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.
addAllObjects() - Method in class owltools.gfx.OWLGraphLayoutRenderer
Adds all objects from the OGW into the rendered graph CAUTION: do this only for small ontologies
addEdge(OWLGraphEdge) - Method in class owltools.gfx.OWLGraphLayoutRenderer
Adds 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. 
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
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
 
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
 
buildViewOntology(IRI, IRI) - Method in class owltools.mooncat.PropertyViewOntologyBuilder
 

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
 
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
 
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
 
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
 
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
score is the IC of the intersection of all attributes; it's recommended this used as a sub-method of a MultiSimilarity check
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
 
createSubOntologyFromDLQuery(String, OWLGraphWrapper, OWLGraphWrapper, OWLReasonerFactory) - Method in class owltools.mooncat.QuerySubsetGenerator
Create a new sub ontology from a given DL query and source ontology.
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.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

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
Create an ontology with EL as description logic profile.
equals(Object) - Method in class owltools.graph.OWLGraphEdge
 
equals(Object) - Method in class owltools.graph.OWLQuantifiedProperty
 
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.
excludeClassesInComparison - Variable in class owltools.sim.SimEngine
 
excludeMetaClass - Variable in class owltools.graph.OWLGraphWrapper.Config
 
excludeProperty(OWLObjectProperty) - Method in class owltools.graph.OWLGraphWrapper.Config
Deprecated. 
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
 
ExpressionMaterializingReasoner(OWLOntology, OWLReasonerConfiguration, BufferingMode) - Constructor for class owltools.reasoner.ExpressionMaterializingReasoner
 
ExpressionMaterializingReasoner(OWLOntology) - Constructor for class owltools.reasoner.ExpressionMaterializingReasoner
 

F

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
 
fontName - Variable in class owltools.gfx.GraphStyle
 
fontSize - Variable in class owltools.gfx.GraphStyle
 
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
getAnyLabel(OWLEntity) - Method in class owltools.mooncat.PropertyViewOntologyBuilder
 
getAssertedViewOntology() - Method in class owltools.mooncat.PropertyViewOntologyBuilder
 
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
 
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
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
 
getDomain(OWLObjectProperty) - Method in class owltools.graph.OWLGraphWrapper
It returns the value of the domain tag
getEdgesBetween(OWLObject, OWLObject) - Method in class owltools.graph.OWLGraphWrapper
 
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.
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.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) - 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
 
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
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.
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.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
 
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
 
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
 
getMinCardinality() - Method in class owltools.graph.OWLQuantifiedProperty
 
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"
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 array of synonyms as encoded by OBO2OWL.
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.
getOutgoingEdgesClosureReflexive(OWLObject) - Method in class owltools.graph.OWLGraphWrapper
as getOutgoingEdgesClosure(s), but also includes an identity edge
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
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)
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
 
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
 
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
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
 
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
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
 
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
 
getViewRootClass() - Method in class owltools.mooncat.PropertyViewOntologyBuilder
 
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
 
GraphStyle(Map<String, String>) - Constructor for class owltools.gfx.GraphStyle
 

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
 
hashCode() - Method in class owltools.graph.OWLGraphEdge
 
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
 
hasProperty() - Method in class owltools.graph.OWLQuantifiedProperty
 
height - Variable in class owltools.gfx.GraphStyle
 
height - Variable in class owltools.gfx.OWLGraphLayoutNode
 
hideIds() - Method in class owltools.io.OWLPrettyPrinter
 

I

id - Variable in class owltools.gfx.OWLGraphLayoutNode
 
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
 
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
 
inferredEdgeBySource - Variable in class owltools.graph.OWLGraphWrapper
 
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
 
isCacheClosure - Variable in class owltools.graph.OWLGraphWrapper.Config
 
isCardinality() - Method in class owltools.graph.OWLQuantifiedProperty
 
isChain - Variable in class owltools.io.ChadoGraphClosureRenderer
 
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
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
 

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
 

L

label - Variable in class owltools.gfx.OWLGraphLayoutNode
 
label(OWLObject) - Method in class owltools.sim.SimEngine
 
lcsIntersectionSet - Variable in class owltools.sim.ConjunctiveSetInformationContentRatioSimilarity
 
left() - Method in class owltools.gfx.OWLGraphLayoutNode
 
left - Variable in class owltools.gfx.OWLGraphLayoutNode.SVGRectangle
 
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.gfx.GraphStyle
 
main(String[]) - Static method in class owltools.gfx.SampleGraphDraw
 
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
 
makeViewClassIRI(OWLClass) - Method in class owltools.mooncat.PropertyViewOntologyBuilder
 
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() - Constructor for class owltools.sim.MaximumInformationContentSimilarity
 
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
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
 
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
 
nonSignificantObjects() - Method in class owltools.sim.SimEngine
 

O

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
 
OWLGraphStrokeEdge - Class in owltools.gfx
Represents an edge in a layour graph Adapted from QuickGO
OWLGraphStrokeEdge(OWLGraphLayoutNode, OWLGraphLayoutNode, OWLGraphEdge) - 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
 
owlObject - Variable in class owltools.gfx.OWLGraphLayoutNode
 
owlObject - Variable in class owltools.gfx.OWLGraphLayoutNode.SVGRectangle
 
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) - 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
 
owltools - package owltools
OWLTools - an OWL API wrapper
owltools.gfx - package owltools.gfx
GFX - OWL Graphics and Visualization
owltools.graph - package owltools.graph
OWLGraph -- OBO-like Graph Wrapper for OWL Ontologies
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
 
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
 
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
 
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
 
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
 
relationConfigMap - Variable in class owltools.gfx.GraphicsConfig
 
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
 
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
 
removeExternalOntologyClasses(boolean) - Method in class owltools.mooncat.Mooncat
 
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.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(OWLGraphWrapper) - Method in class owltools.io.CompactGraphClosureRenderer
 
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
 
right() - Method in class owltools.gfx.OWLGraphLayoutNode
 
right - Variable in class owltools.gfx.OWLGraphLayoutNode.SVGRectangle
 
rowToAxioms(String[]) - Method in class owltools.io.TableToAxiomConverter
 

S

SampleGraphDraw - Class in owltools.gfx
Draw an example graph.
SampleGraphDraw() - Constructor for class owltools.gfx.SampleGraphDraw
 
saveOWL(OWLOntology, String) - Method in class owltools.io.ParserWrapper
 
saveOWL(OWLOntology, OWLOntologyFormat, String) - Method in class owltools.io.ParserWrapper
 
saveOWL(OWLOntology, OWLOntologyFormat, OutputStream) - Method in class owltools.io.ParserWrapper
 
search(OWLObject) - Method in class owltools.sim.SimSearch
Given a query object (e.g.
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
 
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
 
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
 
setDataFactory(OWLDataFactory) - Method in class owltools.graph.OWLGraphWrapper
 
setDistance(int) - Method in class owltools.graph.OWLGraphEdge
 
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.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.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.graph.OWLGraphWrapper
 
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
 
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. 
setRelationType() - Method in class owltools.gfx.OWLGraphStrokeEdge
Sets the value of relType based on OWLGraphEdge properties TODO : this is too hacky.
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
 
setViewEntities(Set<OWLEntity>) - Method in class owltools.mooncat.PropertyViewOntologyBuilder
 
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.
slimColours - Variable in class owltools.gfx.GraphStyle
 
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
 
subSimMethod - Variable in class owltools.sim.MultiSimilarity
 
subsumes(OWLQuantifiedProperty) - Method in class owltools.graph.OWLQuantifiedProperty
 
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
 
termIds - Variable in class owltools.gfx.GraphStyle
 
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
 
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
 
typeIxMap - Variable in class owltools.idmap.IDMappingPIRParser
 
typeMap - Variable in class owltools.idmap.IDMapHandler
 

U

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.OWLGraphLayoutNode
 

X

x - Variable in class owltools.gfx.OWLGraphLayoutNode
 

Y

y - Variable in class owltools.gfx.OWLGraphLayoutNode
 

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