiomConverter.Config
 

B

Base - Interface in owltools.frame
 
BaseLD - Class in owltools.frame.jsonld
 
BaseLD() - Constructor for class owltools.frame.jsonld.BaseLD
 
belongsToSource(OWLEntity) - Method in class owltools.mooncat.Mooncat
 
BloomFilter<E> - Class in owltools.util
Implementation of a Bloom-filter, as described here: http://en.wikipedia.org/wiki/Bloom_filter Inspired by the SimpleBloomFilter-class written by Ian Clarke.
BloomFilter(double, int, int) - Constructor for class owltools.util.BloomFilter
Constructs an empty Bloom filter.
BloomFilter(int, int) - Constructor for class owltools.util.BloomFilter
Constructs an empty Bloom filter.
BloomFilter(double, int) - Constructor for class owltools.util.BloomFilter
Constructs an empty Bloom filter with a given false positive probability.
BloomFilter(int, int, int, BitSet) - Constructor for class owltools.util.BloomFilter
Construct a new Bloom filter based on existing Bloom filter data.
border - Variable in class owltools.gfx.OWLGraphLayoutNode
 
bottom() - Method in class owltools.gfx.OWLGraphLayoutNode
 
bottom - Variable in class owltools.gfx.OWLGraphLayoutNode.SVGRectangle
 
bottomMargin - Static variable in class owltools.gfx.HierarchyImage
 
BridgeExtractor - Class in owltools.mooncat
 
BridgeExtractor(OWLOntology) - Constructor for class owltools.mooncat.BridgeExtractor
 
BridgeExtractor.Combo - Class in owltools.mooncat
Maps a set of ontologies (e.g.
build(OWLReasonerFactory) - Method in class owltools.mooncat.PropertyViewOntologyBuilder
 
buildClassMap(OWLGraphWrapper) - Method in class owltools.io.TableToAxiomConverter
 
buildInferences() - Method in class owltools.InferenceBuilder
 
buildInferences(boolean) - Method in class owltools.InferenceBuilder
if alwaysAssertSuperClasses then ensure that superclasses are always asserted for every equivalence axiom, except in the case where a more specific superclass is already in the set of inferences.
buildInferredViewOntology(OWLReasoner) - Method in class owltools.mooncat.PropertyViewOntologyBuilder
Once the PVO has been constructed, this uses a reasoner to classify it.
buildViewOntology() - Method in class owltools.mooncat.PropertyViewOntologyBuilder
As PropertyViewOntologyBuilder.buildViewOntology(IRI, IRI), but both O(P) and O(P)' have automatically generated IRIs
buildViewOntology(IRI) - Method in class owltools.mooncat.PropertyViewOntologyBuilder
as PropertyViewOntologyBuilder.buildViewOntology(IRI,IRI), but sets the asserted and inferred view ontologies to be the same
buildViewOntology(IRI, IRI) - Method in class owltools.mooncat.PropertyViewOntologyBuilder
Constructs a property view ontology O(P) or O(P,E) from source ontology O, such that every class C in O has a corresponding view class C' in O(P), such that C' EquivalentTo = P some C O(P) imports both the O, and optionally the elements ontology E - in which case we call the ontology O(P,E).

C

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 Lists neQp and extEdgeQp and assigned the resulting OWLQuantifiedPropertys to mergedEdge.
combineEdgePairWithGCI(OWLObject, OWLGraphEdge, OWLGraphEdge, int) - Method in class owltools.graph.OWLGraphWrapperEdgesExtended
Same as OWLGraphWrapperEdges.combineEdgePair(OWLObject, OWLGraphEdge, OWLGraphEdge, int) except that the GCI filler an GCI relation of the edges are taken into account.
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
Create an OWLPrettyPrinter, which renders in OWL Manchester syntax.
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
 

D

DEFAULT_IRI_PREFIX - Static variable in class owltools.graph.OWLGraphWrapper
 
defaultCol1 - Variable in class owltools.io.TableToAxiomConverter.Config
 
defaultCol2 - Variable in class owltools.io.TableToAxiomConverter.Config
 
defaultPrefix - Variable in class owltools.io.StanzaToOWLConverter.Config
 
description - Variable in enum owltools.gfx.RelationType
 
deserialize(JsonElement, Type, JsonDeserializationContext) - Method in class owltools.io.GeneralObjectDeserializer
 
directRestrictions - Variable in class owltools.frame.jsonld.ClassFrameLD
 
directSuperclasses - Variable in class owltools.frame.jsonld.ClassFrameLD
 
dispose() - Method in class owltools.InferenceBuilder
Dispose the internal reasoner
dispose() - Method in class owltools.io.OWLPrettyPrinter.LabelProvider
 
dispose() - Method in class owltools.reasoner.LazyExpressionMaterializingReasoner
Deprecated.
 
DLQueryTool - Class in owltools.mooncat
Tools for running DL queries on OWLOntology.
DLQueryTool() - Constructor for class owltools.mooncat.DLQueryTool
 
doInferencesForClass(OWLClass, OWLOntology) - Method in class owltools.InferenceBuilder
Only create inferences for an OWLClass, if this method returns true.

E

edges - Variable in class owltools.graph.shunt.OWLShuntGraph
 
EdgeTableRenderer - Class in owltools.io
renders all edges in a simple TSV format
EdgeTableRenderer(PrintStream) - Constructor for class owltools.io.EdgeTableRenderer
 
EdgeTableRenderer(String) - Constructor for class owltools.io.EdgeTableRenderer
 
edgeToSourceExpression(OWLGraphEdge) - Method in class owltools.graph.OWLGraphWrapperEdgesExtended
Translates the source of an OWLGraphEdge into an OWLClassExpression (but, as the method OWLGraphEdge.getSource() returns an OWLObject, this method also returns an OWLObject).
edgeToTargetExpression(OWLGraphEdge) - Method in class owltools.graph.OWLGraphWrapperEdges
pack/translate an edge (either asserted or a graph closure edge) into an OWL class expression according to the OWLGraph to OWLOntology translation rules.
endTaskNotify(String) - Method in class owltools.profile.Profiler
 
enforceEL(OWLGraphWrapper) - Static method in class owltools.InferenceBuilder
 
enforceEL(OWLGraphWrapper, IRI) - Static method in class owltools.InferenceBuilder
Create an ontology with EL as description logic profile.
equals(Object) - Method in class owltools.gfx.OWLGraphStrokeEdge
 
equals(Object) - Method in class owltools.graph.OWLGraphEdge
 
equals(Object) - Method in class owltools.graph.OWLGraphWrapper.Synonym
 
equals(Object) - Method in class owltools.graph.OWLQuantifiedProperty
 
equals(Object) - Method in class owltools.graph.shunt.OWLShuntEdge
 
equals(Object) - Method in class owltools.graph.shunt.OWLShuntNode
 
equals(Object) - Method in class owltools.phenolog.GenePheno
 
equals(Object) - Method in class owltools.phenolog.Individual
 
equals(Object) - Method in class owltools.phenolog.IndividualPair
 
equals(Object) - Method in class owltools.phenolog.Pheno
 
equals(Object) - Method in class owltools.RedundantInferences.RedundantAxiom
 
equals(Object) - Method in class owltools.util.BloomFilter
Compares the contents of two instances to see if they are equal.
equals(Object) - Method in class owltools.util.ClassExpressionPair
 
equalsGCI(OWLGraphEdge) - Method in class owltools.graph.OWLGraphEdge
Checks that the gciFiller and gciRelation of this OWLGraphEdge an of e are equals.
equalsIgnoreOntology(Object) - Method in class owltools.graph.OWLGraphEdge
Equals method ignoring the OWLOntology the OWLGraphEdges compared belong to, as opposed to the #equals() method, that takes into account the ontologies for comparison.
equalsIgnoreOntologyAndGCI(Object) - Method in class owltools.graph.OWLGraphEdge
Equals method ignoring the OWLOntology the OWLGraphEdges compared belong to, and ignoring their gciFillers and gciRelations (as opposed to the #equals() method, that takes into account everything for comparison).
EquivalenceSetMergeUtil - Class in owltools.mooncat
 
EquivalenceSetMergeUtil(OWLGraphWrapper, OWLReasoner) - Constructor for class owltools.mooncat.EquivalenceSetMergeUtil
 
equivalentClasses - Variable in class owltools.frame.jsonld.ClassFrameLD
 
errorFontName - Variable in class owltools.gfx.GraphStyle
 
errorFontSize - Variable in class owltools.gfx.GraphStyle
 
errorMessage - Variable in class owltools.gfx.HierarchyImage
 
errors - Variable in class owltools.InferenceBuilder.ConsistencyReport
 
excludeAllWith(OWLAnnotationProperty, OWLOntology) - Method in class owltools.graph.OWLGraphWrapperEdges.Config
 
excludeMetaClass - Variable in class owltools.graph.OWLGraphWrapperEdges.Config
 
excludeProperty(OWLObjectProperty, OWLQuantifiedProperty.Quantifier) - Method in class owltools.graph.OWLGraphWrapperEdges.Config
 
excludeProperty(OWLObjectProperty) - Method in class owltools.graph.OWLGraphWrapperEdges.Config
 
executeDLQuery(String, OWLGraphWrapper, OWLReasonerFactory) - Static method in class owltools.mooncat.DLQueryTool
Execute the DL query on the given ontology graph.
executeTarjan(Adjacency<NODE>) - Method in class owltools.util.AbstractTarjan
 
executeTarjan(Adjacency<NODE>) - Method in interface owltools.util.Tarjan
Create the strongly connected components for the given graph.
expandPropertyChain(List<OWLObjectPropertyExpression>) - Method in class owltools.mooncat.PropertyViewOntologyBuilder
 
expandPropertyChain(List<OWLObjectPropertyExpression>, int) - Method in class owltools.mooncat.PropertyViewOntologyBuilder
 
expandPropertyChain(List<OWLObjectPropertyExpression>, OWLClassExpression) - Method in class owltools.mooncat.PropertyViewOntologyBuilder
 
expandRelationChain(OWLObjectProperty) - Method in class owltools.graph.OWLGraphWrapperEdges
If available, return the elements of the equivalent property chain.
expectedFalsePositiveProbability() - Method in class owltools.util.BloomFilter
Calculates the expected probability of false positives based on the number of expected filter elements and the size of the Bloom filter.
expectedNumCols - Variable in class owltools.idmap.AbstractMappingParser
 
explainTaxonConstraint(Collection<String>, Collection<String>) - Method in class owltools.mooncat.SpeciesSubsetterUtil
Provides explanations about the sources of some taxon constraints on the OWLClasses provided through clsIds, related to the taxa provided through taxonIds.
Expression - Interface in owltools.frame
 
ExpressionLD - Class in owltools.frame.jsonld
 
ExpressionLD() - Constructor for class owltools.frame.jsonld.ExpressionLD
 
extractBridgeOntologies(String, boolean) - Method in class owltools.mooncat.BridgeExtractor
given a source ontology O:
extractModules() - Method in class owltools.mooncat.Mooncat
 
extractModules(OWLOntology) - Method in class owltools.mooncat.Mooncat
 
extractModules(Set<OWLClass>, Set<OWLClass>) - Method in class owltools.mooncat.Mooncat
 
extractOntologyMetadata(OWLGraphWrapper, String) - Static method in class owltools.mooncat.ontologymetadata.ImportChainExtractor
 
extractPropertyOntology() - Method in class owltools.mooncat.PropertyExtractor
 
extractPropertyOntology(IRI) - Method in class owltools.mooncat.PropertyExtractor
 
extractPropertyOntology(IRI, OWLOntology) - Method in class owltools.mooncat.PropertyExtractor
 
extractPropertyOntology(IRI, Set<OWLProperty>) - Method in class owltools.mooncat.PropertyExtractor
Returns a new ontology containing declarations for each prop in props, its closure, together with associated axioms

F

fail() - Method in class owltools.cli.Opts
Send a fail.
fill - Variable in class owltools.gfx.GraphStyle
 
fill - Variable in class owltools.gfx.OWLGraphLayoutNode
 
filterClasses(Set<OWLClass>) - Method in class owltools.graph.OWLGraphManipulator
Filter from the ontologies all OWLClasses present in classesToKeep, and then update the OWLGraphWrapper container.
filterEdges(Set<OWLGraphEdge>, Set<? extends OWLPropertyExpression>) - Method in class owltools.graph.OWLGraphWrapperEdges
 
filterRelations(Collection<String>, boolean) - Method in class owltools.graph.OWLGraphManipulator
Filter the OWLAxioms in the ontologies to keep only those that correspond to OWLObjectPropertys listed in allowedRels, as OBO-style IDs.
filterSubgraphs(Collection<String>) - Method in class owltools.graph.OWLGraphManipulator
Keep in the ontologies only the subgraphs starting from the provided OWLClasses, and their ancestors.
filterWhere - Variable in class owltools.idmap.IDMappingPIRParser
 
findCardinalityConstraints(OWLOntology) - Static method in class owltools.graph.CardinalityContraintsTools
Find the axioms with cardinality constraints.
findCommonAncestors(OWLGraphWrapper, OWLObject, OWLObject) - Static method in class owltools.graph.OWLGraphUtil
 
findCommonAncestors(OWLGraphWrapper, OWLObject, OWLObject, Set<OWLPropertyExpression>) - Static method in class owltools.graph.OWLGraphUtil
Find common ancestors to x and y that can be reached over the specified set of relations.
findCommonSubsumersAsEdges(OWLGraphWrapper, OWLObject, OWLObject) - Static method in class owltools.graph.OWLGraphUtil
 
findLeastCommonAncestors(OWLGraphWrapper, OWLObject, OWLObject) - Static method in class owltools.graph.OWLGraphUtil
 
findLeastCommonAncestors(OWLGraphWrapper, OWLObject, OWLObject, Set<OWLPropertyExpression>) - Static method in class owltools.graph.OWLGraphUtil
Find lest common ancestors to x and y that can be reached over the specified set of relations.
findLeastCommonSubsumersAsEdges(OWLGraphWrapper, OWLObject, OWLObject) - Static method in class owltools.graph.OWLGraphUtil
 
findRedundantSubClassAxioms(Iterable<OWLClass>, OWLOntology, OWLReasoner) - Static method in class owltools.RedundantInferences
Find redundant and marked as inferred axioms for each class in the given ontology.
findRelatedAxioms(Set<OWLObject>, OWLGraphWrapper) - Static method in class owltools.mooncat.Mooncat
 
findTaggedEntities(OWLAnnotationProperty, Set<OWLAnnotationValue>, OWLGraphWrapper) - Static method in class owltools.mooncat.Mooncat
 
flush() - Method in class owltools.io.OWLGsonParser
 
flush() - Method in class owltools.io.OWLGsonRenderer
 
flush() - Method in class owltools.reasoner.LazyExpressionMaterializingReasoner
Deprecated.
 
font - Variable in class owltools.gfx.OWLGraphLayoutNode
 
forCodes(String) - Static method in enum owltools.gfx.RelationType
 
formalCode - Variable in enum owltools.gfx.RelationType
 
Frame - Interface in owltools.frame
 
FrameLD - Class in owltools.frame.jsonld
 
FrameLD() - Constructor for class owltools.frame.jsonld.FrameLD
 
FrameMaker - Class in owltools.frame
 
FrameMaker() - Constructor for class owltools.frame.FrameMaker
 
FrameMakerLD - Class in owltools.frame.jsonld
 
FrameMakerLD(OWLGraphWrapper) - Constructor for class owltools.frame.jsonld.FrameMakerLD
 
fromJson(String) - Static method in class owltools.io.GeneralObjectDeserializer
This is a convenience routine which deserializes a string into one of the five general Java types as described above.
fromJson(Reader) - Static method in class owltools.io.GeneralObjectDeserializer
This is a convenience routine deserializes the Json read from the specified reader into one of the five general Java types as described above.

G

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
Get all OWLClasses from all ontologies, that are neither top entity (owl:thing), nor bottom entity (owl:nothing), nor deprecated (OWLGraphWrapperExtended.isObsolete(OWLObject) returns false).
getAllOWLClassesFromSource() - Method in class owltools.graph.OWLGraphWrapperEdgesExtended
Get only the OWLClasses from the OWLOntology returned by OWLGraphWrapperBasic.getSourceOntology(), that are neither top entity (owl:thing), nor bottom entity (owl:nothing), nor deprecated (OWLGraphWrapperExtended.isObsolete(OWLObject) returns false).
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 OWLObjects 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 OWLAxioms 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
finds all classes for which Mooncat.isDangling(OWLOntology, OWLEntity) is true
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 OWLGraphEdges.
getGCIOutgoingEdges(OWLClass) - Method in class owltools.graph.OWLGraphWrapperEdgesExtended
Retrieve OBO GCI relations outgoing from s as a Set of OWLGraphEdges.
getGCIOutgoingEdges(OWLClass, Set<OWLPropertyExpression>) - Method in class owltools.graph.OWLGraphWrapperEdgesExtended
Same as OWLGraphWrapperEdgesExtended.getGCIOutgoingEdges(OWLClass), but with a Set of OWLPropertyExpression allowing to filter the relations retrieved.
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
Same as OWLGraphWrapperExtended.getIdentifier(OWLObject) but a different profile to support the FlexLoader.
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
As OWLGraphWrapperEdges.getIncomingEdgesClosure(OWLObject t), but allows the option of including 'complete' edge list.
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
Similar to OWLGraphWrapperEdges.getIncomingEdges(OWLObject), but the returned Set also includes OBO GCI incoming edges (see OWLGraphWrapperEdgesExtended.getGCIIncomingEdges(OWLClass)).
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
Generated after running PropertyViewOntologyBuilder.buildInferredViewOntology(OWLReasoner) Note that O(P) and O(P)' can share the same object, i.e the assertedViewOntology is augmented to become the inferred view ontology
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
Similar to OWLGraphWrapperEdges.getNamedAncestors(OWLObject) but also considering GCI relations.
getNamedAncestorsWithGCI(OWLObject, Set<OWLPropertyExpression>) - Method in class owltools.graph.OWLGraphWrapperEdgesExtended
Similar to OWLGraphWrapperEdgesExtended.getNamedAncestorsWithGCI(OWLObject, Set) but allowing to filter the relations considered.
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 OWLClasses leaves of any ontology (OWLClasses with no incoming edges as returned by {OWLGraphWrapperEdges#getIncomingEdgesWithGCI(OWLObject)}), and not deprecated (OWLGraphWrapperExtended.isObsolete(OWLObject) returns false; edges incoming from an obsolete class are not considered)
getOntologyRoots() - Method in class owltools.graph.OWLGraphWrapperEdgesExtended
Return the OWLClasses root of any ontology (OWLClasses with no outgoing edges as returned by {OWLGraphWrapperEdges#getOutgoingEdgesWithGCI(OWLObject)}), and not deprecated (OWLGraphWrapperExtended.isObsolete(OWLObject) returns false)).
getOntologyRoots(Set<OWLPropertyExpression>) - Method in class owltools.graph.OWLGraphWrapperEdgesExtended
Return the OWLClasses root of any ontology over the specified OWLPropertyExpressions (OWLClasses with no outgoing edges of the specified type, as returned by {OWLGraphWrapperEdges#getOutgoingEdgesWithGCI(OWLObject, Set)}), and not deprecated (OWLGraphWrapperExtended.isObsolete(OWLObject) returns false); edges going to obsolete classes are not taken into account).
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
As OWLGraphWrapperEdges.getOutgoingEdgesClosure(OWLObject s), but only consider the specified set of properties when walking the graph.
getOutgoingEdgesClosure(OWLObject, boolean) - Method in class owltools.graph.OWLGraphWrapperEdges
getOutgoingEdgesClosureReflexive(OWLObject) - Method in class owltools.graph.OWLGraphWrapperEdges
as OWLGraphWrapperEdges.getOutgoingEdgesClosure(OWLObject), but also includes an identity edge
getOutgoingEdgesClosureReflexive(OWLObject, Set<? extends OWLPropertyExpression>) - Method in class owltools.graph.OWLGraphWrapperEdges
getOutgoingEdgesClosureWithGCI(OWLObject) - Method in class owltools.graph.OWLGraphWrapperEdgesExtended
Similar to OWLGraphWrapperEdges.getOutgoingEdgesClosure(OWLObject), but also considering OBO GCI relations.
getOutgoingEdgesNamedClosureOverSupProps(OWLObject) - Method in class owltools.graph.OWLGraphWrapperEdgesExtended
Same method as OWLGraphWrapperEdges.getOutgoingEdgesClosure(OWLObject), except that only the OWLGraphEdges going to a named target are returned, and that the list of connecting edge properties are not only combined using the composition rules as usual, but also over super properties (see for instance #combineEdgePairWithSuperPropsAndGCI(OWLGraphEdge, OWLGraphEdge).
getOutgoingEdgesNamedClosureOverSupPropsWithGCI(OWLObject) - Method in class owltools.graph.OWLGraphWrapperEdgesExtended
Similar to OWLGraphWrapperEdgesExtended.getOutgoingEdgesNamedClosureOverSupProps(OWLObject) but with the OBO GCI relations also taken into account.
getOutgoingEdgesWithGCI(OWLObject) - Method in class owltools.graph.OWLGraphWrapperEdgesExtended
Similar to OWLGraphWrapperEdges.getOutgoingEdges(OWLObject), but the returned Set also includes OBO GCI outgoing edges (see OWLGraphWrapperEdgesExtended.getGCIOutgoingEdges(OWLClass)).
getOutgoingEdgesWithGCI(OWLObject, Set<OWLPropertyExpression>) - Method in class owltools.graph.OWLGraphWrapperEdgesExtended
Similar to OWLGraphWrapperEdges.getOutgoingEdges(OWLObject, Set), but the returned Set also includes OBO GCI outgoing edges (see OWLGraphWrapperEdgesExtended.getGCIOutgoingEdges(OWLClass)).
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 OWLClasses 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
As OWLGraphWrapperExtended.getOWLClassByIdentifier(String) but include pre-resolution step using altId map.
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 OWLClasses descendant of parentClass.
getOWLClassDescendantsWithGCI(OWLClass) - Method in class owltools.graph.OWLGraphWrapperEdgesExtended
Similar to OWLGraphWrapperEdgesExtended.getOWLClassDescendants(OWLClass) but also considering GCI relations.
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 OWLClasses that are direct parent of subClass.
getOWLClassDirectDescendants(OWLClass) - Method in class owltools.graph.OWLGraphWrapperEdgesExtended
Return the OWLClasses directly descendant of parentClass.
getOWLClassDirectDescendantsWithGCI(OWLClass) - Method in class owltools.graph.OWLGraphWrapperEdgesExtended
Similar to OWLGraphWrapperEdgesExtended.getOWLClassDirectDescendants(OWLClass) but also considering GCI relations.
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 OWLObjects 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
Returns only the OWLSubClassOfAxioms among the OWLAxioms returned by OWLGraphEdge.getAxioms().
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.

H

handleChanges(Set<OWLAxiom>, Set<OWLAxiom>) - Method in class owltools.reasoner.GraphReasoner
 
handleChanges(Set<OWLAxiom>, Set<OWLAxiom>) - Method in class owltools.reasoner.LazyExpressionMaterializingReasoner
Deprecated.
 
handler - Variable in class owltools.idmap.IDMappingPIRParser
 
hasArgs() - Method in class owltools.cli.Opts
 
hasAssertedSubClassAxiom(OWLClass, OWLClassExpression, OWLOntology) - Method in class owltools.InferenceBuilder
Check the ontology for an existing subClassOf axiom with the given sub- and superclass.
hasEdge(OWLShuntEdge) - Method in class owltools.graph.shunt.OWLShuntGraph
Check to see if an edge is in the graph.
hasFirstEdgeMoreGeneralGCIParams(OWLGraphEdge, OWLGraphEdge) - Method in class owltools.graph.OWLGraphWrapperEdgesExtended
Determines whether the GCI parameters of the GCI relation firstEdge are more general than the GCI parameters of the GCI relation otherEdge.
hashCode() - Method in class owltools.gfx.OWLGraphStrokeEdge
 
hashCode() - Method in class owltools.graph.OWLGraphEdge
 
hashCode() - Method in class owltools.graph.OWLGraphWrapper.Synonym
 
hashCode() - Method in class owltools.graph.OWLQuantifiedProperty
 
hashCode() - Method in class owltools.graph.shunt.OWLShuntEdge
 
hashCode() - Method in class owltools.graph.shunt.OWLShuntNode
 
hashCode() - Method in class owltools.phenolog.GenePheno
 
hashCode() - Method in class owltools.phenolog.Individual
 
hashCode() - Method in class owltools.phenolog.IndividualPair
 
hashCode() - Method in class owltools.phenolog.Pheno
 
hashCode() - Method in class owltools.RedundantInferences.RedundantAxiom
 
hashCode() - Method in class owltools.util.BloomFilter
Calculates a hash code for this class.
hashCode() - Method in class owltools.util.ClassExpressionPair
 
hasNext() - Method in class owltools.graph.shunt.OWLShuntGraphDFIterator
 
hasNode(OWLShuntNode) - Method in class owltools.graph.shunt.OWLShuntGraph
Check to see if a node is in the graph.
hasOpt(String) - Method in class owltools.cli.Opts
Check if the option flag is in the remaining parameters
hasOpts() - Method in class owltools.cli.Opts
 
hasProperty() - Method in class owltools.graph.OWLQuantifiedProperty
 
height - Variable in class owltools.gfx.GraphStyle
 
height - Variable in class owltools.gfx.ImageRender
 
height - Variable in class owltools.gfx.OWLGraphLayoutNode
 
hideIds() - Method in class owltools.io.OWLPrettyPrinter
 
HierarchyImage - Class in owltools.gfx
Adapted from QuickGO
HierarchyImage(String) - Constructor for class owltools.gfx.HierarchyImage
 
HierarchyImage(int, int, Collection<OWLGraphLayoutNode>, Collection<OWLGraphStrokeEdge>, GraphStyle, Set<RelationType>) - Constructor for class owltools.gfx.HierarchyImage
 

I

id() - Method in class owltools.gfx.HierarchyImage
 
id - Variable in class owltools.gfx.OWLGraphLayoutNode
 
id - Variable in class owltools.graph.shunt.OWLShuntGraph
 
id - Variable in class owltools.graph.shunt.OWLShuntNode
 
idColour - Variable in class owltools.gfx.OWLGraphLayoutNode
 
idField - Variable in class owltools.io.StanzaToOWLConverter.Config
 
idMap - Variable in class owltools.idmap.UniProtIDMapParser
 
IDMapHandler - Class in owltools.idmap
 
IDMapHandler() - Constructor for class owltools.idmap.IDMapHandler
 
IDMapPairWriter - Class in owltools.idmap
 
IDMapPairWriter() - Constructor for class owltools.idmap.IDMapPairWriter
 
IDMappingPIRParser - Class in owltools.idmap
Parses the IDMapping file available here: ftp://ftp.pir.georgetown.edu/databases/idmapping/idmapping.tb.gz
IDMappingPIRParser() - Constructor for class owltools.idmap.IDMappingPIRParser
 
IDMappingPIRParser.Types - Enum in owltools.idmap
 
idTypes - Variable in class owltools.idmap.UniProtIDMapParser
 
ImageRender - Class in owltools.gfx
Adapted from QuickGO
ImageRender(int, int) - Constructor for class owltools.gfx.ImageRender
 
ImportChainDotWriter - Class in owltools.mooncat.ontologymetadata
Rudimentary implementation of a DOT writer for the LEGO annotations in OWL.
ImportChainDotWriter(OWLGraphWrapper) - Constructor for class owltools.mooncat.ontologymetadata.ImportChainDotWriter
Create a new writer for the given ontology and reasoner.
ImportChainDotWriter.UnExpectedStructureException - Exception in owltools.mooncat.ontologymetadata
 
ImportChainExtractor - Class in owltools.mooncat.ontologymetadata
 
ImportChainExtractor() - Constructor for class owltools.mooncat.ontologymetadata.ImportChainExtractor
 
ImportClosureSlurper - Class in owltools.io
 
ImportClosureSlurper(OWLOntology) - Constructor for class owltools.io.ImportClosureSlurper
 
includeAllWith(OWLAnnotationProperty, OWLOntology) - Method in class owltools.graph.OWLGraphWrapperEdges.Config
 
includedProperties - Variable in class owltools.mooncat.SpeciesMergeUtil
 
includeProperty(OWLObjectProperty) - Method in class owltools.graph.OWLGraphWrapperEdges.Config
 
includeProperty(OWLObjectProperty, OWLQuantifiedProperty.Quantifier) - Method in class owltools.graph.OWLGraphWrapperEdges.Config
 
Individual - Class in owltools.phenolog
represents an attribute-bearing entity; for example, a gene.
Individual(String, String, Set<Attribute>) - Constructor for class owltools.phenolog.Individual
 
Individual(String, Set<Attribute>) - Constructor for class owltools.phenolog.Individual
 
Individual(String, String) - Constructor for class owltools.phenolog.Individual
 
Individual(String, String, int) - Constructor for class owltools.phenolog.Individual
 
Individual(String) - Constructor for class owltools.phenolog.Individual
 
IndividualPair - Class in owltools.phenolog
 
IndividualPair() - Constructor for class owltools.phenolog.IndividualPair
 
IndividualPair(Individual, Individual) - Constructor for class owltools.phenolog.IndividualPair
 
individualsType - Variable in class owltools.io.TableToAxiomConverter.Config
 
InferenceBuilder - Class in owltools
This class build inferred axioms of an ontology.
InferenceBuilder(OWLGraphWrapper) - Constructor for class owltools.InferenceBuilder
 
InferenceBuilder(OWLGraphWrapper, String) - Constructor for class owltools.InferenceBuilder
 
InferenceBuilder(OWLGraphWrapper, String, boolean) - Constructor for class owltools.InferenceBuilder
 
InferenceBuilder(OWLGraphWrapper, OWLReasonerFactory, boolean) - Constructor for class owltools.InferenceBuilder
 
InferenceBuilder.ConsistencyReport - Class in owltools
 
InferenceBuilder.OWLClassFilter - Interface in owltools
Filter for relevant OWLClasses during the inference Building process.
InferenceBuilder.PotentialRedundant - Class in owltools
 
inferredEdgeBySource - Variable in class owltools.graph.OWLGraphWrapperEdges
 
InferredParentRenderer - Class in owltools.io
Renders the most specific parent over a set of Objectproperties using an extended reasoner.
InferredParentRenderer(PrintStream) - Constructor for class owltools.io.InferredParentRenderer
 
InferredParentRenderer(String) - Constructor for class owltools.io.InferredParentRenderer
 
info(String, String) - Method in class owltools.cli.Opts
Write an info.
infoFontName - Variable in class owltools.gfx.GraphStyle
 
infoFontSize - Variable in class owltools.gfx.GraphStyle
 
init() - Method in class owltools.idmap.IDMapHandler
 
init() - Method in class owltools.idmap.IDMapPairWriter
 
interrupt() - Method in class owltools.reasoner.GraphReasoner
 
interrupt() - Method in class owltools.reasoner.LazyExpressionMaterializingReasoner
Deprecated.
 
intersection(Collection<E>) - Method in class owltools.util.BloomFilter
 
IntersectionOf - Interface in owltools.frame
 
IntersectionOfLD - Class in owltools.frame.jsonld
 
IntersectionOfLD(Set<ExpressionLD>) - Constructor for class owltools.frame.jsonld.IntersectionOfLD
 
iriPrefixMap - Variable in class owltools.io.TableToAxiomConverter.Config
 
ISA_PARTOF - Static variable in class owltools.graph.RelationSets
 
isAllValuesFrom() - Method in class owltools.graph.OWLQuantifiedProperty
 
isAnnotation - Variable in class owltools.io.StanzaToOWLConverter.Mapping
 
isAPartOfEdge(OWLGraphEdge) - Method in class owltools.graph.OWLGraphManipulator
Determine if edge represents a part_of relation or one of its sub-relations (e.g., "deep_part_of").
isAssumeOBOStyleIRIs() - Method in class owltools.mooncat.PropertyViewOntologyBuilder
 
isASubClassOfEdge(OWLGraphEdge) - Method in class owltools.graph.OWLGraphManipulator
Determine if edge represents an is_a relation.
isCacheClosure - Variable in class owltools.graph.OWLGraphWrapperEdges.Config
 
isCardinality() - Method in class owltools.graph.OWLQuantifiedProperty
 
isChain - Variable in class owltools.io.ChadoGraphClosureRenderer
 
isCheckOboDoc() - Method in class owltools.io.ParserWrapper
 
isClassifyIndividuals() - Method in class owltools.mooncat.PropertyViewOntologyBuilder
 
isConsistent() - Method in class owltools.reasoner.GraphReasoner
 
isConsistent() - Method in class owltools.reasoner.LazyExpressionMaterializingReasoner
Deprecated.
 
isCreateReflexiveClasses() - Method in class owltools.mooncat.PropertyViewOntologyBuilder
 
isCreateShorthand - Variable in class owltools.mooncat.PropertyExtractor
 
isDangling(OWLOntology, OWLEntity) - Method in class owltools.mooncat.Mooncat
Here a dangling entity is one that has no annotation assertions; this is not a perfect test, as conceivable a class could lack assertions; however, this would not be the case for any ontology following obo library principles.
isDebug() - Method in class owltools.InferenceBuilder
 
isEdgeEntailed(ProvenanceReasonerWrapper.OWLEdge, OWLOntology, OWLReasoner) - Method in class owltools.mooncat.ProvenanceReasonerWrapper
 
isEntailed(OWLAxiom) - Method in class owltools.reasoner.GraphReasoner
 
isEntailed(Set<? extends OWLAxiom>) - Method in class owltools.reasoner.GraphReasoner
 
isEntailed(OWLAxiom) - Method in class owltools.reasoner.LazyExpressionMaterializingReasoner
Deprecated.
 
isEntailed(Set<? extends OWLAxiom>) - Method in class owltools.reasoner.LazyExpressionMaterializingReasoner
Deprecated.
 
isEntailmentCheckingSupported(AxiomType<?>) - Method in class owltools.reasoner.GraphReasoner
 
isEntailmentCheckingSupported(AxiomType<?>) - Method in class owltools.reasoner.LazyExpressionMaterializingReasoner
Deprecated.
 
isExcluded(OWLQuantifiedProperty) - Method in class owltools.graph.OWLGraphWrapperEdges
 
isExcludeEdge(OWLGraphEdge) - Method in class owltools.graph.OWLGraphWrapperEdges
 
isFilterUnused() - Method in class owltools.mooncat.PropertyViewOntologyBuilder
 
isFollowComplementOfInClosure - Variable in class owltools.graph.OWLGraphWrapperEdges.Config
 
isGCI() - Method in class owltools.graph.OWLGraphEdge
Determines whether this OWLGraphEdge corresponds to an OBO gci_relation.
isHasValue() - Method in class owltools.graph.OWLQuantifiedProperty
 
isHelpMode() - Method in class owltools.cli.Opts
 
isIdentity() - Method in class owltools.graph.OWLQuantifiedProperty
 
isImportMarkedEntity(OWLNamedObject, OWLOntology) - Static method in class owltools.mooncat.Mooncat
Check, if the named object has the annotation property IAO:0000412, declaring the object as imported.
isIncludeClassExpressionsInClosure - Variable in class owltools.graph.OWLGraphWrapperEdges.Config
 
isInferred() - Method in class owltools.graph.OWLQuantifiedProperty
 
isInStack(Stack<NODE>, NODE) - Method in class owltools.util.AbstractTarjan
Check: is the NODE n in the given stack

WARNING: This is currently an inefficient implementation.
isInstanceOf() - Method in class owltools.graph.OWLQuantifiedProperty
 
isInverseOf() - Method in class owltools.graph.OWLQuantifiedProperty
 
isMarkedAsInferredAxiom(OWLAxiom) - Static method in class owltools.graph.AxiomAnnotationTools
Check if there as an annotation with is_inferred="true" for the given axiom.
isMonitorMemory - Variable in class owltools.graph.OWLGraphWrapperEdges.Config
 
isObjectLiteral - Variable in class owltools.io.TableToAxiomConverter.Config
 
isOboIdentifiers - Variable in class owltools.io.StanzaToOWLConverter.Config
 
isOboIdentifiers - Variable in class owltools.io.TableToAxiomConverter.Config
 
isObsolete(OWLObject) - Method in class owltools.graph.OWLGraphWrapperExtended
tests if an OWLObject has been declared obsolete in the graph.
isOWLObjectInSubsets(OWLObject, Collection<String>) - Method in class owltools.graph.OWLGraphWrapperEdgesExtended
Determine if testObject belongs to at least one of the subsets in subsets.
isPrecomputed(InferenceType) - Method in class owltools.reasoner.GraphReasoner
 
isPrecomputed(InferenceType) - Method in class owltools.reasoner.LazyExpressionMaterializingReasoner
Deprecated.
 
isPrefixOWLOntologyFormat() - Method in class owltools.io.OWLJSONFormat
 
isPreserveObjectPropertyIRIs() - Method in class owltools.mooncat.OWLInAboxTranslator
 
isPropertyAssertion() - Method in class owltools.graph.OWLQuantifiedProperty
 
isQuantified() - Method in class owltools.graph.OWLQuantifiedProperty
 
isRealClass(OWLObject) - Method in class owltools.graph.OWLGraphWrapperEdgesExtended
Determines that object is an OWLClass that is neither owl:thing, nor owl:nothing, and that it is not deprecated (OWLGraphWrapperExtended.isObsolete(OWLObject) returns false).
isReplace - Variable in class owltools.tr.TemplatedTransformer.Mapping
 
isSatisfiable(OWLClassExpression) - Method in class owltools.reasoner.GraphReasoner
 
isSatisfiable(OWLClassExpression) - Method in class owltools.reasoner.LazyExpressionMaterializingReasoner
Deprecated.
 
isSkippable(OWLClass) - Method in class owltools.mooncat.SpeciesMergeUtil
 
isSomeValuesFrom() - Method in class owltools.graph.OWLQuantifiedProperty
 
isSourceNamedObject() - Method in class owltools.graph.OWLGraphEdge
 
isStrict - Variable in class owltools.io.StanzaToOWLConverter.Config
 
isSubClassOf() - Method in class owltools.graph.OWLQuantifiedProperty
 
isSwitchSubjectObject - Variable in class owltools.io.TableToAxiomConverter.Config
 
isTargetNamedObject() - Method in class owltools.graph.OWLGraphEdge
 
isToObject - Variable in class owltools.io.StanzaToOWLConverter.Mapping
 
isTransitive(OWLObjectPropertyExpression, OWLOntology) - Static method in class owltools.util.OwlHelper
 
isTransitive(OWLObjectPropertyExpression, Set<OWLOntology>) - Static method in class owltools.util.OwlHelper
 
isUseOriginalClassIRIs() - Method in class owltools.mooncat.PropertyViewOntologyBuilder
 
isUseSubProperties - Variable in class owltools.mooncat.PropertyExtractor
 
isWriteHeader - Variable in class owltools.io.TableRenderer
 
iteratorDF() - Method in class owltools.graph.shunt.OWLShuntGraph
Get a depth-first iterator for the graph.

J

join(List<String>, String) - Static method in class owltools.io.InferredParentRenderer
 
JustifyAssertionsTool - Class in owltools
Methods to test/justify, whether certain axioms can be inferred from the ontology.
JustifyAssertionsTool() - Constructor for class owltools.JustifyAssertionsTool
 
JustifyAssertionsTool.JustifyResult - Class in owltools
Generic result for a justify.
JustifyResult() - Constructor for class owltools.JustifyAssertionsTool.JustifyResult
 
justifySubClasses(OWLOntology, OWLReasoner, Set<OWLSubClassOfAxiom>) - Static method in class owltools.JustifyAssertionsTool
Justify the given set of subClass axioms from the given ontology.
justifySubClasses(OWLOntology, InferenceBuilder, Set<OWLSubClassOfAxiom>) - Static method in class owltools.JustifyAssertionsTool
Justify the given set of subClass axioms from the given ontology.
justifySubClasses(OWLOntology, OWLReasoner, Set<OWLSubClassOfAxiom>, Collection<OWLAxiom>) - Static method in class owltools.JustifyAssertionsTool
Justify the given set of subClass axioms from the given ontology.

K

key - Variable in class owltools.gfx.GraphStyle
 
keyMap - Variable in class owltools.io.StanzaToOWLConverter.Config
 
keyMargin - Static variable in class owltools.gfx.HierarchyImage
 

L

label - Variable in class owltools.gfx.OWLGraphLayoutNode
 
labelFontName - Variable in class owltools.gfx.GraphStyle
 
labelFontSize - Variable in class owltools.gfx.GraphStyle
 
LabelProvider(OWLGraphWrapperExtended) - Constructor for class owltools.io.OWLPrettyPrinter.LabelProvider
 
LazyExpressionMaterializingReasoner - Class in owltools.reasoner
Deprecated.
This is no longer necessary as ELK 0.4 supports queries using class expressions.
LazyExpressionMaterializingReasoner(OWLOntology, OWLReasonerConfiguration, BufferingMode) - Constructor for class owltools.reasoner.LazyExpressionMaterializingReasoner
Deprecated.
 
LazyExpressionMaterializingReasoner(OWLOntology) - Constructor for class owltools.reasoner.LazyExpressionMaterializingReasoner
Deprecated.
 
LazyExpressionMaterializingReasonerFactory - Class in owltools.reasoner
Deprecated.
LazyExpressionMaterializingReasonerFactory() - Constructor for class owltools.reasoner.LazyExpressionMaterializingReasonerFactory
Deprecated.
 
lbl - Variable in class owltools.graph.shunt.OWLShuntNode
 
left() - Method in class owltools.gfx.OWLGraphLayoutNode
 
left - Variable in class owltools.gfx.OWLGraphLayoutNode.SVGRectangle
 
legend - Variable in class owltools.gfx.HierarchyImage
 
line - Variable in class owltools.gfx.OWLGraphLayoutNode
 
lineNumber - Variable in class owltools.idmap.AbstractMappingParser
 
LinkMaker - Class in owltools.tr
Hard coded version to create relationships based on matching genus differentia patterns, such as:
LinkMaker(OWLGraphWrapper, OWLReasoner) - Constructor for class owltools.tr.LinkMaker
 
LinkMaker.LinkMakerResult - Class in owltools.tr
 
LinkMaker.LinkPattern - Class in owltools.tr
Set of variables for a pattern.
LinkMakerResult(Set<OWLAxiom>, Set<OWLAxiom>, Set<OWLAxiom>) - Constructor for class owltools.tr.LinkMaker.LinkMakerResult
 
LinkPattern(OWLClass, OWLClass, OWLObjectProperty, OWLObjectProperty) - Constructor for class owltools.tr.LinkMaker.LinkPattern
 
literalPrototype - Variable in class owltools.io.StanzaToOWLConverter.Mapping
 
LocalMirrorIRIMapper - Class in owltools.io
This mapper allows for IRI resolution based on matching *parts* of URIs.
LocalMirrorIRIMapper(String) - Constructor for class owltools.io.LocalMirrorIRIMapper
Create an instance from the given directory file.
LocalMirrorIRIMapper(File) - Constructor for class owltools.io.LocalMirrorIRIMapper
Create an mappingXmlIRIMapper from the given mapping.xml file.
LocalMirrorIRIMapper(File, File) - Constructor for class owltools.io.LocalMirrorIRIMapper
Create an mappingXmlIRIMapper from the given mapping.xml file.
LocalMirrorIRIMapper(URL) - Constructor for class owltools.io.LocalMirrorIRIMapper
Create an instance from the given mapping URL.
LocalMirrorIRIMapper(URL, File) - Constructor for class owltools.io.LocalMirrorIRIMapper
Create an instance from the given mapping URL.
logDebug(String) - Method in class owltools.InferenceBuilder
 
logger - Static variable in class owltools.InferenceBuilder
 
logInfo(String) - Method in class owltools.InferenceBuilder
 

M

main(String[]) - Static method in class owltools.diff.ResonerDiffCommandLine
 
main(String[]) - Static method in class owltools.gfx.GraphStyle
Deprecated.
main(String[]) - Static method in class owltools.io.OWLGsonParser
 
main(String[]) - Static method in class owltools.io.OWLGsonRenderer
 
Main - Class in owltools.phenolog
Author : Neeral Beladia Date Created : September 5, 2010 Class Purpose : The Main Class is the kickoff Class consisting of Main() method Methods : Main() printhash() Program Logic : 1.
Main() - Constructor for class owltools.phenolog.Main
 
main(String[]) - Static method in class owltools.phenolog.Main
 
makeAnnotationValue(OWLAnnotationValue) - Method in class owltools.frame.jsonld.FrameMakerLD
 
makeClassFrame(OWLClass) - Method in class owltools.frame.FrameMaker
 
makeClassFrame(OWLClass) - Method in class owltools.frame.jsonld.FrameMakerLD
 
makeClassStub(OWLObject) - Method in class owltools.frame.FrameMaker
 
makeClassStub(OWLObject) - Method in class owltools.frame.jsonld.FrameMakerLD
 
makeClosureSubsetOntology(Set<OWLClass>, IRI) - Method in class owltools.mooncat.Mooncat
 
makeEdge(OWLGraphEdge) - Method in class owltools.gfx.OWLGraphLayoutRenderer
Make a layout edge from a OWLGraphEdge make private?
makeExpression(OWLClassExpression) - Method in class owltools.frame.FrameMaker
 
makeExpression(OWLClassExpression) - Method in class owltools.frame.jsonld.FrameMakerLD
 
makeIntersectionOf(OWLObjectIntersectionOf) - Method in class owltools.frame.FrameMaker
 
makeIntersectionOf(OWLObjectIntersectionOf) - Method in class owltools.frame.jsonld.FrameMakerLD
 
makeLinks(List<LinkMaker.LinkPattern>, OWLAnnotation, boolean) - Method in class owltools.tr.LinkMaker
Start search for matches of the given patterns.
makeMinimalSubsetOntology(Set<OWLClass>, IRI) - Method in class owltools.mooncat.Mooncat
 
makeMinimalSubsetOntology(Set<OWLClass>, IRI, boolean) - Method in class owltools.mooncat.Mooncat
 
makeMinimalSubsetOntology(Set<OWLClass>, IRI, boolean, Boolean) - Method in class owltools.mooncat.Mooncat
Given a set of classes (e.g.
makeOntologyFrame(Set<OWLClass>) - Method in class owltools.frame.jsonld.FrameMakerLD
 
makeOntologyFrame(String, Set<OWLClass>) - Method in class owltools.frame.jsonld.FrameMakerLD
 
makePropertyStub(OWLObject) - Method in class owltools.frame.FrameMaker
 
makePropertyStub(OWLObject) - Method in class owltools.frame.jsonld.FrameMakerLD
 
makeSimpleOntology() - Method in class owltools.graph.OWLGraphManipulator
Make a basic ontology, with only is_a, part_of, and develops_from relations, and redundant relations removed, and redundant relations over is_a/part_of removed.
makeSomeValuesFrom(OWLObjectSomeValuesFrom) - Method in class owltools.frame.FrameMaker
 
makeSomeValuesFrom(OWLObjectSomeValuesFrom) - Method in class owltools.frame.jsonld.FrameMakerLD
 
makeStub(OWLObject) - Method in class owltools.frame.FrameMaker
 
makeStub(OWLObject) - Method in class owltools.frame.jsonld.FrameMakerLD
 
makeViewClassIRI(IRI, IRI, String) - Method in class owltools.mooncat.PropertyViewOntologyBuilder
 
Mapping() - Constructor for class owltools.io.StanzaToOWLConverter.Mapping
 
Mapping() - Constructor for class owltools.tr.TemplatedTransformer.Mapping
 
MappingTarjan<T> - Class in owltools.util
Extension of the AbstractTarjan implementation to use internal map for handling the required information for a node.
MappingTarjan(boolean) - Constructor for class owltools.util.MappingTarjan
 
mapRelationsToParent(Collection<String>) - Method in class owltools.graph.OWLGraphManipulator
Replace the sub-relations of parentRelations by these parent relations.
mapRelationsToParent(Collection<String>, Collection<String>) - Method in class owltools.graph.OWLGraphManipulator
Identical to OWLGraphManipulator.mapRelationsToParent(Collection), except that this method allows to filter relations not to be mapped to parents:
markAsInferredAxiom(OWLAxiom, OWLOntology) - Static method in class owltools.graph.AxiomAnnotationTools
Mark the given axiom as inferred.
Side effect: Removes the axiom in the given ontology and creates a new axiom with the changed annotations.
markAsInferredAxiom(OWLAxiom, OWLDataFactory) - Static method in class owltools.graph.AxiomAnnotationTools
Mark the given axiom as inferred.
markAsInferredAxiom(Set<OWLAxiom>, OWLOntology) - Static method in class owltools.graph.AxiomAnnotationTools
Mark the given axioms as inferred.
Side effect: Removes the axiom in the given ontology and creates a new axiom with the changed annotations.
markAsInferredAxiom(Set<OWLAxiom>, OWLDataFactory) - Static method in class owltools.graph.AxiomAnnotationTools
Mark the given axioms as inferred.
maxDepthChain - Variable in class owltools.gfx.GraphicsConfig.RelationConfig
 
maxDepthTotal - Variable in class owltools.gfx.GraphicsConfig.RelationConfig
 
merge(OWLGraphEdge) - Method in class owltools.graph.OWLGraphEdge
Merges this OWLGraphEdge and edge into a new one, containing the union of their underlying OWLAxioms, as returned by getAxioms().
merge() - Method in class owltools.mooncat.EquivalenceSetMergeUtil
 
merge() - Method in class owltools.mooncat.SpeciesMergeUtil
 
mergeImportClosure() - Method in class owltools.graph.OWLGraphWrapperBasic
note: may move to mooncat
mergeImportClosure(boolean) - Method in class owltools.graph.OWLGraphWrapperBasic
 
mergeIntoReferenceOntology(OWLOntology) - Method in class owltools.mooncat.Mooncat
 
mergeOntologies() - Method in class owltools.mooncat.Mooncat
merge minimal subset of referenced ontologies into the source ontology.
mergeOntology(OWLOntology) - Method in class owltools.graph.OWLGraphWrapperBasic
Adds all axioms from extOnt into source ontology
mergeOntology(OWLOntology, boolean) - Method in class owltools.graph.OWLGraphWrapperBasic
 
mergeSpecificImport(IRI) - Method in class owltools.graph.OWLGraphWrapperBasic
Merge a specific ontology from the import closure into the main ontology.
mergeSupportOntology(String, boolean) - Method in class owltools.graph.OWLGraphWrapperBasic
mergeSupportOntology(IRI, boolean) - Method in class owltools.graph.OWLGraphWrapperBasic
 
mergeSupportOntology(String) - Method in class owltools.graph.OWLGraphWrapperBasic
mergeSupportOntology(IRI) - Method in class owltools.graph.OWLGraphWrapperBasic
 
meta - Variable in class owltools.graph.shunt.OWLShuntEdge
 
meta - Variable in class owltools.graph.shunt.OWLShuntNode
 
minWidth - Static variable in class owltools.gfx.HierarchyImage
 
Mooncat - Class in owltools.mooncat
Given one source ontology referencing one or more referenced ontologies (e.g.
Mooncat(OWLOntologyManager, OWLDataFactory, OWLOntology) - Constructor for class owltools.mooncat.Mooncat
 
Mooncat(OWLGraphWrapper) - Constructor for class owltools.mooncat.Mooncat
 

N

nameObjectSomeValuesFrom(OWLOntology, OWLOntology, Map<OWLClass, OWLClassExpression>, boolean) - Static method in class owltools.mooncat.TransformationUtils
Names all inner ObjectSomeValuesFrom expressions
NaryBooleanClassExpression - Interface in owltools.frame
 
NaryBooleanClassExpressionLD - Class in owltools.frame.jsonld
 
NaryBooleanClassExpressionLD() - Constructor for class owltools.frame.jsonld.NaryBooleanClassExpressionLD
 
next() - Method in class owltools.graph.shunt.OWLShuntGraphDFIterator
 
next() - Method in class owltools.idmap.IDMappingPIRParser
 
nextArgIsHelp() - Method in class owltools.cli.Opts
 
nextEq(String) - Method in class owltools.cli.Opts
 
nextEq(Collection<String>) - Method in class owltools.cli.Opts
 
nextFile() - Method in class owltools.cli.Opts
 
nextList() - Method in class owltools.cli.Opts
 
nextOpt() - Method in class owltools.cli.Opts
 
nl() - Method in class owltools.io.AbstractRenderer
 
nodes - Variable in class owltools.graph.shunt.OWLShuntGraph
 
NonDeterministicUnfoldException(String) - Constructor for exception owltools.TBoxUnFoldingTool.NonDeterministicUnfoldException
 
noQuoteLabels() - Method in class owltools.io.OWLPrettyPrinter
 
notEquals(NODE, NODE) - Method in class owltools.util.AbstractTarjan
 
notEquals(T, T) - Method in class owltools.util.MappingTarjan
 

O

obj - Variable in class owltools.graph.shunt.OWLShuntEdge
 
OBO - Static variable in enum owltools.vocab.OBOUpperVocabulary
 
OboAndOwlNameProvider(OBODoc, OWLGraphWrapper) - Constructor for class owltools.io.ParserWrapper.OboAndOwlNameProvider
 
OBONamespaces - Enum in owltools.vocab
 
OBOUpperVocabulary - Enum in owltools.vocab
 
ontologies - Variable in class owltools.mooncat.ontologymetadata.OntologySetMetadata
 
OntologyAnnotation - Class in owltools.mooncat.ontologymetadata
 
OntologyAnnotation(OWLAnnotation) - Constructor for class owltools.mooncat.ontologymetadata.OntologyAnnotation
 
OntologyFrame - Interface in owltools.frame
 
OntologyFrameLD - Class in owltools.frame.jsonld
 
OntologyFrameLD() - Constructor for class owltools.frame.jsonld.OntologyFrameLD
 
OntologyMetadata - Class in owltools.mooncat.ontologymetadata
 
OntologyMetadata(OWLOntology) - Constructor for class owltools.mooncat.ontologymetadata.OntologyMetadata
 
OntologyMetadataMarkdownWriter - Class in owltools.mooncat.ontologymetadata
 
OntologyMetadataMarkdownWriter() - Constructor for class owltools.mooncat.ontologymetadata.OntologyMetadataMarkdownWriter
 
OntologySetMetadata - Class in owltools.mooncat.ontologymetadata
 
OntologySetMetadata(OWLOntology) - Constructor for class owltools.mooncat.ontologymetadata.OntologySetMetadata
 
open(String) - Method in class owltools.mooncat.ontologymetadata.ImportChainDotWriter
 
Opts - Class in owltools.cli
Helper for easy handling of command line parameters and input.
Opts(String[]) - Constructor for class owltools.cli.Opts
Create a new instance for the given command-line parameters.
Opts(List<String>) - Constructor for class owltools.cli.Opts
Create a new instance for the given command-line parameters.
outputOntology - Variable in class owltools.mooncat.ProvenanceReasonerWrapper
 
OWLGraphEdge - Class in owltools.graph
Note that when storing OWLGraphEdges in a Set, an OWLGraphEdge.OWLGraphEdgeSet should be used.
OWLGraphEdge(OWLObject, OWLObject, OWLOntology, OWLQuantifiedProperty) - Constructor for class owltools.graph.OWLGraphEdge
 
OWLGraphEdge(OWLRestriction, OWLObject, OWLQuantifiedProperty, OWLOntology) - Constructor for class owltools.graph.OWLGraphEdge
 
OWLGraphEdge(OWLObject, OWLObject, List<OWLQuantifiedProperty>, OWLOntology) - Constructor for class owltools.graph.OWLGraphEdge
 
OWLGraphEdge(OWLObject, OWLObject, List<OWLQuantifiedProperty>, OWLOntology, Set<OWLAxiom>, OWLClass, OWLObjectPropertyExpression) - Constructor for class owltools.graph.OWLGraphEdge
 
OWLGraphEdge(OWLObject, OWLObject, OWLOntology) - Constructor for class owltools.graph.OWLGraphEdge
 
OWLGraphEdge(OWLObject, OWLObject, OWLOntology, Set<OWLAxiom>, OWLClass, OWLObjectPropertyExpression) - Constructor for class owltools.graph.OWLGraphEdge
 
OWLGraphEdge(OWLObject, OWLObject) - Constructor for class owltools.graph.OWLGraphEdge
 
OWLGraphEdge(OWLObject, OWLObject, OWLObjectPropertyExpression, OWLQuantifiedProperty.Quantifier, OWLOntology) - Constructor for class owltools.graph.OWLGraphEdge
 
OWLGraphEdge(OWLObject, OWLObject, OWLObjectPropertyExpression, OWLQuantifiedProperty.Quantifier, OWLOntology, OWLAxiom) - Constructor for class owltools.graph.OWLGraphEdge
 
OWLGraphEdge(OWLObject, OWLObject, OWLObjectPropertyExpression, OWLQuantifiedProperty.Quantifier, OWLOntology, OWLAxiom, OWLClass, OWLObjectPropertyExpression) - Constructor for class owltools.graph.OWLGraphEdge
 
OWLGraphEdge(OWLObject, OWLObject, OWLQuantifiedProperty.Quantifier) - Constructor for class owltools.graph.OWLGraphEdge
 
OWLGraphEdge(OWLGraphEdge) - Constructor for class owltools.graph.OWLGraphEdge
Copy constructor.
OWLGraphEdge.OWLGraphEdgeSet - Class in owltools.graph
Represents a Set of OWLGraphEdges.
OWLGraphEdgeSet() - Constructor for class owltools.graph.OWLGraphEdge.OWLGraphEdgeSet
 
OWLGraphEdgeSet(OWLGraphEdge.OWLGraphEdgeSet) - Constructor for class owltools.graph.OWLGraphEdge.OWLGraphEdgeSet
 
OWLGraphEdgeSet(Set<OWLGraphEdge>) - Constructor for class owltools.graph.OWLGraphEdge.OWLGraphEdgeSet
 
OWLGraphLayoutNode - Class in owltools.gfx
 
OWLGraphLayoutNode(OWLGraphWrapper, OWLObject) - Constructor for class owltools.gfx.OWLGraphLayoutNode
 
OWLGraphLayoutNode(OWLGraphWrapper, OWLObject, GraphStyle) - Constructor for class owltools.gfx.OWLGraphLayoutNode
 
OWLGraphLayoutNode.SVGRectangle - Class in owltools.gfx
 
OWLGraphLayoutRenderer - Class in owltools.gfx
Render a portion of an ontology using the QuickGO graphics code This should be capable of rendering relationships between any OWLObjects - as well as class hierarchies, also object property hierarchies.
OWLGraphLayoutRenderer(OWLGraphWrapper) - Constructor for class owltools.gfx.OWLGraphLayoutRenderer
Create a new renderer with default graph style.
OWLGraphLayoutRenderer(OWLGraphWrapper, GraphStyle) - Constructor for class owltools.gfx.OWLGraphLayoutRenderer
 
OWLGraphManipulator - Class in owltools.graph
This class provides functionalities to modify an ontology to simplify its graph structure.
OWLGraphManipulator(OWLOntology) - Constructor for class owltools.graph.OWLGraphManipulator
Constructor providing the OWLOntology on which modifications will be performed, that will be wrapped in a OWLGraphWrapper.
OWLGraphManipulator(OWLGraphWrapper) - Constructor for class owltools.graph.OWLGraphManipulator
Constructor providing the OWLGraphWrapper wrapping the ontology on which modifications will be performed.
OWLGraphManipulator(OWLGraphWrapper, boolean) - Constructor for class owltools.graph.OWLGraphManipulator
Constructor providing the OWLGraphWrapper wrapping the ontology on which modifications will be performed.
OWLGraphStrokeEdge - Class in owltools.gfx
Represents an edge in a layout graph Adapted from QuickGO
OWLGraphStrokeEdge(OWLGraphLayoutNode, OWLGraphLayoutNode, OWLGraphEdge, OWLGraphWrapper) - Constructor for class owltools.gfx.OWLGraphStrokeEdge
 
OWLGraphStrokeEdge.SVGEdge - Class in owltools.gfx
 
OWLGraphUtil - Class in owltools.graph
general static methods for additional graph operations
OWLGraphUtil() - Constructor for class owltools.graph.OWLGraphUtil
 
OWLGraphvizRenderer - Class in owltools.gfx
IN-PROGRESS GraphViz renderer TODO - make a common abstract class for all renderers
OWLGraphvizRenderer(OWLGraphWrapper) - Constructor for class owltools.gfx.OWLGraphvizRenderer
 
owlGraphWrapper - Variable in class owltools.gfx.OWLGraphLayoutRenderer
 
OWLGraphWrapper - Class in owltools.graph
Wraps one or more OWLOntology objects providing convenient OBO-like operations
OWLGraphWrapper(OWLOntology) - Constructor for class owltools.graph.OWLGraphWrapper
Create a new wrapper for an OWLOntology
OWLGraphWrapper(OWLOntology, boolean) - Constructor for class owltools.graph.OWLGraphWrapper
Deprecated. 
OWLGraphWrapper(String) - Constructor for class owltools.graph.OWLGraphWrapper
creates a new OWLOntology as the source ontology
OWLGraphWrapper.ISynonym - Interface in owltools.graph
 
OWLGraphWrapper.Synonym - Class in owltools.graph
 
OWLGraphWrapperBasic - Class in owltools.graph
Basic methods for handling multiple OWLOntology objects as one graph.
OWLGraphWrapperBasic(OWLOntology) - Constructor for class owltools.graph.OWLGraphWrapperBasic
 
OWLGraphWrapperBasic(String) - Constructor for class owltools.graph.OWLGraphWrapperBasic
 
OWLGraphWrapperEdges - Class in owltools.graph
Methods to extract and traverse relation in the graph.
OWLGraphWrapperEdges(OWLOntology) - Constructor for class owltools.graph.OWLGraphWrapperEdges
 
OWLGraphWrapperEdges(String) - Constructor for class owltools.graph.OWLGraphWrapperEdges
 
OWLGraphWrapperEdges.Config - Class in owltools.graph
Configuration options.
OWLGraphWrapperEdgesAdvanced - Class in owltools.graph
 
OWLGraphWrapperEdgesAdvanced(OWLOntology) - Constructor for class owltools.graph.OWLGraphWrapperEdgesAdvanced
 
OWLGraphWrapperEdgesAdvanced(String) - Constructor for class owltools.graph.OWLGraphWrapperEdgesAdvanced
 
OWLGraphWrapperEdgesExtended - Class in owltools.graph
This class groups methods that could be modified, or added to OWLGraphWrapper and parent classes.
OWLGraphWrapperEdgesExtended(OWLOntology) - Constructor for class owltools.graph.OWLGraphWrapperEdgesExtended
Default constructor.
OWLGraphWrapperEdgesExtended(String) - Constructor for class owltools.graph.OWLGraphWrapperEdgesExtended
 
OWLGraphWrapperExtended - Class in owltools.graph
Methods to extract values from entities in the graph with potential multiple OWLOntology objects.
OWLGraphWrapperExtended(OWLOntology) - Constructor for class owltools.graph.OWLGraphWrapperExtended
 
OWLGraphWrapperExtended(String) - Constructor for class owltools.graph.OWLGraphWrapperExtended
 
OWLGraphWrapperNameProvider(OWLGraphWrapper) - Constructor for class owltools.io.ParserWrapper.OWLGraphWrapperNameProvider
 
OWLGraphWrapperNameProvider(OWLGraphWrapper, String) - Constructor for class owltools.io.ParserWrapper.OWLGraphWrapperNameProvider
 
OWLGraphWrapperNameProvider(OWLGraphWrapper, OBODoc) - Constructor for class owltools.io.ParserWrapper.OWLGraphWrapperNameProvider
Deprecated.
OWLGsonParser - Class in owltools.io
Counterpart to OWLGsonRenderer UNTESTED
OWLGsonParser() - Constructor for class owltools.io.OWLGsonParser
 
OWLGsonRenderer - Class in owltools.io
 
OWLGsonRenderer(PrintWriter) - Constructor for class owltools.io.OWLGsonRenderer
 
OwlHelper - Class in owltools.util
 
OWLInAboxTranslator - Class in owltools.mooncat
Translates an OWL TBox into a "shadow" representation in the ABox.
OWLInAboxTranslator(OWLOntology) - Constructor for class owltools.mooncat.OWLInAboxTranslator
 
OWLJSONFormat - Class in owltools.io
 
OWLJSONFormat() - Constructor for class owltools.io.OWLJSONFormat
 
OWLPrettyPrinter - Class in owltools.io
Use a OWLGraphWrapper or OWLGraphWrapperExtended to render OWLAxiom, OWLGraphEdge, or OWLQuantifiedProperty in better human readable form.

Hint: Every OWLGraphWrapper is also a OWLGraphWrapperExtended.
OWLPrettyPrinter(OWLGraphWrapperExtended, OWLObjectRenderer) - Constructor for class owltools.io.OWLPrettyPrinter
 
OWLPrettyPrinter(OWLGraphWrapperExtended) - Constructor for class owltools.io.OWLPrettyPrinter
 
OWLPrettyPrinter.LabelProvider - Class in owltools.io
 
OWLQuantifiedProperty - Class in owltools.graph
 
OWLQuantifiedProperty(OWLObjectPropertyExpression, OWLQuantifiedProperty.Quantifier) - Constructor for class owltools.graph.OWLQuantifiedProperty
 
OWLQuantifiedProperty() - Constructor for class owltools.graph.OWLQuantifiedProperty
 
OWLQuantifiedProperty(OWLQuantifiedProperty.Quantifier) - Constructor for class owltools.graph.OWLQuantifiedProperty
 
OWLQuantifiedProperty.Quantifier - Enum in owltools.graph
 
OWLShuntEdge - Class in owltools.graph.shunt
An edge reduced to nothing; for use with OWLShuntGraph.
OWLShuntEdge(String, String) - Constructor for class owltools.graph.shunt.OWLShuntEdge
 
OWLShuntEdge(String, String, String) - Constructor for class owltools.graph.shunt.OWLShuntEdge
 
OWLShuntEdge(OWLObject, OWLObject, String, OWLGraphWrapper) - Constructor for class owltools.graph.shunt.OWLShuntEdge
 
OWLShuntGraph - Class in owltools.graph.shunt
A simple (and easily serializable through GSON) graph model to move data from the OWL model out to more standard graph resources.
OWLShuntGraph() - Constructor for class owltools.graph.shunt.OWLShuntGraph
Empty constructor.
OWLShuntGraphDFIterator - Class in owltools.graph.shunt
Iterate over an OWLShuntGraph.
OWLShuntGraphDFIterator(OWLShuntGraph) - Constructor for class owltools.graph.shunt.OWLShuntGraphDFIterator
Constructor.
OWLShuntNode - Class in owltools.graph.shunt
A node reduced to nothing; for use with OWLShuntGraph.
OWLShuntNode(String) - Constructor for class owltools.graph.shunt.OWLShuntNode
 
OWLShuntNode(String, String) - Constructor for class owltools.graph.shunt.OWLShuntNode
 
OWLShuntNode(OWLGraphWrapper, OWLObject) - Constructor for class owltools.graph.shunt.OWLShuntNode
 
owltools - package owltools
OWLTools - an OWL API wrapper
owltools.cli - package owltools.cli
 
owltools.diff - package owltools.diff
 
owltools.frame - package owltools.frame
 
owltools.frame.jsonld - package owltools.frame.jsonld
 
owltools.gfx - package owltools.gfx
GFX - OWL Graphics and Visualization
owltools.graph - package owltools.graph
OWLGraph -- OBO-like Graph Wrapper for OWL Ontologies
owltools.graph.shunt - package owltools.graph.shunt
OWL Shunt
owltools.idmap - package owltools.idmap
 
owltools.io - package owltools.io
IO - Input/Output
owltools.mooncat - package owltools.mooncat
Mooncat -- Multiple OWL ONtology Catenation
owltools.mooncat.ontologymetadata - package owltools.mooncat.ontologymetadata
OntologyMetadata
owltools.phenolog - package owltools.phenolog
Phenolog - Calculation of class similarity based on instance data
owltools.profile - package owltools.profile
 
owltools.reasoner - package owltools.reasoner
 
owltools.tr - package owltools.tr
 
owltools.util - package owltools.util
 
owltools.version - package owltools.version
 
owltools.vocab - package owltools.vocab
 

P

parentArrowShape - Variable in class owltools.gfx.GraphicsConfig.RelationConfig
 
parse(String) - Method in class owltools.idmap.AbstractMappingParser
 
parse(Reader) - Method in class owltools.idmap.AbstractMappingParser
 
parse(File) - Method in class owltools.idmap.AbstractMappingParser
 
parse(Reader) - Method in class owltools.idmap.IDMappingPIRParser
 
parse(Reader) - Method in class owltools.idmap.UniProtIDMapParser
 
parse(String) - Method in class owltools.io.GMTParser
 
parse(String) - Method in class owltools.io.ParserWrapper
 
parse(String) - Method in class owltools.io.StanzaToOWLConverter
parses a stanza file and generates axioms in targetOntology
parse(File) - Method in class owltools.io.StanzaToOWLConverter
 
parse(String) - Method in class owltools.io.TableToAxiomConverter
 
parse(File) - Method in class owltools.io.TableToAxiomConverter
 
parse(String) - Method in class owltools.phenolog.GenePhenoTsvParser
 
parseOBO(String) - Method in class owltools.io.ParserWrapper
 
parseOWL(String) - Method in class owltools.io.ParserWrapper
 
parseOWL(IRI) - Method in class owltools.io.ParserWrapper
 
ParserWrapper - Class in owltools.io
Convenience class wrapping org.oboformat that abstracts away underlying details of ontology format or location
ParserWrapper() - Constructor for class owltools.io.ParserWrapper
 
ParserWrapper.OboAndOwlNameProvider - Class in owltools.io
Provide names for the OBOFormatWriter using an OBODoc first and an OWLGraphWrapper as secondary.
ParserWrapper.OWLGraphWrapperNameProvider - Class in owltools.io
Provide names for the OBOFormatWriter using an OWLGraphWrapper.
parseToOWLGraph(String) - Method in class owltools.io.ParserWrapper
 
parseToOWLGraph(String, boolean) - Method in class owltools.io.ParserWrapper
 
peekArg() - Method in class owltools.cli.Opts
 
performConsistencyChecks() - Method in class owltools.InferenceBuilder
 
performtransiviteclosure() - Method in class owltools.phenolog.PhenoTransitiveClosure
 
performtransiviteclosure(String, String, HashSet<Pheno>, HashMap<String, Pheno>, HashMap<String, IndividualPair>) - Method in class owltools.phenolog.PhenoTransitiveClosure
 
Pheno - Class in owltools.phenolog
represents an attribute-bearing entity; for example, a phenotype.
Pheno() - Constructor for class owltools.phenolog.Pheno
 
Pheno(String) - Constructor for class owltools.phenolog.Pheno
 
Pheno(String, String) - Constructor for class owltools.phenolog.Pheno
 
Pheno(String, String, HashSet<Individual>) - Constructor for class owltools.phenolog.Pheno
 
Pheno(String, String, HashSet<Individual>, boolean) - Constructor for class owltools.phenolog.Pheno
 
PhenologEngine - Class in owltools.phenolog
 
PhenologEngine() - Constructor for class owltools.phenolog.PhenologEngine
 
PhenoTransitiveClosure - Class in owltools.phenolog
 
PhenoTransitiveClosure() - Constructor for class owltools.phenolog.PhenoTransitiveClosure
 
polarity - Variable in enum owltools.gfx.RelationType
 
PotentialRedundant(OWLAxiom, OWLAxiom, OWLClass, OWLObjectProperty, OWLClass) - Constructor for class owltools.InferenceBuilder.PotentialRedundant
 
precomputeInferences(InferenceType...) - Method in class owltools.reasoner.GraphReasoner
 
precomputeInferences(InferenceType...) - Method in class owltools.reasoner.LazyExpressionMaterializingReasoner
Deprecated.
 
pred - Variable in class owltools.graph.shunt.OWLShuntEdge
 
prefix - Variable in class owltools.io.GMTParser
 
prepare() - Method in class owltools.gfx.ImageRender
 
prettyPrinter - Variable in class owltools.io.AbstractRenderer
 
primitiveEdgeToFullEdges(OWLGraphEdge) - Method in class owltools.graph.OWLGraphWrapperEdges
 
print(OWLObject) - Method in class owltools.io.AbstractRenderer
 
print(String) - Method in class owltools.io.AbstractRenderer
 
print(OWLObject) - Method in class owltools.io.OWLPrettyPrinter
 
print(Set<OWLAxiom>) - Method in class owltools.io.OWLPrettyPrinter
 
print(String) - Method in class owltools.io.OWLPrettyPrinter
 
PRINT_COMPARATOR - Static variable in class owltools.InferenceBuilder.PotentialRedundant
 
printresults(String, ArrayList<Pheno>, double, int) - Static method in class owltools.phenolog.Main
 
process(String[]) - Method in class owltools.idmap.IDMapHandler
 
process(String[]) - Method in class owltools.idmap.IDMapPairWriter
 
process(String[]) - Method in class owltools.idmap.IDMappingPIRParser
 
profiler - Variable in class owltools.graph.OWLGraphWrapperEdges
 
Profiler - Class in owltools.profile
 
Profiler() - Constructor for class owltools.profile.Profiler
 
property - Variable in class owltools.gfx.GraphicsConfig.RelationConfig
 
property - Variable in class owltools.io.StanzaToOWLConverter.Mapping
 
property - Variable in class owltools.io.TableToAxiomConverter.Config
 
PropertyExtractor - Class in owltools.mooncat
 
PropertyExtractor(OWLOntology) - Constructor for class owltools.mooncat.PropertyExtractor
Creates a new PE object
PropertyExtractor(OWLOntology, OWLOntology) - Constructor for class owltools.mooncat.PropertyExtractor
 
PropertyStub - Interface in owltools.frame
 
PropertyStubLD - Class in owltools.frame.jsonld
 
PropertyStubLD() - Constructor for class owltools.frame.jsonld.PropertyStubLD
 
PropertyStubLD(String, String) - Constructor for class owltools.frame.jsonld.PropertyStubLD
 
PropertyViewOntologyBuilder - Class in owltools.mooncat
This class will create a property view or *faceted* view over an ontology using a specified property (relation).
PropertyViewOntologyBuilder(OWLOntology, OWLOntology, OWLObjectProperty) - Constructor for class owltools.mooncat.PropertyViewOntologyBuilder
 
PropertyViewOntologyBuilder(OWLOntology, OWLObjectProperty) - Constructor for class owltools.mooncat.PropertyViewOntologyBuilder
 
PropertyViewOntologyBuilder(OWLDataFactory, OWLOntologyManager, OWLOntology, OWLOntology, OWLObjectProperty) - Constructor for class owltools.mooncat.PropertyViewOntologyBuilder
 
ProvenanceReasonerWrapper - Class in owltools.mooncat
 
ProvenanceReasonerWrapper(OWLOntology, OWLReasonerFactory) - Constructor for class owltools.mooncat.ProvenanceReasonerWrapper
 

Q

queryDescendants(OWLGraphEdge) - Method in class owltools.graph.OWLGraphWrapperEdges
Treats an edge as a path and performs a query.
queryDescendants(OWLClassExpression) - Method in class owltools.graph.OWLGraphWrapperEdges
Performs a closed-world query using a DL expression as a set of boolean database-style constraints.
queryDescendants(OWLClassExpression, boolean, boolean) - Method in class owltools.graph.OWLGraphWrapperEdges
 
QuerySubsetGenerator - Class in owltools.mooncat
Tools for creating a sub ontology spanning multiple ontologies.
QuerySubsetGenerator() - Constructor for class owltools.mooncat.QuerySubsetGenerator
 

R

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 OWLClasses 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 OWLObjects 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
Remove classes invalid for SpeciesSubsetterUtil.taxClass over SpeciesSubsetterUtil.viewProperty, related to rootClass.
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 OWLAxioms in the ontologies corresponding to the OWLObjectPropertys listed in forbiddenRels, as OBO-style IDs.
removeRelsToSubsets(Collection<String>) - Method in class owltools.graph.OWLGraphManipulator
Delegates method call to OWLGraphManipulator.removeRelsToSubsets(Collection, Collection), with no OWLClasses excluded specified.
removeRelsToSubsets(Collection<String>, Collection<String>) - Method in class owltools.graph.OWLGraphManipulator
Remove is_a and part_of incoming edges to OWLClasses in subsets, only if the source of the incoming edge will not be left orphan of other is_a/part_of relations to OWLClasses not in subsets.
removeSpecies() - Method in class owltools.mooncat.SpeciesSubsetterUtil
removeSubgraphs(Collection<String>, boolean) - Method in class owltools.graph.OWLGraphManipulator
Delegates to OWLGraphManipulator.removeSubgraphs(Collection, boolean, Collection), with the last Collection argument being null.
removeSubgraphs(Collection<String>, boolean, Collection<String>) - Method in class owltools.graph.OWLGraphManipulator
Remove from the ontology the subgraphs starting from the OWLClasses 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 OWLObjectPropertys 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
Wrapper for ReasonerDiff as command-line tool.
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
 

S

save() - Method in class owltools.io.ImportClosureSlurper
 
save(String) - Method in class owltools.io.ImportClosureSlurper
 
save(String, String) - Method in class owltools.io.ImportClosureSlurper
 
save(File, OutputStream) - Method in class owltools.io.ImportClosureSlurper
 
save(File, BufferedWriter) - Method in class owltools.io.ImportClosureSlurper
 
save(String, OWLDocumentFormat, OWLOntology) - Method in class owltools.mooncat.BridgeExtractor
 
saveBridgeOntologies(String) - Method in class owltools.mooncat.BridgeExtractor
 
saveBridgeOntologies(String, OWLDocumentFormat) - Method in class owltools.mooncat.BridgeExtractor
 
saveOWL(OWLOntology, String) - Method in class owltools.io.ParserWrapper
 
saveOWL(OWLOntology, OWLDocumentFormat, String) - Method in class owltools.io.ParserWrapper
 
saveOWL(OWLOntology, OWLDocumentFormat, OutputStream) - Method in class owltools.io.ParserWrapper
 
selected - Variable in class owltools.gfx.HierarchyImage
 
sep() - Method in class owltools.io.AbstractRenderer
 
serialise() - Method in class owltools.gfx.OWLGraphLayoutNode
 
serialise() - Method in class owltools.gfx.OWLGraphStrokeEdge
 
serverManifestVersion - Variable in class owltools.mooncat.ontologymetadata.OntologySetMetadata
 
setancestors(HashSet<Pheno>) - Method in class owltools.phenolog.Pheno
 
setAssertedViewOntology(OWLOntology) - Method in class owltools.mooncat.PropertyViewOntologyBuilder
 
setAssumeOBOStyleIRIs(boolean) - Method in class owltools.mooncat.PropertyViewOntologyBuilder
set to false if IRIs are not OBO purls.
setAttributes(Set<Attribute>) - Method in class owltools.phenolog.Individual
 
setAxiomType(String) - Method in class owltools.io.TableToAxiomConverter.Config
 
setBit(int, boolean) - Method in class owltools.util.BloomFilter
Set a single bit in the Bloom filter.
setCheckOboDoc(boolean) - Method in class owltools.io.ParserWrapper
 
setClassifyIndividuals(boolean) - Method in class owltools.mooncat.PropertyViewOntologyBuilder
 
setClosest(Pheno) - Method in class owltools.phenolog.Pheno
 
setClosestDistance(double) - Method in class owltools.phenolog.Pheno
 
setClosestOverlap(int) - Method in class owltools.phenolog.Pheno
 
setClosestOverlapPairs(HashSet<IndividualPair>) - Method in class owltools.phenolog.Pheno
 
setConfig(OWLGraphWrapperEdges.Config) - Method in class owltools.graph.OWLGraphWrapperEdges
 
setConfigForFlyMine() - Method in class owltools.phenolog.GenePhenoTsvParser
 
setConfigForMGIPhenoGeno() - Method in class owltools.phenolog.GenePhenoTsvParser
 
setCreateReflexiveClasses(boolean) - Method in class owltools.mooncat.PropertyViewOntologyBuilder
 
setDefaults() - Method in class owltools.io.StanzaToOWLConverter
 
setDistance(int) - Method in class owltools.graph.OWLGraphEdge
 
setEdgesAdvancedCacheSize(int) - Method in class owltools.graph.OWLGraphWrapperEdgesAdvanced
 
setElementsOntology(OWLOntology) - Method in class owltools.mooncat.PropertyViewOntologyBuilder
 
setExcludedClasses(Set<OWLClass>) - Method in class owltools.mooncat.PropertyViewOntologyBuilder
 
setFilterUnused(boolean) - Method in class owltools.mooncat.PropertyViewOntologyBuilder
 
setGciFillers(List<OWLClass>) - Method in class owltools.io.InferredParentRenderer
 
setGciProperty(OWLObjectProperty) - Method in class owltools.io.InferredParentRenderer
 
setGraph(OWLGraphWrapper) - Method in class owltools.mooncat.Mooncat
 
setHelpMode(boolean) - Method in class owltools.cli.Opts
 
sethmp(HashMap<String, Pheno>) - Method in class owltools.phenolog.PhenoTransitiveClosure
 
sethmpair(HashMap<String, IndividualPair>) - Method in class owltools.phenolog.PhenoTransitiveClosure
 
sethsp(HashSet<Pheno>) - Method in class owltools.phenolog.PhenoTransitiveClosure
 
setId(String) - Method in class owltools.graph.shunt.OWLShuntNode
 
setId(String) - Method in class owltools.phenolog.Attribute
 
setid(String) - Method in class owltools.phenolog.GenePheno
 
setId(String) - Method in class owltools.phenolog.Individual
 
setId(String) - Method in class owltools.phenolog.Pheno
 
setIndex(NODE, int) - Method in class owltools.util.AbstractTarjan
 
setIndex(T, int) - Method in class owltools.util.MappingTarjan
 
setIndividualPairs(Set<IndividualPair>) - Method in class owltools.phenolog.PhenologEngine
 
setIndividuals(HashSet<Individual>) - Method in class owltools.phenolog.Pheno
 
setInferred(boolean) - Method in class owltools.graph.OWLQuantifiedProperty
 
setInferredViewOntology(OWLOntology) - Method in class owltools.mooncat.PropertyViewOntologyBuilder
 
setInverseOf(boolean) - Method in class owltools.graph.OWLQuantifiedProperty
 
setisFromTC(boolean) - Method in class owltools.phenolog.Pheno
 
setLabel(String) - Method in class owltools.graph.shunt.OWLShuntNode
 
setLabel(String) - Method in class owltools.phenolog.Attribute
 
setlabel(String) - Method in class owltools.phenolog.GenePheno
 
setLabel(String) - Method in class owltools.phenolog.Individual
 
setLabel(String) - Method in class owltools.phenolog.Pheno
 
setLeafClasses(Set<OWLClass>) - Method in class owltools.mooncat.PropertyViewOntologyBuilder
 
setLocation(int, int) - Method in class owltools.gfx.OWLGraphLayoutNode
 
setLowlink(NODE, int) - Method in class owltools.util.AbstractTarjan
 
setLowlink(T, int) - Method in class owltools.util.MappingTarjan
 
setManager(OWLOntologyManager) - Method in class owltools.io.ParserWrapper
 
setManager(OWLOntologyManager) - Method in class owltools.mooncat.Mooncat
 
setMaxCardinality(Integer) - Method in class owltools.graph.OWLQuantifiedProperty
 
setMember1(Individual) - Method in class owltools.phenolog.IndividualPair
 
setMember2(Individual) - Method in class owltools.phenolog.IndividualPair
 
setMetadata(Map<String, String>) - Method in class owltools.graph.shunt.OWLShuntEdge
 
setMetadata(Map<String, Object>) - Method in class owltools.graph.shunt.OWLShuntNode
 
setMinCardinality(Integer) - Method in class owltools.graph.OWLQuantifiedProperty
 
setNonTCIndividualSize(int) - Method in class owltools.phenolog.Pheno
 
setobolink(String) - Method in class owltools.phenolog.PhenoTransitiveClosure
 
setOntology(OWLOntology) - Method in class owltools.graph.OWLGraphEdge
 
setOntology(OWLOntology) - Method in class owltools.graph.OWLGraphWrapper
Deprecated.
setOntology(OWLOntology) - Method in class owltools.mooncat.Mooncat
 
setOrthologs(int) - Method in class owltools.phenolog.Individual
 
setOWLGraphWrapper(OWLGraphWrapper) - Method in class owltools.InferenceBuilder
 
setPair(String, String) - Method in class owltools.idmap.IDMapPairWriter
 
setphenoid(String) - Method in class owltools.phenolog.GenePheno
 
setphenolabel(String) - Method in class owltools.phenolog.GenePheno
 
setprefix(String) - Method in class owltools.phenolog.PhenoTransitiveClosure
 
setPrefixScore(Map<String, Double>, String, Double) - Method in class owltools.mooncat.EquivalenceSetMergeUtil
 
setPrefixScore(String, Double) - Method in class owltools.mooncat.EquivalenceSetMergeUtil
 
setPreserveObjectPropertyIRIs(boolean) - Method in class owltools.mooncat.OWLInAboxTranslator
 
setProfiler(Profiler) - Method in class owltools.graph.OWLGraphWrapperEdges
 
setProperties(List<OWLObjectProperty>) - Method in class owltools.io.InferredParentRenderer
 
setProperty(OWLObjectProperty) - Method in class owltools.graph.OWLQuantifiedProperty
 
setPropertyPrefixScore(OWLAnnotationProperty, String, Double) - Method in class owltools.mooncat.EquivalenceSetMergeUtil
 
setPropertyToComment() - Method in class owltools.io.TableToAxiomConverter.Config
 
setPropertyToLabel() - Method in class owltools.io.TableToAxiomConverter.Config
 
setQuantifiedPropertyList(List<OWLQuantifiedProperty>) - Method in class owltools.graph.OWLGraphEdge
 
setQuantifier(OWLQuantifiedProperty.Quantifier) - Method in class owltools.graph.OWLQuantifiedProperty
 
setReasoner(OWLReasoner) - Method in class owltools.graph.OWLGraphWrapperEdges
 
setReasoner(OWLReasoner) - Method in class owltools.InferenceBuilder
 
setReasoner(OWLExtendedReasoner) - Method in class owltools.io.InferredParentRenderer
 
setReferencedOntologies(Set<OWLOntology>) - Method in class owltools.mooncat.Mooncat
Deprecated.
setSingleQuantifiedProperty(OWLQuantifiedProperty) - Method in class owltools.graph.OWLGraphEdge
 
setSource(OWLObject) - Method in class owltools.graph.OWLGraphEdge
 
setSourceOntology(OWLOntology) - Method in class owltools.graph.OWLGraphWrapperBasic
 
setSourceOntologyPrefixes(Set<String>) - Method in class owltools.mooncat.Mooncat
Set the source ontology prefixes.
setStream(InputStream) - Method in class owltools.io.AbstractClosureReader
 
setStream(String) - Method in class owltools.io.AbstractClosureReader
 
setStream(PrintStream) - Method in class owltools.io.AbstractRenderer
 
setStream(String) - Method in class owltools.io.AbstractRenderer
 
setSupportOntologySet(Set<OWLOntology>) - Method in class owltools.graph.OWLGraphWrapperBasic
 
setTarget(OWLObject) - Method in class owltools.graph.OWLGraphEdge
 
setType(String) - Method in class owltools.graph.shunt.OWLShuntNode
 
setUseOriginalClassIRIs(boolean) - Method in class owltools.mooncat.PropertyViewOntologyBuilder
 
setViewEntities(Set<OWLEntity>) - Method in class owltools.mooncat.PropertyViewOntologyBuilder
 
setViewLabelPrefix(String) - Method in class owltools.mooncat.PropertyViewOntologyBuilder
Set this to prefix all class labels in O(P)
setViewLabelPrefixAndSuffix(String, String) - Method in class owltools.mooncat.PropertyViewOntologyBuilder
 
setViewLabelSuffix(String) - Method in class owltools.mooncat.PropertyViewOntologyBuilder
Set this to suffix all class labels in O(P)
setWrappedReasoner(OWLReasoner) - Method in class owltools.reasoner.LazyExpressionMaterializingReasoner
Deprecated.
 
setWrappedReasonerFactory(OWLReasonerFactory) - Method in class owltools.reasoner.LazyExpressionMaterializingReasoner
Deprecated.
 
SharedLabelException - Exception in owltools.graph
 
SharedLabelException(String, IRI, IRI) - Constructor for exception owltools.graph.SharedLabelException
 
ShuntGraphPair(OWLShuntGraph, OWLShuntGraph) - Constructor for class owltools.util.ShuntGraphUtils.ShuntGraphPair
 
ShuntGraphUtils - Class in owltools.util
Alternative method for generating ShuntGraphs - experimental
ShuntGraphUtils() - Constructor for class owltools.util.ShuntGraphUtils
 
ShuntGraphUtils.ShuntGraphPair - Class in owltools.util
Result object containing two corresponding shunt graphs.
simplifies(Collection<String>, Collection<String>, Collection<String>, Collection<String>, Collection<String>) - Method in class owltools.graph.OWLGraphManipulator
Helper method to perform standard simplifications.
size() - Method in class owltools.util.BloomFilter
Returns the number of bits in the Bloom filter.
SomeValuesFrom - Interface in owltools.frame
 
SomeValuesFromLD - Class in owltools.frame.jsonld
 
SomeValuesFromLD(StubLD, StubLD) - Constructor for class owltools.frame.jsonld.SomeValuesFromLD
 
sourceOntology - Variable in class owltools.graph.OWLGraphWrapperBasic
 
SpeciesMergeUtil - Class in owltools.mooncat
This utility is for making "composite" ontologies from the combination of a species-specific ontology (e.g.
SpeciesMergeUtil(OWLGraphWrapper) - Constructor for class owltools.mooncat.SpeciesMergeUtil
 
SpeciesMergeUtil.UnmergeableOntologyException - Exception in owltools.mooncat
 
SpeciesSubsetterUtil - Class in owltools.mooncat
This implements species subsetting (module generation) using OWL reasoning.
SpeciesSubsetterUtil(OWLGraphWrapper) - Constructor for class owltools.mooncat.SpeciesSubsetterUtil
Constructor providing the OWLGraphWrapper wrapping the OWLOntology used for species subsetting.
split(String) - Method in class owltools.idmap.IDMapHandler
 
Stanza() - Constructor for class owltools.io.StanzaToOWLConverter.Stanza
 
StanzaToOWLConverter - Class in owltools.io
reads in a stanza-formatted file (e.g.
StanzaToOWLConverter(OWLGraphWrapper) - Constructor for class owltools.io.StanzaToOWLConverter
 
StanzaToOWLConverter.Config - Class in owltools.io
 
StanzaToOWLConverter.Mapping - Class in owltools.io
incomplete.
StanzaToOWLConverter.Stanza - Class in owltools.io
A stanza is set of key-value pairs E.g
startTaskNotify(String) - Method in class owltools.profile.Profiler
 
stream - Variable in class owltools.io.AbstractClosureReader
 
stream - Variable in class owltools.io.AbstractRenderer
 
Stub - Interface in owltools.frame
 
StubLD - Class in owltools.frame.jsonld
 
StubLD() - Constructor for class owltools.frame.jsonld.StubLD
 
StubLD(String, String) - Constructor for class owltools.frame.jsonld.StubLD
 
sub - Variable in class owltools.graph.shunt.OWLShuntEdge
 
subDir - Variable in class owltools.mooncat.BridgeExtractor
 
subsumes(OWLQuantifiedProperty) - Method in class owltools.graph.OWLQuantifiedProperty
true if this is equal to other.
suffix - Variable in class owltools.mooncat.SpeciesMergeUtil
 
supportOntologySet - Variable in class owltools.graph.OWLGraphWrapperBasic
 
svgPath - Variable in class owltools.gfx.OWLGraphStrokeEdge.SVGEdge
 
SVGRectangle() - Constructor for class owltools.gfx.OWLGraphLayoutNode.SVGRectangle
 
Synonym(String, String, String, Set<String>) - Constructor for class owltools.graph.OWLGraphWrapper.Synonym
 

T

t1 - Variable in class owltools.idmap.IDMapPairWriter
 
t2 - Variable in class owltools.idmap.IDMapPairWriter
 
TableRenderer - Class in owltools.io
Renders the graph closure - i.e.
TableRenderer(PrintStream) - Constructor for class owltools.io.TableRenderer
 
TableRenderer(String) - Constructor for class owltools.io.TableRenderer
 
TableToAxiomConverter - Class in owltools.io
reads in a table (e.g.
TableToAxiomConverter(OWLGraphWrapper) - Constructor for class owltools.io.TableToAxiomConverter
 
TableToAxiomConverter.Config - Class in owltools.io
If AxiomType is ClassAssertion, then axioms will be of form ClassAssertion(sub obj) If AxiomType is SubClassOf, then axioms will be of form SubClassOf(sub obj) if a property P is specified, then obj is transformed to a class expression "P some obj'" where obj' is the original value for obj
targetOntology - Variable in class owltools.io.StanzaToOWLConverter.Config
 
Tarjan<NODE> - Interface in owltools.util
Interface for the Tarjan's strongly connected components algorithm.
taxClass - Variable in class owltools.mooncat.SpeciesMergeUtil
 
taxClass - Variable in class owltools.mooncat.SpeciesSubsetterUtil
 
TBoxUnFoldingTool - Class in owltools
Provide TBox unfolding methods.
TBoxUnFoldingTool(OWLGraphWrapper, Set<String>, String) - Constructor for class owltools.TBoxUnFoldingTool
Create a new instance for the given ontology graph.
TBoxUnFoldingTool.NonDeterministicUnfoldException - Exception in owltools
Exception indication, that the unfold operation is not deterministic.
TemplatedTransformer - Class in owltools.tr
Examples:
TemplatedTransformer(OWLOntology) - Constructor for class owltools.tr.TemplatedTransformer
 
TemplatedTransformer.Mapping - Class in owltools.tr
 
termIds - Variable in class owltools.gfx.GraphStyle
 
terms - Variable in class owltools.gfx.HierarchyImage
 
toJSON() - Method in class owltools.graph.shunt.OWLShuntGraph
 
top - Variable in class owltools.gfx.OWLGraphLayoutNode.SVGRectangle
 
top() - Method in class owltools.gfx.OWLGraphLayoutNode
 
topLine - Variable in class owltools.gfx.OWLGraphLayoutNode
 
toString() - Method in class owltools.graph.OWLGraphEdge
 
toString() - Method in class owltools.graph.OWLGraphWrapper.Synonym
 
toString() - Method in class owltools.graph.OWLQuantifiedProperty
 
toString() - Method in class owltools.io.StanzaToOWLConverter.Mapping
 
toString() - Method in class owltools.tr.TemplatedTransformer.Mapping
 
toString() - Method in enum owltools.vocab.OBOUpperVocabulary
 
tr(OWLSubClassOfAxiom) - Method in class owltools.mooncat.SpeciesMergeUtil
 
tr(OWLEquivalentClassesAxiom) - Method in class owltools.mooncat.SpeciesMergeUtil
 
tr() - Method in class owltools.tr.TemplatedTransformer
 
tr(TemplatedTransformer.Mapping) - Method in class owltools.tr.TemplatedTransformer
 
tr(OWLOntology, TemplatedTransformer.Mapping) - Method in class owltools.tr.TemplatedTransformer
 
tr(OWLAxiom, TemplatedTransformer.Mapping) - Method in class owltools.tr.TemplatedTransformer
 
transferAxiomsUsingIdSpace(String, OWLOntology) - Method in class owltools.mooncat.Mooncat
Assumes OBO-style IDspaces; specifically URI contains "..../IDSPACE_..."
TransformationUtils - Class in owltools.mooncat
Static methods for performing common logical transforms and view creation on OWL ontologies
TransformationUtils() - Constructor for class owltools.mooncat.TransformationUtils
 
translate(StanzaToOWLConverter.Stanza) - Method in class owltools.io.StanzaToOWLConverter
Translates a stanza to axioms (triples) and adds these to the targetOntology
translate() - Method in class owltools.mooncat.OWLInAboxTranslator
 
translateABoxToTBox(OWLOntology) - Method in class owltools.mooncat.PropertyViewOntologyBuilder
Deprecated.
translateABoxToTBox() - Method in class owltools.mooncat.PropertyViewOntologyBuilder
Deprecated.
translateDisjointsToEquivalents() - Method in class owltools.mooncat.Mooncat
For every pair X DisjointWith Y, generate an axiom A and Y = Nothing (may become deprecated after Elk supports disjoints)
translateDisjointsToEquivalents(OWLOntology, OWLOntologyManager, OWLDataFactory) - Static method in class owltools.mooncat.Mooncat
For every pair X DisjointWith Y, generate an axiom A and Y = Nothing (may become deprecated after Elk supports disjoints)
translateInto(OWLOntology) - Method in class owltools.mooncat.OWLInAboxTranslator
Adds all shadow axioms of original ontology to target
translateToJson(Frame) - Method in class owltools.frame.FrameMaker
 
type - Variable in class owltools.graph.shunt.OWLShuntNode
 
typeIxMap - Variable in class owltools.idmap.IDMappingPIRParser
 
typeMap - Variable in class owltools.idmap.IDMapHandler
 

U

UnExpectedStructureException(String, Throwable) - Constructor for exception owltools.mooncat.ontologymetadata.ImportChainDotWriter.UnExpectedStructureException
 
UnExpectedStructureException(String) - Constructor for exception owltools.mooncat.ontologymetadata.ImportChainDotWriter.UnExpectedStructureException
 
unfold(String) - Method in class owltools.TBoxUnFoldingTool
Unfold the equivalence axiom of the OWLClass for the given id.
unfold(OWLClass) - Method in class owltools.TBoxUnFoldingTool
Unfold the equivalence axiom of the OWLClass
unfold(OWLEquivalentClassesAxiom, OWLClass) - Method in class owltools.TBoxUnFoldingTool
Unfold the OWLEquivalentClassesAxiom of the OWLClass.
unfoldToString(String) - Method in class owltools.TBoxUnFoldingTool
Unfold the equivalence axiom of the OWLClass for the given id.
unfoldToString(OWLClass) - Method in class owltools.TBoxUnFoldingTool
Unfold the equivalence axiom of the OWLClass
unify(OWLClassExpression, OWLClassExpression, Set<IRI>) - Method in class owltools.tr.TemplatedTransformer
 
unifyAll(OWLClassExpression, OWLClassExpression, Set<IRI>) - Method in class owltools.tr.TemplatedTransformer
 
UniProtIDMapParser - Class in owltools.idmap
 
UniProtIDMapParser() - Constructor for class owltools.idmap.UniProtIDMapParser
 
UnmergeableOntologyException(String) - Constructor for exception owltools.mooncat.SpeciesMergeUtil.UnmergeableOntologyException
 
unsafeToJSON() - Method in class owltools.graph.shunt.OWLShuntGraph
 
unsatisfiable - Variable in class owltools.InferenceBuilder.ConsistencyReport
 
updateRedundant(OWLClass, OWLOntology, Set<OWLAxiom>, OWLReasoner, OWLDataFactory) - Static method in class owltools.InferenceBuilder
Update the set of redundant axioms for the given OWLClass cls.
useImportClosureForQueries() - Method in class owltools.graph.OWLGraphWrapper
Deprecated.
useOWLClass(OWLClass, OWLOntology) - Method in interface owltools.InferenceBuilder.OWLClassFilter
Return true, if the inferences are to made for the given OWLClass and OWLOntology; otherwise false.

V

valueOf(String) - Static method in enum owltools.gfx.RelationType.Polarity
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum owltools.gfx.RelationType
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum owltools.graph.OWLQuantifiedProperty.Quantifier
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum owltools.idmap.IDMappingPIRParser.Types
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum owltools.vocab.OBONamespaces
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum owltools.vocab.OBOUpperVocabulary
Returns the enum constant of this type with the specified name.
values() - Static method in enum owltools.gfx.RelationType.Polarity
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum owltools.gfx.RelationType
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum owltools.graph.OWLQuantifiedProperty.Quantifier
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum owltools.idmap.IDMappingPIRParser.Types
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum owltools.vocab.OBONamespaces
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum owltools.vocab.OBOUpperVocabulary
Returns an array containing the constants of this enum type, in the order they are declared.
VersionInfo - Class in owltools.version
 
viewProperty - Variable in class owltools.mooncat.SpeciesMergeUtil
 
viewProperty - Variable in class owltools.mooncat.SpeciesSubsetterUtil
 
visit(OWLSubAnnotationPropertyOfAxiom) - Method in class owltools.graph.AxiomAnnotationTools.AxiomAnnotationsChanger
 
visit(OWLAnnotationPropertyDomainAxiom) - Method in class owltools.graph.AxiomAnnotationTools.AxiomAnnotationsChanger
 
visit(OWLAnnotationPropertyRangeAxiom) - Method in class owltools.graph.AxiomAnnotationTools.AxiomAnnotationsChanger
 
visit(OWLSubClassOfAxiom) - Method in class owltools.graph.AxiomAnnotationTools.AxiomAnnotationsChanger
 
visit(OWLNegativeObjectPropertyAssertionAxiom) - Method in class owltools.graph.AxiomAnnotationTools.AxiomAnnotationsChanger
 
visit(OWLAsymmetricObjectPropertyAxiom) - Method in class owltools.graph.AxiomAnnotationTools.AxiomAnnotationsChanger
 
visit(OWLReflexiveObjectPropertyAxiom) - Method in class owltools.graph.AxiomAnnotationTools.AxiomAnnotationsChanger
 
visit(OWLDisjointClassesAxiom) - Method in class owltools.graph.AxiomAnnotationTools.AxiomAnnotationsChanger
 
visit(OWLDataPropertyDomainAxiom) - Method in class owltools.graph.AxiomAnnotationTools.AxiomAnnotationsChanger
 
visit(OWLObjectPropertyDomainAxiom) - Method in class owltools.graph.AxiomAnnotationTools.AxiomAnnotationsChanger
 
visit(OWLEquivalentObjectPropertiesAxiom) - Method in class owltools.graph.AxiomAnnotationTools.AxiomAnnotationsChanger
 
visit(OWLNegativeDataPropertyAssertionAxiom) - Method in class owltools.graph.AxiomAnnotationTools.AxiomAnnotationsChanger
 
visit(OWLDifferentIndividualsAxiom) - Method in class owltools.graph.AxiomAnnotationTools.AxiomAnnotationsChanger
 
visit(OWLDisjointDataPropertiesAxiom) - Method in class owltools.graph.AxiomAnnotationTools.AxiomAnnotationsChanger
 
visit(OWLDisjointObjectPropertiesAxiom) - Method in class owltools.graph.AxiomAnnotationTools.AxiomAnnotationsChanger
 
visit(OWLObjectPropertyRangeAxiom) - Method in class owltools.graph.AxiomAnnotationTools.AxiomAnnotationsChanger
 
visit(OWLObjectPropertyAssertionAxiom) - Method in class owltools.graph.AxiomAnnotationTools.AxiomAnnotationsChanger
 
visit(OWLFunctionalObjectPropertyAxiom) - Method in class owltools.graph.AxiomAnnotationTools.AxiomAnnotationsChanger
 
visit(OWLSubObjectPropertyOfAxiom) - Method in class owltools.graph.AxiomAnnotationTools.AxiomAnnotationsChanger
 
visit(OWLDisjointUnionAxiom) - Method in class owltools.graph.AxiomAnnotationTools.AxiomAnnotationsChanger
 
visit(OWLDeclarationAxiom) - Method in class owltools.graph.AxiomAnnotationTools.AxiomAnnotationsChanger
 
visit(OWLAnnotationAssertionAxiom) - Method in class owltools.graph.AxiomAnnotationTools.AxiomAnnotationsChanger
 
visit(OWLSymmetricObjectPropertyAxiom) - Method in class owltools.graph.AxiomAnnotationTools.AxiomAnnotationsChanger
 
visit(OWLDataPropertyRangeAxiom) - Method in class owltools.graph.AxiomAnnotationTools.AxiomAnnotationsChanger
 
visit(OWLFunctionalDataPropertyAxiom) - Method in class owltools.graph.AxiomAnnotationTools.AxiomAnnotationsChanger
 
visit(OWLEquivalentDataPropertiesAxiom) - Method in class owltools.graph.AxiomAnnotationTools.AxiomAnnotationsChanger
 
visit(OWLClassAssertionAxiom) - Method in class owltools.graph.AxiomAnnotationTools.AxiomAnnotationsChanger
 
visit(OWLEquivalentClassesAxiom) - Method in class owltools.graph.AxiomAnnotationTools.AxiomAnnotationsChanger
 
visit(OWLDataPropertyAssertionAxiom) - Method in class owltools.graph.AxiomAnnotationTools.AxiomAnnotationsChanger
 
visit(OWLTransitiveObjectPropertyAxiom) - Method in class owltools.graph.AxiomAnnotationTools.AxiomAnnotationsChanger
 
visit(OWLIrreflexiveObjectPropertyAxiom) - Method in class owltools.graph.AxiomAnnotationTools.AxiomAnnotationsChanger
 
visit(OWLSubDataPropertyOfAxiom) - Method in class owltools.graph.AxiomAnnotationTools.AxiomAnnotationsChanger
 
visit(OWLInverseFunctionalObjectPropertyAxiom) - Method in class owltools.graph.AxiomAnnotationTools.AxiomAnnotationsChanger
 
visit(OWLSameIndividualAxiom) - Method in class owltools.graph.AxiomAnnotationTools.AxiomAnnotationsChanger
 
visit(OWLSubPropertyChainOfAxiom) - Method in class owltools.graph.AxiomAnnotationTools.AxiomAnnotationsChanger
 
visit(OWLInverseObjectPropertiesAxiom) - Method in class owltools.graph.AxiomAnnotationTools.AxiomAnnotationsChanger
 
visit(OWLHasKeyAxiom) - Method in class owltools.graph.AxiomAnnotationTools.AxiomAnnotationsChanger
 
visit(OWLDatatypeDefinitionAxiom) - Method in class owltools.graph.AxiomAnnotationTools.AxiomAnnotationsChanger
 
visit(SWRLRule) - Method in class owltools.graph.AxiomAnnotationTools.AxiomAnnotationsChanger
 

W

width - Variable in class owltools.gfx.GraphStyle
 
width - Variable in class owltools.gfx.ImageRender
 
width - Variable in class owltools.gfx.OWLGraphLayoutNode
 

X

x - Variable in class owltools.gfx.OWLGraphLayoutNode
 

Y

y - Variable in class owltools.gfx.OWLGraphLayoutNode
 
A B C D E F G H I J K L M N O P Q R S T U V W X Y 
Skip navigation links

Copyright © 2010–2016. All rights reserved.