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
 
add(E) - Method in class owltools.util.BloomFilter
Adds an object to the Bloom filter.
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.
addAncestorsToShuntGraph(OWLObject, OWLShuntGraph) - Method in class owltools.graph.OWLGraphWrapper
Add a set of edges, as ancestors to x in OWLShuntGraph g.
addDirectDescendentsToShuntGraph(OWLObject, OWLShuntGraph) - Method in class owltools.graph.OWLGraphWrapper
Add a set of edges, as descendents to x in OWLShuntGraph g.
addEdge(OWLGraphEdge) - Method in class owltools.gfx.OWLGraphLayoutRenderer
Adds an edge to the graph.
addEdge(OWLShuntEdge) - Method in class owltools.graph.shunt.OWLShuntGraph
Simply "add" an edge to the graph.
addImport(OWLOntology) - Method in class owltools.graph.OWLGraphWrapper
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.OWLGraphWrapper
 
addIRIMapper(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
 
addQueryOntology(OWLOntology) - Method in class owltools.graph.OWLGraphWrapper
Deprecated. 
addReferencedOntology(OWLOntology) - Method in class owltools.mooncat.Mooncat
 
addResultsToOWLOntology(OWLOntology) - Method in class owltools.sim.Similarity
translates similarity results into OWL Axioms and saves axioms into an OWL Ontology
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.
addSupportOntologiesFromImportsClosure() - Method in class owltools.graph.OWLGraphWrapper
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.OWLGraphWrapper
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.OWLGraphWrapper
 
addViewEntities(Set<OWLEntity>) - Method in class owltools.mooncat.PropertyViewOntologyBuilder
 
alternativeCode - Variable in enum owltools.gfx.RelationType
 
annotationIRI(String) - Method in class owltools.sim.Similarity
 
aScore - Variable in class owltools.sim.MultiSimilarity
 
AsymmetricJaccardSimilarity - Class in owltools.sim
 
AsymmetricJaccardSimilarity() - Constructor for class owltools.sim.AsymmetricJaccardSimilarity
 
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
 
AvgInformationContentBestMatchesSimilarity - Class in owltools.sim
Deprecated. 
AvgInformationContentBestMatchesSimilarity() - Constructor for class owltools.sim.AvgInformationContentBestMatchesSimilarity
Deprecated.  
AvgInformationContentLCSSimilarity - Class in owltools.sim
Deprecated. 
AvgInformationContentLCSSimilarity() - Constructor for class owltools.sim.AvgInformationContentLCSSimilarity
Deprecated.  
axiomType - Variable in class owltools.io.TableToAxiomConverter.Config
 

B

belongsToSource(OWLEntity) - Method in class owltools.mooncat.Mooncat
 
bestSubsumers - Variable in class owltools.sim.ConjunctiveSetSimilarity
 
bestSubsumers - Variable in class owltools.sim.DisjunctiveSetSimilarity
 
bestSubsumers - Variable in class owltools.sim.MaximumInformationContentSimilarity
 
bloomFilter - Variable in class owltools.sim.SimSearch
 
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
 
bScore - Variable in class owltools.sim.MultiSimilarity
 
buildClassMap(OWLGraphWrapper) - Method in class owltools.io.TableToAxiomConverter
 
buildDescription(OWLObject, OWLObject) - Method in class owltools.sim.DescriptionTreeSimilarity
Recursively build a class expression that subsumes a and b.
buildDescription(OWLObject, OWLObject, Set<OWLObject>) - Method in class owltools.sim.DescriptionTreeSimilarity
 
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, 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

cacheEdges() - Method in class owltools.graph.OWLGraphWrapper
caches full outgoing and incoming edges in general you should not need to call this directly; used internally by this class.
calculate(SimEngine, OWLObject, OWLObject) - Method in class owltools.sim.AsymmetricJaccardSimilarity
 
calculate(SimEngine, OWLObject, OWLObject) - Method in class owltools.sim.AvgInformationContentBestMatchesSimilarity
Deprecated.  
calculate(SimEngine, OWLObject, OWLObject) - Method in class owltools.sim.AvgInformationContentLCSSimilarity
Deprecated.  
calculate(SimEngine, OWLObject, OWLObject) - Method in class owltools.sim.CombinedJaccardConjunctiveSetSimilarity
 
calculate(SimEngine, OWLObject, OWLObject) - Method in class owltools.sim.CombinedSimilarity
 
calculate(SimEngine, OWLObject, OWLObject) - Method in class owltools.sim.CombinedSimilarity2
 
calculate(SimEngine, OWLObject, OWLObject) - Method in class owltools.sim.ConjunctiveSetInformationContentRatioSimilarity
 
calculate(SimEngine, OWLObject, OWLObject) - Method in class owltools.sim.ConjunctiveSetSimilarity
 
calculate(SimEngine, OWLObject, OWLObject) - Method in class owltools.sim.DescriptionTreeSimilarity
 
calculate(SimEngine, OWLObject, OWLObject) - Method in class owltools.sim.DisjunctiveSetSimilarity
 
calculate(SimEngine, OWLObject, OWLObject) - Method in class owltools.sim.JaccardBloomSimilarity
 
calculate(SimEngine, OWLObject, OWLObject) - Method in class owltools.sim.JaccardSimilarity
 
calculate(SimEngine, OWLObject, OWLObject) - Method in class owltools.sim.MaximumInformationContentSimilarity
 
calculate(SimEngine, OWLObject, OWLObject) - Method in class owltools.sim.MultiSimilarity
 
calculate(SimEngine, OWLObject, OWLObject) - Method in class owltools.sim.OverlapSimilarity
 
calculate(SimEngine, OWLObject, OWLObject) - Method in class owltools.sim.Similarity
 
calculate_overlap(Pheno, Pheno, HashMap<String, IndividualPair>) - Static method in class owltools.phenolog.Main
 
calculateAllSimilarity(OWLObject, OWLObject) - Method in class owltools.sim.SimEngine
iterates through ALL similarity metrics and calculates
calculateSimilarity(Similarity, OWLObject, OWLObject) - Method in class owltools.sim.SimEngine
Calculates the similarity between two OWLObjects this is the core method of the SimEngine
calculateSimilarity(OWLObject, OWLObject) - Method in interface owltools.sim.SimilarityCalculator
given two objects, calculate their similarity, returning a number between zero (no similarity) and 1 (equivalence)
calculateSimilarityAllByAll(String, Double) - Method in class owltools.sim.SimEngine
 
calculateSimilarityScore(Similarity, OWLObject, OWLObject) - Method in class owltools.sim.SimEngine
 
candidates - Variable in class owltools.sim.SimSearch
 
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.
ChadoGraphClosureRenderer - Class in owltools.io
implements a graph closure writer suitable for imports into Chado; in particular: (i) all identifiers are translated to OBO IDs (ii) relationship chains of length > 1 are ignored (iii) 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
 
checkAnnotationCardinality(OWLOntology, OntologyMetaDataTools.AnnotationCardinalityConfictHandler) - Static method in class owltools.mooncat.OntologyMetaDataTools
Check the annotations for cardinality violations.
checkAnnotationCardinality(OWLOntology) - Static method in class owltools.mooncat.OntologyMetaDataTools
Check the annotations for cardinality violations.
childArrowShape - Variable in class owltools.gfx.GraphicsConfig.RelationConfig
 
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
 
classMap - Variable in class owltools.io.TableToAxiomConverter.Config
 
clear() - Method in class owltools.util.BloomFilter
Sets all bits to false in the Bloom filter.
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
 
CombinedJaccardConjunctiveSetSimilarity - Class in owltools.sim
filters first based on SimJ, if passes threshold performs full ConjunctiveSetSimilarity
CombinedJaccardConjunctiveSetSimilarity() - Constructor for class owltools.sim.CombinedJaccardConjunctiveSetSimilarity
 
CombinedSimilarity - Class in owltools.sim
 
CombinedSimilarity() - Constructor for class owltools.sim.CombinedSimilarity
 
CombinedSimilarity2 - Class in owltools.sim
 
CombinedSimilarity2() - Constructor for class owltools.sim.CombinedSimilarity2
 
combineEdgePair(OWLObject, OWLGraphEdge, OWLGraphEdge, int) - Method in class owltools.graph.OWLGraphWrapper
Composes two graph edges into a new edge, using axioms in the ontology to determine the correct composition For example, Edge(x,SUBCLASS_OF,y) * Edge(y,SUBCLASS_OF,z) yields Edge(x,SUBCLASS_OF,z) Note that property chains of length>2 are currently ignored
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
 
comparisonClass - Variable in class owltools.sim.SimEngine
 
comparisonProperty - Variable in class owltools.sim.SimEngine
 
comparisonSuperclass - Variable in class owltools.sim.SimEngine
 
config - Variable in class owltools.io.TableToAxiomConverter
 
ConjunctiveSetInformationContentRatioSimilarity - Class in owltools.sim
score is the IC of the intersection of all attributes divided my min IC of a or b it's recommended this used as a sub-method of a MultiSimilarity check
ConjunctiveSetInformationContentRatioSimilarity() - Constructor for class owltools.sim.ConjunctiveSetInformationContentRatioSimilarity
 
ConjunctiveSetSimilarity - Class in owltools.sim
ConjunctiveSetSimilarity(a,b) = IC( LCA_1(a,b) ^ LCA_2(a,b) ...
ConjunctiveSetSimilarity() - Constructor for class owltools.sim.ConjunctiveSetSimilarity
 
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(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
 
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.
createNonBufferingReasoner(OWLOntology) - Method in class owltools.reasoner.GraphReasonerFactory
 
createNonBufferingReasoner(OWLOntology, OWLReasonerConfiguration) - Method in class owltools.reasoner.GraphReasonerFactory
 
createNonBufferingReasoner(OWLOntology) - Method in class owltools.reasoner.PlaceholderJcelFactory
 
createNonBufferingReasoner(OWLOntology, OWLReasonerConfiguration) - Method in class owltools.reasoner.PlaceholderJcelFactory
 
createOWLOntologyFromResults() - Method in class owltools.sim.Similarity
 
createReasoner(OWLOntology) - Method in class owltools.reasoner.GraphReasonerFactory
 
createReasoner(OWLOntology, OWLReasonerConfiguration) - Method in class owltools.reasoner.GraphReasonerFactory
 
createReasoner(OWLOntology) - Method in class owltools.reasoner.PlaceholderJcelFactory
 
createReasoner(OWLOntology, OWLReasonerConfiguration) - Method in class owltools.reasoner.PlaceholderJcelFactory
 
createReasonerDiff(OWLGraphWrapper, OWLGraphWrapper, String) - Static method in class owltools.diff.ReasonerDiff
 
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
 
createUnionExpression(OWLObject, OWLObject, OWLObject) - Method in class owltools.sim.SimEngine
 
crender(OWLObject) - Method in class owltools.io.CompactGraphClosureRenderer
 
currentCols - Variable in class owltools.idmap.AbstractMappingParser
 
currentRow - Variable in class owltools.idmap.AbstractMappingParser
 

D

deepSimMethods - Variable in class owltools.sim.MultiSimilarity
 
DEFAULT_HANDLER - Static variable in class owltools.mooncat.OntologyMetaDataTools
 
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
 
description - Variable in enum owltools.gfx.RelationType
 
DescriptionTreeSimilarity - Class in owltools.sim
A similarity between two entities constructed by threading two description trees together.
DescriptionTreeSimilarity() - Constructor for class owltools.sim.DescriptionTreeSimilarity
 
DisjunctiveSetSimilarity - Class in owltools.sim
 
DisjunctiveSetSimilarity() - Constructor for class owltools.sim.DisjunctiveSetSimilarity
 
dispose() - Method in class owltools.InferenceBuilder
Dispose the internal reasoner
dispose() - Method in class owltools.io.OWLPrettyPrinter.LabelProvider
 
dispose() - Method in class owltools.reasoner.ExpressionMaterializingReasoner
 
DLQueryTool - Class in owltools.mooncat
Tools for running DL queries on OWLOntology.
DLQueryTool() - Constructor for class owltools.mooncat.DLQueryTool
 

E

edges - Variable in class owltools.graph.shunt.OWLShuntGraph
 
edgeSetToExpression(Set<OWLGraphEdge>) - Method in class owltools.sim.SimEngine
 
edgeToTargetExpression(OWLGraphEdge) - Method in class owltools.graph.OWLGraphWrapper
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.sim.OWLObjectPair
 
equals(Object) - Method in class owltools.util.BloomFilter
Compares the contents of two instances to see if they are equal.
errorFontName - Variable in class owltools.gfx.GraphStyle
 
errorFontSize - Variable in class owltools.gfx.GraphStyle
 
errorMessage - Variable in class owltools.gfx.HierarchyImage
 
excludeAllWith(OWLAnnotationProperty, OWLOntology) - Method in class owltools.graph.OWLGraphWrapper.Config
 
excludeClassesInComparison - Variable in class owltools.sim.SimEngine
 
excludeMetaClass - Variable in class owltools.graph.OWLGraphWrapper.Config
 
excludeProperty(OWLObjectProperty, OWLQuantifiedProperty.Quantifier) - Method in class owltools.graph.OWLGraphWrapper.Config
 
excludeProperty(OWLObjectProperty) - Method in class owltools.graph.OWLGraphWrapper.Config
 
executeDLQuery(String, OWLGraphWrapper, OWLReasonerFactory) - Static method in class owltools.mooncat.DLQueryTool
Execute the DL query on the given ontology graph.
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
 
ExpressionMaterializingReasoner - Class in owltools.reasoner
This wraps an existing reasoner to implement OWLExtendedReasoner.
ExpressionMaterializingReasoner(OWLOntology, OWLReasonerConfiguration, BufferingMode) - Constructor for class owltools.reasoner.ExpressionMaterializingReasoner
 
ExpressionMaterializingReasoner(OWLOntology) - Constructor for class owltools.reasoner.ExpressionMaterializingReasoner
 
extendEdge(OWLGraphEdge) - Method in class owltools.sim.SimEngine
 

F

factory - Variable in class owltools.InferenceBuilder.FactoryDetails
 
featureToAttributeMap - Variable in class owltools.sim.MultiSimilarity
 
fill - Variable in class owltools.gfx.GraphStyle
 
fill - Variable in class owltools.gfx.OWLGraphLayoutNode
 
filterObjects(Set<OWLObject>) - Method in class owltools.sim.SimEngine
 
filterWhere - Variable in class owltools.idmap.IDMappingPIRParser
 
findCommonAncestors(OWLGraphWrapper, OWLObject, OWLObject) - Static method in class owltools.graph.OWLGraphUtil
 
findCommonSubsumersAsEdges(OWLGraphWrapper, OWLObject, OWLObject) - Static method in class owltools.graph.OWLGraphUtil
 
findLeastCommonAncestors(OWLGraphWrapper, OWLObject, OWLObject) - Static method in class owltools.graph.OWLGraphUtil
 
findLeastCommonSubsumersAsEdges(OWLGraphWrapper, OWLObject, OWLObject) - Static method in class owltools.graph.OWLGraphUtil
 
flush() - Method in class owltools.reasoner.ExpressionMaterializingReasoner
 
font - Variable in class owltools.gfx.OWLGraphLayoutNode
 
forceReflexivePropertyCreation - Variable in class owltools.sim.DescriptionTreeSimilarity
 
forCodes(String) - Static method in enum owltools.gfx.RelationType
 
formalCode - Variable in enum owltools.gfx.RelationType
 

G

g - Variable in class owltools.gfx.OWLGraphLayoutRenderer
 
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
 
getA() - Method in class owltools.sim.OWLObjectPair
 
getAllOntologies() - Method in class owltools.graph.OWLGraphWrapper
in general application code need not call this - it is mostly used internally
getAllOntologies() - Method in class owltools.mooncat.Mooncat
 
getAllOWLObjects() - Method in class owltools.graph.OWLGraphWrapper
fetches all classes, individuals and object properties in all ontologies
getAllSimilarityAlgorithmClasses() - Method in class owltools.sim.SimEngine
 
getAllUsedSubsets() - Method in class owltools.graph.OWLGraphWrapper
fetches all subset names that are used
getAltIds(OWLObject) - Method in class owltools.graph.OWLGraphWrapper
It returns the values of the alt_id tag
getAncestors(OWLObject) - Method in class owltools.graph.OWLGraphWrapper
returns all ancestors of an object.
getAncestors(OWLObject, Set<OWLPropertyExpression>) - Method in class owltools.graph.OWLGraphWrapper
returns all ancestors that can be reached over subclass or the specified set of relations
getancestors() - Method in class owltools.phenolog.Pheno
 
getAncestorsReflexive(OWLObject) - Method in class owltools.graph.OWLGraphWrapper
 
getAncestorsReflexive(OWLObject, Set<OWLPropertyExpression>) - Method in class owltools.graph.OWLGraphWrapper
 
getAnnotationProperty(String) - Method in class owltools.graph.OWLGraphWrapper
It translates a oboformat tag into an OWL annotation property
getAnnotationValue(OWLObject, OWLAnnotationProperty) - Method in class owltools.graph.OWLGraphWrapper
fetches the value of a single-valued annotation property for an OWLObject TODO: provide a flag that determines behavior in the case of >1 value
getAnnotationValues(OWLObject, OWLAnnotationProperty) - Method in class owltools.graph.OWLGraphWrapper
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
getAttributeClosureFor(OWLObject) - Method in class owltools.sim.SimEngine
 
getAttributes() - Method in class owltools.phenolog.Individual
 
getAttributesFor(OWLObject) - Method in class owltools.sim.SimEngine
 
getAxiomsForSubset(Set<OWLObject>) - Method in class owltools.mooncat.Mooncat
"slim down" an ontology.
getB() - Method in class owltools.sim.OWLObjectPair
 
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.ExpressionMaterializingReasoner
 
getBottomClassNode() - Method in class owltools.reasoner.GraphReasoner
 
getBottomDataPropertyNode() - Method in class owltools.reasoner.ExpressionMaterializingReasoner
 
getBottomDataPropertyNode() - Method in class owltools.reasoner.GraphReasoner
 
getBottomObjectPropertyNode() - Method in class owltools.reasoner.ExpressionMaterializingReasoner
 
getBottomObjectPropertyNode() - Method in class owltools.reasoner.GraphReasoner
 
getBufferingMode() - Method in class owltools.reasoner.ExpressionMaterializingReasoner
 
getBuiltin(OWLObject) - Method in class owltools.graph.OWLGraphWrapper
Deprecated. 
getCategory() - Method in interface owltools.graph.OWLGraphWrapper.ISynonym
 
getCategory() - Method in class owltools.graph.OWLGraphWrapper.Synonym
 
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.OWLGraphWrapper
gets the value of rdfs:comment for an OWLObject
getCommonSubsumers(OWLObject, OWLObject) - Method in class owltools.sim.SimEngine
 
getCommonSubsumersSize(OWLObject, OWLObject) - Method in class owltools.sim.SimEngine
 
getCompleteEdgesBetween(OWLObject, OWLObject) - Method in class owltools.graph.OWLGraphWrapper
 
getCompleteOutgoingEdgesClosure(OWLObject) - Method in class owltools.graph.OWLGraphWrapper
See OWLGraphWrapper.getIncomingEdgesClosure(OWLObject s, boolean isComplete)
getConfig() - Method in class owltools.graph.OWLGraphWrapper
 
getConsider(OWLObject) - Method in class owltools.graph.OWLGraphWrapper
It returns the values of the consider tag.
getCorpusSize() - Method in class owltools.sim.SimEngine
 
getCreatedBy(OWLObject) - Method in class owltools.graph.OWLGraphWrapper
It returns the value of the created_by tag
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.OWLGraphWrapper
 
getDataPropertyDomains(OWLDataProperty, boolean) - Method in class owltools.reasoner.ExpressionMaterializingReasoner
 
getDataPropertyDomains(OWLDataProperty, boolean) - Method in class owltools.reasoner.GraphReasoner
 
getDataPropertyValues(OWLNamedIndividual, OWLDataProperty) - Method in class owltools.reasoner.ExpressionMaterializingReasoner
 
getDataPropertyValues(OWLNamedIndividual, OWLDataProperty) - Method in class owltools.reasoner.GraphReasoner
 
getDef(OWLObject) - Method in class owltools.graph.OWLGraphWrapper
Gets the textual definition of an OWLObject assumes zero or one def It returns the definition text (encoded as def in obo format and IAO_0000115 annotation property in OWL format) of a class
getDefaultOboNamespace() - Method in class owltools.io.ParserWrapper.OWLGraphWrapperNameProvider
 
getDefXref(OWLObject) - Method in class owltools.graph.OWLGraphWrapper
Get the definition xrefs (IAO_0000115)
getDescendants(OWLObject) - Method in class owltools.graph.OWLGraphWrapper
gets all descendants d of x, where d is reachable by any path.
getDescendantsReflexive(OWLObject) - Method in class owltools.graph.OWLGraphWrapper
gets all reflexive descendants d of x, where d is reachable by any path.
getDifferentIndividuals(OWLNamedIndividual) - Method in class owltools.reasoner.ExpressionMaterializingReasoner
 
getDifferentIndividuals(OWLNamedIndividual) - Method in class owltools.reasoner.GraphReasoner
 
getDisjointClasses(OWLClassExpression) - Method in class owltools.reasoner.ExpressionMaterializingReasoner
 
getDisjointClasses(OWLClassExpression) - Method in class owltools.reasoner.GraphReasoner
 
getDisjointDataProperties(OWLDataPropertyExpression) - Method in class owltools.reasoner.ExpressionMaterializingReasoner
 
getDisjointDataProperties(OWLDataPropertyExpression) - Method in class owltools.reasoner.GraphReasoner
 
getDisjointObjectProperties(OWLObjectPropertyExpression) - Method in class owltools.reasoner.ExpressionMaterializingReasoner
 
getDisjointObjectProperties(OWLObjectPropertyExpression) - Method in class owltools.reasoner.GraphReasoner
 
getDistance() - Method in class owltools.graph.OWLGraphEdge
 
getDocumentIRI(IRI) - Method in class owltools.io.CatalogXmlIRIMapper
 
getDomain(OWLObjectProperty) - Method in class owltools.graph.OWLGraphWrapper
It returns the value of the domain tag
getEdgeLabel(OWLGraphEdge) - Method in class owltools.graph.OWLGraphWrapper
Get the human readable label for an edge.
getEdgesBetween(OWLObject, OWLObject) - Method in class owltools.graph.OWLGraphWrapper
 
getElementsOntology() - Method in class owltools.mooncat.PropertyViewOntologyBuilder
 
getEquivalentClasses(OWLClassExpression) - Method in class owltools.reasoner.ExpressionMaterializingReasoner
 
getEquivalentClasses(OWLClassExpression) - Method in class owltools.reasoner.GraphReasoner
 
getEquivalentDataProperties(OWLDataProperty) - Method in class owltools.reasoner.ExpressionMaterializingReasoner
 
getEquivalentDataProperties(OWLDataProperty) - Method in class owltools.reasoner.GraphReasoner
 
getEquivalentNamedClassPairs() - Method in class owltools.InferenceBuilder
 
getEquivalentObjectProperties(OWLObjectPropertyExpression) - Method in class owltools.reasoner.ExpressionMaterializingReasoner
 
getEquivalentObjectProperties(OWLObjectPropertyExpression) - Method in class owltools.reasoner.GraphReasoner
 
getExcludedLabels() - Method in class owltools.sim.SimEngine
any class whose label matches any of the strings returned here will be excluded from any analysis.
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.
getFinalQuantifiedProperty() - Method in class owltools.graph.OWLGraphEdge
 
getFirstQuantifiedProperty() - Method in class owltools.graph.OWLGraphEdge
 
getFrequency(OWLObject) - Method in class owltools.sim.SimEngine
 
getFrequency(Set<OWLObject>) - Method in class owltools.sim.SimEngine
as getFrequency(obj), treats objs as a conjunction
getFreshEntityPolicy() - Method in class owltools.reasoner.ExpressionMaterializingReasoner
 
getGraph() - Method in class owltools.mooncat.Mooncat
 
getGraph() - Method in class owltools.sim.SimEngine
 
getGraph() - Method in interface owltools.sim.SimilarityCalculator
 
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.OWLGraphWrapper
gets the OBO-style ID of the specified object.
getIdentifier(IRI) - Method in class owltools.graph.OWLGraphWrapper
gets the OBO-style ID of the specified object.
getIncomingEdges(OWLObject) - Method in class owltools.graph.OWLGraphWrapper
 
getIncomingEdgesClosure(OWLObject, boolean) - Method in class owltools.graph.OWLGraphWrapper
As OWLGraphWrapper.getIncomingEdgesClosure(OWLObject t), but allows the option of including 'complete' edge list.
getIncomingEdgesClosure(OWLObject) - Method in class owltools.graph.OWLGraphWrapper
gets all inferred edges coming in to the target edge for every s, if t is reachable from s, then include the inferred edge between s and t.
getIndividualDescendants(OWLObject) - Method in class owltools.graph.OWLGraphWrapper
return all individuals i where x is reachable from i
getIndividualNodeSetPolicy() - Method in class owltools.reasoner.ExpressionMaterializingReasoner
 
getIndividualPairs() - Method in class owltools.phenolog.PhenologEngine
 
getIndividuals() - Method in class owltools.phenolog.Pheno
 
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
getInformationContent(OWLObject) - Method in class owltools.sim.SimEngine
The IC of an OWLObject is freq(Obj)/corpusSize here the frequency of an object is the number of individuals with a graph path up to the object, and the corpus size is the number of individuals in the graph
getInformationContent(Set<OWLObject>) - Method in class owltools.sim.SimEngine
 
getInstanceChainsFromClosure(OWLClass) - Method in class owltools.graph.OWLGraphWrapper
Finds all edges between an instance i and he given class c.
getInstances(OWLClassExpression, boolean) - Method in class owltools.reasoner.ExpressionMaterializingReasoner
 
getInstances(OWLClassExpression, boolean) - Method in class owltools.reasoner.GraphReasoner
 
getInstancesFromClosure(OWLClass) - Method in class owltools.graph.OWLGraphWrapper
Find all edges of the form [i INST c] in the graph closure.
getInverseObjectProperties(OWLObjectPropertyExpression) - Method in class owltools.reasoner.ExpressionMaterializingReasoner
 
getInverseObjectProperties(OWLObjectPropertyExpression) - Method in class owltools.reasoner.GraphReasoner
 
getIRIByIdentifier(String) - Method in class owltools.graph.OWLGraphWrapper
 
getIRIByLabel(String) - Method in class owltools.graph.OWLGraphWrapper
fetches an OWL IRI by rdfs:label
getIRIByLabel(String, boolean) - Method in class owltools.graph.OWLGraphWrapper
fetches an OWL IRI by rdfs:label, optionally testing for uniqueness TODO: index labels.
getIsAnonymous(OWLObject) - Method in class owltools.graph.OWLGraphWrapper
Deprecated. 
getIsAntiSymmetric(OWLObject) - Method in class owltools.graph.OWLGraphWrapper
It returns the value of the is_anti_symmetric tag or IAO_0000427 annotation
getIsaPartofClosureMap(OWLObject) - Method in class owltools.graph.OWLGraphWrapper
Return a overlaps with getIsaPartofLabelClosure and stuff in GafSolrDocumentLoader.
getIsaPartofIDClosure(OWLObject) - Method in class owltools.graph.OWLGraphWrapper
Return a overlaps with getIsaPartofLabelClosure and stuff in GafSolrDocumentLoader.
getIsaPartofLabelClosure(OWLObject) - Method in class owltools.graph.OWLGraphWrapper
Return a overlaps with getIsaPartofIDClosure and stuff in GafSolrDocumentLoader.
getIsCyclic(OWLObject) - Method in class owltools.graph.OWLGraphWrapper
It returns the value of the is_cyclic tag
getisFromTC() - Method in class owltools.phenolog.Pheno
 
getIsFunctional(OWLObjectProperty) - Method in class owltools.graph.OWLGraphWrapper
true if c is functional in the source ontology
getIsInverseFunctional(OWLObjectProperty) - Method in class owltools.graph.OWLGraphWrapper
 
getIsMetaTag(OWLObject) - Method in class owltools.graph.OWLGraphWrapper
It returns the value of the is_metadata_tag tag.
getIsObsolete(OWLObject) - Method in class owltools.graph.OWLGraphWrapper
It returns the value of the is-obsolete tag.
getIsObsoleteBinaryString(OWLObject) - Method in class owltools.graph.OWLGraphWrapper
It returns the value of the is-obsolete tag.
getIsReflexive(OWLObjectProperty) - Method in class owltools.graph.OWLGraphWrapper
 
getIsSymmetric(OWLObjectProperty) - Method in class owltools.graph.OWLGraphWrapper
 
getIsTransitive(OWLObjectProperty) - Method in class owltools.graph.OWLGraphWrapper
true if c is transitive in the source ontology
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.
getLabel(OWLObject) - Method in class owltools.graph.OWLGraphWrapper
fetches the rdfs:label for an OWLObject assumes zero or one rdfs:label
getLabel() - Method in interface owltools.graph.OWLGraphWrapper.ISynonym
 
getLabel() - Method in class owltools.graph.OWLGraphWrapper.Synonym
 
getLabel() - Method in class owltools.graph.shunt.OWLShuntNode
 
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.OWLGraphWrapper
 
getLabelOrId(OWLEntity) - Method in class owltools.io.OWLPrettyPrinter.LabelProvider
 
getLastQuantifiedProperty() - Method in class owltools.graph.OWLGraphEdge
 
getLCS() - Method in class owltools.sim.ConjunctiveSetInformationContentRatioSimilarity
 
getLeastCommonSubsumers(OWLObject, OWLObject) - Method in class owltools.sim.SimEngine
note that this performs caching by default
getLeastCommonSubsumerSimpleClassExpression(OWLObject, OWLObject) - Method in class owltools.sim.SimEngine
 
getLeastCommonSubsumerSimpleClassExpression(OWLObject, OWLObject, boolean) - Method in class owltools.sim.SimEngine
 
getLeastCommonSubsumersSize(OWLObject, OWLObject) - Method in class owltools.sim.SimEngine
 
getManager() - Method in class owltools.graph.OWLGraphWrapper
 
getManager() - Method in class owltools.io.ParserWrapper
 
getManager() - Method in class owltools.mooncat.Mooncat
 
getMaxCardinality() - Method in class owltools.graph.OWLQuantifiedProperty
 
getMaxHits() - Method in class owltools.sim.SimSearch
 
getMember1() - Method in class owltools.phenolog.IndividualPair
 
getMember2() - Method in class owltools.phenolog.IndividualPair
 
getMetadata() - Method in class owltools.graph.shunt.OWLShuntNode
 
getMinCardinality() - Method in class owltools.graph.OWLQuantifiedProperty
 
getName(String) - Method in class owltools.io.ParserWrapper.OWLGraphWrapperNameProvider
 
getNamedAncestors(OWLObject) - Method in class owltools.graph.OWLGraphWrapper
Gets all ancestors that are OWLNamedObjects i.e.
getNamedAncestorsReflexive(OWLObject) - Method in class owltools.graph.OWLGraphWrapper
 
getNamespace(OWLObject) - Method in class owltools.graph.OWLGraphWrapper
It returns the value of the OBO-namespace tag Example: if the OWLObject is the GO class GO:0008150, this would return "biological_process"
getNewAxioms() - Method in class owltools.diff.ReasonerDiff
 
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
 
getObjectPropertyDomains(OWLObjectPropertyExpression, boolean) - Method in class owltools.reasoner.ExpressionMaterializingReasoner
 
getObjectPropertyDomains(OWLObjectPropertyExpression, boolean) - Method in class owltools.reasoner.GraphReasoner
 
getObjectPropertyRanges(OWLObjectPropertyExpression, boolean) - Method in class owltools.reasoner.ExpressionMaterializingReasoner
 
getObjectPropertyRanges(OWLObjectPropertyExpression, boolean) - Method in class owltools.reasoner.GraphReasoner
 
getObjectPropertyValues(OWLNamedIndividual, OWLObjectPropertyExpression) - Method in class owltools.reasoner.ExpressionMaterializingReasoner
 
getObjectPropertyValues(OWLNamedIndividual, OWLObjectPropertyExpression) - Method in class owltools.reasoner.GraphReasoner
 
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) - Method in class owltools.graph.OWLGraphWrapper
It returns String Listof synonyms.
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.OWLGraphWrapper
gets the OBO-style ID of the source ontology IRI.
getOrthologs() - Method in class owltools.phenolog.Individual
 
getOutgoingEdges(OWLObject) - Method in class owltools.graph.OWLGraphWrapper
retrieves direct edges from a source to the direct **named** target e.g.
getOutgoingEdges(OWLObject, boolean, boolean) - Method in class owltools.graph.OWLGraphWrapper
 
getOutgoingEdgesClosure(OWLObject) - Method in class owltools.graph.OWLGraphWrapper
Retrieves the graph closure originating from source.
getOutgoingEdgesClosure(OWLObject, boolean) - Method in class owltools.graph.OWLGraphWrapper
See OWLGraphWrapper.getIncomingEdgesClosure(OWLObject s, boolean isComplete)
getOutgoingEdgesClosureReflexive(OWLObject) - Method in class owltools.graph.OWLGraphWrapper
as getOutgoingEdgesClosure(s), but also includes an identity edge
getOWLAnnotationProperty(IRI) - Method in class owltools.graph.OWLGraphWrapper
 
getOWLClass(String) - Method in class owltools.graph.OWLGraphWrapper
Returns an OWLClass given an IRI string the class must be declared in either the source ontology, or in a support ontology, otherwise null is returned
getOWLClass(IRI) - Method in class owltools.graph.OWLGraphWrapper
Returns an OWLClass given an IRI the class must be declared in either the source ontology, or in a support ontology, otherwise null is returned
getOWLClass(OWLObject) - Method in class owltools.graph.OWLGraphWrapper
 
getOWLClassByIdentifier(String) - Method in class owltools.graph.OWLGraphWrapper
Given an OBO-style ID, return the corresponding OWLClass, if it is declared - otherwise null
getOWLClassesInSubset(String) - Method in class owltools.graph.OWLGraphWrapper
given a subset name, find all OWLClasses assigned to that subset
getOWLGraphEdgeSubsumers(OWLGraphEdge) - Method in class owltools.graph.OWLGraphWrapper
generalizes over quantified properties
getOWLGraphEdgeSubsumers(OWLGraphEdge, int) - Method in class owltools.graph.OWLGraphWrapper
 
getOWLGraphWrapper() - Method in class owltools.InferenceBuilder
 
getOWLIndividual(IRI) - Method in class owltools.graph.OWLGraphWrapper
Returns an OWLNamedIndividual with this IRI if it has been declared in the source or support ontologies.
getOWLIndividual(String) - Method in class owltools.graph.OWLGraphWrapper
 
getOWLIndividualByIdentifier(String) - Method in class owltools.graph.OWLGraphWrapper
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.OWLGraphWrapper
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.OWLGraphWrapper
Returns the OWLObject with this IRI Must have been declared in one of the ontologies Currently OWLObject must be one of OWLClass, OWLObjectProperty or OWLNamedIndividual If the ontology employs punning and there different entities with the same IRI, then the order of precedence is OWLClass then OWLObjectProperty then OWLNamedIndividual
getOWLObjectByIdentifier(String) - Method in class owltools.graph.OWLGraphWrapper
Given an OBO-style ID, return the corresponding OWLObject, if it is declared - otherwise null
getOWLObjectByLabel(String) - Method in class owltools.graph.OWLGraphWrapper
fetches an OWL Object by rdfs:label if there is >1 match, return the first one encountered
getOWLObjectProperty(String) - Method in class owltools.graph.OWLGraphWrapper
Returns the OWLObjectProperty with this IRI Must have been declared in one of the ontologies
getOWLObjectProperty(IRI) - Method in class owltools.graph.OWLGraphWrapper
 
getOWLObjectPropertyByIdentifier(String) - Method in class owltools.graph.OWLGraphWrapper
Given an OBO-style ID, return the corresponding OWLObjectProperty, if it is declared - otherwise null
getOWLObjectsInSubset(String) - Method in class owltools.graph.OWLGraphWrapper
given a subset name, find all OWLObjects (typically OWLClasses) assigned to that subset
getPendingAxiomAdditions() - Method in class owltools.reasoner.ExpressionMaterializingReasoner
 
getPendingAxiomRemovals() - Method in class owltools.reasoner.ExpressionMaterializingReasoner
 
getPendingChanges() - Method in class owltools.reasoner.ExpressionMaterializingReasoner
 
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.ExpressionMaterializingReasoner
 
getPrecomputableInferenceTypes() - Method in class owltools.reasoner.GraphReasoner
 
getprefix() - Method in class owltools.phenolog.PhenoTransitiveClosure
 
getPreSimMethod() - Method in class owltools.sim.MultiSimilarity
 
getPrimitiveIncomingEdges(OWLObject) - Method in class owltools.graph.OWLGraphWrapper
 
getPrimitiveOutgoingEdges(OWLObject) - Method in class owltools.graph.OWLGraphWrapper
primitive edges connect any combination of named objects and expressions e.g.
getProfiler() - Method in class owltools.graph.OWLGraphWrapper
 
getProperty() - Method in class owltools.graph.OWLQuantifiedProperty
 
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.OWLGraphWrapper
It returns the value of the range tag
getReasoner() - Method in class owltools.graph.OWLGraphWrapper
 
getReasoner(OWLOntology) - Method in class owltools.InferenceBuilder
 
getReasonerName() - Method in class owltools.reasoner.ExpressionMaterializingReasoner
 
getReasonerName() - Method in class owltools.reasoner.GraphReasoner
 
getReasonerName() - Method in class owltools.reasoner.GraphReasonerFactory
 
getReasonerName() - Method in class owltools.reasoner.PlaceholderJcelFactory
 
getReasonerVersion() - Method in class owltools.reasoner.ExpressionMaterializingReasoner
 
getReasonerVersion() - Method in class owltools.reasoner.GraphReasoner
 
getRedundantAxioms() - Method in class owltools.InferenceBuilder
 
getReferencedOntologies() - Method in class owltools.mooncat.Mooncat
delegates to OWLGraphWrapper support ontologies
getRelationType(OWLGraphEdge, OWLGraphWrapper) - Static method in class owltools.gfx.OWLGraphStrokeEdge
Sets the value of relType based on OWLGraphEdge properties TODO : this is too hacky.
getRemovedInferredAxioms() - Method in class owltools.diff.ReasonerDiff
 
getReplacedBy(OWLObject) - Method in class owltools.graph.OWLGraphWrapper
It returns the values of the replaced_by tag or IAO_0100001 annotation.
getRootOntology() - Method in class owltools.reasoner.ExpressionMaterializingReasoner
 
getSameIndividuals(OWLNamedIndividual) - Method in class owltools.reasoner.ExpressionMaterializingReasoner
 
getSameIndividuals(OWLNamedIndividual) - Method in class owltools.reasoner.GraphReasoner
 
getScope() - Method in interface owltools.graph.OWLGraphWrapper.ISynonym
 
getScope() - Method in class owltools.graph.OWLGraphWrapper.Synonym
 
getScore() - Method in class owltools.sim.Similarity
 
getSegmentShuntGraph(OWLObject) - Method in class owltools.graph.OWLGraphWrapper
Gets all ancestors and direct descendents (distance == 1) that are OWLNamedObjects.
getSegmentShuntGraphJSON(OWLObject) - Method in class owltools.graph.OWLGraphWrapper
Return a JSONized version of the output of getSegmentShuntGraph
getShortForm(OWLEntity) - Method in class owltools.io.OWLPrettyPrinter.LabelProvider
 
getSimEngine() - Method in class owltools.sim.SimSearch
 
getSimilarityAlgorithm(String) - Method in class owltools.sim.SimEngine
factory class for generating a Similarity instance based on its name
getSimilarityAlgorithm(Class) - Method in class owltools.sim.SimEngine
 
getSingleQuantifiedProperty() - Method in class owltools.graph.OWLGraphEdge
 
getSource() - Method in class owltools.graph.OWLGraphEdge
 
getSourceId() - Method in class owltools.graph.OWLGraphEdge
 
getSourceOntology() - Method in class owltools.graph.OWLGraphWrapper
Every OWLGraphWrapper objects wraps zero or one source ontologies.
getSourceOntologyPrefixes() - Method in class owltools.mooncat.Mooncat
E.g.
getStream() - Method in class owltools.io.AbstractClosureReader
 
getStream() - Method in class owltools.io.AbstractClosureRenderer
 
getSubClasses(OWLClassExpression, boolean) - Method in class owltools.reasoner.ExpressionMaterializingReasoner
 
getSubClasses(OWLClassExpression, boolean) - Method in class owltools.reasoner.GraphReasoner
 
getSubClassesNames(OWLClass) - Method in class owltools.graph.OWLGraphWrapper
Deprecated. 
getSubDataProperties(OWLDataProperty, boolean) - Method in class owltools.reasoner.ExpressionMaterializingReasoner
 
getSubDataProperties(OWLDataProperty, boolean) - Method in class owltools.reasoner.GraphReasoner
 
getSubObjectProperties(OWLObjectPropertyExpression, boolean) - Method in class owltools.reasoner.ExpressionMaterializingReasoner
 
getSubObjectProperties(OWLObjectPropertyExpression, boolean) - Method in class owltools.reasoner.GraphReasoner
 
getSubsets(OWLObject) - Method in class owltools.graph.OWLGraphWrapper
It returns the value of the subset tag.
getSubSimMethod() - Method in class owltools.sim.MultiSimilarity
 
getSubsumersFromClosure(OWLObject) - Method in class owltools.graph.OWLGraphWrapper
find the set of classes or class expressions subsuming source, using the graph closure.
getSuperClasses(OWLClassExpression, boolean) - Method in class owltools.reasoner.ExpressionMaterializingReasoner
 
getSuperClasses(OWLClassExpression, boolean) - Method in class owltools.reasoner.GraphReasoner
 
getSuperClassExpressions(OWLClassExpression, boolean) - Method in class owltools.reasoner.ExpressionMaterializingReasoner
note that this is not a standard reasoner method
getSuperClassExpressions(OWLClassExpression, boolean) - Method in class owltools.reasoner.GraphReasoner
note that this is not a standard reasoner method
getSuperClassExpressions(OWLClassExpression, boolean) - Method in interface owltools.reasoner.OWLExtendedReasoner
 
getSuperDataProperties(OWLDataProperty, boolean) - Method in class owltools.reasoner.ExpressionMaterializingReasoner
 
getSuperDataProperties(OWLDataProperty, boolean) - Method in class owltools.reasoner.GraphReasoner
 
getSuperObjectProperties(OWLObjectPropertyExpression, boolean) - Method in class owltools.reasoner.ExpressionMaterializingReasoner
 
getSuperObjectProperties(OWLObjectPropertyExpression, boolean) - Method in class owltools.reasoner.GraphReasoner
 
getSuperPropertiesOf(OWLObjectPropertyExpression) - Method in class owltools.graph.OWLGraphWrapper
returns parent properties of p in all ontologies
getSuperPropertyClosureOf(OWLObjectPropertyExpression) - Method in class owltools.graph.OWLGraphWrapper
 
getSuperPropertyReflexiveClosureOf(OWLObjectPropertyExpression) - Method in class owltools.graph.OWLGraphWrapper
 
getSupportOntologySet() - Method in class owltools.graph.OWLGraphWrapper
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.ExpressionMaterializingReasoner
 
getTopClassNode() - Method in class owltools.reasoner.ExpressionMaterializingReasoner
 
getTopClassNode() - Method in class owltools.reasoner.GraphReasoner
 
getTopDataPropertyNode() - Method in class owltools.reasoner.ExpressionMaterializingReasoner
 
getTopDataPropertyNode() - Method in class owltools.reasoner.GraphReasoner
 
getTopObjectPropertyNode() - Method in class owltools.reasoner.ExpressionMaterializingReasoner
 
getTopObjectPropertyNode() - Method in class owltools.reasoner.GraphReasoner
 
getTruncatedId(OWLEntity) - Method in class owltools.io.OWLPrettyPrinter.LabelProvider
 
getType() - Method in class owltools.graph.shunt.OWLShuntNode
 
getTypes(OWLNamedIndividual, boolean) - Method in class owltools.reasoner.ExpressionMaterializingReasoner
 
getTypes(OWLNamedIndividual, boolean) - Method in class owltools.reasoner.GraphReasoner
 
getUnionSubsumers(OWLObject, OWLObject) - Method in class owltools.sim.SimEngine
 
getUnionSubsumersSize(OWLObject, OWLObject) - Method in class owltools.sim.SimEngine
 
getUnsatisfiableClasses() - Method in class owltools.reasoner.ExpressionMaterializingReasoner
 
getUnsatisfiableClasses() - Method in class owltools.reasoner.GraphReasoner
 
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.ExpressionMaterializingReasoner
 
getXref(OWLObject) - Method in class owltools.graph.OWLGraphWrapper
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
 
graph - Variable in class owltools.io.AbstractClosureRenderer
 
graph - Variable in class owltools.io.TableToAxiomConverter
 
graph - Variable in class owltools.sim.SimEngine
 
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.OWLGraphWrapper.Config
 
graphEdgeIncludeSet - Variable in class owltools.graph.OWLGraphWrapper.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
 
GraphicsConfig.RelationConfig() - Constructor for class owltools.gfx.GraphicsConfig.RelationConfig
 
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.ExpressionMaterializingReasoner
 
handleChanges(Set<OWLAxiom>, Set<OWLAxiom>) - Method in class owltools.reasoner.GraphReasoner
 
handleConflict(OWLEntity, OWLAnnotationProperty, Collection<OWLAnnotationAssertionAxiom>) - Method in interface owltools.mooncat.OntologyMetaDataTools.AnnotationCardinalityConfictHandler
Resolve a conflict for a given annotation property and axioms.
handler - Variable in class owltools.idmap.IDMappingPIRParser
 
hasEdge(OWLShuntEdge) - Method in class owltools.graph.shunt.OWLShuntGraph
Check to see if an edge is in the graph.
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.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.sim.OWLObjectPair
 
hashCode() - Method in class owltools.util.BloomFilter
Calculates a hash code for this class.
hasInformationContent(OWLObject) - Method in class owltools.sim.SimEngine
 
hasNode(OWLShuntNode) - Method in class owltools.graph.shunt.OWLShuntGraph
Check to see if a node is in the graph.
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
 
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
 
ImportClosureSlurper - Class in owltools.io
 
ImportClosureSlurper(OWLOntology) - Constructor for class owltools.io.ImportClosureSlurper
 
includeAllWith(OWLAnnotationProperty, OWLOntology) - Method in class owltools.graph.OWLGraphWrapper.Config
 
includeProperty(OWLObjectProperty) - Method in class owltools.graph.OWLGraphWrapper.Config
 
includeProperty(OWLObjectProperty, OWLQuantifiedProperty.Quantifier) - Method in class owltools.graph.OWLGraphWrapper.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.FactoryDetails - Class in owltools
 
inferredEdgeBySource - Variable in class owltools.graph.OWLGraphWrapper
 
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.ExpressionMaterializingReasoner
 
interrupt() - Method in class owltools.reasoner.GraphReasoner
 
intersection(Collection<E>) - Method in class owltools.util.BloomFilter
 
iriPrefixMap - Variable in class owltools.io.TableToAxiomConverter.Config
 
isAboveMinScore() - Method in class owltools.sim.Similarity
 
isAllValuesFrom() - Method in class owltools.graph.OWLQuantifiedProperty
 
isAssumeOBOStyleIRIs() - Method in class owltools.mooncat.PropertyViewOntologyBuilder
 
isCacheClosure - Variable in class owltools.graph.OWLGraphWrapper.Config
 
isCardinality() - Method in class owltools.graph.OWLQuantifiedProperty
 
isChain - Variable in class owltools.io.ChadoGraphClosureRenderer
 
isClassifyIndividuals() - Method in class owltools.mooncat.PropertyViewOntologyBuilder
 
isConsistent() - Method in class owltools.reasoner.ExpressionMaterializingReasoner
 
isConsistent() - Method in class owltools.reasoner.GraphReasoner
 
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.
isEntailed(OWLAxiom) - Method in class owltools.reasoner.ExpressionMaterializingReasoner
 
isEntailed(Set<? extends OWLAxiom>) - Method in class owltools.reasoner.ExpressionMaterializingReasoner
 
isEntailed(OWLAxiom) - Method in class owltools.reasoner.GraphReasoner
 
isEntailed(Set<? extends OWLAxiom>) - Method in class owltools.reasoner.GraphReasoner
 
isEntailmentCheckingSupported(AxiomType<?>) - Method in class owltools.reasoner.ExpressionMaterializingReasoner
 
isEntailmentCheckingSupported(AxiomType<?>) - Method in class owltools.reasoner.GraphReasoner
 
isEq(Object, Object) - Method in class owltools.graph.OWLGraphEdge
 
isExcludedFromAnalysis(OWLObject) - Method in class owltools.sim.SimEngine
A class is excluded from the analysis if: it is a named entity, and the label for that entity matches the exclude labels list OR: it is a class expression, and the signature contains an excluded class
isExcludeEdge(OWLGraphEdge) - Method in class owltools.graph.OWLGraphWrapper
 
isFilterUnused() - Method in class owltools.mooncat.PropertyViewOntologyBuilder
 
isFollowComplementOfInClosure - Variable in class owltools.graph.OWLGraphWrapper.Config
 
isHasValue() - Method in class owltools.graph.OWLQuantifiedProperty
 
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.OWLGraphWrapper.Config
 
isInferred() - Method in class owltools.graph.OWLQuantifiedProperty
 
isInstanceOf() - Method in class owltools.graph.OWLQuantifiedProperty
 
isInverseOf() - Method in class owltools.graph.OWLQuantifiedProperty
 
isMonitorMemory - Variable in class owltools.graph.OWLGraphWrapper.Config
 
isOboIdentifiers - Variable in class owltools.io.TableToAxiomConverter.Config
 
isObsolete(OWLObject) - Method in class owltools.graph.OWLGraphWrapper
tests if an OWLObject has been declared obsolete in the source ontology
isPrecomputed(InferenceType) - Method in class owltools.reasoner.ExpressionMaterializingReasoner
 
isPrecomputed(InferenceType) - Method in class owltools.reasoner.GraphReasoner
 
isPropertyAssertion() - Method in class owltools.graph.OWLQuantifiedProperty
 
isQuantified() - Method in class owltools.graph.OWLQuantifiedProperty
 
isSatisfiable(OWLClassExpression) - Method in class owltools.reasoner.ExpressionMaterializingReasoner
 
isSatisfiable(OWLClassExpression) - Method in class owltools.reasoner.GraphReasoner
 
isSomeValuesFrom() - Method in class owltools.graph.OWLQuantifiedProperty
 
isSourceNamedObject() - Method in class owltools.graph.OWLGraphEdge
 
isSubClassOf() - Method in class owltools.graph.OWLQuantifiedProperty
 
isSwitchSubjectObject - Variable in class owltools.io.TableToAxiomConverter.Config
 
isTargetNamedObject() - Method in class owltools.graph.OWLGraphEdge
 
isUseOriginalClassIRIs() - Method in class owltools.mooncat.PropertyViewOntologyBuilder
 

J

JaccardBloomSimilarity - Class in owltools.sim
 
JaccardBloomSimilarity() - Constructor for class owltools.sim.JaccardBloomSimilarity
 
JaccardSimilarity - Class in owltools.sim
 
JaccardSimilarity() - Constructor for class owltools.sim.JaccardSimilarity
 

K

key - Variable in class owltools.gfx.GraphStyle
 
keyMargin - Static variable in class owltools.gfx.HierarchyImage
 

L

label - Variable in class owltools.gfx.OWLGraphLayoutNode
 
label - Variable in class owltools.graph.shunt.OWLShuntNode
 
label(OWLObject) - Method in class owltools.sim.SimEngine
 
labelFontName - Variable in class owltools.gfx.GraphStyle
 
labelFontSize - Variable in class owltools.gfx.GraphStyle
 
lcsIntersectionSet - Variable in class owltools.sim.ConjunctiveSetInformationContentRatioSimilarity
 
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
 
logger - Static variable in class owltools.InferenceBuilder
 
logger - Static variable in class owltools.OWLReasonerRunner
 

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.OWLGsonRenderer
 
main(String[]) - Static method in class owltools.OWLReasonerRunner
 
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
 
makeEdge(OWLGraphEdge) - Method in class owltools.gfx.OWLGraphLayoutRenderer
Make a layout edge from a OWLGraphEdge make private?
makeIntersectionPair(OWLClassExpression, OWLClassExpression) - Method in class owltools.sim.SimEngine
 
makeNonRedundant(Set<OWLObject>) - Method in class owltools.sim.SimEngine
An object x is redundant with a set S if: there exists an element y of S, such that ymakeNonRedundant(Set<OWLObject>, boolean) - Method in class owltools.sim.SimEngine
 
makeSubsetOntology(Set<OWLClass>, IRI) - Method in class owltools.mooncat.Mooncat
Given a set of classes (e.g.
makeUnionPair(OWLClassExpression, OWLClassExpression) - Method in class owltools.sim.SimEngine
 
materializeExpressions(OWLOntology) - Method in class owltools.reasoner.ExpressionMaterializingReasoner
 
materializeExpressions() - Method in class owltools.reasoner.ExpressionMaterializingReasoner
 
maxDepthChain - Variable in class owltools.gfx.GraphicsConfig.RelationConfig
 
maxDepthTotal - Variable in class owltools.gfx.GraphicsConfig.RelationConfig
 
maxHits - Variable in class owltools.sim.SimSearch
 
MaximumInformationContentSimilarity - Class in owltools.sim
MaximumInformationContentSimilarity(a,b) = max { IC(LCA_1(a,b)) ...
MaximumInformationContentSimilarity() - Constructor for class owltools.sim.MaximumInformationContentSimilarity
 
mergeImportClosure() - Method in class owltools.graph.OWLGraphWrapper
note: may move to mooncat
mergeImportClosure(boolean) - Method in class owltools.graph.OWLGraphWrapper
 
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.OWLGraphWrapper
Adds all axioms from extOnt into source ontology
mergeOntology(OWLOntology, boolean) - Method in class owltools.graph.OWLGraphWrapper
 
mergeSupportOntology(String, boolean) - Method in class owltools.graph.OWLGraphWrapper
 
mergeSupportOntology(String) - Method in class owltools.graph.OWLGraphWrapper
 
metadata - Variable in class owltools.graph.shunt.OWLShuntNode
 
minIC - Variable in class owltools.sim.SimSearch
 
minimumIC - Variable in class owltools.sim.SimEngine
 
minScore - Variable in class owltools.sim.Similarity
 
minScore - Variable in class owltools.sim.SimSearch
 
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
 
MultiSimilarity - Class in owltools.sim
This is the standard method to use when comparing entities with multiple attributes.
MultiSimilarity() - Constructor for class owltools.sim.MultiSimilarity
 

N

next() - Method in class owltools.idmap.IDMappingPIRParser
 
nl() - Method in class owltools.io.AbstractClosureRenderer
 
nodes - Variable in class owltools.graph.shunt.OWLShuntGraph
 
nonSignificantObjects() - Method in class owltools.sim.SimEngine
 
noQuoteLabels() - Method in class owltools.io.OWLPrettyPrinter
 

O

object_id - Variable in class owltools.graph.shunt.OWLShuntEdge
 
OntologyMetaDataTools - Class in owltools.mooncat
Tools for checking and managing ontology data.
OntologyMetaDataTools() - Constructor for class owltools.mooncat.OntologyMetaDataTools
 
OntologyMetaDataTools.AnnotationCardinalityConfictHandler - Interface in owltools.mooncat
Functor for resolving conflicts for an annotation property and its cardinality constraint.
OntologyMetaDataTools.AnnotationCardinalityException - Exception in owltools.mooncat
Exception indication a non-resolvable conflict for an annotation property and its cardinality constraint.
OntologyMetaDataTools.AnnotationCardinalityException(String, Throwable) - Constructor for exception owltools.mooncat.OntologyMetaDataTools.AnnotationCardinalityException
Create a new Exception.
OntologyMetaDataTools.AnnotationCardinalityException(String) - Constructor for exception owltools.mooncat.OntologyMetaDataTools.AnnotationCardinalityException
Create a new Exception.
OverlapSimilarity - Class in owltools.sim
 
OverlapSimilarity() - Constructor for class owltools.sim.OverlapSimilarity
 
OWLExtendedReasoner - Interface in owltools.reasoner
Extends standard OWL reasoning to allow for querying of ancestor class expressions
OWLGraphEdge - Class in owltools.graph
 
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, OWLOntology) - 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, OWLQuantifiedProperty.Quantifier) - Constructor for class owltools.graph.OWLGraphEdge
 
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
 
OWLGraphLayoutNode.SVGRectangle() - Constructor for class owltools.gfx.OWLGraphLayoutNode.SVGRectangle
 
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
 
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.Config - Class in owltools.graph
Configuration options.
OWLGraphWrapper.Config() - Constructor for class owltools.graph.OWLGraphWrapper.Config
 
OWLGraphWrapper.ISynonym - Interface in owltools.graph
 
OWLGraphWrapper.Synonym - Class in owltools.graph
 
OWLGraphWrapper.Synonym(String, String, String, Set<String>) - Constructor for class owltools.graph.OWLGraphWrapper.Synonym
 
OWLGsonRenderer - Class in owltools.io
 
OWLGsonRenderer(PrintWriter) - Constructor for class owltools.io.OWLGsonRenderer
 
OWLObjectPair - Class in owltools.sim
 
OWLObjectPair(OWLObject, OWLObject) - Constructor for class owltools.sim.OWLObjectPair
 
OWLObjectPair(OWLObject, OWLObject, boolean) - Constructor for class owltools.sim.OWLObjectPair
 
OWLPrettyPrinter - Class in owltools.io
 
OWLPrettyPrinter(OWLGraphWrapper, OWLObjectRenderer) - Constructor for class owltools.io.OWLPrettyPrinter
 
OWLPrettyPrinter(OWLGraphWrapper) - Constructor for class owltools.io.OWLPrettyPrinter
 
OWLPrettyPrinter.LabelProvider - Class in owltools.io
 
OWLPrettyPrinter.LabelProvider(OWLGraphWrapper) - Constructor for class owltools.io.OWLPrettyPrinter.LabelProvider
 
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
 
OWLReasonerRunner - Class in owltools
Adapted from Matthew Horridge's OWLAPI examples by Chris Mungall.
OWLReasonerRunner() - Constructor for class owltools.OWLReasonerRunner
 
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
 
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.
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.diff - package owltools.diff
 
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
 
owltools.idmap - package owltools.idmap
 
owltools.io - package owltools.io
IO - Input/Output
owltools.mooncat - package owltools.mooncat
Mooncat -- Multiple OWL ONtology Catenation
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.sim - package owltools.sim
OWLSim -- Semantic Similarity over OWL ontologies
owltools.util - package owltools.util
 

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.ParserWrapper
 
parse(String) - Method in class owltools.io.TableToAxiomConverter
 
parse(String) - Method in class owltools.phenolog.GenePhenoTsvParser
 
parseOBO(String) - Method in class owltools.io.ParserWrapper
 
parseOBOFiles(List<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.OWLGraphWrapperNameProvider - Class in owltools.io
Provide names for the OBOFormatWriter using an OWLGraphWrapper.
ParserWrapper.OWLGraphWrapperNameProvider(OWLGraphWrapper) - Constructor for class owltools.io.ParserWrapper.OWLGraphWrapperNameProvider
 
ParserWrapper.OWLGraphWrapperNameProvider(OWLGraphWrapper, String) - Constructor for class owltools.io.ParserWrapper.OWLGraphWrapperNameProvider
 
ParserWrapper.OWLGraphWrapperNameProvider(OWLGraphWrapper, OBODoc) - Constructor for class owltools.io.ParserWrapper.OWLGraphWrapperNameProvider
 
parseToOWLGraph(String) - Method in class owltools.io.ParserWrapper
 
parseToOWLGraph(String, boolean) - Method in class owltools.io.ParserWrapper
 
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
 
PHYSICAL_IRI - Static variable in class owltools.OWLReasonerRunner
 
PlaceholderJcelFactory - Class in owltools.reasoner
 
PlaceholderJcelFactory() - Constructor for class owltools.reasoner.PlaceholderJcelFactory
 
polarity - Variable in enum owltools.gfx.RelationType
 
precomputeInferences(InferenceType...) - Method in class owltools.reasoner.ExpressionMaterializingReasoner
 
precomputeInferences(InferenceType...) - Method in class owltools.reasoner.GraphReasoner
 
predicate_id - Variable in class owltools.graph.shunt.OWLShuntEdge
 
prepare() - Method in class owltools.gfx.ImageRender
 
preSimMethod - Variable in class owltools.sim.MultiSimilarity
 
prettyPrinter - Variable in class owltools.io.AbstractClosureRenderer
 
print(OWLObject) - Method in class owltools.io.AbstractClosureRenderer
 
print(String) - Method in class owltools.io.AbstractClosureRenderer
 
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(PrintStream) - Method in class owltools.sim.AvgInformationContentBestMatchesSimilarity
Deprecated.  
print(PrintStream) - Method in class owltools.sim.AvgInformationContentLCSSimilarity
Deprecated.  
print(PrintStream) - Method in class owltools.sim.CombinedJaccardConjunctiveSetSimilarity
 
print(PrintStream) - Method in class owltools.sim.CombinedSimilarity
 
print(PrintStream) - Method in class owltools.sim.CombinedSimilarity2
 
print(PrintStream) - Method in class owltools.sim.ConjunctiveSetInformationContentRatioSimilarity
 
print(PrintStream) - Method in class owltools.sim.ConjunctiveSetSimilarity
 
print(PrintStream) - Method in class owltools.sim.DescriptionTreeSimilarity
 
print(PrintStream) - Method in class owltools.sim.DisjunctiveSetSimilarity
 
print(PrintStream) - Method in class owltools.sim.MultiSimilarity
 
print() - Method in class owltools.sim.Similarity
 
print(PrintStream) - Method in class owltools.sim.Similarity
 
print(PrintStream, OWLObject) - Method in class owltools.sim.Similarity
 
printDescription(PrintStream, OWLObject) - Method in class owltools.sim.Similarity
 
printDescription(PrintStream, OWLObject, int) - Method in class owltools.sim.Similarity
 
printresults(String, ArrayList<Pheno>, double, int) - Static method in class owltools.phenolog.Main
 
printX(PrintStream, OWLObject) - Method in class owltools.sim.DescriptionTreeSimilarity
 
printX(PrintStream, OWLObject, int) - Method in class owltools.sim.DescriptionTreeSimilarity
 
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 - 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.TableToAxiomConverter.Config
 
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(OWLDataFactory, OWLOntologyManager, OWLOntology, OWLOntology, OWLObjectProperty) - Constructor for class owltools.mooncat.PropertyViewOntologyBuilder
 

Q

queryDescendants(OWLGraphEdge) - Method in class owltools.graph.OWLGraphWrapper
Treats an edge as a path and performs a query.
queryDescendants(OWLClassExpression) - Method in class owltools.graph.OWLGraphWrapper
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.OWLGraphWrapper
 
QuerySubsetGenerator - Class in owltools.mooncat
Tools for creating a sub ontology spanning multiple ontologies.
QuerySubsetGenerator() - Constructor for class owltools.mooncat.QuerySubsetGenerator
 
quickScore(Set<OWLObject>, Set<OWLObject>) - Method in class owltools.sim.DescriptionTreeSimilarity
 

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
 
REASONER_ELK - Static variable in class owltools.InferenceBuilder
 
REASONER_HERMIT - Static variable in class owltools.InferenceBuilder
 
REASONER_JCEL - Static variable in class owltools.InferenceBuilder
 
REASONER_PELLET - Static variable in class owltools.InferenceBuilder
 
ReasonerDiff - Class in owltools.diff
 
ReasonerDiff(List<OWLAxiom>, List<OWLAxiom>) - Constructor for class owltools.diff.ReasonerDiff
 
relationConfigMap - Variable in class owltools.gfx.GraphicsConfig
 
relations - Variable in class owltools.gfx.HierarchyImage
 
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.OWLGraphWrapper
 
remakeOntologiesFromImportsClosure(IRI) - Method in class owltools.graph.OWLGraphWrapper
 
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
 
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
 
removeExternalOntologyClasses(boolean) - Method in class owltools.mooncat.Mooncat
Removes all classes that have IAO_0000412 'imported from' set to another ontology.
removeIRIMapper(OWLOntologyIRIMapper) - Method in class owltools.io.ParserWrapper
 
removeSubsetComplementClasses(Set<OWLClass>, boolean) - Method in class owltools.mooncat.Mooncat
Remove all classes *not* in subset.
removeSupportOntology(OWLOntology) - Method in class owltools.graph.OWLGraphWrapper
 
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(OWLGraphEdge) - Method in class owltools.io.GraphClosureRenderer
 
render(OWLGraphWrapper) - Method in interface owltools.io.GraphRenderer
 
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
 
renderDot() - Method in class owltools.gfx.OWLGraphvizRenderer
 
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
 
report() - Method in class owltools.profile.Profiler
 
report(Reporter) - Method in class owltools.sim.AsymmetricJaccardSimilarity
 
report(Reporter) - Method in class owltools.sim.ConjunctiveSetInformationContentRatioSimilarity
 
report(Reporter) - Method in class owltools.sim.JaccardSimilarity
 
report(Reporter) - Method in class owltools.sim.MultiSimilarity
 
report(Object...) - Method in class owltools.sim.Reporter
 
report(Reporter) - Method in class owltools.sim.Similarity
 
Reporter - Class in owltools.sim
 
Reporter(PrintStream, OWLGraphWrapper) - Constructor for class owltools.sim.Reporter
 
Reporter(OWLGraphWrapper) - Constructor for class owltools.sim.Reporter
 
reporter - Variable in class owltools.sim.SimSearch
 
ResonerDiffCommandLine - Class in owltools.diff
Wrapper for ReasonerDiff as command-line tool.
ResonerDiffCommandLine() - Constructor for class owltools.diff.ResonerDiffCommandLine
 
right() - Method in class owltools.gfx.OWLGraphLayoutNode
 
right - Variable in class owltools.gfx.OWLGraphLayoutNode.SVGRectangle
 
rightMargin - Static variable in class owltools.gfx.HierarchyImage
 
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(String, OutputStream) - Method in class owltools.io.ImportClosureSlurper
 
save(String, BufferedWriter) - Method in class owltools.io.ImportClosureSlurper
 
save(String, OWLOntologyFormat, BufferedWriter) - Method in class owltools.io.ImportClosureSlurper
 
saveOWL(OWLOntology, String, OWLGraphWrapper) - Method in class owltools.io.ParserWrapper
 
saveOWL(OWLOntology, OWLOntologyFormat, String, OWLGraphWrapper) - Method in class owltools.io.ParserWrapper
 
saveOWL(OWLOntology, OWLOntologyFormat, OutputStream, OWLGraphWrapper) - Method in class owltools.io.ParserWrapper
 
search(OWLObject) - Method in class owltools.sim.SimSearch
Given a query object (e.g.
selected - Variable in class owltools.gfx.HierarchyImage
 
sep() - Method in class owltools.io.AbstractClosureRenderer
 
serialise() - Method in class owltools.gfx.OWLGraphLayoutNode
 
serialise() - Method in class owltools.gfx.OWLGraphStrokeEdge
 
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.
setCandidates(Set<OWLObject>) - Method in class owltools.sim.SimSearch
 
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(OWLGraphWrapper.Config) - Method in class owltools.graph.OWLGraphWrapper
 
setConfigForFlyMine() - Method in class owltools.phenolog.GenePhenoTsvParser
 
setConfigForMGIPhenoGeno() - Method in class owltools.phenolog.GenePhenoTsvParser
 
setDistance(int) - Method in class owltools.graph.OWLGraphEdge
 
setElementsOntology(OWLOntology) - Method in class owltools.mooncat.PropertyViewOntologyBuilder
 
setFilterUnused(boolean) - Method in class owltools.mooncat.PropertyViewOntologyBuilder
 
setGraph(OWLGraphWrapper) - Method in class owltools.mooncat.Mooncat
 
setGraph(OWLGraphWrapper) - Method in class owltools.sim.SimEngine
 
setGraph(OWLGraphWrapper) - Method in interface owltools.sim.SimilarityCalculator
 
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
 
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
 
setLocation(int, int) - Method in class owltools.gfx.OWLGraphLayoutNode
 
setManager(OWLOntologyManager) - Method in class owltools.io.ParserWrapper
 
setManager(OWLOntologyManager) - Method in class owltools.mooncat.Mooncat
 
setMaxCardinality(Integer) - Method in class owltools.graph.OWLQuantifiedProperty
 
setMaxHits(int) - Method in class owltools.sim.SimSearch
 
setMember1(Individual) - Method in class owltools.phenolog.IndividualPair
 
setMember2(Individual) - Method in class owltools.phenolog.IndividualPair
 
setMetadata(String) - 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
 
setPreSimMethod(String) - Method in class owltools.sim.MultiSimilarity
 
setProfiler(Profiler) - Method in class owltools.graph.OWLGraphWrapper
 
setProperty(OWLObjectProperty) - Method in class owltools.graph.OWLQuantifiedProperty
 
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.OWLGraphWrapper
 
setReasoner(OWLReasoner) - Method in class owltools.InferenceBuilder
 
setReferencedOntologies(Set<OWLOntology>) - Method in class owltools.mooncat.Mooncat
Deprecated. 
setScore(Double) - Method in class owltools.sim.Similarity
 
setScore(int) - Method in class owltools.sim.Similarity
 
setSimEngine(SimEngine) - Method in class owltools.sim.SimSearch
 
setSingleQuantifiedProperty(OWLQuantifiedProperty) - Method in class owltools.graph.OWLGraphEdge
 
setSource(OWLObject) - Method in class owltools.graph.OWLGraphEdge
 
setSourceOntology(OWLOntology) - Method in class owltools.graph.OWLGraphWrapper
 
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.AbstractClosureRenderer
 
setStream(String) - Method in class owltools.io.AbstractClosureRenderer
 
setSubSimMethod(String) - Method in class owltools.sim.MultiSimilarity
 
setSupportOntologySet(Set<OWLOntology>) - Method in class owltools.graph.OWLGraphWrapper
 
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.ExpressionMaterializingReasoner
 
SharedLabelException - Exception in owltools.graph
 
SharedLabelException(String, IRI, IRI) - Constructor for exception owltools.graph.SharedLabelException
 
showMemory() - Static method in class owltools.OWLReasonerRunner
 
SimEngine - Class in owltools.sim
SimEngine provides access to multiple similarity calculation procedures (see Similarity).
SimEngine(OWLGraphWrapper) - Constructor for class owltools.sim.SimEngine
 
simEngine - Variable in class owltools.sim.SimSearch
 
SimEngine.SimilarityAlgorithmException - Exception in owltools.sim
 
SimEngine.SimilarityAlgorithmException(String) - Constructor for exception owltools.sim.SimEngine.SimilarityAlgorithmException
 
Similarity - Class in owltools.sim
Represents a pairwise similarity between two OWLObjects.
Similarity() - Constructor for class owltools.sim.Similarity
 
SimilarityCalculator - Interface in owltools.sim
 
SimSearch - Class in owltools.sim
quick search for best matches
SimSearch(SimEngine) - Constructor for class owltools.sim.SimSearch
 
SimSearch(SimEngine, Reporter) - Constructor for class owltools.sim.SimSearch
 
size() - Method in class owltools.util.BloomFilter
Returns the number of bits in the Bloom filter.
sortMapByScore(Map<OWLObject, Similarity>) - Method in class owltools.sim.MultiSimilarity
 
split(String) - Method in class owltools.idmap.IDMapHandler
 
splitIRI(IRI) - Method in class owltools.sim.Similarity
 
startTaskNotify(String) - Method in class owltools.profile.Profiler
 
stream - Variable in class owltools.io.AbstractClosureReader
 
stream - Variable in class owltools.io.AbstractClosureRenderer
 
subject_id - Variable in class owltools.graph.shunt.OWLShuntEdge
 
subSimMethod - Variable in class owltools.sim.MultiSimilarity
 
subsumes(OWLQuantifiedProperty) - Method in class owltools.graph.OWLQuantifiedProperty
true if this is equal to other.
svgPath - Variable in class owltools.gfx.OWLGraphStrokeEdge.SVGEdge
 

T

t1 - Variable in class owltools.idmap.IDMapPairWriter
 
t2 - Variable in class owltools.idmap.IDMapPairWriter
 
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
TableToAxiomConverter.Config() - Constructor for class owltools.io.TableToAxiomConverter.Config
 
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.
TBoxUnFoldingTool.NonDeterministicUnfoldException(String) - Constructor for exception owltools.TBoxUnFoldingTool.NonDeterministicUnfoldException
 
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.sim.ConjunctiveSetInformationContentRatioSimilarity
 
toString() - Method in class owltools.sim.ConjunctiveSetSimilarity
 
toString() - Method in class owltools.sim.DisjunctiveSetSimilarity
 
toString() - Method in class owltools.sim.MaximumInformationContentSimilarity
 
toString() - Method in class owltools.sim.OWLObjectPair
 
toString() - Method in class owltools.sim.Similarity
 
translateABoxToTBox(OWLOntology) - Method in class owltools.mooncat.PropertyViewOntologyBuilder
generates SubClassOf axioms from ClassAssertion axioms Note that property assertions are currently ignored
translateABoxToTBox() - Method in class owltools.mooncat.PropertyViewOntologyBuilder
 
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)
translateResultsToOWLAxioms(String, OWLNamedIndividual, Set<OWLAxiom>) - Method in class owltools.sim.AsymmetricJaccardSimilarity
 
translateResultsToOWLAxioms(String, OWLNamedIndividual, Set<OWLAxiom>) - Method in class owltools.sim.AvgInformationContentBestMatchesSimilarity
Deprecated.  
translateResultsToOWLAxioms(String, OWLNamedIndividual, Set<OWLAxiom>) - Method in class owltools.sim.AvgInformationContentLCSSimilarity
Deprecated.  
translateResultsToOWLAxioms(String, OWLNamedIndividual, Set<OWLAxiom>) - Method in class owltools.sim.CombinedJaccardConjunctiveSetSimilarity
 
translateResultsToOWLAxioms(String, OWLNamedIndividual, Set<OWLAxiom>) - Method in class owltools.sim.CombinedSimilarity
 
translateResultsToOWLAxioms(String, OWLNamedIndividual, Set<OWLAxiom>) - Method in class owltools.sim.CombinedSimilarity2
 
translateResultsToOWLAxioms(String, OWLNamedIndividual, Set<OWLAxiom>) - Method in class owltools.sim.ConjunctiveSetInformationContentRatioSimilarity
 
translateResultsToOWLAxioms(String, OWLNamedIndividual, Set<OWLAxiom>) - Method in class owltools.sim.ConjunctiveSetSimilarity
 
translateResultsToOWLAxioms(String, OWLNamedIndividual, Set<OWLAxiom>) - Method in class owltools.sim.DescriptionTreeSimilarity
adds additional axioms specific to this method.
translateResultsToOWLAxioms(String, OWLNamedIndividual, Set<OWLAxiom>) - Method in class owltools.sim.DisjunctiveSetSimilarity
 
translateResultsToOWLAxioms(String, OWLNamedIndividual, Set<OWLAxiom>) - Method in class owltools.sim.JaccardBloomSimilarity
 
translateResultsToOWLAxioms(String, OWLNamedIndividual, Set<OWLAxiom>) - Method in class owltools.sim.JaccardSimilarity
 
translateResultsToOWLAxioms(String, OWLNamedIndividual, Set<OWLAxiom>) - Method in class owltools.sim.MaximumInformationContentSimilarity
 
translateResultsToOWLAxioms(String, OWLNamedIndividual, Set<OWLAxiom>) - Method in class owltools.sim.MultiSimilarity
adds additional axioms specific to this method.
translateResultsToOWLAxioms(String, OWLNamedIndividual, Set<OWLAxiom>) - Method in class owltools.sim.OverlapSimilarity
 
translateResultsToOWLAxioms() - Method in class owltools.sim.Similarity
 
translateResultsToOWLAxioms(String, OWLNamedIndividual, Set<OWLAxiom>) - Method in class owltools.sim.Similarity
 
type - Variable in class owltools.graph.shunt.OWLShuntNode
 
typeIxMap - Variable in class owltools.idmap.IDMappingPIRParser
 
typeMap - Variable in class owltools.idmap.IDMapHandler
 

U

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
UniProtIDMapParser - Class in owltools.idmap
 
UniProtIDMapParser() - Constructor for class owltools.idmap.UniProtIDMapParser
 
useImportClosureForQueries() - Method in class owltools.graph.OWLGraphWrapper
Deprecated. 

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.
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.

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
 

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