Index (OWLTools-Parent 0.2.2-SNAPSHOT API)

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

a - Variable in class owltools.sim2.io.SimResultRenderer.AttributesSimScores
ABNORMAL - Variable in class owltools.sim2.preprocessor.PhenoSimHQEPreProcessor
aboutCommand() - Method in class owltools.web.OWLHandler: information about an ontology object (class, property, individual)
ABoxUtils - Class in owltools.sim2.preprocessor
ABoxUtils() - Constructor for class owltools.sim2.preprocessor.ABoxUtils
AbstractAnnotationPredictor - Class in owltools.gaf.inference
AbstractAnnotationPredictor(GafDocument, OWLGraphWrapper) - Constructor for class owltools.gaf.inference.AbstractAnnotationPredictor
AbstractAnnotationRule - Class in owltools.gaf.rules
AbstractAnnotationRule() - Constructor for class owltools.gaf.rules.AbstractAnnotationRule
AbstractCheck - Class in owltools.ontologyverification.impl: Helper to reduce boiler plate code for an OntologyCheck.
AbstractCheck(String, String, boolean, OntologyCheckRunner.TimePoint) - Constructor for class owltools.ontologyverification.impl.AbstractCheck
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
AbstractGafWriter - Class in owltools.gaf.io: General utility to write a GafDocument or GeneAnnotation.
AbstractGafWriter() - Constructor for class owltools.gaf.io.AbstractGafWriter
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
AbstractOBOSimPreProcessor - Class in owltools.sim2.preprocessor
AbstractOBOSimPreProcessor() - Constructor for class owltools.sim2.preprocessor.AbstractOBOSimPreProcessor
AbstractOwlSim - Class in owltools.sim2
AbstractOwlSim() - Constructor for class owltools.sim2.AbstractOwlSim
AbstractRenderer - Class in owltools.io: Renders the graph closure - i.e.
AbstractRenderer(PrintStream) - Constructor for class owltools.io.AbstractRenderer
AbstractRenderer(String) - Constructor for class owltools.io.AbstractRenderer
AbstractRenderer - Class in owltools.sim2.io
AbstractRenderer() - Constructor for class owltools.sim2.io.AbstractRenderer
AbstractRetrieveGolr - Class in org.bbop.golr.java
AbstractRetrieveGolr(String) - Constructor for class org.bbop.golr.java.AbstractRetrieveGolr
AbstractRetrieveGolr(String, int) - Constructor for class org.bbop.golr.java.AbstractRetrieveGolr
AbstractSimPreProcessor - Class in owltools.sim2.preprocessor
AbstractSimPreProcessor() - Constructor for class owltools.sim2.preprocessor.AbstractSimPreProcessor
AbstractSolrLoader - Class in owltools.solrj: Root class for loading ontologies or ontology-related data into a Solr instance using web services and the solrj library
AbstractSolrLoader(SolrServer) - Constructor for class owltools.solrj.AbstractSolrLoader
AbstractSolrLoader(String) - Constructor for class owltools.solrj.AbstractSolrLoader
AbstractTarjan<NODE> - Class in owltools.util: Basic implementation for the Tarjan algorithm.
AbstractTarjan(boolean) - Constructor for class owltools.util.AbstractTarjan
AbstractXmlWriter - Class in owltools.gaf.io: Helper to write properly formated XML using an XMLStreamWriter.
AbstractXmlWriter(String) - Constructor for class owltools.gaf.io.AbstractXmlWriter
accept(String, int, T) - Method in interface owltools.gaf.parser.LineFilter: Given a line in a annotation file, decide whether to load the line.
add(FlexLine) - Method in class owltools.flex.FlexDocument: Add a line to the document.
add(boolean, OWLClass, OWLClass) - Method in class owltools.gaf.inference.ClassTaxonMatrix
add(Bioentity) - Method in class owltools.gaf.io.OpenAnnotationRDFWriter: Adds a single Bioentity to a model
add(GeneAnnotation) - Method in class owltools.gaf.io.OpenAnnotationRDFWriter: Adds a single GeneAnnotation to a model
add(OWLOntology, OWLAxiom) - Method in class owltools.graph.CardinalityContraintsTools.CardinalityReporter
add(OWLGraphEdge) - Method in class owltools.graph.OWLGraphEdge.OWLGraphEdgeSet: Try to add edge to this OWLGraphEdgeSet, or, if it already contains an equal OWLGraphEdge, merges their underlying OWLAxioms (as returned by their getOWLAxioms methods).
add(SolrInputDocument) - Method in class owltools.solrj.AbstractSolrLoader
add(E) - Method in class owltools.util.BloomFilter: Adds an object to the Bloom filter.
add(String) - Method in class owltools.yaml.golrconfig.ConfigManager: Work with a flexible document definition from a configuration file.
addAll(Collection<? extends OWLGraphEdge>) - Method in class owltools.graph.OWLGraphEdge.OWLGraphEdgeSet: Try to add or merge each element of edges into this OWLGraphEdgeSet, as performed by the method OWLGraphEdge.OWLGraphEdgeSet.add(OWLGraphEdge).
addAll(Collection<SolrInputDocument>) - Method in class owltools.solrj.AbstractSolrLoader
addAll(Collection<? extends E>) - Method in class owltools.util.BloomFilter: Adds all elements from a Collection to the Bloom filter.
addAllAndCommit() - Method in class owltools.solrj.AbstractSolrLoader
addAllClasses() - Method in class owltools.gfx.OWLGraphLayoutRenderer: Adds all classes from the OGW into the rendered graph CAUTION: do this only for small ontologies
addAllObjects() - Method in class owltools.gfx.OWLGraphLayoutRenderer: Adds all objects from the OGW into the rendered graph.
addAltId(OWLOntology, String, String, OWLAnnotationProperty) - Static method in class owltools.ncbi.NCBIOWL: Add an alternative identifier for a main term.
addAnnotation(PropertyStubLD, Object) - Method in interface owltools.frame.Frame
addAnnotation(PropertyStubLD, Object) - Method in class owltools.frame.jsonld.FrameLD
addAnnotation(GeneAnnotation) - Method in class owltools.gaf.Bioentity
addAssociatedGeneProduct(String, String) - Method in class owltools.panther.PANTHERTree: Add an associated id/label for a term in this tree.
addAttributeClass(OWLClassExpression) - Method in class owltools.sim.OldSimpleOwlSim.ScoreAttributesPair
addAttributeClass(OWLClass) - Method in class owltools.sim2.OwlSim.ScoreAttributeSetPair: Adds am attribute to set (first creating empty set if not already present)
addAttributeIC(double) - Method in class owltools.sim2.SimStats
addAxioms(Set<OWLAxiom>) - Method in class owltools.gaf.owl.GAFOWLBridge
addAxiomsToOutput(Set<OWLAxiom>, boolean) - Method in class owltools.sim2.preprocessor.AbstractSimPreProcessor
addAxiomToOutput(OWLAxiom, boolean) - Method in class owltools.sim2.preprocessor.AbstractSimPreProcessor
addBioentity(Bioentity) - Method in class owltools.gaf.BioentityDocument: Add a Bioentity object to the document.
addBioentity(Bioentity) - Method in class owltools.gaf.GafDocument: Add a Bioentity object to the document.
addBridgeOntology(String) - Method in class owltools.ontologyrelease.OortConfiguration
addClassFrame(ClassFrame) - Method in class owltools.frame.jsonld.OntologyFrameLD
addClassFrame(ClassFrame) - Method in interface owltools.frame.OntologyFrame
addCombo(String, Set<String>) - Method in class owltools.mooncat.BridgeExtractor
addComment(String) - Method in class owltools.gaf.BioentityDocument: Add a comment line.
addComment(String) - Method in class owltools.gaf.GafDocument: Add a comment line.
addCommentListener(CommentListener) - Method in class owltools.gaf.parser.GAFParser
addDbXref(String) - Method in class owltools.gaf.Bioentity
addDirectDescendentsToShuntGraph(OWLObject, OWLShuntGraph, List<String>) - Method in class owltools.graph.OWLGraphWrapperEdgesAdvanced: Add a set of edges, as descendants to x in OWLShuntGraph g.
addEdge(OWLGraphEdge) - Method in class owltools.gfx.OWLGraphLayoutRenderer: Adds an edge to the graph.
addEdge(OWLGraphEdge) - Method in class owltools.graph.OWLGraphManipulator: Add edge to its related ontology.
addEdge(OWLShuntEdge) - Method in class owltools.graph.shunt.OWLShuntGraph: Simply "add" an edge to the graph.
addEdges(Set<OWLGraphEdge>) - Method in class owltools.graph.OWLGraphManipulator: Add edges to their related ontology.
addElementLabels(OWLOntology, String) - Static method in class owltools.sim2.OwlSimUtil
addElementLabels(OWLOntology, File) - Static method in class owltools.sim2.OwlSimUtil
addElementToAttributeAssociationsFromFile(OWLOntology, File) - Static method in class owltools.sim2.OwlSimUtil
addExperimentalInferences(List<Prediction>) - Method in class owltools.gaf.rules.AnnotationRulesEngine.AnnotationRulesEngineResult
addFieldUnique(SolrInputDocument, String, String) - Method in class owltools.solrj.AbstractSolrLoader
addFilter(LineFilter<GAFParser>) - Method in class owltools.gaf.parser.GafObjectsBuilder: Add a filter to object builder.
addFilter(InferenceBuilder.OWLClassFilter) - Method in class owltools.InferenceBuilder
addGafDocument(GafDocument) - Method in class owltools.gaf.godb.Dumper
addGeneAnnotation(GeneAnnotation) - Method in class owltools.gaf.GafDocument: Add a single annotation to the document.
addGpadFilter(LineFilter<GpadParser>) - Method in class owltools.gaf.parser.GpadGpiObjectsBuilder
addGpiFilter(LineFilter<GpiParser>) - Method in class owltools.gaf.parser.GpadGpiObjectsBuilder
addHeaderInfo(GafDocument) - Method in class owltools.gaf.io.OpenAnnotationRDFWriter: Adds header info from a GAF, use the comments from the GafDocument.
addIgnoreSubClassesOf(OWLClass) - Method in class owltools.sim.OldSimpleOwlSim
addIgnoreSubClassesOf(IRI) - Method in class owltools.sim.OldSimpleOwlSim
addIgnoreSubClassesOf(OWLClass) - Method in class owltools.sim2.SimpleOwlSim: e.g.
addIgnoreSubClassesOf(IRI) - Method in class owltools.sim2.SimpleOwlSim
addImport(OWLOntology) - Method in class owltools.graph.OWLGraphWrapperBasic: adds an imports declaration between the source ontology and extOnt
addImport(String) - Method in class owltools.mooncat.Mooncat: Deprecated.
addImportsFromSupportOntologies() - Method in class owltools.graph.OWLGraphWrapperBasic
addIndividualIC(double) - Method in class owltools.sim2.SimStats
addInferences(List<Prediction>) - Method in class owltools.gaf.rules.AnnotationRulesEngine.AnnotationRulesEngineResult
addIRIMapper(OWLOntologyIRIMapper) - Method in class owltools.io.ParserWrapper
addIRIMappers(List<OWLOntologyIRIMapper>) - Method in class owltools.io.ParserWrapper
addIssueListener(IssueListener) - Method in class owltools.gaf.parser.GpadGpiObjectsBuilder
addLabelField(SolrInputDocument, String, String) - Method in class owltools.solrj.AbstractSolrLoader: Resolve the list of id to a label and add it to the doc.
addLabelFields(SolrInputDocument, String, List<String>) - Method in class owltools.solrj.AbstractSolrLoader: Resolve the list of ids to labels and add them to the doc.
addListener(QuestForOrthologsSeqXMLParser.ProteinListener) - Method in class owltools.gaf.bioentities.QuestForOrthologsSeqXMLParser: Add a QuestForOrthologsSeqXMLParser.ProteinListener.
addListener(QuestForOrthologsSeqXMLParser.MoreInfoProteinListener) - Method in class owltools.gaf.bioentities.QuestForOrthologsSeqXMLParser: Add a QuestForOrthologsSeqXMLParser.MoreInfoProteinListener.
addNode(OWLShuntNode) - Method in class owltools.graph.shunt.OWLShuntGraph: Simply "add" a node to the graph.
addObject(OWLObject) - Method in class owltools.gfx.OWLGraphLayoutRenderer: Adds an object to the graph to be rendered This will also add all ancestors of the focusObj, and all direct edges from each ancestor
addObjects(Set<OWLObject>) - Method in class owltools.gfx.OWLGraphLayoutRenderer
addParserListener(ParserListener) - Method in class owltools.gaf.parser.GAFParser
addPath(String) - Method in class owltools.ontologyrelease.OortConfiguration
addProblem(String) - Method in class owltools.gaf.godb.Dumper
addPropertiesForMaterialization(Iterable<OWLObjectProperty>) - Method in class owltools.graph.OWLGraphWrapperEdgesAdvanced
addProperty(String, String) - Method in class owltools.gaf.Bioentity
addProperty(String, String) - Method in class owltools.gaf.GeneAnnotation
addPropertyChain(String, String, String) - Method in class owltools.sim2.preprocessor.AbstractOBOSimPreProcessor
addPropertyForMaterialization(OWLObjectProperty) - Method in class owltools.graph.OWLGraphWrapperEdgesAdvanced
addPropertyIdsForMaterialization(Iterable<String>) - Method in class owltools.graph.OWLGraphWrapperEdgesAdvanced
addQueryOntology(OWLOntology) - Method in class owltools.graph.OWLGraphWrapper: Deprecated.
addReferencedOntology(OWLOntology) - Method in class owltools.mooncat.Mooncat
addReferenceId(String) - Method in class owltools.gaf.GeneAnnotation
addReferenceIds(Collection<String>) - Method in class owltools.gaf.GeneAnnotation
addResultsToOWLOntology(OWLOntology) - Method in class owltools.sim.Similarity: translates similarity results into OWL Axioms and saves axioms into an OWL Ontology
addRewriteIRIMap(IRI, IRI) - Method in class owltools.ontologyrelease.OortConfiguration: Adds entry to rewrite map
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.
addSourceOntologyPrefix(String) - Method in class owltools.ontologyrelease.OortConfiguration
addSourceViewProperty(OWLObjectProperty) - Method in class owltools.sim.OldSimpleOwlSim: Deprecated.
addSourceViewProperty(IRI) - Method in class owltools.sim.OldSimpleOwlSim
addSpeciesLabel(String) - Method in class owltools.gaf.Bioentity
addStepwiseAncestorsToShuntGraph(OWLObject, OWLShuntGraph, List<String>) - Method in class owltools.graph.OWLGraphWrapperEdgesAdvanced: Add a set of edges, as ancestors to x in OWLShuntGraph g.
addSupportOntologiesFromImportsClosure() - Method in class owltools.graph.OWLGraphWrapperBasic: Each ontology in the import closure of the source ontology is added to the list of support ontologies
addSupportOntologiesFromImportsClosure(boolean) - Method in class owltools.graph.OWLGraphWrapperBasic: Each ontology in the import closure of the source ontology (and the import closure of each existing support ontology, if doForAllSupportOntologies is true) is added to the list of support ontologies
addSupportOntology(OWLOntology) - Method in class owltools.graph.OWLGraphWrapperBasic
addSynonym(String) - Method in class owltools.gaf.Bioentity
addToServer(Collection<SolrInputDocument>) - Method in class owltools.solrj.AbstractSolrLoader
addToSkipFormatSet(String) - Method in class owltools.ontologyrelease.OortConfiguration
addTransitiveAncestorsToShuntGraph(OWLObject, OWLShuntGraph, List<String>) - Method in class owltools.graph.OWLGraphWrapperEdgesAdvanced: Add a set of edges, as ancestors to x in OWLShuntGraph g.
addValues(String, Collection<String>) - Static method in class owltools.ontologyrelease.OortConfiguration: Only public for testing purposes.
addViewEntities(Set<OWLEntity>) - Method in class owltools.mooncat.PropertyViewOntologyBuilder
addViewMapping(OWLClass, OWLObjectProperty, OWLClass) - Method in class owltools.sim2.preprocessor.AbstractSimPreProcessor
addViewProperty(OWLObjectProperty) - Method in class owltools.sim.OldSimpleOwlSim: Deprecated.
addViewProperty(IRI) - Method in class owltools.sim.OldSimpleOwlSim: Deprecated.
addViolations(Iterable<AnnotationRuleViolation>) - Method in class owltools.gaf.rules.AnnotationRulesEngine.AnnotationRulesEngineResult
Adjacency<T> - Interface in owltools.util: Representation of a graph (i.e.
afterLoading(OWLGraphWrapper) - Method in class owltools.ontologyverification.OntologyCheckHandler: Run tests for the ontology after loading it.
afterMireot(OWLGraphWrapper) - Method in class owltools.ontologyverification.OntologyCheckHandler: Run tests for the ontology after mireoting.
afterReasoning(OWLGraphWrapper) - Method in class owltools.ontologyverification.OntologyCheckHandler: Run tests for the ontology after reasoning.
aggregate - Variable in class owltools.sim2.OwlSim.StatsPerIndividual
allClassIC(Opts) - Method in class owltools.cli.SimCommandRunner
allowFileOverwrite(File) - Method in class owltools.ontologyrelease.OboOntologyReleaseRunner: Hook method to handle an unexpected file overwrite request.
allSubClassOfCommand() - Method in class owltools.web.OWLHandler: Params: direct
allTypesDirectCount - Variable in class owltools.sim2.OwlSimMetadata
allTypesInferredCount - Variable in class owltools.sim2.OwlSimMetadata
alternativeCode - Variable in enum owltools.gfx.RelationType
AltIdInSignature - Class in owltools.ontologyverification.impl
AltIdInSignature() - Constructor for class owltools.ontologyverification.impl.AltIdInSignature
analysisRelation - Variable in class owltools.sim2.preprocessor.PropertyViewSimPreProcessor
analysisStats - Variable in class owltools.sim2.SimStats
annotate(OWLOntology, OWLEntity, OWLAnnotationProperty, OWLAnnotationValue) - Static method in class owltools.ncbi.OWLConverter: Convenience method for adding an annotation assertion to the ontology.
annotate(OWLOntology, OWLEntity, String, OWLAnnotationValue) - Static method in class owltools.ncbi.OWLConverter: Convenience method for adding an annotation assertion to the ontology, taking a CURIE for the property.
annotate(OWLOntology, OWLEntity, String, String) - Static method in class owltools.ncbi.OWLConverter: Convenience method for adding an annotation assertion to the ontology, taking a CURIE for the property and a string literal.
annotate(OWLOntology, OWLEntity, String, boolean) - Static method in class owltools.ncbi.OWLConverter: Convenience method for adding an annotation assertion to the ontology, taking a CURIE for the property and an Boolean literal.
annotate(OWLOntology, String, IRI) - Static method in class owltools.ncbi.OWLConverter: Convenience method for adding an annotation assertion to the ontology itself, taking a CURIE for the property and an Boolean literal.
annotate(OWLOntology, String, String) - Static method in class owltools.ncbi.OWLConverter: Convenience method for adding an annotation assertion to the ontology itself, taking a CURIE for the property and an Boolean literal.
annotatedEntityCount - Variable in class owltools.gaf.metadata.AnnotationDocumentMetadata
Annotation - Interface in owltools.frame
ANNOTATION_IRI_IS_INFERRED - Static variable in class owltools.graph.AxiomAnnotationTools: IRI for the default annotation marking an axiom as inferred.
ANNOTATION_XP - Static variable in class owltools.gaf.parser.GAFParser
annotationCount - Variable in class owltools.gaf.metadata.AnnotationDocumentMetadata
annotationCountExcludingIEA - Variable in class owltools.gaf.metadata.AnnotationDocumentMetadata
AnnotationDocumentMetadata - Class in owltools.gaf.metadata
AnnotationDocumentMetadata() - Constructor for class owltools.gaf.metadata.AnnotationDocumentMetadata
AnnotationExtensionFolder - Class in owltools.gaf.owl
AnnotationExtensionFolder(OWLGraphWrapper) - Constructor for class owltools.gaf.owl.AnnotationExtensionFolder
AnnotationExtensionUnfolder - Class in owltools.gaf.owl
AnnotationExtensionUnfolder(OWLGraphWrapper) - Constructor for class owltools.gaf.owl.AnnotationExtensionUnfolder
annotationIRI(String) - Method in class owltools.sim.Similarity
AnnotationLD - Class in owltools.frame.jsonld
AnnotationLD() - Constructor for class owltools.frame.jsonld.AnnotationLD
AnnotationLD(PropertyStubLD, Object) - Constructor for class owltools.frame.jsonld.AnnotationLD
AnnotationPredictor - Interface in owltools.gaf.inference: given a bioentity, predict a set of annotations
AnnotationRegularExpressionFromXMLRule - Class in owltools.gaf.rules: This class implements execution of the regular expression rules.
AnnotationRegularExpressionFromXMLRule() - Constructor for class owltools.gaf.rules.AnnotationRegularExpressionFromXMLRule
AnnotationRule - Interface in owltools.gaf.rules
AnnotationRulesEngine - Class in owltools.gaf.rules
AnnotationRulesEngine(AnnotationRulesFactory, boolean, boolean) - Constructor for class owltools.gaf.rules.AnnotationRulesEngine
AnnotationRulesEngine.AnnotationRuleCheckException - Exception in owltools.gaf.rules: This exception is thrown when an exception occurs during the execution of annotation rules.
AnnotationRulesEngine.AnnotationRuleCheckException() - Constructor for exception owltools.gaf.rules.AnnotationRulesEngine.AnnotationRuleCheckException
AnnotationRulesEngine.AnnotationRuleCheckException(String) - Constructor for exception owltools.gaf.rules.AnnotationRulesEngine.AnnotationRuleCheckException
AnnotationRulesEngine.AnnotationRuleCheckException(Throwable) - Constructor for exception owltools.gaf.rules.AnnotationRulesEngine.AnnotationRuleCheckException
AnnotationRulesEngine.AnnotationRuleCheckException(String, Throwable) - Constructor for exception owltools.gaf.rules.AnnotationRulesEngine.AnnotationRuleCheckException
AnnotationRulesEngine.AnnotationRulesEngineResult - Class in owltools.gaf.rules: Results for a run of the AnnotationRulesEngine.
AnnotationRulesEngine.AnnotationRulesEngineResult() - Constructor for class owltools.gaf.rules.AnnotationRulesEngine.AnnotationRulesEngineResult
AnnotationRulesFactory - Interface in owltools.gaf.rules
AnnotationRulesFactoryImpl - Class in owltools.gaf.rules: This class reads the annotation_qc.xml file and builds AnnotationRule objects from the qc file.
AnnotationRulesFactoryImpl(String, OWLGraphWrapper) - Constructor for class owltools.gaf.rules.AnnotationRulesFactoryImpl
AnnotationRulesReportWriter - Class in owltools.gaf.rules: Write reports for the results of annotations validation and prediction.
AnnotationRulesReportWriter(String, String, String, String, String, String) - Constructor for class owltools.gaf.rules.AnnotationRulesReportWriter
AnnotationRulesReportWriter(File, File, File, File, File, File) - Constructor for class owltools.gaf.rules.AnnotationRulesReportWriter
AnnotationRulesReportWriter(PrintWriter, PrintWriter, PrintStream, PrintWriter, PrintStream, PrintWriter) - Constructor for class owltools.gaf.rules.AnnotationRulesReportWriter
AnnotationRuleViolation - Class in owltools.gaf.rules: Data associated with a rule violation
AnnotationRuleViolation(String, String) - Constructor for class owltools.gaf.rules.AnnotationRuleViolation: Create a simple violation from with a given message.
AnnotationRuleViolation(String, String, GeneAnnotation) - Constructor for class owltools.gaf.rules.AnnotationRuleViolation: Create a violation object with a message and a the corresponding source annotation.
AnnotationRuleViolation(String, String, GeneAnnotation, AnnotationRuleViolation.ViolationType) - Constructor for class owltools.gaf.rules.AnnotationRuleViolation: Create a violation object with a message and a the corresponding source annotation.
AnnotationRuleViolation(String, String, String) - Constructor for class owltools.gaf.rules.AnnotationRuleViolation: Create a violation object with a message and a the corresponding annotation row.
AnnotationRuleViolation(String, String, String, AnnotationRuleViolation.ViolationType) - Constructor for class owltools.gaf.rules.AnnotationRuleViolation: Create a violation object with a message and a the corresponding annotation row and AnnotationRuleViolation.ViolationType.
AnnotationRuleViolation.ViolationType - Enum in owltools.gaf.rules
AnnotationSource - Class in owltools.gaf
AnnotationSource(String, int, String) - Constructor for class owltools.gaf.AnnotationSource
AnnotationTaxonRule - Class in owltools.gaf.rules: Checks if an annotation is valid according to taxon constraints.
AnnotationTaxonRule(OWLGraphWrapper) - Constructor for class owltools.gaf.rules.AnnotationTaxonRule
appendLine(CharSequence) - Method in class org.geneontology.lego.dot.LegoDotWriter: Deprecated.

Write a line to the file.
appendLine(CharSequence) - Method in class owltools.mooncat.ontologymetadata.ImportChainDotWriter
aScore - Variable in class owltools.sim.MultiSimilarity
ASPECT - Static variable in class owltools.gaf.parser.GAFParser
assertAboxInferences(Opts) - Method in class owltools.cli.CommandRunner
assertAllInferences(OWLGraphWrapper, String) - Static method in class owltools.cli.AssertInferenceTool
assertEnabledByCommand() - Method in class owltools.web.OWLHandler
assertFactCommand() - Method in class owltools.web.OWLHandler: Deprecated.
assertInferences(OWLGraphWrapper, boolean, boolean, boolean, boolean, boolean, InferenceBuilder.OWLClassFilter, BufferedWriter) - Static method in class owltools.cli.AssertInferenceTool: Assert inferred super class relationships and (optional) remove redundant ones.
assertInferences(OWLGraphWrapper, boolean, boolean, boolean, boolean, boolean, boolean, boolean, InferenceBuilder.OWLClassFilter, BufferedWriter) - Static method in class owltools.cli.AssertInferenceTool
assertInferences(boolean) - Method in class owltools.sim.OldSimpleOwlSim
AssertInferenceTool - Class in owltools.cli: Simple command-line tool to assert inferences and (optional) remove redundant relations
AssertInferenceTool() - Constructor for class owltools.cli.AssertInferenceTool
AssertInferredClassExpressions - Class in owltools.cli
AssertInferredClassExpressions() - Constructor for class owltools.cli.AssertInferredClassExpressions
AssertInferredClassExpressions.OWLClassFilter - Interface in owltools.cli
assertInferredForAttributeClasses() - Method in class owltools.sim2.preprocessor.AbstractSimPreProcessor
assertInferredSubClassAxioms(Opts) - Method in class owltools.cli.CommandRunner
assertOccursInCommand() - Method in class owltools.web.OWLHandler
assertSubAnnotationProperty(OWLOntology, OWLAnnotationProperty, OWLAnnotationProperty) - Static method in class owltools.ncbi.OWLConverter: Convenience method for asserting a subAnnotationProperty relation between a parent and child property in an ontology.
assertSubClass(OWLOntology, OWLClass, String) - Static method in class owltools.ncbi.NCBIConverter: Convenience method for asserting a subClass relation between a parent and child class in an ontology.
assertSubClass(OWLOntology, OWLClass, OWLClass) - Static method in class owltools.ncbi.OWLConverter: Convenience method for asserting a subClass relation between a parent and child class in an ontology.
assertTypeCommand() - Method in class owltools.web.OWLHandler: Deprecated.
assignDefaultInformationContentForAllClasses() - Method in class owltools.sim2.AbstractOwlSim
assignDefaultInformationContentForAllClasses() - Method in class owltools.sim2.FastOwlSim
ASSIGNED_BY - Static variable in class owltools.gaf.parser.GAFParser
associatedIdentifierSet() - Method in class owltools.panther.PANTHERTree: Return a set of all identifiers associated with this family.
AsymmetricJaccardSimilarity - Class in owltools.sim
AsymmetricJaccardSimilarity() - Constructor for class owltools.sim.AsymmetricJaccardSimilarity
asymmetricSimGIC - Variable in class owltools.sim2.scores.ElementPairScores
asymmetricSimjScore - Variable in class owltools.sim2.scores.AttributePairScores
asymmetricSimjScore - Variable in class owltools.sim2.scores.ElementPairScores
AsymSimJScore - Variable in class owltools.sim2.io.SimResultRenderer.AttributesSimScores
AsymSimJScoreLabel - Variable in class owltools.sim2.io.SimResultRenderer.AttributesSimScores
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
attributeAllByAll(OwlSim, Opts) - Method in class owltools.cli.Sim2CommandRunner
attributeAllByAllOld(Opts) - Method in class owltools.cli.Sim2CommandRunner
attributeClass - Variable in class owltools.sim.OldSimpleOwlSim.ScoreAttributePair
attributeClass - Variable in class owltools.sim2.SimpleOwlSim.ScoreAttributePair
attributeClassSet - Variable in class owltools.sim.OldSimpleOwlSim.ScoreAttributesPair
attributeClassSet - Variable in class owltools.sim2.OwlSim.ScoreAttributeSetPair: Set of attributes that have the score
attributeInformationContentCutoff - Variable in class owltools.sim.OldSimpleOwlSim.EnrichmentConfig
attributeInformationContentCutoff - Variable in class owltools.sim2.EnrichmentConfig
AttributePairScores - Class in owltools.sim2.scores: A set of scores for any given pair of attributes classes
AttributePairScores(OWLClass, OWLClass) - Constructor for class owltools.sim2.scores.AttributePairScores
attributesIC - Variable in class owltools.sim2.SimStats
attributeSimilarityAllByAllPairwise(Opts) - Method in class owltools.cli.Sim2CommandRunner: Iterates through all individuals, generating similarity calculations for each of its attributes (ontology classes).
attributeSimilarityByPair(OWLNamedIndividual, OWLNamedIndividual) - Method in class owltools.cli.Sim2CommandRunner: Given two individuals, this fetches their respective attributes, computes their similarity (LCS), and renders the scores for all attribute-pairs.
AutomaticSimPreProcessor - Class in owltools.sim2.preprocessor: uses all properties as view properties, no role chains
AutomaticSimPreProcessor() - Constructor for class owltools.sim2.preprocessor.AutomaticSimPreProcessor
avgIC - Variable in class owltools.sim2.scores.ElementPairScores
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.
AxiomAnnotationTools - Class in owltools.graph: These are helper methods to check and modify axiom annotations.
AxiomAnnotationTools() - Constructor for class owltools.graph.AxiomAnnotationTools
AxiomAnnotationTools.AxiomAnnotationsChanger - Class in owltools.graph: Visitor which returns a new axiom of the same type with the new annotations.
AxiomAnnotationTools.AxiomAnnotationsChanger(Set<OWLAnnotation>, OWLDataFactory) - Constructor for class owltools.graph.AxiomAnnotationTools.AxiomAnnotationsChanger
axiomType - Variable in class owltools.io.TableToAxiomConverter.Config

B

b - Variable in class owltools.sim2.io.SimResultRenderer.AttributesSimScores
Base - Interface in owltools.frame
baseFileName - Variable in class owltools.sim.OldSimpleOwlSim
BaseLD - Class in owltools.frame.jsonld
BaseLD() - Constructor for class owltools.frame.jsonld.BaseLD
BasicABox - Class in owltools.gaf.owl.mapping
BasicABox(OWLGraphWrapper) - Constructor for class owltools.gaf.owl.mapping.BasicABox
BasicAnnotationPropagator - Class in owltools.gaf.inference: This performs basic annotation inferences involving propagation between the 3 sub-ontologies in GO MF -> BP over part_of BP -> CC over occurs_in This approach pre-computes the possible non-redundant propagations classes for each class during the setup.
BasicAnnotationPropagator(GafDocument, OWLGraphWrapper, boolean) - Constructor for class owltools.gaf.inference.BasicAnnotationPropagator: Create instance.
BasicChecksRule - Class in owltools.gaf.rules.go: This class performs basic checks.
BasicChecksRule(String, TraversingEcoMapper) - Constructor for class owltools.gaf.rules.go.BasicChecksRule
BasicStatistics - Class in owltools.sim2.kb
BasicStatistics(DescriptiveStatistics) - Constructor for class owltools.sim2.kb.BasicStatistics
belongsToSource(OWLEntity) - Method in class owltools.mooncat.Mooncat
bestForC - Variable in class owltools.sim2.scores.ScoreMatrix
bestForD - Variable in class owltools.sim2.scores.ScoreMatrix
bestSubsumers - Variable in class owltools.sim.ConjunctiveSetSimilarity
bestSubsumers - Variable in class owltools.sim.DisjunctiveSetSimilarity
bestSubsumers - Variable in class owltools.sim.MaximumInformationContentSimilarity
BioChebiGenerator - Class in owltools.cli: Methods for creating the BioChEBI wrapper file for ChEBI.
BioChebiGenerator(Map<OWLObjectProperty, Set<OWLObjectProperty>>) - Constructor for class owltools.cli.BioChebiGenerator
bioentities - Variable in class owltools.gaf.BioentityDocument
bioentity - Variable in class org.bbop.golr.java.RetrieveGolrBioentities.GolrBioentityDocument
Bioentity - Class in owltools.gaf
Bioentity() - Constructor for class owltools.gaf.Bioentity
Bioentity(String, String, String, String, String, String) - Constructor for class owltools.gaf.Bioentity
bioentity_label - Variable in class org.bbop.golr.java.RetrieveGolrBioentities.GolrBioentityDocument
bioentity_name - Variable in class org.bbop.golr.java.RetrieveGolrBioentities.GolrBioentityDocument
bioentityDocument - Variable in class owltools.cli.GafCommandRunner
BioentityDocument - Class in owltools.gaf
BioentityDocument(String) - Constructor for class owltools.gaf.BioentityDocument
BioentityDocument(String, List<Bioentity>) - Constructor for class owltools.gaf.BioentityDocument
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.
bmaAsymIC - Variable in class owltools.sim2.io.SimResultRenderer.IndividualSimScores
bmaAsymIC - Variable in class owltools.sim2.scores.ElementPairScores
bmaAsymICLabel - Variable in class owltools.sim2.io.SimResultRenderer.IndividualSimScores
bmaAsymJ - Variable in class owltools.sim2.io.SimResultRenderer.IndividualSimScores
bmaAsymJLabel - Variable in class owltools.sim2.io.SimResultRenderer.IndividualSimScores
bmaInverseAsymIC - Variable in class owltools.sim2.scores.ElementPairScores
bmaSymIC - Variable in class owltools.sim2.io.SimResultRenderer.IndividualSimScores
bmaSymIC - Variable in class owltools.sim2.scores.ElementPairScores
bmaSymICLabel - Variable in class owltools.sim2.io.SimResultRenderer.IndividualSimScores
bmaSymJ - Variable in class owltools.sim2.io.SimResultRenderer.IndividualSimScores
bmaSymJLabel - Variable in class owltools.sim2.io.SimResultRenderer.IndividualSimScores
boost_weights - Variable in class owltools.yaml.golrconfig.GOlrConfig
boost_weights - Variable in class owltools.yaml.golrconfig.GOlrField
border - Variable in class owltools.gfx.OWLGraphLayoutNode
bottom() - Method in class owltools.gfx.OWLGraphLayoutNode
bottom - Variable in class owltools.gfx.OWLGraphLayoutNode.SVGRectangle
bottomMargin - Static variable in class owltools.gfx.HierarchyImage
bp - Variable in class org.geneontology.lego.model.LegoTools: Deprecated.
BridgeExtractor - Class in owltools.mooncat
BridgeExtractor(OWLOntology) - Constructor for class owltools.mooncat.BridgeExtractor
BridgeExtractor.Combo - Class in owltools.mooncat: Maps a set of ontologies (e.g.
BridgeExtractor.Combo(Set<String>, String) - Constructor for class owltools.mooncat.BridgeExtractor.Combo
BruteForceSimPreProcessor - Class in owltools.sim2.preprocessor: uses ClassAssertions to determine view property
BruteForceSimPreProcessor() - Constructor for class owltools.sim2.preprocessor.BruteForceSimPreProcessor
bScore - Variable in class owltools.sim.MultiSimilarity
build(OWLReasonerFactory) - Method in class owltools.mooncat.PropertyViewOntologyBuilder
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
buildDocument(Reader, String, String) - Method in class owltools.gaf.parser.GafObjectsBuilder
buildDocument(String, String, String) - Method in class owltools.gaf.parser.GafObjectsBuilder
buildDocument(File) - Method in class owltools.gaf.parser.GafObjectsBuilder
buildDocument(String) - Method in class owltools.gaf.parser.GafObjectsBuilder
BuilderTools - Class in owltools.gaf.parser
BuilderTools() - Constructor for class owltools.gaf.parser.BuilderTools
buildExtensionExpression(List<List<ExtensionExpression>>) - Static method in class owltools.gaf.parser.BuilderTools
buildGafQualifierString(GeneAnnotation) - Static method in class owltools.gaf.parser.BuilderTools
buildGpadQualifierString(GeneAnnotation) - Static method in class owltools.gaf.parser.BuilderTools
buildInferences() - Method in class owltools.InferenceBuilder
buildInferences(boolean) - Method in class owltools.InferenceBuilder: if alwaysAssertSuperClasses then ensure that superclasses are always asserted for every equivalence axiom, except in the case where a more specific superclass is already in the set of inferences.
buildInferredViewOntology(OWLReasoner) - Method in class owltools.mooncat.PropertyViewOntologyBuilder: Once the PVO has been constructed, this uses a reasoner to classify it.
buildPropertyExpression(List<Pair<String, String>>) - Static method in class owltools.gaf.parser.BuilderTools
buildReferenceIdsString(List<String>) - Static method in class owltools.gaf.parser.BuilderTools
buildTaxonString(String, Pair<String, String>) - Static method in class owltools.gaf.parser.BuilderTools
buildTaxonString(Pair<String, String>) - Static method in class owltools.gaf.parser.BuilderTools
BuildVersionId - Class in owltools.ontologyrelease: Deprecated.
BuildVersionId() - Constructor for class owltools.ontologyrelease.BuildVersionId: Deprecated.
buildViewOntology() - Method in class owltools.mooncat.PropertyViewOntologyBuilder: As PropertyViewOntologyBuilder.buildViewOntology(IRI, IRI), but both O(P) and O(P)' have automatically generated IRIs
buildViewOntology(IRI) - Method in class owltools.mooncat.PropertyViewOntologyBuilder: as PropertyViewOntologyBuilder.buildViewOntology(IRI,IRI), but sets the asserted and inferred view ontologies to be the same
buildViewOntology(IRI, IRI) - Method in class owltools.mooncat.PropertyViewOntologyBuilder: Constructs a property view ontology O(P) or O(P,E) from source ontology O, such that every class C in O has a corresponding view class C' in O(P), such that C' EquivalentTo = P some C O(P) imports both the O, and optionally the elements ontology E - in which case we call the ontology O(P,E).
buildWithString(Collection<String>) - Static method in class owltools.gaf.parser.BuilderTools
buildWithString(Collection<String>, String) - Static method in class owltools.gaf.parser.BuilderTools

C

c - Variable in class owltools.sim2.FastOwlSim.ClassCount
c - Variable in class owltools.sim2.scores.AttributePairScores
c1 - Variable in class owltools.sim.OldSimpleOwlSim.OWLClassExpressionPair
c1 - Variable in class owltools.sim.OWLClassExpressionPair
c1 - Variable in class owltools.util.ClassExpressionPair
c2 - Variable in class owltools.sim.OldSimpleOwlSim.OWLClassExpressionPair
c2 - Variable in class owltools.sim.OWLClassExpressionPair
c2 - Variable in class owltools.util.ClassExpressionPair
cacheEdges() - Method in class owltools.graph.OWLGraphWrapperEdges: caches full outgoing and incoming edges
cacheInformationContentInOntology() - Method in class owltools.sim2.AbstractOwlSim
cacheInformationContentInOntology() - Method in interface owltools.sim2.OwlSim: Generates an ontology containing annotation assertion axioms connecting a class to an IC value.
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
calculateAllByAllEnrichment(OWLClass, OWLClass, OWLClass) - Method in class owltools.sim.OldSimpleOwlSim
calculateAllByAllEnrichment() - Method in class owltools.sim2.AbstractOwlSim
calculateAllByAllEnrichment(OWLClass, OWLClass, OWLClass) - Method in class owltools.sim2.AbstractOwlSim
calculateAllByAllEnrichment(OWLClass, OWLClass, OWLClass) - Method in interface owltools.sim2.OwlSim: For every c ∈ sample set, test c against all classes ∈ enriched class set.
calculateAllByAllEnrichment() - Method in interface owltools.sim2.OwlSim
calculateAllSimilarity(OWLObject, OWLObject) - Method in class owltools.sim.SimEngine: iterates through ALL similarity metrics and calculates
calculateCombinedScore(ElementPairScores, double, double) - Method in class owltools.sim2.AbstractOwlSim
calculateCombinedScore(ElementPairScores, double, double) - Method in interface owltools.sim2.OwlSim
calculateCombinedScore(ElementPairScores, double, double) - Method in class owltools.sim2.SimpleOwlSim
calculateCombinedScores(List<ElementPairScores>, double, double) - Method in class owltools.sim2.FastOwlSim: Given a set of scorings between an individual i, and a set of individuals j1 ..jn ∈ J, calculate the combined score for each i,j pair where j ∈ J
calculateCombinedScores(List<ElementPairScores>, double, double) - Method in interface owltools.sim2.OwlSim
calculateCombinedScores(List<ElementPairScores>, double, double) - Method in class owltools.sim2.SimpleOwlSim
calculateEnrichment(OWLClass, OWLClass) - Method in class owltools.sim.EnrichmentEngine
calculateEnrichment(OWLClass, OWLClass) - Method in class owltools.sim.OldSimpleOwlSim
calculateEnrichment(OWLClass, OWLClass) - Method in class owltools.sim2.AbstractOwlSim
calculateEnrichment(OWLClass, OWLClass) - Method in interface owltools.sim2.OwlSim: Uses OwlSim.calculatePairwiseEnrichment(OWLClass, OWLClass, OWLClass)}
calculateGenusDifferentiaEnrichment(OWLClass, OWLClass, OWLClass) - Method in class owltools.sim2.ClassDifferentiaLearner
calculateMetricStats(Set<OWLNamedIndividual>, Set<OWLNamedIndividual>) - Method in class owltools.sim2.FastOwlSim
calculateMetricStats(Set<OWLNamedIndividual>, Set<OWLNamedIndividual>) - Method in interface owltools.sim2.OwlSim
calculateMetricStats(Set<OWLNamedIndividual>, Set<OWLNamedIndividual>) - Method in class owltools.sim2.SimpleOwlSim
calculateOverallAnnotationSufficiencyForAttributeSet(Set<OWLClass>) - Method in class owltools.sim2.AbstractOwlSim
calculateOverallAnnotationSufficiencyForAttributeSet(Set<OWLClass>) - Method in interface owltools.sim2.OwlSim
calculateOverallAnnotationSufficiencyForIndividual(OWLNamedIndividual) - Method in class owltools.sim2.AbstractOwlSim
calculateOverallAnnotationSufficiencyForIndividual(OWLNamedIndividual) - Method in interface owltools.sim2.OwlSim
calculatePairwiseEnrichment(OWLClass, OWLClass, OWLClass) - Method in class owltools.sim.OldSimpleOwlSim
calculatePairwiseEnrichment(OWLClass, OWLClass, OWLClass) - Method in class owltools.sim2.AbstractOwlSim
calculatePairwiseEnrichment(OWLClass, OWLClass, OWLClass) - Method in interface owltools.sim2.OwlSim: Pairwise enrichment test
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
calculateSubgraphAnnotationSufficiencyForAttributeSet(Set<OWLClass>, OWLClass) - Method in class owltools.sim2.AbstractOwlSim
calculateSubgraphAnnotationSufficiencyForAttributeSet(Set<OWLClass>, OWLClass) - Method in interface owltools.sim2.OwlSim
calculateSubgraphAnnotationSufficiencyForIndividual(OWLNamedIndividual, OWLClass) - Method in class owltools.sim2.AbstractOwlSim
candidates - Variable in class owltools.sim.SimSearch
cardinality - Variable in class owltools.yaml.golrconfig.GOlrField
CardinalityContraintsTools - Class in owltools.graph: Tools to handle cardinality constraints in OWL.
CardinalityContraintsTools() - Constructor for class owltools.graph.CardinalityContraintsTools
CardinalityContraintsTools.CardinalityReporter - Class in owltools.graph
CatalogXmlIRIMapper - Class in owltools.io: OWLOntologyIRIMapper using the mappings from a catalog.xml file.
CatalogXmlIRIMapper(String) - Constructor for class owltools.io.CatalogXmlIRIMapper: Create an CatalogXmlIRIMapper from the given catalog.xml file.
CatalogXmlIRIMapper(File) - Constructor for class owltools.io.CatalogXmlIRIMapper: Create an CatalogXmlIRIMapper from the given catalog.xml file.
CatalogXmlIRIMapper(File, File) - Constructor for class owltools.io.CatalogXmlIRIMapper: Create an CatalogXmlIRIMapper from the given catalog.xml file.
CatalogXmlIRIMapper(URL) - Constructor for class owltools.io.CatalogXmlIRIMapper: Create an CatalogXmlIRIMapper from the given catalog URL.
CatalogXmlIRIMapper(URL, File) - Constructor for class owltools.io.CatalogXmlIRIMapper: Create an CatalogXmlIRIMapper from the given catalog URL.
categorizeNamespace(OWLObject, Map<String, Object>) - Method in class owltools.graph.OWLGraphWrapperEdgesAdvanced
categorizeObject(OWLNamedObject, Map<String, String>, Set<String>, boolean) - Method in class owltools.graph.OWLGraphWrapperEdgesAdvanced: Create a category for a given named object.
CellularLocationTools - Class in org.geneontology.lego.model: Deprecated.
CellularLocationTools() - Constructor for class org.geneontology.lego.model.CellularLocationTools: Deprecated.
ChadoGraphClosureRenderer - Class in owltools.io: implements a graph closure writer suitable for imports into Chado; in particular: all identifiers are translated to OBO IDs relationship chains of length > 1 are ignored SUBCLASS is written as is_a, and only existential restrictions are emitted
ChadoGraphClosureRenderer(PrintStream) - Constructor for class owltools.io.ChadoGraphClosureRenderer
ChadoGraphClosureRenderer(String) - Constructor for class owltools.io.ChadoGraphClosureRenderer
changeAxiomAnnotations(OWLAxiom, Set<OWLAnnotation>, OWLOntology) - Static method in class owltools.graph.AxiomAnnotationTools: Update the given axiom to a new set of axiom annotation.
Side effect: This removes the old axiom and adds the new axiom to the given ontology.
changeAxiomAnnotations(OWLAxiom, Set<OWLAnnotation>, OWLDataFactory) - Static method in class owltools.graph.AxiomAnnotationTools: Update the given axiom to the new set of axiom annotation.
check(OWLGraphWrapper, Collection<OWLObject>) - Method in class owltools.ontologyverification.impl.AltIdInSignature
check(OWLClass, OWLGraphWrapper, Map<String, OWLObject>, List<CheckWarning>, OWLPrettyPrinter) - Method in class owltools.ontologyverification.impl.AltIdInSignature
check(OWLGraphWrapper, Collection<OWLObject>) - Method in class owltools.ontologyverification.impl.CycleCheck
check(OWLGraphWrapper, Collection<OWLObject>) - Method in class owltools.ontologyverification.impl.DanglingReferenceCheck
check(OWLClass, OWLGraphWrapper, List<CheckWarning>, OWLPrettyPrinter) - Method in class owltools.ontologyverification.impl.DanglingReferenceCheck
check(OWLGraphWrapper, Collection<OWLObject>) - Method in class owltools.ontologyverification.impl.NameRedundancyCheck
check(OWLGraphWrapper, Collection<OWLObject>) - Method in class owltools.ontologyverification.impl.ObsoleteClassInSignature
check(OWLClass, OWLGraphWrapper, List<CheckWarning>, OWLPrettyPrinter) - Method in class owltools.ontologyverification.impl.ObsoleteClassInSignature
check(OWLGraphWrapper, Collection<OWLObject>) - Method in class owltools.ontologyverification.impl.SelfReferenceInDefinition
check(OWLGraphWrapper, Collection<OWLObject>) - Method in interface owltools.ontologyverification.OntologyCheck: Run the check for the given ontology.
checkAxioms(String, String) - Static method in class owltools.ncbi.NCBI2OWL: Load an ontology from a file and then print a list of its axioms.
checkNew(File) - Method in class owltools.ontologyrelease.OboOntologyReleaseRunner: Check whether the file is new.
checkPotentialRedundantSubClassAxioms(Collection<? extends OWLAxiom>) - Method in class owltools.InferenceBuilder: Check the list of axioms for potential redundant subClass axioms of type:
checkPotentialRedundantSubClassAxioms() - Method in class owltools.InferenceBuilder: Check all classes for potential redundant subClass axioms of type:
checkTaxon(OWLOntology, OWLClass) - Static method in class owltools.ncbi.NCBIConverter: Check to make sure that this taxon has the required properties.
CheckWarning - Class in owltools.ontologyverification: Information about an error or warning as a result of an ontology check.
CheckWarning(String, String, boolean, IRI) - Constructor for class owltools.ontologyverification.CheckWarning
CheckWarning(String, String, boolean, IRI, String) - Constructor for class owltools.ontologyverification.CheckWarning
CheckWarning(String, String, boolean, List<IRI>, String) - Constructor for class owltools.ontologyverification.CheckWarning
childArrowShape - Variable in class owltools.gfx.GraphicsConfig.RelationConfig
classCommand() - Method in class owltools.web.OWLHandler
classCount - Variable in class owltools.sim2.OwlSimMetadata
ClassCountComparator - Static variable in class owltools.sim2.FastOwlSim
ClassDifferentiaLearner - Class in owltools.sim2
ClassDifferentiaLearner(OwlSim) - Constructor for class owltools.sim2.ClassDifferentiaLearner
ClassDifferentiaLearner.InferredClassDefinition - Class in owltools.sim2
ClassDifferentiaLearner.InferredClassDefinition(OWLClass, OWLClass, OWLClass, Double) - Constructor for class owltools.sim2.ClassDifferentiaLearner.InferredClassDefinition
classesToSkip - Variable in class owltools.sim2.preprocessor.AbstractSimPreProcessor
ClassExpression - Interface in owltools.frame
classExpression - Variable in class owltools.gaf.owl.GAFOWLBridge.GAFDescription
ClassExpressionGraphClosureRenderer - Class in owltools.io: Writes graph closure as class expressions
ClassExpressionGraphClosureRenderer(PrintStream) - Constructor for class owltools.io.ClassExpressionGraphClosureRenderer
ClassExpressionGraphClosureRenderer(String) - Constructor for class owltools.io.ClassExpressionGraphClosureRenderer
ClassExpressionLD - Class in owltools.frame.jsonld
ClassExpressionLD() - Constructor for class owltools.frame.jsonld.ClassExpressionLD
ClassExpressionPair - Class in owltools.util
ClassExpressionPair(OWLClassExpression, OWLClassExpression) - Constructor for class owltools.util.ClassExpressionPair
ClassFrame - Interface in owltools.frame
ClassFrameLD - Class in owltools.frame.jsonld
ClassFrameLD() - Constructor for class owltools.frame.jsonld.ClassFrameLD
classICPairs(Opts) - Method in class owltools.cli.Sim2CommandRunner
classifyRelationship(OWLGraphEdge, OWLObject, Set<? extends OWLPropertyExpression>) - Method in class owltools.graph.OWLGraphWrapperEdgesAdvanced: Classify the an edge and target as a human readable string for further processing.
classIndexSize - Variable in class owltools.sim2.OwlSimMetadata
classMap - Variable in class owltools.io.TableToAxiomConverter.Config
classPairCount - Variable in class owltools.sim2.SimStats
classSetCommand() - Method in class owltools.web.OWLHandler
ClassStub - Interface in owltools.frame
ClassStubLD - Class in owltools.frame.jsonld
ClassStubLD() - Constructor for class owltools.frame.jsonld.ClassStubLD
ClassStubLD(String, String) - Constructor for class owltools.frame.jsonld.ClassStubLD
ClassTaxonMatrix - Class in owltools.gaf.inference: Matrix representing the applicability of classes and taxa.
ClassTaxonMatrix(int, int) - Constructor for class owltools.gaf.inference.ClassTaxonMatrix
cleanup() - Method in class owltools.gaf.godb.DatabaseDumper
clear() - Method in class owltools.util.BloomFilter: Sets all bits to false in the Bloom filter.
clearCachedEdges() - Method in class owltools.graph.OWLGraphWrapperEdges: Clear the current edge cache.
clearCachedEdges() - Method in class owltools.graph.OWLGraphWrapperEdgesExtended
clearFilters() - Method in class owltools.InferenceBuilder
clearInformationContentCache() - Method in class owltools.sim2.AbstractOwlSim
clearInformationContentCache() - Method in class owltools.sim2.FastOwlSim
clearInformationContentCache() - Method in class owltools.sim2.SimpleOwlSim
clearLCSCache() - Method in class owltools.sim2.FastOwlSim
clearTaxonSubsetName() - Method in class owltools.solrj.GafSolrDocumentLoader
CLIMethod - Annotation Type in owltools.cli.tools: Annotation indicating, that this method can be called from the command line interface.
close() - Method in class org.geneontology.lego.dot.LegoDotWriter: Deprecated.

Overwrite this method to implement a custom close() function for the writer.
close() - Method in class owltools.gaf.io.GafWriter
close() - Method in class owltools.gaf.rules.AnnotationRulesReportWriter
close() - Method in class owltools.graph.OWLGraphWrapperEdgesAdvanced
close() - Method in class owltools.mooncat.ontologymetadata.ImportChainDotWriter
closeAllPrintStreams() - Method in class owltools.gaf.godb.DatabaseDumper
closePrintStream(String) - Method in class owltools.gaf.godb.DatabaseDumper
cls - Variable in class owltools.gaf.ExtensionExpression
code - Variable in enum owltools.gfx.RelationType
COL_SUBSET - Variable in class owltools.idmap.IDMappingPIRParser
colIxSubset - Variable in class owltools.idmap.IDMappingPIRParser
collect(FlexDocument) - Method in class owltools.solrj.FlexSolrDocumentLoader: Take args and add it index (no commits) Main wrapping for adding ontology documents to GOlr.
collect(OWLObject, OWLGraphWrapper) - Method in class owltools.solrj.OntologyGeneralSolrDocumentLoader
collect(OWLObject, OWLGraphWrapper) - Method in class owltools.solrj.OntologySolrLoader: Deprecated.
collect_unit_info(LegoUnit, String, String, String, OWLShuntGraph) - Method in class owltools.solrj.ComplexAnnotationSolrDocumentLoader: Take args and add it index (no commits) Main wrapping for adding complex annotation documents to GOlr.
COLOCATES_WITH_MASK - Static variable in class owltools.gaf.GeneAnnotation
color - Variable in class owltools.gfx.GraphicsConfig.RelationConfig
color - Variable in enum owltools.gfx.RelationType
colour - Variable in class owltools.gfx.OWLGraphStrokeEdge.SVGEdge
COLS - Static variable in class owltools.idmap.IDMappingPIRParser
CombinedJaccardConjunctiveSetSimilarity - Class in owltools.sim: filters first based on SimJ, if passes threshold performs full ConjunctiveSetSimilarity
CombinedJaccardConjunctiveSetSimilarity() - Constructor for class owltools.sim.CombinedJaccardConjunctiveSetSimilarity
combinedQuantifiedPropertyPair(OWLQuantifiedProperty, OWLQuantifiedProperty) - Method in class owltools.graph.OWLGraphWrapperEdges: Edge composition rules TODO - property chains of length > 2
combinedScore - Variable in class owltools.sim2.scores.ElementPairScores
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.OWLGraphWrapperEdges: Composes two graph edges into a new edge, using axioms in the ontology to determine the correct composition
combineEdgePair(OWLGraphEdge, List<OWLQuantifiedProperty>, List<OWLQuantifiedProperty>, int) - Method in class owltools.graph.OWLGraphWrapperEdges: Combine the OWLQuantifiedProperty Lists neQp and extEdgeQp and assigned the resulting OWLQuantifiedPropertys to mergedEdge.
combineEdgePairWithGCI(OWLObject, OWLGraphEdge, OWLGraphEdge, int) - Method in class owltools.graph.OWLGraphWrapperEdgesExtended: Same as OWLGraphWrapperEdges.combineEdgePair(OWLObject, OWLGraphEdge, OWLGraphEdge, int) except that the GCI filler an GCI relation of the edges are taken into account.
combineEdgePairWithSuperPropsAndGCI(OWLGraphEdge, OWLGraphEdge) - Method in class owltools.graph.OWLGraphWrapperEdgesExtended: Combines firstEdge and secondEdge to create a new edge from the source of firstEdge to the target of secondEdge, with properties combined in a regular way, and over super properties.
CommandLineInterface - Class in owltools.cli: Wrapper class to provide a stable class name for the main method.
CommandLineInterface() - Constructor for class owltools.cli.CommandLineInterface
CommandRunner - Class in owltools.cli: An instance of this class can execute owltools commands in sequence.
CommandRunner() - Constructor for class owltools.cli.CommandRunner
CommandRunner.OptionException - Exception in owltools.cli
CommandRunner.OptionException(String) - Constructor for exception owltools.cli.CommandRunner.OptionException
CommentListener - Interface in owltools.gaf.parser
COMMON - Static variable in class owltools.graph.RelationSets
CompactGraphClosureReader - Class in owltools.io: Note that the ontology must be loaded prior to restored a closure table
CompactGraphClosureReader(OWLGraphWrapper) - Constructor for class owltools.io.CompactGraphClosureReader
CompactGraphClosureRenderer - Class in owltools.io: Similar to GraphClosureRenderer, writes in a more compact format
CompactGraphClosureRenderer(PrintStream) - Constructor for class owltools.io.CompactGraphClosureRenderer
CompactGraphClosureRenderer(String) - Constructor for class owltools.io.CompactGraphClosureRenderer
compareAllAttributes(OWLClass, Set<OWLClass>) - Method in class owltools.sim2.FastOwlSim
compareAllAttributes(OWLClass, Set<OWLClass>) - Method in interface owltools.sim2.OwlSim
compareAllAttributes(OWLClass, Set<OWLClass>) - Method in class owltools.sim2.SimpleOwlSim
compareAttributeSetPair(Set<OWLClass>, Set<OWLClass>) - Method in class owltools.sim2.SimJSONEngine
compareAttributeSetPair(Set<OWLClass>, Set<OWLClass>, boolean) - Method in class owltools.sim2.SimJSONEngine
compareAttributeSetsCommand() - Method in class owltools.web.OWLHandler
compareLCSWithEnrichmentGrouping(OWLOntology, Double, OWLPrettyPrinter) - Static method in class owltools.sim2.OwlSimUtil
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
compareTo(OldSimpleOwlSim.EnrichmentResult) - Method in class owltools.sim.OldSimpleOwlSim.EnrichmentResult
compareTo(ClassDifferentiaLearner.InferredClassDefinition) - Method in class owltools.sim2.ClassDifferentiaLearner.InferredClassDefinition
compareTo(EnrichmentResult) - Method in class owltools.sim2.EnrichmentResult
compareTo(OwlSim.ScoreAttributeSetPair) - Method in class owltools.sim2.OwlSim.ScoreAttributeSetPair
compareTo(ElementPairScores) - Method in class owltools.sim2.scores.ElementPairScores
compareTo(SimpleOwlSim.ScoreAttributePair) - Method in class owltools.sim2.SimpleOwlSim.ScoreAttributePair
comparisonClass - Variable in class owltools.sim.SimEngine
comparisonProperty - Variable in class owltools.sim.SimEngine
comparisonSuperclass - Variable in class owltools.sim.SimEngine
ComplexAnnotationSolrDocumentLoader - Class in owltools.solrj: A very specific class for the specific use case of loading in complex annotations from owl.
ComplexAnnotationSolrDocumentLoader(String, OWLGraphWrapper, OWLReasoner, Set<OWLNamedIndividual>, Set<OWLAnnotation>, String, String, String) - Constructor for class owltools.solrj.ComplexAnnotationSolrDocumentLoader
COMPOSED_PRIMARILY_OF - Variable in class owltools.sim2.preprocessor.AbstractOBOSimPreProcessor
CompositionalClassPredictor - Class in owltools.gaf.inference: Deprecated.
CompositionalClassPredictor(GafDocument, OWLGraphWrapper) - Constructor for class owltools.gaf.inference.CompositionalClassPredictor: Deprecated.
compute(OWLClass, OWLClass) - Method in class owltools.sim2.ClassDifferentiaLearner
computeAttributeSetSimilarityStats(Set<OWLClass>) - Method in class owltools.sim2.AbstractOwlSim
computeAttributeSetSimilarityStats(Set<OWLClass>) - Method in interface owltools.sim2.OwlSim
computeAttributeSetSimilarityStatsForSubgraph(Set<OWLClass>, OWLClass) - Method in class owltools.sim2.AbstractOwlSim
computeAttributeSetSimilarityStatsForSubgraph(Set<OWLClass>, OWLClass) - Method in interface owltools.sim2.OwlSim
computeDescriptiveStatistics(OWLNamedIndividual) - Method in class owltools.sim2.kb.OWLSimReferenceBasedStatistics
computeDescriptiveStatistics(Set<OWLClass>) - Method in class owltools.sim2.kb.OWLSimReferenceBasedStatistics
computeIndividualSimilarityStats(OWLNamedIndividual) - Method in class owltools.sim2.AbstractOwlSim
computeIndividualStats(OWLNamedIndividual) - Method in class owltools.sim2.AbstractOwlSim
computeIndividualStats(OWLNamedIndividual) - Method in interface owltools.sim2.OwlSim: This will compute the individual summary statistics over the set of anntoated classes to an individual i.
computeIndividualStats(OWLNamedIndividual) - Method in class owltools.sim2.SimpleOwlSim
computeIndividualStatsForSubgraph(OWLNamedIndividual, OWLClass) - Method in class owltools.sim2.AbstractOwlSim
computeSystemStats() - Method in class owltools.sim2.AbstractOwlSim
computeSystemStats() - Method in interface owltools.sim2.OwlSim: This function will compute the IC-based summary statistics over the set of individuals for direct annotations.
computeSystemStats() - Method in class owltools.sim2.SimpleOwlSim
computeSystemStatsForSubgraph(OWLClass) - Method in class owltools.sim2.AbstractOwlSim
computeSystemStatsForSubgraph(OWLClass) - Method in interface owltools.sim2.OwlSim
computeTFIDFMatrix(int[][], int, int[][], int) - Method in class owltools.sim2.FastOwlSim
computeTFIDFMatrix(int[][], int, int[][], int) - Method in interface owltools.sim2.OwlSim
computeTFIDFMatrix(int[][], int, int[][], int) - Method in class owltools.sim2.SimpleOwlSim
config - Variable in class owltools.flex.FlexCollection
config - Variable in class owltools.io.StanzaToOWLConverter
config - Variable in class owltools.io.TableToAxiomConverter
ConfigManager - Class in owltools.yaml.golrconfig
ConfigManager() - Constructor for class owltools.yaml.golrconfig.ConfigManager: Constructor.
configRead(Opts) - Method in class owltools.cli.SolrCommandRunner: Output (STDOUT) a XML segment to put into the Solr schema file after reading the YAML file.
ConjunctiveSetInformationContentRatioSimilarity - Class in owltools.sim: score is the IC of the intersection of all attributes divided my min IC of a or b it's recommended this used as a sub-method of a MultiSimilarity check
ConjunctiveSetInformationContentRatioSimilarity() - Constructor for class owltools.sim.ConjunctiveSetInformationContentRatioSimilarity
ConjunctiveSetSimilarity - Class in owltools.sim: ConjunctiveSetSimilarity(a,b) = IC( LCA_1(a,b) ^ LCA_2(a,b) ...
ConjunctiveSetSimilarity() - Constructor for class owltools.sim.ConjunctiveSetSimilarity
contains(E) - Method in class owltools.util.BloomFilter: Returns true if the element could have been inserted into the Bloom filter.
containsAll(Collection<? extends E>) - Method in class owltools.util.BloomFilter: Returns true if all the elements of a Collection could have been inserted into the Bloom filter.
CONTRIBUTES_TO_MASK - Static variable in class owltools.gaf.GeneAnnotation
convert(List<RetrieveGolrAnnotations.GolrAnnotationDocument>) - Method in class org.bbop.golr.java.RetrieveGolrAnnotations
convert(List<RetrieveGolrAnnotations.GolrAnnotationDocument>, Map<String, Bioentity>, GafDocument) - Method in class org.bbop.golr.java.RetrieveGolrAnnotations
convert() - Method in class owltools.io.OWLGsonParser
convert(OWLObject) - Method in class owltools.io.OWLGsonParser
convert(OWLOntology) - Method in class owltools.io.OWLGsonParser
convert(OWLAxiom) - Method in class owltools.io.OWLGsonParser
convert(OWLGraphEdge) - Method in class owltools.io.OWLGsonParser
convert(OWLImportsDeclaration) - Method in class owltools.io.OWLGsonRenderer
convert(OWLObject) - Method in class owltools.io.OWLGsonRenderer
convert(OWLOntology) - Method in class owltools.io.OWLGsonRenderer
convert(OWLAxiom) - Method in class owltools.io.OWLGsonRenderer
convert(OWLGraphEdge) - Method in class owltools.io.OWLGsonRenderer
convertAxiom(Map) - Method in class owltools.io.OWLGsonParser
convertAxioms(Object[]) - Method in class owltools.io.OWLGsonParser
convertCountMatrixToFrequency(int[][], int) - Method in class owltools.sim2.FastOwlSim
convertCountMatrixToFrequency(int[][], int) - Method in interface owltools.sim2.OwlSim
convertCountMatrixToFrequency(int[][], int) - Method in class owltools.sim2.SimpleOwlSim
convertOntology(Map<Object, Object>) - Method in class owltools.io.OWLGsonParser
convertToMultiline(String) - Static method in class owltools.ontologyrelease.OboOntologyReleaseRunnerGui
convertToOWL(String, Map<String, String>) - Static method in class owltools.ncbi.NCBI2OWL: Read a data file and create an OWL representation.
convertToOWL(String, String, Map<String, String>) - Static method in class owltools.ncbi.NCBI2OWL: Read a data file, create an OWL representation, and save an OWL file.
convertToOWL(String, String, InputStream, InputStream, Map<String, String>) - Static method in class owltools.ncbi.NCBI2OWL: Read a data file, create an OWL representation, and save an OWL file.
corpusSize - Variable in class owltools.sim2.AbstractOwlSim
count - Variable in class owltools.sim2.FastOwlSim.ClassCount
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.
countViolations(AnnotationRuleViolation.ViolationType) - Method in class owltools.gaf.rules.AnnotationRulesEngine.AnnotationRulesEngineResult
create(OWLGraphWrapper, Collection<OWLClass>, String...) - Static method in class owltools.gaf.inference.ClassTaxonMatrix: Create a new taxon-class-matrix for the given classes and taxa.
create(OWLGraphWrapper, Collection<OWLClass>, Collection<OWLClass>) - Static method in class owltools.gaf.inference.ClassTaxonMatrix: Create a new taxon-class-matrix for the given classes and taxa.
CREATE_EXPLANATIONS - Static variable in class owltools.gaf.rules.GenericReasonerValidationCheck
createAnnotationProperty(OWLOntology, IRI) - Static method in class owltools.ncbi.OWLConverter: Create an annotation property and add it to the ontology.
createAnnotationProperty(OWLOntology, String) - Static method in class owltools.ncbi.OWLConverter: Convenience method taking a string CURIE instead of an IRI.
createAnnotationProperty(OWLOntology, Obo2OWLConstants.Obo2OWLVocabulary) - Static method in class owltools.ncbi.OWLConverter: Convenience method for adding and labelling OboInOwl annotation properties with its rdfs:label.
createAspectProvider(OWLGraphWrapper, Map<String, String>, OWLReasoner) - Static method in class owltools.gaf.parser.DefaultAspectProvider: Create a new aspect provider from the given super classes and aspects.
createBioChebi(File, String) - Static method in class owltools.cli.BioChebiGenerator: Create the GCIs for BioChEBI.
createBioChebi(OWLGraphWrapper, String) - Static method in class owltools.cli.BioChebiGenerator: Create the GCIs for BioChEBI.
createBioChebi(OWLGraphWrapper, Set<OWLClass>) - Static method in class owltools.cli.BioChebiGenerator: Create the GCIs for BioChEBI.
createBioChebi(Opts) - Method in class owltools.cli.CommandRunner
createDefaultAspectMap(OWLGraphWrapper) - Method in class owltools.gaf.inference.BasicAnnotationPropagator: Create the mapping from the sub ontology to the aspect in the GAF.
createDisjoint(OWLDataFactory, Set<OWLClass>, OWLObjectProperty) - Method in class owltools.cli.TaxonCommandRunner
createDisjoint(OWLDataFactory, OWLClass, OWLClass, OWLObjectProperty) - Method in class owltools.cli.TaxonCommandRunner
createDisjoint(OWLDataFactory, OWLClass, OWLClass) - Method in class owltools.cli.TaxonCommandRunner
createEcoMapper() - Static method in class owltools.gaf.eco.EcoMapperFactory: Create an instance of a EcoMapper.
createEcoMapper(OWLOntologyManager) - Static method in class owltools.gaf.eco.EcoMapperFactory: Create an instance of a EcoMapper.
createEcoMapper(ParserWrapper) - Static method in class owltools.gaf.eco.EcoMapperFactory: Create an instance of a EcoMapper.
createEcoMapper(ParserWrapper, String) - Static method in class owltools.gaf.eco.EcoMapperFactory: Create an instance of a EcoMapper.
createEcoMapper(OWLGraphWrapper) - Static method in class owltools.gaf.eco.EcoMapperFactory: Create an instance of a EcoMapper.
createElementAttributeMapFromOntology() - Method in class owltools.sim.OldSimpleOwlSim: assumes that the ontology contains both attributes (TBox) and elements + associations (ABox)
createElementAttributeMapFromOntology() - Method in class owltools.sim2.FastOwlSim
createElementAttributeMapFromOntology() - Method in interface owltools.sim2.OwlSim: This must be called prior to calculation of any similarity metrics.
createElementAttributeMapFromOntology() - Method in class owltools.sim2.SimpleOwlSim
createExperimentalPredictions(Opts) - Method in class owltools.cli.GafCommandRunner
createExternalMappings(Opts) - Method in class owltools.cli.CommandRunner
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.
createLegoGraph(Collection<OWLNamedIndividual>, Set<OWLAnnotation>) - Method in class org.geneontology.lego.model2.LegoUnitTools: Deprecated.
createLegoNodes(Collection<OWLNamedIndividual>) - Method in class org.geneontology.lego.model.LegoTools: Deprecated.
createManchesterSyntaxPrettyPrinter(OWLGraphWrapperExtended) - Static method in class owltools.io.OWLPrettyPrinter: Create an OWLPrettyPrinter, which renders in OWL Manchester syntax.
createMap() - Method in class owltools.mooncat.SpeciesMergeUtil: builds ecmap, a map between species-classes to generic-classes also populates ssClasses
createModel(GafDocument) - Method in class owltools.gaf.io.OpenAnnotationRDFWriter: Generate an RDF model from a GAF Document
createMultiLineLabel(String) - Static method in class owltools.ontologyrelease.OboOntologyReleaseRunnerGui
createNameFiltered(Set<String>, OortConfiguration) - Static method in class owltools.ontologyrelease.logging.ExplicitReportFileHandler
createNCBIIRI(String) - Static method in class owltools.ncbi.NCBIConverter: Create an NCBI taxon IRI from an NCBI ID string.
createNCBIIRI(int) - Static method in class owltools.ncbi.NCBIConverter: Create an NCBI taxon IRI from an NCBI ID integer.
createNonBufferingReasoner(OWLOntology) - Method in class owltools.reasoner.GraphReasonerFactory
createNonBufferingReasoner(OWLOntology, OWLReasonerConfiguration) - Method in class owltools.reasoner.GraphReasonerFactory
createNonBufferingReasoner(OWLOntology) - Method in class owltools.reasoner.LazyExpressionMaterializingReasonerFactory: Deprecated.
createNonBufferingReasoner(OWLOntology, OWLReasonerConfiguration) - Method in class owltools.reasoner.LazyExpressionMaterializingReasonerFactory: Deprecated.
createNonBufferingReasoner(OWLOntology) - Method in class owltools.reasoner.PlaceholderJcelFactory
createNonBufferingReasoner(OWLOntology, OWLReasonerConfiguration) - Method in class owltools.reasoner.PlaceholderJcelFactory
createNonBufferingReasoner(OWLOntology) - Method in class owltools.reasoner.PrecomputingMoreReasonerFactory
createNonBufferingReasoner(OWLOntology, OWLReasonerConfiguration) - Method in class owltools.reasoner.PrecomputingMoreReasonerFactory
createObjectPropertyView(OWLOntology, OWLOntology, OWLObjectProperty, Map<OWLClass, OWLClass>, boolean) - Static method in class owltools.mooncat.TransformationUtils
createOortConfig(Properties) - Static method in class owltools.ontologyrelease.OortConfiguration: Create an OortConfiguration from the given Properties.
createOWLOntology() - Static method in class owltools.ncbi.NCBIOWL: Create and initialize the ontology.
createOWLOntologyFromResults() - Method in class owltools.sim.Similarity
createOwlSim(OWLOntology) - Method in class owltools.sim2.FastOwlSimFactory
createOwlSim(OWLOntology) - Method in interface owltools.sim2.OwlSimFactory
createOwlSim(OWLOntology) - Method in class owltools.sim2.SimpleOwlSimFactory
createOwlSimFromOntologyFile(String) - Static method in class owltools.sim2.OwlSimUtil: Generates an OwlSim object from an ontology file does *not* call
createOwlSimFromOntologyFile(File) - Static method in class owltools.sim2.OwlSimUtil
createOwlSimFromOntologyFiles(String, Set<String>, Set<String>) - Static method in class owltools.sim2.OwlSimUtil
createPartOfLinks(Opts) - Method in class owltools.cli.CommandRunner: GeneOntology specific function to create links between molecular functions and their corresponding processes.
createPrediction(OWLClass, String, String, GeneAnnotation) - Method in class owltools.gaf.inference.BasicAnnotationPropagator
createPropagationRules(OWLGraphWrapper, OWLReasoner) - Method in class owltools.gaf.inference.BasicAnnotationPropagator: Create the default propagation rule set tailored for the GeneOntology.
createProperties(OortConfiguration) - Static method in class owltools.ontologyrelease.OortConfiguration: Create a Properties object for the given configuration.
createPropertyView(OWLObjectProperty) - Method in class owltools.sim2.preprocessor.AbstractSimPreProcessor
createPropertyView(OWLObjectProperty, OWLClass, String) - Method in class owltools.sim2.preprocessor.AbstractSimPreProcessor
createPropertyView(OWLObjectProperty, Set<OWLClass>) - Method in class owltools.sim2.preprocessor.AbstractSimPreProcessor
createPropertyView(OWLObjectProperty, Set<OWLClass>, String) - Method in class owltools.sim2.preprocessor.AbstractSimPreProcessor
createProteinClassesFromQuestForOrthologs(OWLOntology, InputStream, OWLClass) - Static method in class owltools.gaf.bioentities.ProteinTools: Add a named class for each protein extracted from the InputStream.
createProteinLabelOntology(OWLOntologyManager, IRI, File) - Static method in class owltools.gaf.bioentities.ProteinTools: Create a new ontology (with the given ID) for all proteins in the given Quest for Orthlogs seq XML file.
createProteinOntologies(Set<String>, String, String, String) - Static method in class owltools.gaf.bioentities.ProteinTools: Create protein ontologies from the qfo files.
createProteinOntologyIRI(String) - Static method in class owltools.gaf.bioentities.ProteinTools: Create an protein ontology IRI for the given subset name.
createRandomClassAssertions(OWLOntology, int, int) - Static method in class owltools.sim2.preprocessor.ABoxUtils
createRdfXml(Opts) - Method in class owltools.cli.GafCommandRunner
createReasoner(OWLOntology) - Method in class owltools.reasoner.GraphReasonerFactory
createReasoner(OWLOntology, OWLReasonerConfiguration) - Method in class owltools.reasoner.GraphReasonerFactory
createReasoner(OWLOntology) - Method in class owltools.reasoner.LazyExpressionMaterializingReasonerFactory: Deprecated.
createReasoner(OWLOntology, OWLReasonerConfiguration) - Method in class owltools.reasoner.LazyExpressionMaterializingReasonerFactory: Deprecated.
createReasoner(OWLOntology) - Method in class owltools.reasoner.PlaceholderJcelFactory
createReasoner(OWLOntology, OWLReasonerConfiguration) - Method in class owltools.reasoner.PlaceholderJcelFactory
createReasoner(OWLOntology) - Method in class owltools.reasoner.PrecomputingMoreReasonerFactory
createReasoner(OWLOntology, OWLReasonerConfiguration) - Method in class owltools.reasoner.PrecomputingMoreReasonerFactory
createReasonerDiff(OWLGraphWrapper, OWLGraphWrapper, String) - Static method in class owltools.diff.ReasonerDiff
createRelease() - Method in class owltools.ontologyrelease.OboOntologyReleaseRunner: Create a release, use the OortConfiguration instance specified the in constructor.
createShuntGraph(OWLGraphWrapper, OWLObject, Set<OWLPropertyExpression>, boolean) - Static method in class owltools.util.ShuntGraphUtils: Generate a shunt graph G = (V,E) which is a subset of the ontology G^O = (V^O,E^O) from a focus object X and relationset R such that: V contains every node reachable from X over some relations r1,t2,...
createShuntGraphPair(OWLGraphWrapper, OWLObject, Set<OWLPropertyExpression>, boolean) - Static method in class owltools.util.ShuntGraphUtils: Generate two shunt graphs, one based on the topology and the other based on the inferred graph.
createSimple() - Static method in class owltools.gaf.eco.EcoMapperFactory: Create a new SimpleEcoMapper with from the mapping loaded from the PURL.
createSimple(String) - Static method in class owltools.gaf.eco.EcoMapperFactory: Create a new SimpleEcoMapper with from the mapping loaded from the given source.
createSlim(Opts) - Method in class owltools.cli.CommandRunner
createSubOntologyFromDLQuery(String, OWLGraphWrapper, OWLGraphWrapper, OWLReasonerFactory, Set<OWLOntology>) - Method in class owltools.mooncat.QuerySubsetGenerator: Create a new sub ontology from a given DL query and source ontology.
createSubOntologyFromDLQuery(OWLClass, OWLGraphWrapper, OWLGraphWrapper, OWLReasonerFactory, Set<OWLOntology>) - Method in class owltools.mooncat.QuerySubsetGenerator: Create a new sub ontology from a given DL query and source ontology.
createSubSet(OWLGraphWrapper, Set<OWLClass>, Set<OWLOntology>) - Method in class owltools.mooncat.QuerySubsetGenerator: Given a collection of classes (such as those generated from a reasoner getSubClasses call), create a subset ontology and place it in targetGraph.
createSubSet(OWLGraphWrapper, Set<OWLClass>, Set<OWLOntology>, boolean, boolean) - Method in class owltools.mooncat.QuerySubsetGenerator
createSubsetMap(String) - Method in class owltools.mooncat.Mooncat
createSubsetMap(Set<OWLObject>) - Method in class owltools.mooncat.Mooncat: Note: this assumes you have already filtered any relations not to be propagated over from the graph
createSubsetTags(Opts) - Method in class owltools.cli.CommandRunner: Simple helper to create a subset tag for matching entities, allows to specify exceptions
createSuffixFiltered(Set<String>, OortConfiguration) - Static method in class owltools.ontologyrelease.logging.ExplicitReportFileHandler
createTaxon(OWLOntology, String) - Static method in class owltools.ncbi.NCBIConverter: Create a class for an NCBI Taxonomy ID and add it to the ontology.
createTaxonDisjointOverInTaxon(Opts) - Method in class owltools.cli.TaxonCommandRunner
createTraversingEcoMapper() - Static method in class owltools.gaf.eco.EcoMapperFactory: Create a TraversingEcoMapper instance using a new ParserWrapper to load ECO.
createTraversingEcoMapper(ParserWrapper) - Static method in class owltools.gaf.eco.EcoMapperFactory: Create a TraversingEcoMapper instance using the given ParserWrapper to load ECO.
createTraversingEcoMapper(ParserWrapper, String) - Static method in class owltools.gaf.eco.EcoMapperFactory: Create a TraversingEcoMapper instance using the given ParserWrapper to load ECO from the given location.
createTraversingEcoMapper(OWLGraphWrapper, OWLReasoner, boolean) - Static method in class owltools.gaf.eco.EcoMapperFactory: Create a TraversingEcoMapper instance using the given OWLGraphWrapper.
createUnionExpression(OWLObject, OWLObject, OWLObject) - Method in class owltools.sim.SimEngine
createWriter(OutputStream) - Method in class owltools.gaf.io.AbstractXmlWriter
crender(OWLObject) - Method in class owltools.io.CompactGraphClosureRenderer
cs - Variable in class owltools.sim2.scores.ElementPairScores
currentCols - Variable in class owltools.idmap.AbstractMappingParser
currentRow - Variable in class owltools.idmap.AbstractMappingParser
CUT_MASK - Static variable in class owltools.gaf.GeneAnnotation
CutoffException - Exception in owltools.sim2
CutoffException(String, Double, Double) - Constructor for exception owltools.sim2.CutoffException
CutoffException(String, Integer, Integer) - Constructor for exception owltools.sim2.CutoffException
CycleCheck - Class in owltools.ontologyverification.impl: Simple cycle check using the asserted super/sub class relations.
CycleCheck() - Constructor for class owltools.ontologyverification.impl.CycleCheck

D

d - Variable in class owltools.sim2.scores.AttributePairScores
DanglingReferenceCheck - Class in owltools.ontologyverification.impl: Check for dangling references in equivalence axioms.
DanglingReferenceCheck() - Constructor for class owltools.ontologyverification.impl.DanglingReferenceCheck
DatabaseDumper - Class in owltools.gaf.godb: Generates a relational database dump.
DatabaseDumper() - Constructor for class owltools.gaf.godb.DatabaseDumper
dataFactory - Static variable in class owltools.ncbi.NCBIOWL: Create OWLAPI utilities: A data factory.
DATE - Static variable in class owltools.gaf.parser.GAFParser
DB - Static variable in class owltools.gaf.parser.GAFParser
DB_OBJECT_ID - Static variable in class owltools.gaf.parser.GAFParser
DB_OBJECT_NAME - Static variable in class owltools.gaf.parser.GAFParser
DB_OBJECT_SYMBOL - Static variable in class owltools.gaf.parser.GAFParser
DB_OBJECT_SYNONYM - Static variable in class owltools.gaf.parser.GAFParser
DB_OBJECT_TYPE - Static variable in class owltools.gaf.parser.GAFParser
dbname - Variable in class owltools.gaf.metadata.AnnotationDocumentMetadata
debugClass - Variable in class owltools.sim2.FastOwlSim
declare(OWLOntology, OWLEntity) - Static method in class owltools.ncbi.OWLConverter: Convenience method for adding a declaration axiom to the ontology.
deepSimMethods - Variable in class owltools.sim.MultiSimilarity
DEFAULT_IRI_PREFIX - Static variable in class owltools.graph.OWLGraphWrapper
DefaultAspectProvider - Class in owltools.gaf.parser
DefaultAspectProvider(Map<String, String>) - Constructor for class owltools.gaf.parser.DefaultAspectProvider: Create a new aspect provider with the given (complete) id-aspect mappings.
defaultCol1 - Variable in class owltools.io.TableToAxiomConverter.Config
defaultCol2 - Variable in class owltools.io.TableToAxiomConverter.Config
defaultLCSElementFrequencyThreshold - Variable in class owltools.sim2.preprocessor.LCSEnabledSimPreProcessor
defaultNewIntersectionSimJThreshold - Variable in class owltools.sim2.preprocessor.LCSEnabledSimPreProcessor
defaultPrefix - Variable in class owltools.io.StanzaToOWLConverter.Config
defaultRandomWait() - Method in class org.bbop.golr.java.AbstractRetrieveGolr
defaultValue() - Method in enum owltools.sim2.SimpleOwlSim.SimConfigurationProperty
deleteFactCommand() - Method in class owltools.web.OWLHandler: Deprecated.
DelimitedLineRenderer - Class in owltools.sim2.io
DelimitedLineRenderer(PrintStream, String, String) - Constructor for class owltools.sim2.io.DelimitedLineRenderer
DelimitedLineRenderer(PrintStream) - Constructor for class owltools.sim2.io.DelimitedLineRenderer
DEPENDS_ON - Variable in class owltools.sim2.preprocessor.AbstractOBOSimPreProcessor
description - Variable in enum owltools.gfx.RelationType
description - Variable in class owltools.yaml.golrconfig.GOlrConfig
description - Variable in class owltools.yaml.golrconfig.GOlrField
DescriptionTreeSimilarity - Class in owltools.sim: A similarity between two entities constructed by threading two description trees together.
DescriptionTreeSimilarity() - Constructor for class owltools.sim.DescriptionTreeSimilarity
deserialize(JsonElement, Type, JsonDeserializationContext) - Method in class owltools.io.GeneralObjectDeserializer
destroy() - Method in class owltools.web.OWLServer
DEVELOPS_FROM - Variable in class owltools.sim2.preprocessor.AbstractOBOSimPreProcessor
directRestrictions - Variable in class owltools.frame.jsonld.ClassFrameLD
directSuperclasses - Variable in class owltools.frame.jsonld.ClassFrameLD
disableReleaseButton() - Method in class owltools.ontologyrelease.gui.OortGuiMainFrame
DisjunctiveSetSimilarity - Class in owltools.sim
DisjunctiveSetSimilarity() - Constructor for class owltools.sim.DisjunctiveSetSimilarity
display_name - Variable in class owltools.yaml.golrconfig.GOlrConfig
display_name - Variable in class owltools.yaml.golrconfig.GOlrField
dispose() - Method in interface owltools.gaf.eco.TraversingEcoMapper: Dispose this instance
dispose() - Method in class owltools.gaf.eco.TraversingEcoMapperImpl
dispose() - Method in class owltools.gaf.EcoTools: Deprecated.

Clean up the internal data structures, usually done as last operation.
dispose() - Method in class owltools.gaf.inference.AbstractAnnotationPredictor
dispose() - Method in interface owltools.gaf.inference.AnnotationPredictor
dispose() - Method in class owltools.gaf.inference.BasicAnnotationPropagator
dispose() - Method in class owltools.gaf.inference.FoldBasedPredictor
dispose() - Method in class owltools.gaf.parser.GafObjectsBuilder
dispose() - Method in class owltools.gaf.parser.GAFParser
dispose() - Method in class owltools.gaf.TaxonTools: Clean up the internal data structures, usually done as last operation.
dispose() - Method in class owltools.InferenceBuilder: Dispose the internal reasoner
dispose() - Method in class owltools.io.OWLPrettyPrinter.LabelProvider
dispose() - Method in class owltools.reasoner.LazyExpressionMaterializingReasoner: Deprecated.
dispose() - Method in class owltools.sim2.AbstractOwlSim
dispose() - Method in class owltools.sim2.FastOwlSim
dispose() - Method in class owltools.sim2.io.AbstractRenderer
dispose() - Method in class owltools.sim2.io.JSONRenderer
dispose() - Method in class owltools.sim2.io.OWLRenderer
dispose() - Method in interface owltools.sim2.io.SimResultRenderer
dispose() - Method in interface owltools.sim2.OwlSim: call when owlsim object is no longer required
dispose() - Method in class owltools.sim2.preprocessor.AbstractSimPreProcessor
dispose() - Method in interface owltools.sim2.preprocessor.SimPreProcessor: Clean the current instance, i.e.
DLQueryTool - Class in owltools.mooncat: Tools for running DL queries on OWLOntology.
DLQueryTool() - Constructor for class owltools.mooncat.DLQueryTool
document_category - Variable in class org.bbop.golr.java.RetrieveGolrBioentities.GolrBioentityDocument
document_category - Variable in class owltools.yaml.golrconfig.GOlrConfig
doInferencesForClass(OWLClass, OWLOntology) - Method in class owltools.InferenceBuilder: Only create inferences for an OWLClass, if this method returns true.
doWriteReport(String) - Method in class owltools.ontologyrelease.logging.ExplicitReportFileHandler
ds - Variable in class owltools.sim2.scores.ElementPairScores
dtFormat - Static variable in class owltools.gaf.rules.go.BasicChecksRule
dump() - Method in class owltools.gaf.godb.Dumper: dumps all data
dump() - Method in class owltools.gaf.godb.GoMySQLDatabaseDumper: dumps all tables
dumpAssociationModule() - Method in class owltools.gaf.godb.GoMySQLDatabaseDumper
dumpAssociationRowsForGaf(PrintStream, GafDocument) - Method in class owltools.gaf.godb.GoMySQLDatabaseDumper
dumpAssociationTable() - Method in class owltools.gaf.godb.GoMySQLDatabaseDumper
dumpDbxrefTable() - Method in class owltools.gaf.godb.GoMySQLDatabaseDumper
Dumper - Class in owltools.gaf.godb: Generates a dump of a combined set of ontologies, annotations and related data Currently there is one implementing subclass, for dumping a relational database.
Dumper() - Constructor for class owltools.gaf.godb.Dumper
dumpGeneProductRowsForGaf(PrintStream, GafDocument) - Method in class owltools.gaf.godb.GoMySQLDatabaseDumper
dumpGraphModule() - Method in class owltools.gaf.godb.GoMySQLDatabaseDumper
dumpGraphPathTable() - Method in class owltools.gaf.godb.GoMySQLDatabaseDumper
dumpMetaModule() - Method in class owltools.gaf.godb.GoMySQLDatabaseDumper
dumpOptModule() - Method in class owltools.gaf.godb.GoMySQLDatabaseDumper
dumpRow(PrintStream, Object...) - Method in class owltools.gaf.godb.DatabaseDumper
dumpShuntGraphs(Opts) - Method in class owltools.cli.SolrCommandRunner: Used for generating output for units tests in other languages.
dumpSpeciesRow(PrintStream, String) - Method in class owltools.gaf.godb.GoMySQLDatabaseDumper
dumpSpeciesTable() - Method in class owltools.gaf.godb.GoMySQLDatabaseDumper
dumpTerm2TermTable() - Method in class owltools.gaf.godb.GoMySQLDatabaseDumper
dumpTermSubsetTable() - Method in class owltools.gaf.godb.GoMySQLDatabaseDumper
dumpTermTable() - Method in class owltools.gaf.godb.GoMySQLDatabaseDumper

E

eco - Variable in class owltools.cli.GafCommandRunner
ECO_MAPPING_PURL - Static variable in interface owltools.gaf.eco.EcoMapper: Permanent URL for the mapping of GO evidence codes to ECO classes
ECO_PURL - Static variable in interface owltools.gaf.eco.EcoMapper: Permanent URL for the evidence code ontology (ECO) owl file.
ECO_PURL - Static variable in class owltools.gaf.EcoTools: Deprecated.
ECO_PURL_IRI - Static variable in interface owltools.gaf.eco.EcoMapper: IRI for the evidence code ontology (ECO) owl file.
EcoMapper - Interface in owltools.gaf.eco
EcoMapperFactory - Class in owltools.gaf.eco: Factory to create instances of EcoMapper and TraversingEcoMapper.
EcoMapperFactory.OntologyMapperPair<MAPPER extends EcoMapper> - Class in owltools.gaf.eco
EcoMapperImpl - Class in owltools.gaf.eco
EcoTools - Class in owltools.gaf: Deprecated.
use EcoMapper, TraversingEcoMapper and EcoMapperFactory.
EcoTools(OWLGraphWrapper, OWLReasoner, boolean) - Constructor for class owltools.gaf.EcoTools: Deprecated.

Create an instance for the given graph and reasoner.
EcoTools(ParserWrapper) - Constructor for class owltools.gaf.EcoTools: Deprecated.

Create a new instance using the given ParserWrapper to load the ECO.
EcoTools(OWLGraphWrapper) - Constructor for class owltools.gaf.EcoTools: Deprecated.

Create a new instance using the ECO graph wrapper.
edges - Variable in class owltools.graph.shunt.OWLShuntGraph
edgeSetToExpression(Set<OWLGraphEdge>) - Method in class owltools.sim.SimEngine
EdgeTableRenderer - Class in owltools.io: renders all edges in a simple TSV format
EdgeTableRenderer(PrintStream) - Constructor for class owltools.io.EdgeTableRenderer
EdgeTableRenderer(String) - Constructor for class owltools.io.EdgeTableRenderer
edgeToSourceExpression(OWLGraphEdge) - Method in class owltools.graph.OWLGraphWrapperEdgesExtended: Translates the source of an OWLGraphEdge into an OWLClassExpression (but, as the method OWLGraphEdge.getSource() returns an OWLObject, this method also returns an OWLObject).
edgeToTargetExpression(OWLGraphEdge) - Method in class owltools.graph.OWLGraphWrapperEdges: pack/translate an edge (either asserted or a graph closure edge) into an OWL class expression according to the OWLGraph to OWLOntology translation rules.
eiSetSize - Variable in class owltools.sim2.EnrichmentResult
ElementPairScores - Class in owltools.sim2.scores: A pair of scores for any given pair of individuals
ElementPairScores(OWLNamedIndividual, OWLNamedIndividual) - Constructor for class owltools.sim2.scores.ElementPairScores
enabled_by - Variable in class org.geneontology.lego.model.LegoTools: Deprecated.
enableReleaseButton() - Method in class owltools.ontologyrelease.gui.OortGuiMainFrame
end() - Method in class owltools.gaf.io.AbstractGafWriter: Called after the writing of a GafDocument has been finished.
end() - Method in class owltools.gaf.io.GafWriter.BufferedGafWriter
end() - Method in class owltools.gaf.io.GafWriter
end() - Method in class owltools.gaf.io.GpadWriter: Called after the writing of a GafDocument has been finished.
end() - Method in class owltools.gaf.io.GpiWriter: Called after the writing of a GafDocument has been finished.
end(PrintWriter, OWLGraphWrapper) - Method in class owltools.ontologyrelease.reports.OntologyReportGenerator.AbstractReport
end(PrintWriter, OWLGraphWrapper) - Method in interface owltools.ontologyrelease.reports.OntologyReportGenerator.OntologyReport: End the report.
endTaskNotify(String) - Method in class owltools.profile.Profiler
enforceEL(OWLGraphWrapper) - Static method in class owltools.InferenceBuilder
enforceEL(OWLGraphWrapper, IRI) - Static method in class owltools.InferenceBuilder: Create an ontology with EL as description logic profile.
enrichedClass - Variable in class owltools.sim.OldSimpleOwlSim.EnrichmentResult
enrichedClass - Variable in class owltools.sim2.EnrichmentResult
enrichedClassSize - Variable in class owltools.sim2.EnrichmentResult
enrichmentConfig - Variable in class owltools.sim.OldSimpleOwlSim
enrichmentConfig - Variable in class owltools.sim2.AbstractOwlSim
EnrichmentConfig - Class in owltools.sim2
EnrichmentConfig() - Constructor for class owltools.sim2.EnrichmentConfig
EnrichmentEngine - Class in owltools.sim
EnrichmentEngine() - Constructor for class owltools.sim.EnrichmentEngine
EnrichmentResult - Class in owltools.sim2
EnrichmentResult(OWLClass, OWLClass, double, double) - Constructor for class owltools.sim2.EnrichmentResult
EnrichmentResult(OWLClass, OWLClass, double, double, int, int, int, int) - Constructor for class owltools.sim2.EnrichmentResult
equals(Object) - Method in class owltools.gaf.ExtensionExpression
equals(Object) - Method in class owltools.gaf.inference.Prediction
equals(Object) - Method in class owltools.gfx.OWLGraphStrokeEdge
equals(Object) - Method in class owltools.graph.OWLGraphEdge
equals(Object) - Method in class owltools.graph.OWLGraphWrapper.Synonym
equals(Object) - Method in class owltools.graph.OWLQuantifiedProperty
equals(Object) - Method in class owltools.graph.shunt.OWLShuntEdge
equals(Object) - Method in class owltools.graph.shunt.OWLShuntNode
equals(Object) - Method in class owltools.ontologyverification.CheckWarning
equals(Object) - Method in class owltools.ontologyverification.impl.AbstractCheck
equals(Object) - Method in class owltools.phenolog.GenePheno
equals(Object) - Method in class owltools.phenolog.Individual
equals(Object) - Method in class owltools.phenolog.IndividualPair
equals(Object) - Method in class owltools.phenolog.Pheno
equals(Object) - Method in class owltools.RedundantInferences.RedundantAxiom
equals(Object) - Method in class owltools.sim.OldSimpleOwlSim.OWLClassExpressionPair
equals(Object) - Method in class owltools.sim.OWLClassExpressionPair
equals(Object) - Method in class owltools.sim.OWLObjectPair
equals(Object) - Method in class owltools.sim2.EnrichmentResult
equals(Object) - Method in class owltools.sim2.io.SimResultRenderer.AttributesSimScores
equals(Object) - Method in class owltools.sim2.scores.ElementPairScores
equals(Object) - Method in class owltools.util.BloomFilter: Compares the contents of two instances to see if they are equal.
equals(Object) - Method in class owltools.util.ClassExpressionPair
equalsGCI(OWLGraphEdge) - Method in class owltools.graph.OWLGraphEdge: Checks that the gciFiller and gciRelation of this OWLGraphEdge an of e are equals.
equalsIgnoreOntology(Object) - Method in class owltools.graph.OWLGraphEdge: Equals method ignoring the OWLOntology the OWLGraphEdges compared belong to, as opposed to the #equals() method, that takes into account the ontologies for comparison.
equalsIgnoreOntologyAndGCI(Object) - Method in class owltools.graph.OWLGraphEdge: Equals method ignoring the OWLOntology the OWLGraphEdges compared belong to, and ignoring their gciFillers and gciRelations (as opposed to the #equals() method, that takes into account everything for comparison).
EquivalenceSetMergeUtil - Class in owltools.mooncat
EquivalenceSetMergeUtil(OWLGraphWrapper, OWLReasoner) - Constructor for class owltools.mooncat.EquivalenceSetMergeUtil
equivalentClasses - Variable in class owltools.frame.jsonld.ClassFrameLD
error(String) - Static method in class owltools.ncbi.NCBI2OWL
errorCount - Variable in class owltools.ontologyverification.OntologyCheckHandler.CheckSummary
errorFontName - Variable in class owltools.gfx.GraphStyle
errorFontSize - Variable in class owltools.gfx.GraphStyle
errorMessage - Variable in class owltools.gfx.HierarchyImage
ErrorReportFileHandler - Class in owltools.ontologyrelease.logging
ErrorReportFileHandler(File, String) - Constructor for class owltools.ontologyrelease.logging.ErrorReportFileHandler
errors - Variable in class owltools.InferenceBuilder.ConsistencyReport
escape(String, char) - Static method in class owltools.ontologyrelease.OortConfiguration: Only public for testing purposes.
EVIDENCE - Static variable in class owltools.gaf.parser.GAFParser
excludeAllWith(OWLAnnotationProperty, OWLOntology) - Method in class owltools.graph.OWLGraphWrapperEdges.Config
excludeClassesInComparison - Variable in class owltools.sim.SimEngine
excludeMetaClass - Variable in class owltools.graph.OWLGraphWrapperEdges.Config
excludeProperty(OWLObjectProperty, OWLQuantifiedProperty.Quantifier) - Method in class owltools.graph.OWLGraphWrapperEdges.Config
excludeProperty(OWLObjectProperty) - Method in class owltools.graph.OWLGraphWrapperEdges.Config
execute() - Method in class owltools.ontologyrelease.BuildVersionId: Deprecated.

Run task.
execute() - Method in class owltools.ontologyrelease.GetOntologyId: Deprecated.
execute() - Method in class owltools.ontologyrelease.OboProperty: Deprecated.
executeDLQuery(String, OWLGraphWrapper, OWLReasonerFactory) - Static method in class owltools.mooncat.DLQueryTool: Execute the DL query on the given ontology graph.
executeRelease(OortGuiConfiguration) - Method in class owltools.ontologyrelease.gui.OortGuiMainFrame: Execute the actual release.
executeTarjan(Adjacency<NODE>) - Method in class owltools.util.AbstractTarjan
executeTarjan(Adjacency<NODE>) - Method in interface owltools.util.Tarjan: Create the strongly connected components for the given graph.
exit(int) - Method in class owltools.cli.CommandRunner
exitOnException - Variable in class owltools.cli.CommandRunner
expand(OWLOntology, Set<OWLClass>) - Method in class owltools.cli.BioChebiGenerator: Create the GCIs for BioChEBI.
expandPropertyChain(List<OWLObjectPropertyExpression>) - Method in class owltools.mooncat.PropertyViewOntologyBuilder
expandPropertyChain(List<OWLObjectPropertyExpression>, int) - Method in class owltools.mooncat.PropertyViewOntologyBuilder
expandPropertyChain(List<OWLObjectPropertyExpression>, OWLClassExpression) - Method in class owltools.mooncat.PropertyViewOntologyBuilder
expandRelationChain(OWLObjectProperty) - Method in class owltools.graph.OWLGraphWrapperEdges: If available, return the elements of the equivalent property chain.
expectedFalsePositiveProbability() - Method in class owltools.util.BloomFilter: Calculates the expected probability of false positives based on the number of expected filter elements and the size of the Bloom filter.
expectedNumCols - Variable in class owltools.idmap.AbstractMappingParser
experimentalLoadComplexAnnotationSolr(Opts) - Method in class owltools.cli.SolrCommandRunner: Experimental method for trying out the loading of complex_annotation doc type
experimentalPredictionReportWriter - Variable in class owltools.gaf.rules.AnnotationRulesReportWriter
experimentalPredictionWriter - Variable in class owltools.gaf.rules.AnnotationRulesReportWriter
explainTaxonConstraint(Collection<String>, Collection<String>) - Method in class owltools.mooncat.SpeciesSubsetterUtil: Provides explanations about the sources of some taxon constraints on the OWLClasses provided through clsIds, related to the taxa provided through taxonIds.
ExplicitReportFileHandler - Class in owltools.ontologyrelease.logging
ExplicitReportFileHandler(OortConfiguration) - Constructor for class owltools.ontologyrelease.logging.ExplicitReportFileHandler
EXPRESSED_IN - Variable in class owltools.sim2.preprocessor.AbstractOBOSimPreProcessor
Expression - Interface in owltools.frame
ExpressionLD - Class in owltools.frame.jsonld
ExpressionLD() - Constructor for class owltools.frame.jsonld.ExpressionLD
ExpressionSimPreProcessor - Class in owltools.sim2.preprocessor
ExpressionSimPreProcessor() - Constructor for class owltools.sim2.preprocessor.ExpressionSimPreProcessor
extendEdge(OWLGraphEdge) - Method in class owltools.sim.SimEngine
ExtensionExpression - Class in owltools.gaf: Corresponds to col16 in GAF2.0
ExtensionExpression() - Constructor for class owltools.gaf.ExtensionExpression
ExtensionExpression(String, String) - Constructor for class owltools.gaf.ExtensionExpression
External2GoReports - Class in owltools.ontologyrelease.reports.go: Provide reports for all external to go mappings.
External2GoReports.External2GoKegg - Class in owltools.ontologyrelease.reports.go
External2GoReports.External2GoMetaCyc - Class in owltools.ontologyrelease.reports.go
External2GoReports.External2GoReactome - Class in owltools.ontologyrelease.reports.go
External2GoReports.External2GoResid - Class in owltools.ontologyrelease.reports.go
External2GoReports.External2GoRhea - Class in owltools.ontologyrelease.reports.go
External2GoReports.External2GoUmBbdEnzymeId - Class in owltools.ontologyrelease.reports.go
External2GoReports.External2GoUmBbdPathwayId - Class in owltools.ontologyrelease.reports.go
External2GoReports.External2GoUmBbdReactionId - Class in owltools.ontologyrelease.reports.go
External2GoReports.External2GoWikipedia - Class in owltools.ontologyrelease.reports.go
extractAnnotationValue(Opts) - Method in class owltools.cli.CommandRunner
extractBridgeOntologies(String, boolean) - Method in class owltools.mooncat.BridgeExtractor: given a source ontology O:
extractClassesFromDeclarations(Set<OWLAxiom>) - Method in class owltools.sim2.preprocessor.AbstractSimPreProcessor
extractExtensionFile(Opts) - Method in class owltools.cli.CommandRunner: Extract all xps (OWLEquivalentClassesAxiom) from the loaded ontology.
extractMetadata(LegoMetadata, Iterable<? extends OWLAxiom>) - Static method in class org.geneontology.lego.model.LegoMetadata: Deprecated.
extractMetadata(LegoMetadata, OWLAxiom) - Static method in class org.geneontology.lego.model.LegoMetadata: Deprecated.
extractModules() - Method in class owltools.mooncat.Mooncat
extractModules(OWLOntology) - Method in class owltools.mooncat.Mooncat
extractModules(Set<OWLClass>, Set<OWLClass>) - Method in class owltools.mooncat.Mooncat
extractOntologyMetadata(OWLGraphWrapper, String) - Static method in class owltools.mooncat.ontologymetadata.ImportChainExtractor
extractOntologySubsetByGaf(Opts) - Method in class owltools.cli.GafCommandRunner
extractPropertyOntology() - Method in class owltools.mooncat.PropertyExtractor
extractPropertyOntology(IRI) - Method in class owltools.mooncat.PropertyExtractor
extractPropertyOntology(IRI, OWLOntology) - Method in class owltools.mooncat.PropertyExtractor
extractPropertyOntology(IRI, Set<OWLProperty>) - Method in class owltools.mooncat.PropertyExtractor: Returns a new ontology containing declarations for each prop in props, its closure, together with associated axioms

F

fail() - Method in class owltools.cli.Opts: Send a fail.
FastOwlSim - Class in owltools.sim2: Faster implementation of OwlSim Makes use of integers to index classes, and bitmaps to represent class sets.
FastOwlSim(OWLOntology) - Constructor for class owltools.sim2.FastOwlSim
FastOwlSim(OWLReasoner) - Constructor for class owltools.sim2.FastOwlSim
FastOwlSim.ClassCount - Class in owltools.sim2
FastOwlSim.ClassCount(OWLClass, Double) - Constructor for class owltools.sim2.FastOwlSim.ClassCount
FastOwlSim.ClassCount(OWLClass, Integer) - Constructor for class owltools.sim2.FastOwlSim.ClassCount
FastOwlSimFactory - Class in owltools.sim2
FastOwlSimFactory() - Constructor for class owltools.sim2.FastOwlSimFactory
featureToAttributeMap - Variable in class owltools.sim.MultiSimilarity
field - Variable in class owltools.flex.FlexLine
field() - Method in class owltools.flex.FlexLine: Return the field name.
fields - Variable in class owltools.yaml.golrconfig.GOlrConfig
fileCount - Variable in class owltools.panther.PANTHERForest
fill - Variable in class owltools.gfx.GraphStyle
fill - Variable in class owltools.gfx.OWLGraphLayoutNode
filter_weights - Variable in class owltools.yaml.golrconfig.GOlrConfig
filter_weights - Variable in class owltools.yaml.golrconfig.GOlrField
filterByDirectProperty(Set<OWLClass>, OWLObjectProperty) - Method in class owltools.sim2.preprocessor.PhenoSimHQEPreProcessor: Note: if the ontology contains Z SubClassOf df some Z2, Z2 SubClassOf U then Z2 will be retained, but U will not.
filterClasses(Set<OWLClass>) - Method in class owltools.graph.OWLGraphManipulator: Filter from the ontologies all OWLClasses present in classesToKeep, and then update the OWLGraphWrapper container.
filterEdges(Set<OWLGraphEdge>, Set<? extends OWLPropertyExpression>) - Method in class owltools.graph.OWLGraphWrapperEdges
filterEnrichmentResults(List<EnrichmentResult>) - Method in class owltools.sim2.AbstractOwlSim
filterExtensionFile(Opts) - Method in class owltools.cli.CommandRunner: Retain only subclass of axioms and intersection of axioms if they contain a class in it's signature of a given set of parent terms.
filterObjects(Set<OWLObject>) - Method in class owltools.sim.SimEngine
filterRelations(Collection<String>, boolean) - Method in class owltools.graph.OWLGraphManipulator: Filter the OWLAxioms in the ontologies to keep only those that correspond to OWLObjectPropertys listed in allowedRels, as OBO-style IDs.
filterSubgraphs(Collection<String>) - Method in class owltools.graph.OWLGraphManipulator: Keep in the ontologies only the subgraphs starting from the provided OWLClasses, and their ancestors.
filterUnused(Set<OWLAxiom>) - Method in class owltools.sim2.preprocessor.AbstractSimPreProcessor: Call after createPropertyView() if the view contains a class C' = P some C, and C' does not classify and individuals or classes in the ontology (excluding other view classes in this set), then C' and related axioms are removed TODO: note that in general this should not be used if P is reflexive, as there will trivially be subclasses of the view class
filterWhere - Variable in class owltools.idmap.IDMappingPIRParser
findCardinalityConstraints(OWLOntology) - Static method in class owltools.graph.CardinalityContraintsTools: Find the axioms with cardinality constraints.
findCommonAncestors(OWLGraphWrapper, OWLObject, OWLObject) - Static method in class owltools.graph.OWLGraphUtil
findCommonAncestors(OWLGraphWrapper, OWLObject, OWLObject, Set<OWLPropertyExpression>) - Static method in class owltools.graph.OWLGraphUtil: Find common ancestors to x and y that can be reached over the specified set of relations.
findCommonSubsumersAsEdges(OWLGraphWrapper, OWLObject, OWLObject) - Static method in class owltools.graph.OWLGraphUtil
findCycles(OWLGraphWrapper) - Static method in class owltools.ontologyrelease.OboBasicDagCheck: Find cycles of any relationship.
findDifferentia(OWLClass, OWLClass, OWLClass) - Method in class owltools.sim2.ClassDifferentiaLearner
findLeastCommonAncestors(OWLGraphWrapper, OWLObject, OWLObject) - Static method in class owltools.graph.OWLGraphUtil
findLeastCommonAncestors(OWLGraphWrapper, OWLObject, OWLObject, Set<OWLPropertyExpression>) - Static method in class owltools.graph.OWLGraphUtil: Find lest common ancestors to x and y that can be reached over the specified set of relations.
findLeastCommonSubsumersAsEdges(OWLGraphWrapper, OWLObject, OWLObject) - Static method in class owltools.graph.OWLGraphUtil
findMatches(Set<OWLClass>, String) - Method in class owltools.sim2.AbstractOwlSim
findMatches(OWLNamedIndividual, String) - Method in class owltools.sim2.AbstractOwlSim
findMatches(OWLNamedIndividual, String, double, double) - Method in class owltools.sim2.AbstractOwlSim
findMatches(Set<OWLClass>, String, double, double) - Method in class owltools.sim2.FastOwlSim
findMatches(Set<OWLClass>, String) - Method in interface owltools.sim2.OwlSim: Find all similar matches to a pseudo-individual with a set of attributes when compared to loaded individuals using getGroupwiseSimilarity with default cutoffs.
findMatches(Set<OWLClass>, String, double, double) - Method in interface owltools.sim2.OwlSim: Find all similar matches to a pseudo-individual with a set of attributes when compared to loaded individuals using getGroupwiseSimilarity with minSimJPct and minMaxIC cutoffs.
findMatches(OWLNamedIndividual, String) - Method in interface owltools.sim2.OwlSim
findMatches(OWLNamedIndividual, String, double, double) - Method in interface owltools.sim2.OwlSim
findMatches(Set<OWLClass>, String) - Method in class owltools.sim2.SimpleOwlSim
findMatches(Set<OWLClass>, String, double, double) - Method in class owltools.sim2.SimpleOwlSim
findMatchesRefactored(Set<OWLClass>, String) - Method in class owltools.sim2.FastOwlSim
findMatchesRefactored(Set<OWLClass>, String, double, double) - Method in class owltools.sim2.FastOwlSim
findMatchesWithin(OWLNamedIndividual, Set<OWLNamedIndividual>) - Method in class owltools.sim2.FastOwlSim
findMatchesWithin(Set<OWLClass>, Set<OWLNamedIndividual>, double, double) - Method in class owltools.sim2.FastOwlSim
findMatchesWithin(OWLNamedIndividual, Set<OWLNamedIndividual>) - Method in interface owltools.sim2.OwlSim
findMatchesWithin(OWLNamedIndividual, Set<OWLNamedIndividual>) - Method in class owltools.sim2.SimpleOwlSim
findRedundantSubClassAxioms(Iterable<OWLClass>, OWLOntology, OWLReasoner) - Static method in class owltools.RedundantInferences: Find redundant and marked as inferred axioms for each class in the given ontology.
findRelatedAxioms(Set<OWLObject>, OWLGraphWrapper) - Static method in class owltools.mooncat.Mooncat
findTaggedEntities(OWLAnnotationProperty, Set<OWLAnnotationValue>, OWLGraphWrapper) - Static method in class owltools.mooncat.Mooncat
FlexCollection - Class in owltools.flex: Pull defined sources into a middle state for output, loading into Solr, etc.
FlexCollection(OWLGraphWrapper) - Constructor for class owltools.flex.FlexCollection: More fun init.
FlexCollection(ConfigManager, OWLGraphWrapper) - Constructor for class owltools.flex.FlexCollection: More fun init.
FlexDocument - Class in owltools.flex: Pull defined sources into a middle state for output, loading into Solr, etc.
FlexDocument() - Constructor for class owltools.flex.FlexDocument: Init.
flexDumpOntologySolr(Opts) - Method in class owltools.cli.SolrCommandRunner: Dump experimental flexible loader output to JSON(?) blob.
FlexLine - Class in owltools.flex: Workalike for a singleton line in a Solr document.
FlexLine(String, String) - Constructor for class owltools.flex.FlexLine: Singleton init.
FlexLine(String, ArrayList<String>) - Constructor for class owltools.flex.FlexLine: List init.
flexLoadOntologySolr(Opts) - Method in class owltools.cli.SolrCommandRunner: Flexible loader for ontologies--uses the YAML config to find loading functions.
FlexSolrDocumentLoader - Class in owltools.solrj: A slightly generic class for loading a Solr index compatible with the constraints defined by a BBOP-JS Solr index.
FlexSolrDocumentLoader(String, FlexCollection) - Constructor for class owltools.solrj.FlexSolrDocumentLoader
FlexSolrDocumentLoader(SolrServer, FlexCollection) - Constructor for class owltools.solrj.FlexSolrDocumentLoader
flush() - Method in class owltools.io.OWLGsonParser
flush() - Method in class owltools.io.OWLGsonRenderer
flush() - Method in class owltools.reasoner.LazyExpressionMaterializingReasoner: Deprecated.
flush() - Method in class owltools.sim2.preprocessor.AbstractSimPreProcessor
fold(GafDocument) - Method in class owltools.gaf.owl.AnnotationExtensionFolder
fold(GafDocument, boolean) - Method in class owltools.gaf.owl.AnnotationExtensionFolder
fold(GafDocument, GeneAnnotation) - Method in class owltools.gaf.owl.AnnotationExtensionFolder: given an annotation to a pre-existing term, this will return a set of zero or more annotations to new terms that are generated from folding the annotation extensions into newly created term
FoldBasedPredictor - Class in owltools.gaf.inference: Use a reasoner to find more specific named classes for annotations with extension expressions.
FoldBasedPredictor(GafDocument, OWLGraphWrapper, boolean) - Constructor for class owltools.gaf.inference.FoldBasedPredictor
foldedClassMap - Variable in class owltools.gaf.owl.AnnotationExtensionFolder
foldGafExtensions(Opts) - Method in class owltools.cli.GafCommandRunner
font - Variable in class owltools.gfx.OWLGraphLayoutNode
forceReflexivePropertyCreation - Variable in class owltools.sim.DescriptionTreeSimilarity
forCodes(String) - Static method in enum owltools.gfx.RelationType
formalCode - Variable in enum owltools.gfx.RelationType
format - Static variable in class owltools.ncbi.OWLConverter: Create OWLAPI utilities: An ontology format.
format(Date) - Static method in class owltools.ontologyrelease.OntologyVersionTools: Format a date into the canonical format of YYYY-MM-DD.
FormattedRenderer - Class in owltools.sim2.io
FormattedRenderer(PrintStream, OWLPrettyPrinter) - Constructor for class owltools.sim2.io.FormattedRenderer
FormattedRenderer(OWLPrettyPrinter) - Constructor for class owltools.sim2.io.FormattedRenderer
FormattedRenderer(OWLGraphWrapper) - Constructor for class owltools.sim2.io.FormattedRenderer
FormattedRenderer(OWLGraphWrapper, PrintStream) - Constructor for class owltools.sim2.io.FormattedRenderer
Frame - Interface in owltools.frame
FrameLD - Class in owltools.frame.jsonld
FrameLD() - Constructor for class owltools.frame.jsonld.FrameLD
FrameMaker - Class in owltools.frame
FrameMaker() - Constructor for class owltools.frame.FrameMaker
FrameMakerLD - Class in owltools.frame.jsonld
FrameMakerLD(OWLGraphWrapper) - Constructor for class owltools.frame.jsonld.FrameMakerLD
fromJson(String) - Static method in class owltools.io.GeneralObjectDeserializer: This is a convenience routine which deserializes a string into one of the five general Java types as described above.
fromJson(Reader) - Static method in class owltools.io.GeneralObjectDeserializer: This is a convenience routine deserializes the Json read from the specified reader into one of the five general Java types as described above.
fsimAttTopSimJ(Opts) - Method in class owltools.cli.Sim2CommandRunner
fsimBasic(Opts) - Method in class owltools.cli.Sim2CommandRunner
fsimCompareAtts(Opts) - Method in class owltools.cli.Sim2CommandRunner
fsimCompareAttsLCS(Opts) - Method in class owltools.cli.Sim2CommandRunner
fsimCompareAttsLite(Opts) - Method in class owltools.cli.Sim2CommandRunner
fsimCompareAttsSimJ(Opts) - Method in class owltools.cli.Sim2CommandRunner
fsimFindMatches(Opts) - Method in class owltools.cli.Sim2CommandRunner
fsimSearchAll(Opts) - Method in class owltools.cli.Sim2CommandRunner
fsimTest(Opts) - Method in class owltools.cli.Sim2CommandRunner

G

g - Variable in class owltools.cli.CommandRunner
g - Variable in class owltools.gfx.OWLGraphLayoutRenderer
gaCalculateSpecificity(Opts) - Method in class owltools.cli.GafCommandRunner
gaf(Opts) - Method in class owltools.cli.GafCommandRunner: Used for loading GAFs into memory
gaf2oa(Opts) - Method in class owltools.cli.GafCommandRunner
gaf2Owl(Opts) - Method in class owltools.cli.GafCommandRunner
gaf2OwlSimple(Opts) - Method in class owltools.cli.GafCommandRunner: Created to mimic the translation to OWL for GAF checks
GAF_Date_Format - Static variable in class owltools.gaf.GeneAnnotation: Provide a thread-safe formatter for a GAF date.
GAF_LINE_NUMBER_ANNOTATION_PROPERTY_IRI - Static variable in class owltools.gaf.owl.GAFOWLBridge
GafCommandRunner - Class in owltools.cli: GAF tools for command-line, includes validation of GAF files.
GafCommandRunner() - Constructor for class owltools.cli.GafCommandRunner
gafCompareBasic(Opts) - Method in class owltools.cli.GafCommandRunner
gafdoc - Variable in class owltools.cli.GafCommandRunner
gafdocs - Variable in class owltools.gaf.godb.Dumper
GafDocument - Class in owltools.gaf: Representation of a gene annotation file (GAF).
GafDocument(String, String) - Constructor for class owltools.gaf.GafDocument: Create a new document instance.
GafDocument(String, String, Map<String, Bioentity>) - Constructor for class owltools.gaf.GafDocument: Create a new document instance.
gafDocumentSizeInBytes - Variable in class owltools.gaf.metadata.AnnotationDocumentMetadata
gafFoldInferences(Opts) - Method in class owltools.cli.GafCommandRunner
GafObjectsBuilder - Class in owltools.gaf.parser: The class builds GafDocument a gaf file.
GafObjectsBuilder() - Constructor for class owltools.gaf.parser.GafObjectsBuilder
GafObjectsBuilder(int) - Constructor for class owltools.gaf.parser.GafObjectsBuilder
GAFOWLBridge - Class in owltools.gaf.owl
GAFOWLBridge(OWLGraphWrapper) - Constructor for class owltools.gaf.owl.GAFOWLBridge
GAFOWLBridge(OWLGraphWrapper, OWLOntology) - Constructor for class owltools.gaf.owl.GAFOWLBridge: The ontology generated from the gaf will be placed in tgtOnt The graphwrapper object should include ontologies required to resolve certain entities, including the relations used in col16.
GAFOWLBridge.BioentityMapping - Enum in owltools.gaf.owl
GAFOWLBridge.GAFDescription - Class in owltools.gaf.owl
GAFOWLBridge.GAFDescription(OWLObjectSomeValuesFrom, String) - Constructor for class owltools.gaf.owl.GAFOWLBridge.GAFDescription
GAFOWLBridge.Vocab - Enum in owltools.gaf.owl
GAFParser - Class in owltools.gaf.parser
GAFParser() - Constructor for class owltools.gaf.parser.GAFParser
gafQuery(Opts) - Method in class owltools.cli.GafCommandRunner
gafRemoveRedundant(Opts) - Method in class owltools.cli.GafCommandRunner
GafSolrDocumentLoader - Class in owltools.solrj: A very specific class for the specific use case of loading in a GAF-like document into a Solr index.
GafSolrDocumentLoader(String) - Constructor for class owltools.solrj.GafSolrDocumentLoader
GafSolrDocumentLoader(SolrServer, int) - Constructor for class owltools.solrj.GafSolrDocumentLoader: Use for test purposes.
gafTermCounts(Opts) - Method in class owltools.cli.GafCommandRunner
gafTermICValues(Opts) - Method in class owltools.cli.GafCommandRunner
GafWriter - Class in owltools.gaf.io: Write a Gene Annotation File to a given stream or file.
GafWriter() - Constructor for class owltools.gaf.io.GafWriter
GafWriter.BufferedGafWriter - Class in owltools.gaf.io: Helper class to create a list of all GeneAnnotation lines, excluding any headers.
Can be used for sorting.
GafWriter.BufferedGafWriter() - Constructor for class owltools.gaf.io.GafWriter.BufferedGafWriter
gafXpPredict(Opts) - Method in class owltools.cli.GafCommandRunner
GENE_PRODUCT_ISOFORM - Static variable in class owltools.gaf.parser.GAFParser
GeneAnnotation - Class in owltools.gaf: Representation of a gene annotation.
GeneAnnotation() - Constructor for class owltools.gaf.GeneAnnotation
GeneAnnotation(GeneAnnotation) - Constructor for class owltools.gaf.GeneAnnotation
GeneOntologyReports - Class in owltools.ontologyrelease.reports.go: Provide all reports for the GeneOntology.
GenePheno - Class in owltools.phenolog: Represents a characteristic of an individual.
GenePheno(String, String, String, String) - Constructor for class owltools.phenolog.GenePheno
GenePheno(String, String) - Constructor for class owltools.phenolog.GenePheno
GenePhenoTsvParser - Class in owltools.phenolog
GenePhenoTsvParser() - Constructor for class owltools.phenolog.GenePhenoTsvParser
generalGson - Static variable in class owltools.io.GeneralObjectDeserializer: generalGson is a Gson instance which provides for general deserializing.
generalLoadOntologySolr(Opts) - Method in class owltools.cli.SolrCommandRunner: Trivial hard-wired (and optional) method for loading collected ontology information into the "general" schema (general-config.yaml) for GO.
GeneralObjectDeserializer - Class in owltools.io: Use this class to create a general object-tree using the Gson parser (see http://code.google.com/p/google-gson/).
GeneralObjectDeserializer() - Constructor for class owltools.io.GeneralObjectDeserializer
generate(OWLGraphWrapper) - Method in class owltools.ontologyrelease.OntologyMetadata
generateAssociations(OWLOntology) - Method in class owltools.gaf.owl.SimpleABoxToGAF
generateAssociations(OWLNamedIndividual, OWLOntology) - Method in class owltools.gaf.owl.SimpleABoxToGAF
generateGroupingClasses() - Method in class owltools.sim.OldSimpleOwlSim: Deprecated.
generateJsonGafStatistics(Opts) - Method in class owltools.cli.GafCommandRunner
generateLabel(OWLClassExpression) - Method in class owltools.sim2.preprocessor.AbstractSimPreProcessor
generateLeastCommonSubsumers(Set<OWLClass>) - Method in class owltools.sim2.preprocessor.LCSEnabledSimPreProcessor: generates new LCS grouping classes
generateLeastCommonSubsumersForAttributeClasses() - Method in class owltools.sim2.preprocessor.LCSEnabledSimPreProcessor
generatePropertyViews() - Method in class owltools.sim.OldSimpleOwlSim: Deprecated.
generateReports(OWLGraphWrapper) - Method in class owltools.ontologyrelease.reports.OntologyReportGenerator: Generate the internal reports for a given ontology.
generateSourcePropertyViews() - Method in class owltools.sim.OldSimpleOwlSim: Deprecated.
GenericReasonerValidationCheck - Class in owltools.gaf.rules: This check using the ElkReasoner will not detect unsatisfiable classes, which result from inverse_of object properties.
GenericReasonerValidationCheck() - Constructor for class owltools.gaf.rules.GenericReasonerValidationCheck
get(OWLClass, OWLClass) - Method in class owltools.gaf.inference.ClassTaxonMatrix
getA() - Method in class owltools.sim.OWLObjectPair
getA() - Method in class owltools.sim2.scores.AttributePairScores
getA() - Method in class owltools.sim2.scores.ElementPairScores
getA() - Method in interface owltools.sim2.scores.PairScores
getAboxProperty() - Method in class owltools.sim2.preprocessor.AbstractSimPreProcessor
getAboxProperty() - Method in class owltools.sim2.preprocessor.ExpressionSimPreProcessor
getAboxProperty() - Method in class owltools.sim2.preprocessor.PropertyViewSimPreProcessor
getAboxProperty() - Method in interface owltools.sim2.preprocessor.SimPreProcessor
getActiveEntity() - Method in class org.geneontology.lego.model.LegoNode: Deprecated.
getActivity() - Method in class org.geneontology.lego.model2.LegoUnit: Deprecated.
getActsOnTaxonId() - Method in class owltools.gaf.GeneAnnotation
getAdded() - Method in class owltools.graph.CardinalityContraintsTools.CardinalityReporter
getAdjacent(T) - Method in interface owltools.util.Adjacency
getAdvancedPanel() - Method in class owltools.ontologyrelease.gui.OortGuiMainFrame: Retrieve advanced panel, create new if it not exists.
getAllAttributeClasses() - Method in class owltools.sim.OldSimpleOwlSim: returns all attribute classes - i.e.
getAllAttributeClasses() - Method in class owltools.sim2.FastOwlSim
getAllAttributeClasses() - Method in interface owltools.sim2.OwlSim: returns all attribute classes - i.e.
getAllAttributeClasses() - Method in class owltools.sim2.SimpleOwlSim
getAllByAllLowestCommonSubsumer() - Method in class owltools.sim.OldSimpleOwlSim: Deprecated.
getAllEcoClassesForCode(String) - Method in interface owltools.gaf.eco.EcoMapper: Retrieve the ECO classes for the given GO evidence code.
getAllEcoClassesForCode(String) - Method in class owltools.gaf.eco.EcoMapperImpl
getAllElements() - Method in class owltools.sim.OldSimpleOwlSim
getAllElements() - Method in class owltools.sim2.FastOwlSim
getAllElements() - Method in interface owltools.sim2.OwlSim
getAllElements() - Method in class owltools.sim2.SimpleOwlSim
getAllOntologies() - Method in class owltools.graph.OWLGraphWrapperBasic: in general application code need not call this - it is mostly used internally
getAllOntologies() - Method in class owltools.mooncat.Mooncat
getAllOWLClasses() - Method in class owltools.graph.OWLGraphWrapperBasic: Fetch all OWLClass objects from all ontologies.
getAllOWLClasses() - Method in class owltools.graph.OWLGraphWrapperEdgesExtended: Get all OWLClasses from all ontologies, that are neither top entity (owl:thing), nor bottom entity (owl:nothing), nor deprecated (OWLGraphWrapperExtended.isObsolete(OWLObject) returns false).
getAllOWLClassesFromSource() - Method in class owltools.graph.OWLGraphWrapperEdgesExtended: Get only the OWLClasses from the OWLOntology returned by OWLGraphWrapperBasic.getSourceOntology(), that are neither top entity (owl:thing), nor bottom entity (owl:nothing), nor deprecated (OWLGraphWrapperExtended.isObsolete(OWLObject) returns false).
getAllOWLObjects() - Method in class owltools.graph.OWLGraphWrapperBasic: fetches all classes, individuals and object properties in all ontologies.
getAllOWLObjectsByAltId() - Method in class owltools.graph.OWLGraphWrapperExtended: Find all corresponding OWLObjects with an OBO-style alternate identifier.
getAllOWLSubClassOfAxiomsForSubClass(OWLClass) - Method in class owltools.graph.OWLGraphWrapperBasic: Fetch all OWLSubClassOfAxiom axioms for a given subClass (OWLClass) from all ontologies.
getAllOWLSubClassOfAxiomsForSuperClass(OWLClass) - Method in class owltools.graph.OWLGraphWrapperBasic: Fetch all OWLSubClassOfAxiom axioms for a given superClass (OWLClass) from all ontologies.
getAllPredictions() - Method in class owltools.gaf.inference.AbstractAnnotationPredictor
getAllPredictions() - Method in interface owltools.gaf.inference.AnnotationPredictor
getAllSimilarityAlgorithmClasses() - Method in class owltools.sim.SimEngine
getAllUsedSubsets() - Method in class owltools.graph.OWLGraphWrapperExtended: fetches all subset names that are used
getAllValidEvidenceIds(String, boolean) - Method in interface owltools.gaf.eco.TraversingEcoMapper: Get all strings which are valid identifiers for a given evidence code.
getAllValidEvidenceIds(Set<String>, boolean) - Method in interface owltools.gaf.eco.TraversingEcoMapper: Get all strings which are valid identifiers for the given evidence codes.
getAllValidEvidenceIds(String, boolean) - Method in class owltools.gaf.eco.TraversingEcoMapperImpl
getAllValidEvidenceIds(Set<String>, boolean) - Method in class owltools.gaf.eco.TraversingEcoMapperImpl
getAltIds(OWLObject) - Method in class owltools.graph.OWLGraphWrapperExtended: It returns the values of the alt_id tag
getAncestorAnnotations(String) - Method in class owltools.panther.PANTHERTree: Return all annotations to ancestor nodes.
getAncestors(Set<OWLClass>, boolean) - Method in interface owltools.gaf.eco.TraversingEcoMapper: Traversing method for the ECO ontology.
getAncestors(OWLClass, boolean) - Method in interface owltools.gaf.eco.TraversingEcoMapper: Traversing method for the ECO ontology.
getAncestors(Set<OWLClass>, boolean) - Method in class owltools.gaf.eco.TraversingEcoMapperImpl
getAncestors(OWLClass, boolean) - Method in class owltools.gaf.eco.TraversingEcoMapperImpl
getAncestors(Set<OWLClass>, boolean) - Method in class owltools.gaf.EcoTools: Deprecated.

Wrapper method for the reasoner.
getAncestors(OWLClass, boolean) - Method in class owltools.gaf.TaxonTools: Wrapper method for the reasoner.
getAncestors(OWLObject) - Method in class owltools.graph.OWLGraphWrapperEdges: returns all ancestors of an object.
getAncestors(OWLObject, Set<OWLPropertyExpression>) - Method in class owltools.graph.OWLGraphWrapperEdges: returns all ancestors that can be reached over subclass or the specified set of relations
getAncestors(OWLObject, Set<OWLPropertyExpression>, boolean) - Method in class owltools.graph.OWLGraphWrapperEdges: As overProps, but if isStrict is true, then only consider paths that include at least one edge with a property in the specified set.
getAncestors(String) - Method in class owltools.panther.PANTHERTree: Return the ancestors of this node as an ID set.
getancestors() - Method in class owltools.phenolog.Pheno
getAncestorsReflexive(OWLObject) - Method in class owltools.graph.OWLGraphWrapperEdges
getAncestorsReflexive(OWLObject, Set<OWLPropertyExpression>) - Method in class owltools.graph.OWLGraphWrapperEdges
getAncestorsThroughIsA(OWLObject) - Method in class owltools.graph.OWLGraphWrapperEdgesExtended: Retrieve OWLClass ancestors of x only using "is_a" relations (SubClassOf).
getAncestorsWithIC(Opts) - Method in class owltools.cli.SimCommandRunner
getAnnotation_Extension() - Method in class owltools.gaf.parser.GpadParser
getAnnotation_Properties() - Method in class owltools.gaf.parser.GpadParser
getAnnotationCount() - Method in class owltools.gaf.rules.AnnotationRulesEngine.AnnotationRulesEngineResult
getAnnotationExtension() - Method in class owltools.gaf.parser.GAFParser
getAnnotationProperty(String) - Method in class owltools.graph.OWLGraphWrapperExtended: It translates a oboformat tag into an OWL annotation property
getAnnotationPropertyValue(OWLObject, String) - Method in class owltools.graph.OWLGraphWrapperExtended: Get the annotation property value for a tag.
getAnnotationPropertyValue(OWLObject, List<String>) - Method in class owltools.graph.OWLGraphWrapperExtended: Get the annotation property value for a tag.
getAnnotationPropertyValues(OWLObject, String) - Method in class owltools.graph.OWLGraphWrapperExtended: Get the annotation property values for a tag.
getAnnotationPropertyValues(OWLObject, List<String>) - Method in class owltools.graph.OWLGraphWrapperExtended: Get the annotation property values for a tag.
getAnnotationRow() - Method in class owltools.gaf.rules.AnnotationRuleViolation
getAnnotationRuleViolations() - Method in class owltools.gaf.parser.GAFParser
getAnnotations() - Method in class owltools.gaf.Bioentity
getAnnotationSufficiencyScore(OWLNamedIndividual) - Method in class owltools.sim2.SimJSONEngine
getAnnotationSufficiencyScore(Set<OWLClass>) - Method in class owltools.sim2.SimJSONEngine
getAnnotationSufficiencyScore(Set<OWLClass>, OWLClass) - Method in class owltools.sim2.SimJSONEngine
getAnnotationSufficiencyScoreCommand() - Method in class owltools.web.OWLHandler
getAnnotationValue(OWLObject, OWLAnnotationProperty) - Method in class owltools.graph.OWLGraphWrapperExtended: fetches the value of a single-valued annotation property for an OWLObject
getAnnotationValues(OWLObject, OWLAnnotationProperty) - Method in class owltools.graph.OWLGraphWrapperExtended: gets the values of all annotation assertions to an OWLObject for a particular annotation property
getAnovaPValue() - Method in class owltools.sim2.kb.PValue
getAnyLabel(OWLEntity) - Method in class owltools.sim2.preprocessor.AbstractSimPreProcessor
getArbitraryAttributeClass() - Method in class owltools.sim2.OwlSim.ScoreAttributeSetPair: Deprecated.
getAspect() - Method in class owltools.gaf.GeneAnnotation
getAspect(String) - Method in class owltools.gaf.parser.DefaultAspectProvider
getAspect() - Method in class owltools.gaf.parser.GAFParser
getAspect(String) - Method in interface owltools.gaf.parser.GpadGpiObjectsBuilder.AspectProvider
getAssertedViewOntology() - Method in class owltools.mooncat.PropertyViewOntologyBuilder: Automatically generated Property View Ontology O(P) containing axioms C' == P some C, for each C in source ontology
getAssigned_by() - Method in class owltools.gaf.parser.GpadParser
getAssignedBy() - Method in class owltools.gaf.GeneAnnotation
getAssignedBy() - Method in class owltools.gaf.parser.GAFParser
getAssociatedGeneProductIDs() - Method in class owltools.panther.PANTHERTree: Return the associated gene/product ids for this tree.
getAssociatedGeneProductJSONMap() - Method in class owltools.panther.PANTHERTree: Return the mapping of associated gene/product ids to labels for this tree.
getAssociatedGeneProductLabels() - Method in class owltools.panther.PANTHERTree: Return the associated gene/product labels for this tree.
getAssociatedTrees(String) - Method in class owltools.panther.PANTHERForest: Return the number of unique bioentity identifiers found in the set.
getAsymmetricAttributeJaccardSimilarity(OWLClass, OWLClass) - Method in class owltools.sim2.FastOwlSim
getAsymmetricAttributeJaccardSimilarity(OWLClass, OWLClass) - Method in interface owltools.sim2.OwlSim: SimJ^ASym(c,d) = | anc(c) ∩ anc(d) | / | anc(d) |
getAsymmetricAttributeJaccardSimilarity(OWLClass, OWLClass) - Method in class owltools.sim2.SimpleOwlSim
getAsymmetricAttributeJaccardSimilarityAsPercent(OWLClass, OWLClass) - Method in class owltools.sim2.AbstractOwlSim
getAsymmetricAttributeJaccardSimilarityAsPercent(OWLClass, OWLClass) - Method in interface owltools.sim2.OwlSim: Equivalent to OwlSim.getAsymmetricAttributeJaccardSimilarity(OWLClass, OWLClass) * 100
getAsymmetricElementGraphInformationContentSimilarity(OWLNamedIndividual, OWLNamedIndividual) - Method in class owltools.sim2.FastOwlSim
getAsymmetricElementJaccardSimilarity(OWLNamedIndividual, OWLNamedIndividual) - Method in class owltools.sim2.FastOwlSim
getAsymmetricElementJaccardSimilarity(OWLNamedIndividual, OWLNamedIndividual) - Method in interface owltools.sim2.OwlSim: SimJ(i,j) = | Type(i) ∩ Type(j) | / | Type(j) |
getAsymmetricElementJaccardSimilarity(OWLNamedIndividual, OWLNamedIndividual) - Method in class owltools.sim2.SimpleOwlSim
getAsymmetricElementJaccardSimilarityAsPercent(OWLNamedIndividual, OWLNamedIndividual) - Method in class owltools.sim2.AbstractOwlSim
getAsymmetricElementJaccardSimilarityAsPercent(OWLNamedIndividual, OWLNamedIndividual) - Method in class owltools.sim2.FastOwlSim
getAsymmetricElementJaccardSimilarityAsPercent(OWLNamedIndividual, OWLNamedIndividual) - Method in interface owltools.sim2.OwlSim: Equivalent to OwlSim.getAsymmetricElementJaccardSimilarity(OWLNamedIndividual, OWLNamedIndividual) * 100
getAttributeClasses() - Method in class owltools.sim2.preprocessor.AbstractSimPreProcessor
getAttributeClosureFor(OWLObject) - Method in class owltools.sim.SimEngine
getAttributeGraphInformationContentSimilarity(OWLClass, OWLClass) - Method in class owltools.sim2.FastOwlSim
getAttributeGraphInformationContentSimilarity(OWLClass, OWLClass) - Method in interface owltools.sim2.OwlSim: sums of IC of the intersection attributes/ sum of IC of union attributes.
getAttributeGraphInformationContentSimilarity(OWLClass, OWLClass) - Method in class owltools.sim2.SimpleOwlSim
getAttributeInformationProfile(Set<OWLClass>) - Method in class owltools.sim2.SimJSONEngine
getAttributeInformationProfile(Set<OWLClass>, Set<OWLClass>) - Method in class owltools.sim2.SimJSONEngine
getAttributeInformationProfileCommand() - Method in class owltools.web.OWLHandler
getAttributeJaccardSimilarity(OWLClassExpression, OWLClassExpression) - Method in class owltools.sim.OldSimpleOwlSim
getAttributeJaccardSimilarity(OWLClass, OWLClass) - Method in class owltools.sim2.FastOwlSim
getAttributeJaccardSimilarity(OWLClass, OWLClass) - Method in interface owltools.sim2.OwlSim: SimJ(a,b) = | anc(a) ∩ anc(b) | / | anc(a) ∪ anc(b) |
getAttributeJaccardSimilarity(OWLClass, OWLClass) - Method in class owltools.sim2.SimpleOwlSim
getAttributeJaccardSimilarityAsPercent(OWLClass, OWLClass) - Method in class owltools.sim2.AbstractOwlSim
getAttributeJaccardSimilarityAsPercent(OWLClass, OWLClass) - Method in class owltools.sim2.FastOwlSim
getAttributeJaccardSimilarityAsPercent(OWLClass, OWLClass) - Method in interface owltools.sim2.OwlSim: Equivalent to OwlSim.getAttributeJaccardSimilarity(OWLClass, OWLClass) * 100
getAttributes() - Method in class owltools.phenolog.Individual
getAttributes(IRI) - Method in class owltools.sim2.kb.OWLSimReferenceBasedStatistics
getAttributesFor(OWLObject) - Method in class owltools.sim.SimEngine
getAttributesForElement(OWLEntity) - Method in class owltools.sim.OldSimpleOwlSim
getAttributesForElement(OWLNamedIndividual) - Method in class owltools.sim2.FastOwlSim
getAttributesForElement(OWLNamedIndividual) - Method in interface owltools.sim2.OwlSim: Gets all attribute classes used to describe individual element e.
getAttributesForElement(OWLNamedIndividual) - Method in class owltools.sim2.SimpleOwlSim
getAttributeSimilarity(OWLClass, OWLClass, SimpleOwlSim.Metric) - Method in class owltools.sim2.FastOwlSim
getAttributeSimilarity(OWLClass, OWLClass, SimpleOwlSim.Metric) - Method in interface owltools.sim2.OwlSim: This method provides a generic wrapper onto other attribute-based similarity methods Compares two classes (attributes) according to the specified metric
getAttributeSimilarity(OWLClass, OWLClass, SimpleOwlSim.Metric) - Method in class owltools.sim2.SimpleOwlSim
getAvailableChecks() - Static method in class owltools.ontologyrelease.OortConfiguration: Provide a list of all OntologyCheck's known to this configuration.
getAxiom() - Method in class owltools.RedundantInferences.RedundantAxiom
getAxiomAnnotationValues(IRI, OWLAxiom) - Static method in class owltools.graph.AxiomAnnotationTools: Retrieve the literal values for the axiom annotations with the given annotation property IRI.
getAxiomOne() - Method in class owltools.InferenceBuilder.PotentialRedundant
getAxioms() - Method in class owltools.graph.OWLGraphEdge: Returns A Set containing the underlying OWLAxioms that allowed to produce this OWLGraphEdge.
getAxiomsCommand() - Method in class owltools.web.OWLHandler: Params: id
getAxiomsForSubset(Set<OWLObject>) - Method in class owltools.mooncat.Mooncat: Given a set of objects (e.g.
getAxiomTwo() - Method in class owltools.InferenceBuilder.PotentialRedundant
getB() - Method in class owltools.sim.OWLObjectPair
getB() - Method in class owltools.sim2.scores.AttributePairScores
getB() - Method in class owltools.sim2.scores.ElementPairScores
getB() - Method in interface owltools.sim2.scores.PairScores
getBase() - Method in class owltools.ontologyrelease.OortConfiguration
getBaseFileName() - Method in class owltools.sim.OldSimpleOwlSim
getBioentities() - Method in class owltools.gaf.BioentityDocument: Get all Bioentity objects.
getBioentities() - Method in class owltools.gaf.GafDocument: Get all registered Bioentity objects.
getBioentity(String) - Method in class owltools.gaf.GafDocument: Retrieve the Bioentity object for the given id.
getBioentity() - Method in class owltools.gaf.GeneAnnotation
getBioentityMapping() - Method in class owltools.gaf.owl.GAFOWLBridge
getBioentityObject() - Method in class owltools.gaf.GeneAnnotation
getBit(int) - Method in class owltools.util.BloomFilter: Read a single bit from the Bloom filter.
getBitSet() - Method in class owltools.util.BloomFilter: Return the bit set used to store the Bloom filter.
getBitsPerElement() - Method in class owltools.util.BloomFilter: Get actual number of bits per element based on the number of elements that have currently been inserted and the length of the Bloom filter.
getBottomClassNode() - Method in class owltools.reasoner.GraphReasoner
getBottomClassNode() - Method in class owltools.reasoner.LazyExpressionMaterializingReasoner: Deprecated.
getBottomDataPropertyNode() - Method in class owltools.reasoner.GraphReasoner
getBottomDataPropertyNode() - Method in class owltools.reasoner.LazyExpressionMaterializingReasoner: Deprecated.
getBottomObjectPropertyNode() - Method in class owltools.reasoner.GraphReasoner
getBottomObjectPropertyNode() - Method in class owltools.reasoner.LazyExpressionMaterializingReasoner: Deprecated.
getBridgeOntologies() - Method in class owltools.ontologyrelease.OortConfiguration
getBufferingMode() - Method in class owltools.reasoner.LazyExpressionMaterializingReasoner: Deprecated.
getBuiltin(OWLObject) - Method in class owltools.graph.OWLGraphWrapperExtended: Deprecated.
getCandidateBasicStatistics() - Method in class owltools.sim2.kb.ICDistribution
getCandidateDistribution() - Method in class owltools.sim2.kb.ICDistribution
getCatalogXML() - Method in class owltools.ontologyrelease.OortConfiguration
getCategory() - Method in interface owltools.graph.OWLGraphWrapper.ISynonym
getCategory() - Method in class owltools.graph.OWLGraphWrapper.Synonym
getCellularLocation() - Method in class org.geneontology.lego.model.LegoNode: Deprecated.
getCheck() - Method in class owltools.ontologyverification.CheckWarning
getChildren() - Method in class owltools.gaf.Bioentity
getChildren(String) - Method in class owltools.graph.shunt.OWLShuntGraph: Return the set of children of a node as IDs.
getClassA() - Method in class owltools.InferenceBuilder.PotentialRedundant
getClassB() - Method in class owltools.InferenceBuilder.PotentialRedundant
getClassesForGoCode(String) - Method in class owltools.gaf.EcoTools: Deprecated.

Retrieve the ECO classes for the given GO annotation codes.
getClassesForGoCodes(OWLGraphWrapper, String...) - Static method in class owltools.gaf.EcoTools: Deprecated.

Retrieve the ECO classes for the given GO annotation codes.
getClassesForGoCodes(OWLGraphWrapper, Set<String>) - Static method in class owltools.gaf.EcoTools: Deprecated.

Retrieve the ECO classes for the given GO annotation codes.
getClassForName(String) - Method in class owltools.gaf.rules.AnnotationRulesFactoryImpl
getClassForName(String) - Method in class owltools.gaf.rules.go.GoAnnotationRulesFactoryImpl
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.
getCls() - Method in class owltools.gaf.ExtensionExpression
getCls() - Method in class owltools.gaf.GeneAnnotation
getCoAnnotatedClassesCommand() - Method in class owltools.web.OWLHandler
getCoannotatedClassesForAttribute(OWLClass) - Method in class owltools.sim2.FastOwlSim
getCoannotatedClassesForAttribute(OWLClass, int) - Method in class owltools.sim2.FastOwlSim
getCoannotatedClassesForAttribute(OWLClass, Double, int) - Method in class owltools.sim2.FastOwlSim
getCoannotatedClassesForAttribute(OWLClass, int) - Method in interface owltools.sim2.OwlSim
getCoannotatedClassesForAttribute(OWLClass) - Method in interface owltools.sim2.OwlSim
getCoannotatedClassesForAttribute(OWLClass, Double, int) - Method in interface owltools.sim2.OwlSim
getCoannotatedClassesForAttribute(OWLClass, int) - Method in class owltools.sim2.SimpleOwlSim
getCoannotatedClassesForAttribute(OWLClass, Double, int) - Method in class owltools.sim2.SimpleOwlSim
getCoannotatedClassesForAttribute(OWLClass) - Method in class owltools.sim2.SimpleOwlSim
getCoAnnotatedClassesForAttributes(Set<OWLClass>) - Method in class owltools.sim2.FastOwlSim
getCoAnnotatedClassesForAttributes(Set<OWLClass>, int) - Method in class owltools.sim2.FastOwlSim
getCoAnnotatedClassesForAttributes(Set<OWLClass>) - Method in interface owltools.sim2.OwlSim
getCoAnnotatedClassesForAttributes(Set<OWLClass>, int) - Method in interface owltools.sim2.OwlSim
getCoAnnotatedClassesForAttributes(Set<OWLClass>) - Method in class owltools.sim2.SimpleOwlSim
getCoAnnotatedClassesForAttributes(Set<OWLClass>, int) - Method in class owltools.sim2.SimpleOwlSim
getCoAnnotatedClassesForIndividual(OWLNamedIndividual) - Method in class owltools.sim2.FastOwlSim
getCoAnnotatedClassesForIndividual(OWLNamedIndividual, int) - Method in class owltools.sim2.FastOwlSim
getCoAnnotatedClassesForIndividual(OWLNamedIndividual) - Method in interface owltools.sim2.OwlSim
getCoAnnotatedClassesForIndividual(OWLNamedIndividual, int) - Method in interface owltools.sim2.OwlSim
getCoAnnotatedClassesForIndividual(OWLNamedIndividual) - Method in class owltools.sim2.SimpleOwlSim
getCoAnnotatedClassesForIndividual(OWLNamedIndividual, int) - Method in class owltools.sim2.SimpleOwlSim
getCoAnnotatedClassesForMatches(List<ElementPairScores>, Set<OWLClass>) - Method in class owltools.sim2.FastOwlSim
getCoAnnotatedClassesForMatches(List<ElementPairScores>, Set<OWLClass>, int) - Method in class owltools.sim2.FastOwlSim
getCoAnnotatedClassesForMatches(List<ElementPairScores>, Set<OWLClass>) - Method in interface owltools.sim2.OwlSim
getCoAnnotatedClassesForMatches(List<ElementPairScores>, Set<OWLClass>) - Method in class owltools.sim2.SimpleOwlSim
getCoAnnotationListForAttribute(OWLClass, int) - Method in class owltools.sim2.SimJSONEngine
getCodes(Set<OWLClass>, OWLGraphWrapper) - Static method in class owltools.gaf.EcoTools: Deprecated.
getCodes(Set<OWLClass>, OWLGraphWrapper, boolean) - Static method in class owltools.gaf.EcoTools: Deprecated.

Retrieve the set of codes for a given set of ECO classes.
getCodesForEcoClasses() - Method in interface owltools.gaf.eco.EcoMapper: Retrieve the mapping from ECO classes to GO evidence codes.
getCodesForEcoClasses() - Method in class owltools.gaf.eco.EcoMapperImpl
getColumn(GpadParser.GpadColumns) - Method in class owltools.gaf.parser.GpadParser
getColumn(GpiParser.GpiColumns) - Method in class owltools.gaf.parser.GpiParser
getCommandName() - Method in class owltools.web.OWLHandler
getComment(OWLObject) - Method in class owltools.graph.OWLGraphWrapperExtended: gets the value of rdfs:comment for an OWLObject
getComment(OWLObject, List<String>) - Method in class owltools.graph.OWLGraphWrapperExtended: gets the value of rdfs:comment for an OWLObject
getComments() - Method in class owltools.gaf.BioentityDocument: Get the current set of comments.
getComments() - Method in class owltools.gaf.GafDocument: Get the current set of comments.
getCommonSubsumers(OWLObject, OWLObject) - Method in class owltools.sim.SimEngine: todo rename - actually gets common named ancestors
getCommonSubsumersSize(OWLObject, OWLObject) - Method in class owltools.sim.SimEngine
getCompleteEdgesBetween(OWLObject, OWLObject) - Method in class owltools.graph.OWLGraphWrapperEdges
getCompleteOutgoingEdgesClosure(OWLObject) - Method in class owltools.graph.OWLGraphWrapperEdges: See OWLGraphWrapperEdges.getIncomingEdgesClosure(OWLObject s, boolean isComplete)
getConditionalProbability(OWLClass, OWLClass) - Method in class owltools.sim2.AbstractOwlSim
getConditionalProbability(OWLClass, OWLClass) - Method in interface owltools.sim2.OwlSim
getConditionalProbability(OWLClass, OWLClass) - Method in class owltools.sim2.SimpleOwlSim
getConfig() - Method in class owltools.graph.OWLGraphWrapperEdges
getConsider(OWLObject) - Method in class owltools.graph.OWLGraphWrapperExtended: It returns the values of the consider tag.
getContributors() - Method in class org.geneontology.lego.model.LegoMetadata: Deprecated.
getCorpusSize() - Method in class owltools.sim.OldSimpleOwlSim
getCorpusSize() - Method in class owltools.sim.SimEngine
getCorpusSize() - Method in class owltools.sim2.AbstractOwlSim
getCorpusSize() - Method in interface owltools.sim2.OwlSim: The number of entities in the entire set being analyzed.
getCorpusSize() - Method in class owltools.sim2.SimpleOwlSim
getCreatedBy(OWLObject) - Method in class owltools.graph.OWLGraphWrapperExtended: It returns the value of the created_by tag
getCurrentEdgesAdvancedCacheSize() - Method in class owltools.graph.OWLGraphWrapperEdgesAdvanced
getCurrentRow() - Method in class owltools.gaf.parser.GAFParser
getDanglingAxioms(OWLOntology) - Method in class owltools.mooncat.Mooncat
getDanglingClasses() - Method in class owltools.mooncat.Mooncat
getDanglingClasses(OWLOntology) - Method in class owltools.mooncat.Mooncat: finds all classes for which Mooncat.isDangling(OWLOntology, OWLEntity) is true
getDataFactory() - Method in class owltools.graph.OWLGraphWrapperBasic
getDataPropertyDomains(OWLDataProperty, boolean) - Method in class owltools.reasoner.GraphReasoner
getDataPropertyDomains(OWLDataProperty, boolean) - Method in class owltools.reasoner.LazyExpressionMaterializingReasoner: Deprecated.
getDataPropertyValues(OWLNamedIndividual, OWLDataProperty) - Method in class owltools.reasoner.GraphReasoner
getDataPropertyValues(OWLNamedIndividual, OWLDataProperty) - Method in class owltools.reasoner.LazyExpressionMaterializingReasoner: Deprecated.
getDate() - Method in class owltools.gaf.parser.GAFParser
getDate() - Method in class owltools.gaf.parser.GpadParser
getDate() - Method in class owltools.gaf.rules.AbstractAnnotationRule
getDate() - Method in interface owltools.gaf.rules.AnnotationRule: Get the status date of this rule.
getDates() - Method in class org.geneontology.lego.model.LegoMetadata: Deprecated.
getDb() - Method in class owltools.gaf.Bioentity
getDb() - Method in class owltools.gaf.parser.GAFParser
getDB() - Method in class owltools.gaf.parser.GpadParser
getDB_Object_ID() - Method in class owltools.gaf.parser.GpadParser
getDB_Object_ID() - Method in class owltools.gaf.parser.GpiParser
getDB_Object_Name() - Method in class owltools.gaf.parser.GpiParser
getDB_Object_Symbol() - Method in class owltools.gaf.parser.GpiParser
getDB_Object_Synonym() - Method in class owltools.gaf.parser.GpiParser
getDB_Object_Type() - Method in class owltools.gaf.parser.GpiParser
getDB_Reference() - Method in class owltools.gaf.parser.GpadParser
getDB_Xref() - Method in class owltools.gaf.parser.GpiParser
getDBID() - Method in class owltools.gaf.Bioentity
getDbObjectId() - Method in class owltools.gaf.parser.GAFParser
getDbObjectName() - Method in class owltools.gaf.parser.GAFParser
getDbObjectSymbol() - Method in class owltools.gaf.parser.GAFParser
getDbObjectSynonym() - Method in class owltools.gaf.parser.GAFParser
getDBObjectType() - Method in class owltools.gaf.parser.GAFParser
getDBs() - Method in interface owltools.gaf.bioentities.QuestForOrthologsSeqXMLParser.MoreInfoProteinListener.MoreInfo: Retrieve the databases for which there are identifiers for the protein.
getDbXrefs() - Method in class owltools.gaf.Bioentity
getDef(OWLObject) - Method in class owltools.graph.OWLGraphWrapperExtended: Gets the textual definition of an OWLObject
getDef(OWLObject, List<String>) - Method in class owltools.graph.OWLGraphWrapperExtended: Gets the textual definition of an OWLObject
getDefaultDbToTaxon() - Static method in class owltools.gaf.bioentities.ProteinTools: Retrieve the default mapping from db name to the numeric part of the NCBI taxon id.
getDefaultFormat() - Method in class owltools.ontologyrelease.OortConfiguration
getDefaultOboNamespace() - Method in class owltools.io.ParserWrapper.OWLGraphWrapperNameProvider
getDefXref(OWLObject) - Method in class owltools.graph.OWLGraphWrapperExtended: Get the definition xrefs (IAO_0000115)
getDefXref(OWLObject, List<String>) - Method in class owltools.graph.OWLGraphWrapperExtended: Get the definition xrefs (IAO_0000115)
getDescendantAnnotations(String) - Method in class owltools.panther.PANTHERTree: Return all annotations to descendant nodes.
getDescendants(OWLObject) - Method in class owltools.graph.OWLGraphWrapperEdges: gets all descendants d of x, where d is reachable by any path.
getDescendants(String) - Method in class owltools.panther.PANTHERTree: Return the descendants of this node as an ID set.
getDescendants(Set<OWLClass>) - Method in class owltools.sim2.kb.OWLSimReferenceBasedStatistics
getDescendantsReflexive(OWLObject) - Method in class owltools.graph.OWLGraphWrapperEdges: gets all reflexive descendants d of x, where d is reachable by any path.
getDescendantsThroughIsA(OWLObject) - Method in class owltools.graph.OWLGraphWrapperEdgesExtended: Retrieve OWLClass descendants of x only using "is_a" relations (SubClassOf).
getDescendents(Set<OWLClass>, boolean) - Method in interface owltools.gaf.eco.TraversingEcoMapper: Traversing method for the ECO ontology.
getDescendents(OWLClass, boolean) - Method in interface owltools.gaf.eco.TraversingEcoMapper: Traversing method for the ECO ontology.
getDescendents(Set<OWLClass>, boolean) - Method in class owltools.gaf.eco.TraversingEcoMapperImpl
getDescendents(OWLClass, boolean) - Method in class owltools.gaf.eco.TraversingEcoMapperImpl
getDescendents(Set<OWLClass>, boolean) - Method in class owltools.gaf.EcoTools: Deprecated.

Wrapper method for the reasoner
getDescendents(Set<OWLClass>, boolean) - Method in class owltools.gaf.TaxonTools: Wrapper method for the reasoner
getDescription(GeneAnnotation) - Method in class owltools.gaf.owl.GAFOWLBridge
getDescription() - Method in class owltools.gaf.rules.AbstractAnnotationRule
getDescription() - Method in interface owltools.gaf.rules.AnnotationRule: Get the description for a rule.
getDifferentiaRelation() - Method in class owltools.tr.LinkMaker.LinkPattern
getDifferentIndividuals(OWLNamedIndividual) - Method in class owltools.reasoner.GraphReasoner
getDifferentIndividuals(OWLNamedIndividual) - Method in class owltools.reasoner.LazyExpressionMaterializingReasoner: Deprecated.
getDirectAttributeClassExpressions() - Method in class owltools.sim2.preprocessor.AbstractSimPreProcessor: Deprecated.
getDirectLinkedClasses(OWLClass, String, OWLGraphWrapper) - Static method in class owltools.gaf.inference.BasicAnnotationPropagator: Lookup relation super classes in graph g for a given sub class c and property p.
getDirectLinkedClasses(OWLClass, Set<OWLObjectProperty>, OWLGraphWrapper, Set<OWLClass>) - Static method in class owltools.gaf.inference.BasicAnnotationPropagator: Lookup relation super classes in graph g for a given sub class c and property p.
getDisjointClasses(OWLClassExpression) - Method in class owltools.reasoner.GraphReasoner
getDisjointClasses(OWLClassExpression) - Method in class owltools.reasoner.LazyExpressionMaterializingReasoner: Deprecated.
getDisjointDataProperties(OWLDataPropertyExpression) - Method in class owltools.reasoner.GraphReasoner
getDisjointDataProperties(OWLDataPropertyExpression) - Method in class owltools.reasoner.LazyExpressionMaterializingReasoner: Deprecated.
getDisjointObjectProperties(OWLObjectPropertyExpression) - Method in class owltools.reasoner.GraphReasoner
getDisjointObjectProperties(OWLObjectPropertyExpression) - Method in class owltools.reasoner.LazyExpressionMaterializingReasoner: Deprecated.
getDistance() - Method in class owltools.graph.OWLGraphEdge
getDistributionBasedPValue() - Method in class owltools.sim2.kb.PValue
getDistributions() - Method in class owltools.sim2.kb.OwlSimICDistribution
getDocumentIRI(IRI) - Method in class owltools.io.CatalogXmlIRIMapper
getDocumentIRI(IRI) - Method in class owltools.io.LocalMirrorIRIMapper
getDocumentPath() - Method in class owltools.gaf.GafDocument: Retrieve the source path for this document
getDomain(OWLObjectProperty) - Method in class owltools.graph.OWLGraphWrapperExtended: It returns the value of the domain tag
getEco(String, String) - Method in interface owltools.gaf.eco.SimpleEcoMapper
getEco(String, Collection<String>) - Method in interface owltools.gaf.eco.SimpleEcoMapper
getEco(String, String) - Method in class owltools.gaf.eco.SimpleEcoMapperImpl
getEco(String, Collection<String>) - Method in class owltools.gaf.eco.SimpleEcoMapperImpl
getEcoClassForCode(String) - Method in interface owltools.gaf.eco.EcoMapper: Retrieve the equivalent ECO class for the given GO evidence code.
getEcoClassForCode(String, String) - Method in interface owltools.gaf.eco.EcoMapper: Retrieve the ECO class for the given GO evidence code and reference.
getEcoClassForCode(String) - Method in class owltools.gaf.eco.EcoMapperImpl
getEcoClassForCode(String, String) - Method in class owltools.gaf.eco.EcoMapperImpl
getEcoEvidenceCls() - Method in class owltools.gaf.GeneAnnotation
getEdgeLabel(OWLGraphEdge) - Method in class owltools.graph.OWLGraphWrapperEdges: Get the human readable label for an edge.
getEdgesBetween(OWLObject, OWLObject) - Method in class owltools.graph.OWLGraphWrapperEdges
getElementGraphInformationContentSimilarity(OWLNamedIndividual, OWLNamedIndividual) - Method in class owltools.sim2.FastOwlSim
getElementGraphInformationContentSimilarity(OWLNamedIndividual, OWLNamedIndividual) - Method in interface owltools.sim2.OwlSim: sums of IC of the intersection attributes/ sum of IC of union attributes.
getElementGraphInformationContentSimilarity(OWLNamedIndividual, OWLNamedIndividual) - Method in class owltools.sim2.SimpleOwlSim
getElementJaccardSimilarity(OWLNamedIndividual, OWLNamedIndividual) - Method in class owltools.sim.OldSimpleOwlSim
getElementJaccardSimilarity(OWLNamedIndividual, OWLNamedIndividual) - Method in class owltools.sim2.FastOwlSim
getElementJaccardSimilarity(OWLNamedIndividual, OWLNamedIndividual) - Method in interface owltools.sim2.OwlSim: SimJ(i,j) = | Type(i) ∩ Type(j) | / | Type(i) ∪ Type(j) |
getElementJaccardSimilarity(OWLNamedIndividual, OWLNamedIndividual) - Method in class owltools.sim2.SimpleOwlSim
getElementJaccardSimilarityAsPercent(OWLNamedIndividual, OWLNamedIndividual) - Method in class owltools.sim2.AbstractOwlSim
getElementJaccardSimilarityAsPercent(OWLNamedIndividual, OWLNamedIndividual) - Method in class owltools.sim2.FastOwlSim
getElementJaccardSimilarityAsPercent(OWLNamedIndividual, OWLNamedIndividual) - Method in interface owltools.sim2.OwlSim: Equivalent to OwlSim.getElementJaccardSimilarity(OWLNamedIndividual, OWLNamedIndividual) * 100
getElementsForAttribute(OWLClass) - Method in class owltools.sim.OldSimpleOwlSim: inferred
getElementsForAttribute(OWLClass) - Method in class owltools.sim2.FastOwlSim
getElementsForAttribute(OWLClass) - Method in interface owltools.sim2.OwlSim: inferred
getElementsForAttribute(OWLClass) - Method in class owltools.sim2.SimpleOwlSim
getElementsOntology() - Method in class owltools.mooncat.PropertyViewOntologyBuilder
getElementToAttributesMap() - Method in class owltools.sim2.FastOwlSim
getElementToAttributesMap() - Method in interface owltools.sim2.OwlSim
getElementToAttributesMap() - Method in class owltools.sim2.SimpleOwlSim
getEnabledBy() - Method in class org.geneontology.lego.model2.LegoUnit: Deprecated.
getEnrichmentConfig() - Method in class owltools.sim.OldSimpleOwlSim
getEnrichmentConfig() - Method in class owltools.sim2.AbstractOwlSim
getEnrichmentConfig() - Method in interface owltools.sim2.OwlSim
getEntropy() - Method in class owltools.sim2.AbstractOwlSim
getEntropy(Set<OWLClass>) - Method in class owltools.sim2.AbstractOwlSim
getEntropy() - Method in interface owltools.sim2.OwlSim
getEntropy(Set<OWLClass>) - Method in interface owltools.sim2.OwlSim
getEntropy() - Method in class owltools.sim2.SimpleOwlSim
getEntropy(Set<OWLClass>) - Method in class owltools.sim2.SimpleOwlSim
getEquivalentClasses(OWLClassExpression) - Method in class owltools.reasoner.GraphReasoner
getEquivalentClasses(OWLClassExpression) - Method in class owltools.reasoner.LazyExpressionMaterializingReasoner: Deprecated.
getEquivalentDataProperties(OWLDataProperty) - Method in class owltools.reasoner.GraphReasoner
getEquivalentDataProperties(OWLDataProperty) - Method in class owltools.reasoner.LazyExpressionMaterializingReasoner: Deprecated.
getEquivalentNamedClassPairs() - Method in class owltools.InferenceBuilder
getEquivalentObjectProperties(OWLObjectPropertyExpression) - Method in class owltools.reasoner.GraphReasoner
getEquivalentObjectProperties(OWLObjectPropertyExpression) - Method in class owltools.reasoner.LazyExpressionMaterializingReasoner: Deprecated.
getErrorCount() - Method in class owltools.gaf.rules.AnnotationRulesEngine.AnnotationRulesEngineResult
getErrorMessage() - Method in class owltools.gaf.rules.AnnotationRegularExpressionFromXMLRule
getErrorReportFile() - Method in class owltools.ontologyrelease.OortConfiguration
getErrors() - Method in class owltools.gaf.parser.IssueListener.DefaultIssueListener
getEvidence() - Method in class org.geneontology.lego.model.LegoMetadata: Deprecated.
getEvidence() - Method in class owltools.gaf.parser.GAFParser
getEvidence_Code() - Method in class owltools.gaf.parser.GpadParser
getExcludedClasses() - Method in class owltools.mooncat.PropertyViewOntologyBuilder
getExcludedLabels() - Method in class owltools.sim.SimEngine: any class whose label matches any of the strings returned here will be excluded from any analysis.
getExisiting() - Method in class owltools.tr.LinkMaker.LinkMakerResult
getExistsEntailed() - Method in class owltools.JustifyAssertionsTool.JustifyResult
getExistsNotEntailed() - Method in class owltools.JustifyAssertionsTool.JustifyResult
getExistsRedundant() - Method in class owltools.JustifyAssertionsTool.JustifyResult
getExpectedBitsPerElement() - Method in class owltools.util.BloomFilter: Get expected number of bits per element when the Bloom filter is full.
getExpectedColumnCount() - Method in class owltools.gaf.parser.GpadParser
getExpectedColumnCount() - Method in class owltools.gaf.parser.GpiParser
getExpectedNumberOfElements() - Method in class owltools.util.BloomFilter: Returns the expected number of elements to be inserted into the filter.
getExperimentalInferenceRules() - Method in interface owltools.gaf.rules.AnnotationRulesFactory: Get the list of rules, which check for inferred annotations.
getExperimentalInferenceRules() - Method in class owltools.gaf.rules.AnnotationRulesFactoryImpl
getExplaination(String, String, OWLQuantifiedProperty.Quantifier) - Method in class owltools.InferenceBuilder
getExpressions(OWLOntology, Set<OWLObjectProperty>, AssertInferredClassExpressions.OWLClassFilter) - Static method in class owltools.cli.AssertInferredClassExpressions
getExtensionExpressions() - Method in class owltools.gaf.GeneAnnotation
getExternalReferencedEntities() - Method in class owltools.mooncat.Mooncat: returns set of entities that belong to a referenced ontology that are referenced in the source ontology.
getExtString(OWLObject, List<String>, Map<String, Object>) - Method in class owltools.flex.FlexCollection: Get properly formatted output from the OWLGraphWrapper.
getExtStringList(OWLObject, List<String>, Map<String, Object>) - Method in class owltools.flex.FlexCollection: Get properly formatted output from the OWLGraphWrapper.
getFactory(String) - Static method in class owltools.InferenceBuilder
getFalsePositiveProbability(double) - Method in class owltools.util.BloomFilter: Calculate the probability of a false positive given the specified number of inserted elements.
getFalsePositiveProbability() - Method in class owltools.util.BloomFilter: Get the current probability of a false positive.
getField() - Method in class owltools.ontologyverification.CheckWarning
getFieldComments(String) - Method in class owltools.yaml.golrconfig.ConfigManager: Return the comments associated with the GOlrCoreField id; empty list if there weren't any.
getFields() - Method in class owltools.yaml.golrconfig.ConfigManager: Get all the fields.
getFile() - Method in class owltools.ontologyrelease.GetOntologyId: Deprecated.
getFileHeader() - Method in class owltools.ontologyrelease.reports.OBOTermsAltIdsReport
getFileHeader() - Method in class owltools.ontologyrelease.reports.OBOTermsIdsObsoleteReport
getFileHeader() - Method in class owltools.ontologyrelease.reports.OBOTermsIdsReport
getFileHeader() - Method in class owltools.ontologyrelease.reports.ObsoletesAllReport
getFileHeader() - Method in class owltools.ontologyrelease.reports.ObsoletesExactReport
getFileHeader() - Method in class owltools.ontologyrelease.reports.ObsoletesInExactReport
getFileHeader() - Method in class owltools.ontologyrelease.reports.OntologyReportGenerator.AbstractReport
getFileName() - Method in class owltools.gaf.AnnotationSource
getFiller() - Method in class owltools.frame.jsonld.RestrictionLD
getFiller() - Method in class owltools.frame.jsonld.SomeValuesFromLD
getFiller() - Method in interface owltools.frame.Restriction
getFilterSimpleProperties() - Method in class owltools.ontologyrelease.OortConfiguration
getFinalQuantifiedProperty() - Method in class owltools.graph.OWLGraphEdge
getFirstLiteral(OWLOntology, OWLEntity, OWLAnnotationProperty) - Static method in class owltools.ncbi.OWLConverter: Convenience method to get the first string literal of an annotation property.
getFirstLiteral(OWLOntology, OWLEntity, IRI) - Static method in class owltools.ncbi.OWLConverter: Convenience method to get the first string literal of an annotation property.
getFirstLiteral(OWLOntology, OWLEntity, String) - Static method in class owltools.ncbi.OWLConverter: Convenience method to get the first string literal of an annotation property.
getFirstQuantifiedProperty() - Method in class owltools.graph.OWLGraphEdge
getFoldedClassMap() - Method in class owltools.gaf.owl.AnnotationExtensionFolder
getFormat() - Method in class owltools.web.OWLHandler
getFragmentID(OWLObject) - Static method in class owltools.mooncat.TransformationUtils
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.LazyExpressionMaterializingReasoner: Deprecated.
getFullName() - Method in class owltools.gaf.Bioentity
getGafdocs() - Method in class owltools.gaf.godb.Dumper
getGafDocument() - Method in class owltools.gaf.inference.AbstractAnnotationPredictor
getGafDocument() - Method in class owltools.gaf.rules.AnnotationRuleViolation
getGafDocument() - Method in class owltools.solrj.GafSolrDocumentLoader
getGafDocumentRules() - Method in interface owltools.gaf.rules.AnnotationRulesFactory: Get the list of rules, which require a global view of the GAF (GafDocument).
getGafDocumentRules() - Method in class owltools.gaf.rules.AnnotationRulesFactoryImpl
getGCIFiller() - Method in class owltools.graph.OWLGraphEdge: Returns the OWLClass that is the OBO gci_filler of this OWLGraphEdge.
getGciFillers() - Method in class owltools.io.InferredParentRenderer
getGCIIncomingEdges(OWLClass) - Method in class owltools.graph.OWLGraphWrapperEdgesExtended: Retrieve OBO GCI relations incoming to t as a Set of OWLGraphEdges.
getGCIOutgoingEdges(OWLClass) - Method in class owltools.graph.OWLGraphWrapperEdgesExtended: Retrieve OBO GCI relations outgoing from s as a Set of OWLGraphEdges.
getGCIOutgoingEdges(OWLClass, Set<OWLPropertyExpression>) - Method in class owltools.graph.OWLGraphWrapperEdgesExtended: Same as OWLGraphWrapperEdgesExtended.getGCIOutgoingEdges(OWLClass), but with a Set of OWLPropertyExpression allowing to filter the relations retrieved.
getGciProperty() - Method in class owltools.io.InferredParentRenderer
getGCIRelation() - Method in class owltools.graph.OWLGraphEdge: Returns the OWLObjectPropertyExpression that is the OBO gci_relation of this OWLGraphEdge.
getGene_Product_Properties() - Method in class owltools.gaf.parser.GpiParser
getGeneAnnotation() - Method in class owltools.gaf.inference.Prediction
getGeneAnnotationByLineNumber(int) - Method in class owltools.gaf.GafDocument: Retrieve the (first) annotation for the given line number or null.
getGeneAnnotationRules() - Method in interface owltools.gaf.rules.AnnotationRulesFactory: Get the list of rules to be applied for each GeneAnnotation
getGeneAnnotationRules() - Method in class owltools.gaf.rules.AnnotationRulesFactoryImpl
getGeneAnnotations() - Method in class owltools.gaf.GafDocument: Get all annotations from this document.
getGeneAnnotations(String) - Method in class owltools.gaf.GafDocument: Get all annotations for a given Bioentity id.
getGeneAnnotationsByDirectGoCls(String) - Method in class owltools.gaf.GafDocument: Search for all annotations with the given cls String.
getGeneId() - Method in class owltools.gaf.Bioentity
getGeneOntologyReports() - Static method in class owltools.ontologyrelease.reports.go.GeneOntologyReports
getGeneProductForm() - Method in class owltools.gaf.GeneAnnotation
getGeneProjectFormId() - Method in class owltools.gaf.parser.GAFParser
getGO_ID() - Method in class owltools.gaf.parser.GpadParser
getGoCode(String) - Method in interface owltools.gaf.eco.SimpleEcoMapper
getGoCode(String) - Method in class owltools.gaf.eco.SimpleEcoMapperImpl
getGOId() - Method in class owltools.gaf.parser.GAFParser
getGolrAnnotations(List<String[]>) - Method in class org.bbop.golr.java.RetrieveGolrAnnotations
getGolrAnnotationsForGene(String) - Method in class org.bbop.golr.java.RetrieveGolrAnnotations
getGolrAnnotationsForGenes(List<String>) - Method in class org.bbop.golr.java.RetrieveGolrAnnotations
getGolrAnnotationsForSynonym(String, String) - Method in class org.bbop.golr.java.RetrieveGolrAnnotations
getGolrAnnotationsForSynonym(String, List<String>) - Method in class org.bbop.golr.java.RetrieveGolrAnnotations
getGolrBioentites(String) - Method in class org.bbop.golr.java.RetrieveGolrBioentities
getGolrBioentities(List<String[]>) - Method in class org.bbop.golr.java.RetrieveGolrBioentities
getGoSubOntology(OWLClass, OWLGraphWrapper) - Method in class owltools.gaf.inference.BasicAnnotationPropagator: Get the specific sub ontology.
getGrandFatheringDate() - Method in class owltools.gaf.rules.AbstractAnnotationRule
getGrandFatheringDate() - Method in interface owltools.gaf.rules.AnnotationRule: Return the cut-off date for grand fathering the rule.
getGraph() - Method in class owltools.gaf.eco.EcoMapperFactory.OntologyMapperPair
getGraph() - Method in class owltools.gaf.inference.AbstractAnnotationPredictor
getGraph() - Method in interface owltools.gaf.rules.AnnotationRulesFactory: Get the underlying ontology graph for this rule factory.
getGraph() - Method in class owltools.gaf.rules.AnnotationRulesFactoryImpl
getGraph() - Method in class owltools.mooncat.Mooncat
getGraph() - Method in class owltools.sim.SimEngine
getGraph() - Method in interface owltools.sim.SimilarityCalculator
getGraph() - Method in class owltools.sim2.io.AbstractRenderer
getGraph() - Method in interface owltools.sim2.io.SimResultRenderer
getGraph() - Method in class owltools.solrj.AbstractSolrLoader
getGroupwiseSimilarity(OWLNamedIndividual, OWLNamedIndividual) - Method in class owltools.sim2.AbstractOwlSim
getGroupwiseSimilarity(OWLNamedIndividual) - Method in class owltools.sim2.FastOwlSim
getGroupwiseSimilarity(Set<OWLClass>, Set<OWLClass>) - Method in class owltools.sim2.FastOwlSim
getGroupwiseSimilarity(OWLNamedIndividual, OWLNamedIndividual) - Method in class owltools.sim2.FastOwlSim
getGroupwiseSimilarity(OWLNamedIndividual, OWLNamedIndividual, double, double) - Method in class owltools.sim2.FastOwlSim
getGroupwiseSimilarity(Set<OWLClass>, OWLNamedIndividual) - Method in class owltools.sim2.FastOwlSim
getGroupwiseSimilarity(Set<OWLClass>, OWLNamedIndividual, double, double) - Method in class owltools.sim2.FastOwlSim
getGroupwiseSimilarity(Set<OWLClass>, Set<OWLClass>, double, double) - Method in class owltools.sim2.FastOwlSim
getGroupwiseSimilarity(OWLNamedIndividual) - Method in interface owltools.sim2.OwlSim: Compare a named individual i to itself.
getGroupwiseSimilarity(OWLNamedIndividual, OWLNamedIndividual) - Method in interface owltools.sim2.OwlSim: Compare two named individuals (i,j).
getGroupwiseSimilarity(OWLNamedIndividual, OWLNamedIndividual, double, double) - Method in interface owltools.sim2.OwlSim: Compare two named individuals i, filtering on minSimJ and minMaxIC
getGroupwiseSimilarity(Set<OWLClass>, OWLNamedIndividual) - Method in interface owltools.sim2.OwlSim: Compare a set of attributes against the named individual i.
getGroupwiseSimilarity(Set<OWLClass>, OWLNamedIndividual, double, double) - Method in interface owltools.sim2.OwlSim: Compare a set of attributes against the named individual i.
getGroupwiseSimilarity(Set<OWLClass>, Set<OWLClass>) - Method in interface owltools.sim2.OwlSim
getGroupwiseSimilarity(Set<OWLClass>, Set<OWLClass>, double, double) - Method in interface owltools.sim2.OwlSim
getGroupwiseSimilarity(OWLNamedIndividual) - Method in class owltools.sim2.SimpleOwlSim
getGroupwiseSimilarity(OWLNamedIndividual, OWLNamedIndividual, double, double) - Method in class owltools.sim2.SimpleOwlSim
getGroupwiseSimilarity(Set<OWLClass>, OWLNamedIndividual) - Method in class owltools.sim2.SimpleOwlSim
getGroupwiseSimilarity(Set<OWLClass>, OWLNamedIndividual, double, double) - Method in class owltools.sim2.SimpleOwlSim
getGroupwiseSimilarity(Set<OWLClass>, Set<OWLClass>) - Method in class owltools.sim2.SimpleOwlSim
getGroupwiseSimilarity(Set<OWLClass>, Set<OWLClass>, double, double) - Method in class owltools.sim2.SimpleOwlSim
getHeight() - Method in class owltools.gfx.OWLGraphLayoutNode
getHint() - Method in exception owltools.ontologyrelease.OboOntologyReleaseRunnerCheckException
gethmp() - Method in class owltools.phenolog.PhenoTransitiveClosure
gethmpair() - Method in class owltools.phenolog.PhenoTransitiveClosure
gethsp() - Method in class owltools.phenolog.PhenoTransitiveClosure
getIC(Opts) - Method in class owltools.cli.SimCommandRunner
getICDistribution(Set<OWLClass>, IRI, double) - Method in class owltools.sim2.kb.OWLSimReferenceBasedStatistics
getICDistribution(Set<OWLClass>, IRI, Set<OWLClass>, double) - Method in class owltools.sim2.kb.OWLSimReferenceBasedStatistics
getICSimDisj(OWLClass, OWLClass) - Method in class owltools.sim2.AbstractOwlSim
getId() - Method in class org.geneontology.lego.model.LegoNode: Deprecated.
getId() - Method in class org.geneontology.lego.model2.LegoUnit: Deprecated.
getId() - Method in class owltools.gaf.Bioentity
getId() - Method in class owltools.gaf.BioentityDocument
getId() - Method in class owltools.gaf.GafDocument
getId(String, Object) - Method in class owltools.gaf.godb.DatabaseDumper
getId(String, Object, boolean) - Method in class owltools.gaf.godb.DatabaseDumper
getId(String) - Method in class owltools.gaf.io.XgmmlWriter
getId() - Method in class owltools.graph.shunt.OWLShuntNode
getID() - Method in class owltools.ontologyverification.impl.AbstractCheck
getID() - Method in interface owltools.ontologyverification.OntologyCheck
getId() - Method in class owltools.phenolog.Attribute
getid() - Method in class owltools.phenolog.GenePheno
getId() - Method in class owltools.phenolog.Individual
getId() - Method in class owltools.phenolog.Pheno
getIdentifier(OWLObject) - Method in class owltools.graph.OWLGraphWrapperExtended: gets the OBO-style ID of the specified object.
getIdentifier(OWLObject, boolean) - Method in class owltools.graph.OWLGraphWrapperExtended: Gets the OBO-style ID of the specified object.
getIdentifier(OWLObject, List<String>) - Method in class owltools.graph.OWLGraphWrapperExtended: Same as OWLGraphWrapperExtended.getIdentifier(OWLObject) but a different profile to support the FlexLoader.
getIdentifier(IRI) - Method in class owltools.graph.OWLGraphWrapperExtended: gets the OBO-style ID of the specified object.
getIds(String) - Method in interface owltools.gaf.bioentities.QuestForOrthologsSeqXMLParser.MoreInfoProteinListener.MoreInfo: Retrieve all identifier of a protein for the given database.
getIdSpaceManager() - Method in class owltools.io.OWLJSONFormat: Gets the OBO id-space manager.
getIgnoreSelectedEquivalentPairSet() - Method in class owltools.ontologyrelease.OortConfiguration
getIgnoreSubClassesOf() - Method in class owltools.sim.OldSimpleOwlSim
getIgnoreSubClassesOf() - Method in class owltools.sim2.SimpleOwlSim
getIncomingEdges(OWLObject) - Method in class owltools.graph.OWLGraphWrapperEdges
getIncomingEdgesClosure(OWLObject, boolean) - Method in class owltools.graph.OWLGraphWrapperEdges: As OWLGraphWrapperEdges.getIncomingEdgesClosure(OWLObject t), but allows the option of including 'complete' edge list.
getIncomingEdgesClosure(OWLObject) - Method in class owltools.graph.OWLGraphWrapperEdges: gets all inferred edges coming in to the target edge
getIncomingEdgesWithGCI(OWLObject) - Method in class owltools.graph.OWLGraphWrapperEdgesExtended: Similar to OWLGraphWrapperEdges.getIncomingEdges(OWLObject), but the returned Set also includes OBO GCI incoming edges (see OWLGraphWrapperEdgesExtended.getGCIIncomingEdges(OWLClass)).
getIndex(NODE) - Method in class owltools.util.AbstractTarjan
getIndex(T) - Method in class owltools.util.MappingTarjan
getIndividual() - Method in class org.geneontology.lego.model.LegoNode: Deprecated.
getIndividualDescendants(OWLObject) - Method in class owltools.graph.OWLGraphWrapperEdges: return all individuals i where x is reachable from i
getIndividualNodeSetPolicy() - Method in class owltools.reasoner.LazyExpressionMaterializingReasoner: Deprecated.
getIndividualPairs() - Method in class owltools.phenolog.PhenologEngine
getIndividuals() - Method in class owltools.phenolog.Pheno
getInferenceRules() - Method in interface owltools.gaf.rules.AnnotationRulesFactory: Get the list of rules, which check for inferred annotations.
getInferenceRules() - Method in class owltools.gaf.rules.AnnotationRulesFactoryImpl
getInferredAttributes(OWLNamedIndividual) - Method in class owltools.sim2.FastOwlSim
getInferredAttributes(OWLNamedIndividual) - Method in interface owltools.sim2.OwlSim
getInferredAttributes(OWLNamedIndividual) - Method in class owltools.sim2.SimpleOwlSim
getInferredGraph() - Method in class owltools.util.ShuntGraphUtils.ShuntGraphPair
getInferredViewOntology() - Method in class owltools.mooncat.PropertyViewOntologyBuilder: Generated after running PropertyViewOntologyBuilder.buildInferredViewOntology(OWLReasoner) Note that O(P) and O(P)' can share the same object, i.e the assertedViewOntology is augmented to become the inferred view ontology
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
getInformationContentForAttribute(OWLClass) - Method in class owltools.sim.OldSimpleOwlSim
getInformationContentForAttribute(OWLClass) - Method in class owltools.sim2.FastOwlSim
getInformationContentForAttribute(OWLClass) - Method in interface owltools.sim2.OwlSim: IC = -(log OwlSim.getNumElementsForAttribute(OWLClass) / corpus size) / log(2)
getInformationContentForAttribute(OWLClass) - Method in class owltools.sim2.SimpleOwlSim
getInputOntology() - Method in class owltools.sim2.preprocessor.AbstractSimPreProcessor
getInputOntology() - Method in interface owltools.sim2.preprocessor.SimPreProcessor
getInstanceChainsFromClosure(OWLClass) - Method in class owltools.graph.OWLGraphWrapperEdges: Finds all edges between an instance i and he given class c.
getInstances(OWLClassExpression, boolean) - Method in class owltools.reasoner.GraphReasoner
getInstances(OWLClassExpression, boolean) - Method in class owltools.reasoner.LazyExpressionMaterializingReasoner: Deprecated.
getInstancesFromClosure(OWLClass) - Method in class owltools.graph.OWLGraphWrapperEdges: Find all edges of the form [i INST c] in the graph closure.
getInteracting_Taxon_ID() - Method in class owltools.gaf.parser.GpadParser
getInverseObjectProperties(OWLObjectPropertyExpression) - Method in class owltools.reasoner.GraphReasoner
getInverseObjectProperties(OWLObjectPropertyExpression) - Method in class owltools.reasoner.LazyExpressionMaterializingReasoner: Deprecated.
getIRI() - Method in enum owltools.vocab.OBOUpperVocabulary
getIRIByIdentifier(String) - Method in class owltools.graph.OWLGraphWrapperExtended
getIRIByIdentifier(String, boolean) - Method in class owltools.graph.OWLGraphWrapperExtended
getIRIByLabel(String) - Method in class owltools.graph.OWLGraphWrapperExtended: fetches an OWL IRI by rdfs:label
getIRIByLabel(String, boolean) - Method in class owltools.graph.OWLGraphWrapperExtended: fetches an OWL IRI by rdfs:label, optionally testing for uniqueness
getIRIMappers() - Method in class owltools.io.ParserWrapper
getIris() - Method in class owltools.ontologyverification.CheckWarning
getIRIViaOBOSuffix(String) - Method in class owltools.sim2.preprocessor.AbstractOBOSimPreProcessor
getIsAnonymous(OWLObject) - Method in class owltools.graph.OWLGraphWrapperExtended: Deprecated.
getIsAntiSymmetric(OWLObject) - Method in class owltools.graph.OWLGraphWrapperExtended: It returns the value of the is_anti_symmetric tag or IAO_0000427 annotation
getIsaPartofClosureMap(OWLObject) - Method in class owltools.graph.OWLGraphWrapperEdgesAdvanced: Deprecated.
getIsaPartofIDClosure(OWLObject) - Method in class owltools.graph.OWLGraphWrapperEdgesAdvanced: Deprecated.
getIsaPartofIDClosure(OWLObject, List<String>) - Method in class owltools.graph.OWLGraphWrapperEdgesAdvanced: Deprecated.
getIsaPartofLabelClosure(OWLObject) - Method in class owltools.graph.OWLGraphWrapperEdgesAdvanced: Deprecated.
getIsaPartofLabelClosure(OWLObject, List<String>) - Method in class owltools.graph.OWLGraphWrapperEdgesAdvanced: Deprecated.
getIsaPartofSuperClassClosure(Collection<OWLClass>, OWLGraphWrapper, OWLReasoner) - Static method in class owltools.gaf.inference.BasicAnnotationPropagator
getIsCyclic(OWLObject) - Method in class owltools.graph.OWLGraphWrapperExtended: It returns the value of the is_cyclic tag
getisFromTC() - Method in class owltools.phenolog.Pheno
getIsFunctional(OWLObjectProperty) - Method in class owltools.graph.OWLGraphWrapperExtended: true if c is functional in the graph
getIsInverseFunctional(OWLObjectProperty) - Method in class owltools.graph.OWLGraphWrapperExtended: true if c is inverse functional in the graph
getIsMetaTag(OWLObject) - Method in class owltools.graph.OWLGraphWrapperExtended: It returns the value of the is_metadata_tag tag.
getIsObsolete(OWLObject) - Method in class owltools.graph.OWLGraphWrapperExtended: It returns the value of the is-obsolete tag.
getIsObsoleteBinaryString(OWLObject, List<String>) - Method in class owltools.graph.OWLGraphWrapperExtended: It returns the value of the is-obsolete tag.
getIsReflexive(OWLObjectProperty) - Method in class owltools.graph.OWLGraphWrapperExtended: true if c is reflexive in the graph
getIsSymmetric(OWLObjectProperty) - Method in class owltools.graph.OWLGraphWrapperExtended: true if c is symmetric in the graph
getIsTransitive(OWLObjectProperty) - Method in class owltools.graph.OWLGraphWrapperExtended: true if c is transitive in the graph
getJsonStringFromUri(URI) - Method in class org.bbop.golr.java.AbstractRetrieveGolr
getJsonStringFromUri(URI, int) - Method in class org.bbop.golr.java.AbstractRetrieveGolr
getJustifyAssertedSubclassesFrom() - Method in class owltools.ontologyrelease.OortConfiguration
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.
getKurtosis() - Method in class owltools.sim2.kb.BasicStatistics
getLabel() - Method in interface owltools.graph.OWLGraphWrapper.ISynonym
getLabel() - Method in class owltools.graph.OWLGraphWrapper.Synonym
getLabel(OWLObject) - Method in class owltools.graph.OWLGraphWrapperExtended: fetches the rdfs:label for an OWLObject
getLabel(OWLObject, List<String>) - Method in class owltools.graph.OWLGraphWrapperExtended: fetches the rdfs:label for an OWLObject
getLabel() - Method in class owltools.graph.shunt.OWLShuntNode
getLabel(OWLEntity, OWLOntology) - Method in class owltools.mooncat.PropertyViewOntologyBuilder
getLabel() - Method in class owltools.ontologyverification.impl.AbstractCheck
getLabel() - Method in interface owltools.ontologyverification.OntologyCheck
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
getLabel(OWLEntity, OWLOntology) - Method in class owltools.sim2.preprocessor.AbstractSimPreProcessor
getLabelOrDisplayId(OWLObject) - Method in class owltools.graph.OWLGraphWrapperExtended
getLabelOrId(OWLEntity) - Method in class owltools.io.OWLPrettyPrinter.LabelProvider
getLastQuantifiedProperty() - Method in class owltools.graph.OWLGraphEdge
getLastUpdateDate() - Method in class owltools.gaf.GeneAnnotation
getLCS() - Method in class owltools.sim.ConjunctiveSetInformationContentRatioSimilarity
getLeafClasses() - Method in class owltools.mooncat.PropertyViewOntologyBuilder
getLeastCommonSubsumers(OWLObject, OWLObject) - Method in class owltools.sim.SimEngine: note that this performs caching by default
getLeastCommonSubsumerSimpleClassExpression(OWLObject, OWLObject) - Method in class owltools.sim.SimEngine
getLeastCommonSubsumerSimpleClassExpression(OWLObject, OWLObject, boolean) - Method in class owltools.sim.SimEngine
getLeastCommonSubsumersSize(OWLObject, OWLObject) - Method in class owltools.sim.SimEngine
getLeaves() - Method in class owltools.graph.shunt.OWLShuntGraph: Return the set of graph leaves (no children) as IDs.
getLineageShuntGraph(OWLObject, List<String>) - Method in class owltools.graph.OWLGraphWrapperEdgesAdvanced: Gets all ancestors that are OWLNamedObjects.
getLineageShuntGraphJSON(OWLObject, List<String>) - Method in class owltools.graph.OWLGraphWrapperEdgesAdvanced: Return a JSONized version of the output of getLineageShuntGraph
getLineNumber() - Method in class owltools.gaf.AnnotationSource
getLineNumber() - Method in class owltools.gaf.parser.GAFParser
getLineNumber() - Method in class owltools.gaf.rules.AnnotationRuleViolation
getLines() - Method in class owltools.gaf.io.GafWriter.BufferedGafWriter
getLinks() - Method in class org.geneontology.lego.model.LegoNode: Deprecated.
getLinks() - Method in class org.geneontology.lego.model2.LegoGraph: Deprecated.

Extract the whole list of links form the nodes
getLocalId() - Method in class owltools.gaf.Bioentity
getLocation() - Method in class org.geneontology.lego.model2.LegoUnit: Deprecated.
getLowestCommonSubsumer(OWLClassExpression, OWLClassExpression) - Method in class owltools.sim.OldSimpleOwlSim: gets the LCS.
getLowestCommonSubsumer(OWLClassExpression, OWLClassExpression) - Method in class owltools.sim2.preprocessor.AbstractSimPreProcessor
getLowestCommonSubsumer(OWLClassExpression, OWLClassExpression) - Method in class owltools.sim2.preprocessor.LCSEnabledSimPreProcessor: gets the LCS.
getLowestCommonSubsumer(OWLClassExpression, OWLClassExpression, Set<OWLClass>) - Method in class owltools.sim2.preprocessor.LCSEnabledSimPreProcessor
getLowestCommonSubsumer(OWLClassExpression, OWLClassExpression) - Method in interface owltools.sim2.preprocessor.SimPreProcessor: Returns the LCS of a and b.
getLowestCommonSubsumerClass(OWLClassExpression, OWLClassExpression) - Method in class owltools.sim.OldSimpleOwlSim: generates a LCS expression and makes it a class if it is a class expression
getLowestCommonSubsumerClass(OWLClassExpression, OWLClassExpression, Set<OWLClass>) - Method in class owltools.sim2.preprocessor.LCSEnabledSimPreProcessor: generates a LCS expression and makes it a class if it is a class expression
getLowestCommonSubsumerIC(OWLClassExpression, OWLClassExpression) - Method in class owltools.sim.OldSimpleOwlSim
getLowestCommonSubsumerIC(OWLClass, OWLClass) - Method in class owltools.sim2.SimpleOwlSim: IC(c) = -log₂(p(c)) p(c) = | Inst(c) | / | Inst(owl:Thing) |
getLowestCommonSubsumerIC(OWLClass, OWLClass, Double) - Method in class owltools.sim2.SimpleOwlSim
getLowestCommonSubsumersCommand() - Method in class owltools.web.OWLHandler
getLowestCommonSubsumerWithIC(OWLClass, OWLClass) - Method in class owltools.sim2.FastOwlSim
getLowestCommonSubsumerWithIC(OWLClass, OWLClass, Double) - Method in class owltools.sim2.FastOwlSim
getLowestCommonSubsumerWithIC(OWLClass, OWLClass) - Method in interface owltools.sim2.OwlSim: Resnick similarity measure, together with all LCSs (MICAs) that have this as IC
getLowestCommonSubsumerWithIC(OWLClass, OWLClass, Double) - Method in interface owltools.sim2.OwlSim
getLowestCommonSubsumerWithIC(OWLClass, OWLClass) - Method in class owltools.sim2.SimpleOwlSim
getLowestCommonSubsumerWithIC(OWLClass, OWLClass, Double) - Method in class owltools.sim2.SimpleOwlSim
getLowestCommonSubsumerWithLinScore(OWLClass, OWLClass) - Method in class owltools.sim2.AbstractOwlSim
getLowestCommonSubsumerWithLinScore(OWLClass, OWLClass) - Method in interface owltools.sim2.OwlSim
getLowlink(NODE) - Method in class owltools.util.AbstractTarjan
getLowlink(T) - Method in class owltools.util.MappingTarjan
getMacroStrategy() - Method in class owltools.ontologyrelease.OortConfiguration
getManager() - Method in class owltools.graph.OWLGraphWrapperBasic
getManager() - Method in class owltools.io.ParserWrapper
getManager() - Method in class owltools.mooncat.Mooncat
getManifestVersion(String) - Static method in class owltools.version.VersionInfo: Try to retrieve the value for the given key from a manifest file.
getMappedErrors() - Method in class owltools.gaf.parser.IssueListener.DefaultIssueListener
getMappedWarnings() - Method in class owltools.gaf.parser.IssueListener.DefaultIssueListener
getMapper() - Method in class owltools.gaf.eco.EcoMapperFactory.OntologyMapperPair
getMappings() - Method in class owltools.io.CatalogXmlIRIMapper
getMappings() - Method in class owltools.tr.TemplatedTransformer
getMappingSource() - Method in class owltools.gaf.IdMapping
getMax() - Method in class owltools.sim2.kb.BasicStatistics
getMax(SimpleOwlSim.Metric) - Method in class owltools.sim2.SimStats
getMaxCardinality() - Method in class owltools.graph.OWLQuantifiedProperty
getMaxHits() - Method in class owltools.sim.SimSearch
getMean() - Method in class owltools.sim2.kb.BasicStatistics
getMember1() - Method in class owltools.phenolog.IndividualPair
getMember2() - Method in class owltools.phenolog.IndividualPair
getMessage() - Method in class owltools.gaf.rules.AnnotationRuleViolation
getMessage() - Method in exception owltools.ontologyrelease.OboOntologyReleaseRunnerCheckException
getMessage() - Method in class owltools.ontologyverification.CheckWarning
getMessage() - Method in exception owltools.sim2.CutoffException
getMetadata() - Method in class owltools.graph.shunt.OWLShuntEdge
getMetadata() - Method in class owltools.graph.shunt.OWLShuntNode
getMetadata() - Method in class owltools.sim2.AbstractOwlSim
getMetadata() - Method in class owltools.sim2.FastOwlSim
getMetadata() - Method in interface owltools.sim2.OwlSim
getMetricStats(OwlSim.Stat) - Method in class owltools.sim2.AbstractOwlSim
getMetricStats(OwlSim.Stat) - Method in interface owltools.sim2.OwlSim
getMin() - Method in class owltools.sim2.kb.BasicStatistics
getMinCardinality() - Method in class owltools.graph.OWLQuantifiedProperty
getMinimumDistanceToAncestor(OWLClass, OWLClass) - Method in class owltools.sim2.AbstractOwlSim
getMinimumDistanceViaMICA(OWLClass, OWLClass) - Method in class owltools.sim2.AbstractOwlSim
getModified() - Method in class owltools.tr.LinkMaker.LinkMakerResult
getMoreHermitFactory() - Static method in class owltools.reasoner.PrecomputingMoreReasonerFactory
getMoreJFactFactory() - Static method in class owltools.reasoner.PrecomputingMoreReasonerFactory
getMoreSpecific() - Method in class owltools.RedundantInferences.RedundantAxiom
getName() - Method in class owltools.gaf.rules.AbstractAnnotationRule
getName() - Method in interface owltools.gaf.rules.AnnotationRule: Return the name of the rule.
getName(String) - Method in class owltools.io.ParserWrapper.OboAndOwlNameProvider
getName(String) - Method in class owltools.io.ParserWrapper.OWLGraphWrapperNameProvider
getNamedAncestors(OWLObject) - Method in class owltools.graph.OWLGraphWrapperEdges: Gets all ancestors that are OWLNamedObjects
getNamedAncestorsReflexive(OWLObject) - Method in class owltools.graph.OWLGraphWrapperEdges
getNamedAncestorsWithGCI(OWLObject) - Method in class owltools.graph.OWLGraphWrapperEdgesExtended: Similar to OWLGraphWrapperEdges.getNamedAncestors(OWLObject) but also considering GCI relations.
getNamedAncestorsWithGCI(OWLObject, Set<OWLPropertyExpression>) - Method in class owltools.graph.OWLGraphWrapperEdgesExtended: Similar to OWLGraphWrapperEdgesExtended.getNamedAncestorsWithGCI(OWLObject, Set) but allowing to filter the relations considered.
getNamedCommonSubsumers(OWLClassExpression, OWLClassExpression) - Method in class owltools.sim.OldSimpleOwlSim
getNamedCommonSubsumers(OWLNamedIndividual, OWLNamedIndividual) - Method in class owltools.sim.OldSimpleOwlSim
getNamedCommonSubsumers(OWLClass, OWLClass) - Method in class owltools.sim2.FastOwlSim
getNamedCommonSubsumers(OWLNamedIndividual, OWLNamedIndividual) - Method in class owltools.sim2.FastOwlSim
getNamedCommonSubsumers(OWLClass, OWLClass) - Method in interface owltools.sim2.OwlSim: CS(a,b) = { c : c ∈ RSub(a), c ∈ RSub(b) }
getNamedCommonSubsumers(OWLNamedIndividual, OWLNamedIndividual) - Method in interface owltools.sim2.OwlSim: CS(i,j) = { c : c ∈ Type(i), c ∈ Type(j) }
getNamedCommonSubsumers(OWLClassExpression, OWLClassExpression) - Method in class owltools.sim2.preprocessor.LCSEnabledSimPreProcessor
getNamedCommonSubsumers(OWLNamedIndividual, OWLNamedIndividual) - Method in class owltools.sim2.preprocessor.LCSEnabledSimPreProcessor
getNamedCommonSubsumers(OWLClass, OWLClass) - Method in class owltools.sim2.SimpleOwlSim
getNamedCommonSubsumers(OWLNamedIndividual, OWLNamedIndividual) - Method in class owltools.sim2.SimpleOwlSim
getNamedCommonSubsumersCount(OWLClass, OWLClass) - Method in class owltools.sim2.FastOwlSim
getNamedCommonSubsumersCount(OWLClass, OWLClass) - Method in interface owltools.sim2.OwlSim: | CS(i,j) | = | { c : c ∈ Type(i), c ∈ Type(j) } |
getNamedCommonSubsumersCount(OWLClass, OWLClass) - Method in class owltools.sim2.SimpleOwlSim
getNamedLowestCommonSubsumers(OWLClassExpression, OWLClassExpression) - Method in class owltools.sim.OldSimpleOwlSim
getNamedLowestCommonSubsumers(OWLClass, OWLClass) - Method in class owltools.sim2.FastOwlSim
getNamedLowestCommonSubsumers(OWLClass, OWLClass) - Method in interface owltools.sim2.OwlSim: CS_redundant(a,b) = { c : c ∈ CS(a,b), &E; c' : c' ∈ CS(a,b), c' &in Sub(c) } LCS(a,b) = CS(a,b) - CS_redundant
getNamedLowestCommonSubsumers(OWLClassExpression, OWLClassExpression) - Method in class owltools.sim2.preprocessor.LCSEnabledSimPreProcessor
getNamedLowestCommonSubsumers(OWLClass, OWLClass) - Method in class owltools.sim2.SimpleOwlSim
getNamedReflexiveSubsumers(OWLClassExpression) - Method in class owltools.sim.OldSimpleOwlSim
getNamedReflexiveSubsumers(OWLClass) - Method in class owltools.sim2.FastOwlSim
getNamedReflexiveSubsumers(OWLClass) - Method in interface owltools.sim2.OwlSim
getNamedReflexiveSubsumers(OWLClassExpression) - Method in class owltools.sim2.preprocessor.LCSEnabledSimPreProcessor
getNamedReflexiveSubsumers(OWLClass) - Method in class owltools.sim2.SimpleOwlSim
getNamedSubsumers(OWLClassExpression) - Method in class owltools.sim.OldSimpleOwlSim
getNamedSubsumers(OWLNamedIndividual) - Method in class owltools.sim.OldSimpleOwlSim
getNamedSubsumers(OWLClass) - Method in class owltools.sim2.AbstractOwlSim
getNamedSubsumers(OWLClass) - Method in interface owltools.sim2.OwlSim
getNamedSubsumers(OWLClassExpression) - Method in class owltools.sim2.preprocessor.LCSEnabledSimPreProcessor
getNamedSubsumers(OWLNamedIndividual) - Method in class owltools.sim2.preprocessor.LCSEnabledSimPreProcessor
getNamedSubsumers(OWLClass) - Method in class owltools.sim2.SimpleOwlSim
getNamedTarget() - Method in class org.geneontology.lego.model.LegoLink: Deprecated.
getNamedUnionSubsumers(OWLClass, OWLClass) - Method in class owltools.sim2.FastOwlSim
getNamespace() - Method in class owltools.gaf.parser.GpiParser
getNamespace(OWLObject) - Method in class owltools.graph.OWLGraphWrapperExtended: It returns the value of the OBO-namespace tag
getNamespace(OWLObject, List<String>) - Method in class owltools.graph.OWLGraphWrapperExtended: It returns the value of the OBO-namespace tag.
getNcbiTaxonId() - Method in class owltools.gaf.Bioentity
getNewAxioms() - Method in class owltools.diff.ReasonerDiff
getNewInferred() - Method in class owltools.JustifyAssertionsTool.JustifyResult
getNewRelation() - Method in class owltools.tr.LinkMaker.LinkPattern
getNextSplitDocument() - Method in class owltools.gaf.parser.GafObjectsBuilder: When this variable reaches the splitSize count, the algorithm in the GafObjectsBuilder.getNextSplitDocument() method stops calling next method of the GAFParser and returns the GafDocument object build with the number of rows
getNHXString() - Method in class owltools.panther.PANTHERTree: Return the raw Newick-type input string.
getNode(OWLObject) - Method in class owltools.gfx.OWLGraphLayoutRenderer: fetch a layout node via the cognate OWLObject make private?
getNodes() - Method in class org.geneontology.lego.model2.LegoGraph: Deprecated.
getNonRedundantLinkedClasses(OWLClass, Set<OWLObjectProperty>, OWLGraphWrapper, OWLReasoner, Set<OWLClass>, Map<Set<OWLClass>, Set<OWLClass>>) - Static method in class owltools.gaf.inference.BasicAnnotationPropagator: Retrieve the non redundant set of linked classes using the given relation.
getNonTCIndividualSize() - Method in class owltools.phenolog.Pheno
getNumberOfAttributesForI() - Method in class owltools.sim2.scores.ElementPairScores
getNumberOfAttributesForJ() - Method in class owltools.sim2.scores.ElementPairScores
getNumberOfFilesInSet() - Method in class owltools.panther.PANTHERForest: Return the number of files read into the set.
getNumberOfIdentifiersInSet() - Method in class owltools.panther.PANTHERForest: Return the number of unique identifiers found in the set.
getNumElementsForAttribute(OWLClass) - Method in class owltools.sim.OldSimpleOwlSim: |{e|e in a(c)}|
getNumElementsForAttribute(OWLClass) - Method in class owltools.sim2.FastOwlSim
getNumElementsForAttribute(OWLClass) - Method in interface owltools.sim2.OwlSim: |{e : e ∈ Inst(c)}|
getNumElementsForAttribute(OWLClass) - Method in class owltools.sim2.SimpleOwlSim
getNumSharedElements(OWLClass, OWLClass) - Method in class owltools.sim2.AbstractOwlSim
getNumSharedElements(OWLClass, OWLClass) - Method in class owltools.sim2.FastOwlSim
getNumSharedElements(OWLClass, OWLClass, OWLClass) - Method in class owltools.sim2.FastOwlSim
getObjectByAltId(String) - Method in class owltools.graph.OWLGraphWrapperExtended
getObjectProperty(OWLDataFactory) - Method in enum owltools.vocab.OBOUpperVocabulary
getObjectProperty(OWLOntology) - Method in enum owltools.vocab.OBOUpperVocabulary
getObjectPropertyByShorthand(String) - Method in class owltools.gaf.owl.GAFOWLBridge
getObjectPropertyDomains(OWLObjectPropertyExpression, boolean) - Method in class owltools.reasoner.GraphReasoner
getObjectPropertyDomains(OWLObjectPropertyExpression, boolean) - Method in class owltools.reasoner.LazyExpressionMaterializingReasoner: Deprecated.
getObjectPropertyRanges(OWLObjectPropertyExpression, boolean) - Method in class owltools.reasoner.GraphReasoner
getObjectPropertyRanges(OWLObjectPropertyExpression, boolean) - Method in class owltools.reasoner.LazyExpressionMaterializingReasoner: Deprecated.
getObjectPropertyValues(OWLNamedIndividual, OWLObjectPropertyExpression) - Method in class owltools.reasoner.GraphReasoner
getObjectPropertyValues(OWLNamedIndividual, OWLObjectPropertyExpression) - Method in class owltools.reasoner.LazyExpressionMaterializingReasoner: Deprecated.
getOBOdoc() - Method in class owltools.io.ParserWrapper
getobolink() - Method in class owltools.phenolog.PhenoTransitiveClosure
getOBOSynonyms(OWLObject) - Method in class owltools.graph.OWLGraphWrapper: It returns list of synonyms as encoded by OBO2OWL.
getOBOSynonymStrings(OWLObject, List<String>) - Method in class owltools.graph.OWLGraphWrapper: It returns String Listof synonyms.
getOntology() - Method in class owltools.graph.OWLGraphEdge
getOntology() - Method in class owltools.graph.OWLGraphWrapper: Deprecated.
getOntology() - Method in class owltools.mooncat.Mooncat
getOntologyCheck(String) - Static method in class owltools.ontologyrelease.OortConfiguration
getOntologyChecks() - Method in class owltools.ontologyrelease.OortConfiguration
getOntologyCheckShortName(OntologyCheck) - Static method in class owltools.ontologyrelease.OortConfiguration
getOntologyId() - Method in class owltools.graph.OWLGraphWrapperExtended: gets the OBO-style ID of the source ontology IRI.
GetOntologyId - Class in owltools.ontologyrelease: Deprecated.
GetOntologyId() - Constructor for class owltools.ontologyrelease.GetOntologyId: Deprecated.
getOntologyLeaves() - Method in class owltools.graph.OWLGraphWrapperEdgesExtended: Return the OWLClasses leaves of any ontology (OWLClasses with no incoming edges as returned by {OWLGraphWrapperEdges#getIncomingEdgesWithGCI(OWLObject)}), and not deprecated (OWLGraphWrapperExtended.isObsolete(OWLObject) returns false; edges incoming from an obsolete class are not considered)
getOntologyRoots() - Method in class owltools.graph.OWLGraphWrapperEdgesExtended: Return the OWLClasses root of any ontology (OWLClasses with no outgoing edges as returned by {OWLGraphWrapperEdges#getOutgoingEdgesWithGCI(OWLObject)}), and not deprecated (OWLGraphWrapperExtended.isObsolete(OWLObject) returns false)).
getOntologyRoots(Set<OWLPropertyExpression>) - Method in class owltools.graph.OWLGraphWrapperEdgesExtended: Return the OWLClasses root of any ontology over the specified OWLPropertyExpressions (OWLClasses with no outgoing edges of the specified type, as returned by {OWLGraphWrapperEdges#getOutgoingEdgesWithGCI(OWLObject, Set)}), and not deprecated (OWLGraphWrapperExtended.isObsolete(OWLObject) returns false); edges going to obsolete classes are not taken into account).
getOriginalClassForViewClass(OWLClass) - Method in class owltools.mooncat.PropertyViewOntologyBuilder
getOrthologs() - Method in class owltools.phenolog.Individual
getOutgoingEdges(OWLObject) - Method in class owltools.graph.OWLGraphWrapperEdges: retrieves direct edges from a source to the direct **named** target e.g.
getOutgoingEdges(OWLObject, Set<? extends OWLPropertyExpression>) - Method in class owltools.graph.OWLGraphWrapperEdges: retrieves direct edges from a source to the direct **named** target for a given set of properties e.g.
getOutgoingEdges(OWLObject, boolean, boolean) - Method in class owltools.graph.OWLGraphWrapperEdges
getOutgoingEdgesClosure(OWLObject) - Method in class owltools.graph.OWLGraphWrapperEdges: Retrieves the graph closure originating from source.
getOutgoingEdgesClosure(OWLObject, Set<? extends OWLPropertyExpression>) - Method in class owltools.graph.OWLGraphWrapperEdges: As OWLGraphWrapperEdges.getOutgoingEdgesClosure(OWLObject s), but only consider the specified set of properties when walking the graph.
getOutgoingEdgesClosure(OWLObject, boolean) - Method in class owltools.graph.OWLGraphWrapperEdges: See OWLGraphWrapperEdges.getIncomingEdgesClosure(OWLObject s, boolean isComplete)
getOutgoingEdgesClosureReflexive(OWLObject) - Method in class owltools.graph.OWLGraphWrapperEdges: as OWLGraphWrapperEdges.getOutgoingEdgesClosure(OWLObject), but also includes an identity edge
getOutgoingEdgesClosureReflexive(OWLObject, Set<? extends OWLPropertyExpression>) - Method in class owltools.graph.OWLGraphWrapperEdges: as OWLGraphWrapperEdges.getOutgoingEdgesClosure(OWLObject, Set), but also include an identify edge
getOutgoingEdgesClosureWithGCI(OWLObject) - Method in class owltools.graph.OWLGraphWrapperEdgesExtended: Similar to OWLGraphWrapperEdges.getOutgoingEdgesClosure(OWLObject), but also considering OBO GCI relations.
getOutgoingEdgesCommand() - Method in class owltools.web.OWLHandler
getOutgoingEdgesNamedClosureOverSupProps(OWLObject) - Method in class owltools.graph.OWLGraphWrapperEdgesExtended: Same method as OWLGraphWrapperEdges.getOutgoingEdgesClosure(OWLObject), except that only the OWLGraphEdges going to a named target are returned, and that the list of connecting edge properties are not only combined using the composition rules as usual, but also over super properties (see for instance #combineEdgePairWithSuperPropsAndGCI(OWLGraphEdge, OWLGraphEdge).
getOutgoingEdgesNamedClosureOverSupPropsWithGCI(OWLObject) - Method in class owltools.graph.OWLGraphWrapperEdgesExtended: Similar to OWLGraphWrapperEdgesExtended.getOutgoingEdgesNamedClosureOverSupProps(OWLObject) but with the OBO GCI relations also taken into account.
getOutgoingEdgesWithGCI(OWLObject) - Method in class owltools.graph.OWLGraphWrapperEdgesExtended: Similar to OWLGraphWrapperEdges.getOutgoingEdges(OWLObject), but the returned Set also includes OBO GCI outgoing edges (see OWLGraphWrapperEdgesExtended.getGCIOutgoingEdges(OWLClass)).
getOutgoingEdgesWithGCI(OWLObject, Set<OWLPropertyExpression>) - Method in class owltools.graph.OWLGraphWrapperEdgesExtended: Similar to OWLGraphWrapperEdges.getOutgoingEdges(OWLObject, Set), but the returned Set also includes OBO GCI outgoing edges (see OWLGraphWrapperEdgesExtended.getGCIOutgoingEdges(OWLClass)).
getOutputOntology() - Method in class owltools.sim2.preprocessor.AbstractSimPreProcessor
getOutputOntology() - Method in interface owltools.sim2.preprocessor.SimPreProcessor
getOWLAnnotationProperty(IRI) - Method in class owltools.graph.OWLGraphWrapperExtended
getOWLClass(String) - Method in class owltools.gaf.inference.CompositionalClassPredictor: Deprecated.
getOWLClass(String) - Method in class owltools.gaf.owl.GAFOWLBridge
getOWLClass(String) - Method in class owltools.graph.OWLGraphWrapperExtended: Returns an OWLClass given an IRI string
getOWLClass(IRI) - Method in class owltools.graph.OWLGraphWrapperExtended: Returns an OWLClass given an IRI
getOWLClass(OWLObject) - Method in class owltools.graph.OWLGraphWrapperExtended
getOWLClass(OWLDataFactory) - Method in enum owltools.vocab.OBOUpperVocabulary
getOWLClass(OWLOntology) - Method in enum owltools.vocab.OBOUpperVocabulary
getOWLClassAncestors(OWLClass) - Method in class owltools.graph.OWLGraphWrapperEdgesExtended: Return the OWLClasses ancestor of sourceClass.
getOWLClassAncestorsWithGCI(OWLObject) - Method in class owltools.graph.OWLGraphWrapperEdgesExtended: Similar to OWLGraphWrapperEdgesExtended.getNamedAncestorsWithGCI(OWLObject) but returning only OWLClasses.
getOWLClassByIdentifier(String) - Method in class owltools.graph.OWLGraphWrapperExtended: Given an OBO-style ID, return the corresponding OWLClass, if it is declared - otherwise null
getOWLClassByIdentifier(String, boolean) - Method in class owltools.graph.OWLGraphWrapperExtended: As OWLGraphWrapperExtended.getOWLClassByIdentifier(String) but include pre-resolution step using altId map.
getOWLClassDescendants(OWLClass) - Method in class owltools.graph.OWLGraphWrapperEdgesExtended: Return the OWLClasses descendant of parentClass.
getOWLClassDescendantsWithGCI(OWLClass) - Method in class owltools.graph.OWLGraphWrapperEdgesExtended: Similar to OWLGraphWrapperEdgesExtended.getOWLClassDescendants(OWLClass) but also considering GCI relations.
getOWLClassDescendantsWithGCI(OWLClass, Set<OWLPropertyExpression>) - Method in class owltools.graph.OWLGraphWrapperEdgesExtended: Similar to #getOWLClassDescendantsWithGCI(OWLObject) but allowing to filter the relations considered.
getOWLClassDirectAncestors(OWLClass) - Method in class owltools.graph.OWLGraphWrapperEdgesExtended: Return the OWLClasses that are direct parent of subClass.
getOWLClassDirectDescendants(OWLClass) - Method in class owltools.graph.OWLGraphWrapperEdgesExtended: Return the OWLClasses directly descendant of parentClass.
getOWLClassDirectDescendantsWithGCI(OWLClass) - Method in class owltools.graph.OWLGraphWrapperEdgesExtended: Similar to OWLGraphWrapperEdgesExtended.getOWLClassDirectDescendants(OWLClass) but also considering GCI relations.
getOWLClassesInSubset(String) - Method in class owltools.graph.OWLGraphWrapperExtended: given a subset name, find all OWLClasses assigned to that subset
getOWLClassFromShortId(String) - Method in class owltools.sim2.AbstractOwlSim
getOWLClassViaOBOSuffix(String) - Method in class owltools.sim2.preprocessor.AbstractOBOSimPreProcessor
getOWLGraphEdgeSubRelsReflexive(OWLGraphEdge) - Method in class owltools.graph.OWLGraphWrapperEdgesExtended: Get the sub-relations of edge.
getOWLGraphEdgeSubsumers(OWLGraphEdge) - Method in class owltools.graph.OWLGraphWrapperEdges: generalizes over quantified properties
getOWLGraphEdgeSubsumers(OWLGraphEdge, int) - Method in class owltools.graph.OWLGraphWrapperEdges
getOwlGraphWrapper() - Method in class owltools.graph.OWLGraphManipulator: Get the OWLGraphWrapper on which modifications are performed.
getOWLGraphWrapper() - Method in class owltools.InferenceBuilder
getOWLIndividual(IRI) - Method in class owltools.graph.OWLGraphWrapperExtended: Returns an OWLNamedIndividual with this IRI if it has been declared in the source or support ontologies.
getOWLIndividual(String) - Method in class owltools.graph.OWLGraphWrapperExtended
getOWLIndividualByIdentifier(String) - Method in class owltools.graph.OWLGraphWrapperExtended: Given an OBO-style ID, return the corresponding OWLNamedIndividual, if it is declared - otherwise null
getOwlObject() - Method in class owltools.gfx.OWLGraphLayoutNode
getOWLObject(String) - Method in class owltools.graph.OWLGraphWrapperExtended: Returns the OWLObject with this IRI (where IRI is specified as a string - e.g http://purl.obolibrary.org/obo/GO_0008150)
getOWLObject(IRI) - Method in class owltools.graph.OWLGraphWrapperExtended: Returns the OWLObject with this IRI
getOWLObjectByAltId(String) - Method in class owltools.graph.OWLGraphWrapperExtended: Find the corresponding OWLObject for a given OBO-style alternate identifier.
getOWLObjectByIdentifier(String) - Method in class owltools.graph.OWLGraphWrapperExtended: Given an OBO-style ID, return the corresponding OWLObject, if it is declared - otherwise null
getOWLObjectByLabel(String) - Method in class owltools.graph.OWLGraphWrapperExtended: fetches an OWL Object by rdfs:label
getOWLObjectProperty(String) - Method in class owltools.graph.OWLGraphWrapperExtended: Returns the OWLObjectProperty with this IRI
getOWLObjectProperty(IRI) - Method in class owltools.graph.OWLGraphWrapperExtended
getOWLObjectPropertyByIdentifier(String) - Method in class owltools.graph.OWLGraphWrapperExtended: Given an OBO-style ID, return the corresponding OWLObjectProperty, if it is declared - otherwise null
getOWLObjectPropertyViaOBOSuffix(String) - Method in class owltools.sim2.preprocessor.AbstractOBOSimPreProcessor
getOWLObjectsByAltId(Set<String>) - Method in class owltools.graph.OWLGraphWrapperExtended: Find the corresponding OWLObjects for a given set of OBO-style alternate identifiers.
getOWLObjectsInSubset(String) - Method in class owltools.graph.OWLGraphWrapperExtended: given a subset name, find all OWLObjects (typically OWLClasses) assigned to that subset
getOwlOfnFormat() - Method in class owltools.ontologyrelease.OortConfiguration
getOwlRules() - Method in interface owltools.gaf.rules.AnnotationRulesFactory: Get the list of rules, which require a global view of the GAF (GafDocument) and OWL.
getOwlRules() - Method in class owltools.gaf.rules.AnnotationRulesFactoryImpl
getOWLShuntGraph() - Method in class owltools.panther.PANTHERTree: Return the complete OWL shunt graph representation of the phylogenic tree.
getOwlSimFactory() - Method in class owltools.cli.Sim2CommandRunner
getOwlSimMetadataCommand() - Method in class owltools.web.OWLHandler
getOwlXMLFormat() - Method in class owltools.ontologyrelease.OortConfiguration
getPaintId() - Method in class owltools.gaf.Bioentity
getPairwiseSimilarity(OWLClass, OWLClass) - Method in class owltools.sim2.FastOwlSim
getPairwiseSimilarity(OWLClass, OWLClass) - Method in interface owltools.sim2.OwlSim: Deprecated.
getPairwiseSimilarity(OWLClass, OWLClass) - Method in class owltools.sim2.SimpleOwlSim
getPANTHERID() - Method in class owltools.panther.PANTHERTree: Return the tree public (PANTHER) identifier.
getParent() - Method in class owltools.gaf.Bioentity
getParent_Object_ID() - Method in class owltools.gaf.parser.GpiParser
getParents(String) - Method in class owltools.graph.shunt.OWLShuntGraph: Return the set of parents of a node as IDs.
getParser() - Method in class owltools.gaf.parser.GafObjectsBuilder
getPaths() - Method in class owltools.ontologyrelease.OortConfiguration
getPaths(OWLClass, OWLClass) - Method in class owltools.sim2.AbstractOwlSim
getPattern() - Method in class owltools.gaf.rules.AnnotationRegularExpressionFromXMLRule
getPendingAxiomAdditions() - Method in class owltools.reasoner.LazyExpressionMaterializingReasoner: Deprecated.
getPendingAxiomRemovals() - Method in class owltools.reasoner.LazyExpressionMaterializingReasoner: Deprecated.
getPendingChanges() - Method in class owltools.reasoner.LazyExpressionMaterializingReasoner: Deprecated.
getpermutedgenes(int, int, ArrayList<Individual>) - Static method in class owltools.phenolog.Main
getPersistantNodeID() - Method in class owltools.gaf.Bioentity
getphenoid() - Method in class owltools.phenolog.GenePheno
getphenolabel() - Method in class owltools.phenolog.GenePheno
getPhenotypeEntityClasses() - Method in class owltools.sim2.preprocessor.PhenoSimHQEPreProcessor
getPrecomputableInferenceTypes() - Method in class owltools.reasoner.GraphReasoner
getPrecomputableInferenceTypes() - Method in class owltools.reasoner.LazyExpressionMaterializingReasoner: Deprecated.
getPredictedAnnotations(GafDocument, OWLGraphWrapper) - Method in class owltools.gaf.rules.AbstractAnnotationRule
getPredictedAnnotations(GafDocument, OWLGraphWrapper) - Method in interface owltools.gaf.rules.AnnotationRule: Given a whole GafDocument in plan and OWL format, check for possible new inferred annotations (Prediction).
getPredictedAnnotations(GafDocument, OWLGraphWrapper) - Method in class owltools.gaf.rules.go.GoAnnotationExperimentalPredictionRule
getPredictedAnnotations(GafDocument, OWLGraphWrapper) - Method in class owltools.gaf.rules.go.GoAnnotationPredictionRule
getPrediction(OWLClass, String, String) - Method in class owltools.gaf.inference.CompositionalClassPredictor: Deprecated.
getPrediction(GeneAnnotation, OWLClass, String, String) - Method in class owltools.gaf.inference.FoldBasedPredictor
getPredictions() - Method in class owltools.tr.LinkMaker.LinkMakerResult
getprefix() - Method in class owltools.phenolog.PhenoTransitiveClosure
getPreSimMethod() - Method in class owltools.sim.MultiSimilarity
getPrettyPrinter() - Method in class owltools.cli.CommandRunner
getPrimitiveIncomingEdges(OWLObject) - Method in class owltools.graph.OWLGraphWrapperEdges
getPrimitiveOutgoingEdges(OWLObject) - Method in class owltools.graph.OWLGraphWrapperEdges: primitive edges connect any combination of named objects and expressions
getPrimitiveOutgoingEdges(OWLObject, Set<? extends OWLPropertyExpression>) - Method in class owltools.graph.OWLGraphWrapperEdges
getPrintStream(String) - Method in class owltools.gaf.godb.DatabaseDumper
getPrintStream(String, boolean) - Method in class owltools.gaf.godb.DatabaseDumper
getProcess() - Method in class org.geneontology.lego.model2.LegoUnit: Deprecated.
getProfiler() - Method in class owltools.graph.OWLGraphWrapperEdges
getProperties() - Method in class owltools.gaf.Bioentity
getProperties() - Method in class owltools.gaf.GeneAnnotation
getProperties() - Method in class owltools.io.InferredParentRenderer
getProperty() - Method in class org.geneontology.lego.model.LegoLink: Deprecated.
getProperty(SimpleOwlSim.SimConfigurationProperty) - Method in class owltools.cli.Sim2CommandRunner
getProperty(SimpleOwlSim.SimConfigurationProperty) - Method in class owltools.cli.SimCommandRunner
getProperty() - Method in class owltools.graph.OWLQuantifiedProperty
getProperty() - Method in class owltools.InferenceBuilder.PotentialRedundant
getProperty(SimpleOwlSim.SimConfigurationProperty) - Method in class owltools.sim2.AbstractOwlSim
getProperty(String) - Method in class owltools.sim2.preprocessor.AbstractSimPreProcessor
getPropertyAsBoolean(SimpleOwlSim.SimConfigurationProperty) - Method in class owltools.sim2.AbstractOwlSim
getPropertyAsDouble(SimpleOwlSim.SimConfigurationProperty) - Method in class owltools.sim2.AbstractOwlSim
getPropertyAsDouble(SimpleOwlSim.SimConfigurationProperty, Double) - Method in class owltools.sim2.AbstractOwlSim
getPropertyChains(OWLObjectProperty) - Method in class owltools.mooncat.PropertyViewOntologyBuilder
getPropertyId() - Method in class owltools.graph.OWLQuantifiedProperty
getPropertyViews() - Method in class owltools.ontologyrelease.OortConfiguration
getPValue(Set<OWLClass>, IRI) - Method in class owltools.sim2.kb.OwlSimPValue
getPValue(Set<OWLClass>, IRI, Set<OWLClass>) - Method in class owltools.sim2.kb.OwlSimPValue
getPValue(Set<OWLClass>, IRI) - Method in class owltools.sim2.kb.OWLSimReferenceBasedStatistics
getPValue(Set<OWLClass>, IRI, Set<OWLClass>) - Method in class owltools.sim2.kb.OWLSimReferenceBasedStatistics
getQualifier() - Method in class owltools.gaf.parser.GAFParser
getQualifier() - Method in class owltools.gaf.parser.GpadParser
getQualifiers() - Method in class owltools.gaf.GeneAnnotation
getQualityClasses() - Method in class owltools.sim2.preprocessor.PhenoSimHQEPreProcessor
getQuantifiedPropertyList() - Method in class owltools.graph.OWLGraphEdge
getQuantifier() - Method in class owltools.graph.OWLQuantifiedProperty
getQueryOntology() - Method in class owltools.ontologyrelease.OortConfiguration
getQueryOntologyReference() - Method in class owltools.ontologyrelease.OortConfiguration
getRange(OWLObjectProperty) - Method in class owltools.graph.OWLGraphWrapperExtended: It returns the value of the range tag
getReason() - Method in class owltools.gaf.inference.Prediction
getReasoner() - Method in class owltools.graph.OWLGraphWrapperEdges
getReasoner(OWLOntology) - Method in class owltools.InferenceBuilder
getReasoner() - Method in class owltools.io.InferredParentRenderer
getReasoner() - Method in class owltools.sim.OldSimpleOwlSim
getReasoner() - Method in class owltools.sim2.AbstractOwlSim
getReasoner() - Method in interface owltools.sim2.OwlSim
getReasoner() - Method in class owltools.sim2.preprocessor.AbstractSimPreProcessor
getReasoner() - Method in interface owltools.sim2.preprocessor.SimPreProcessor
getReasoner() - Method in class owltools.sim2.SimpleOwlSim
getReasoner(String) - Method in class owltools.web.OWLServer
getReasonerFactory() - Method in class owltools.sim.OldSimpleOwlSim
getReasonerName() - Method in class owltools.ontologyrelease.OortConfiguration
getReasonerName() - Method in class owltools.reasoner.GraphReasoner
getReasonerName() - Method in class owltools.reasoner.GraphReasonerFactory
getReasonerName() - Method in class owltools.reasoner.LazyExpressionMaterializingReasoner: Deprecated.
getReasonerName() - Method in class owltools.reasoner.LazyExpressionMaterializingReasonerFactory: Deprecated.
getReasonerName() - Method in class owltools.reasoner.PlaceholderJcelFactory
getReasonerName() - Method in class owltools.reasoner.PrecomputingMoreReasonerFactory
getReasonerVersion() - Method in class owltools.reasoner.GraphReasoner
getReasonerVersion() - Method in class owltools.reasoner.LazyExpressionMaterializingReasoner: Deprecated.
getReasons() - Method in exception owltools.ontologyrelease.OboOntologyReleaseRunnerCheckException
getRecommendationCount() - Method in class owltools.gaf.rules.AnnotationRulesEngine.AnnotationRulesEngineResult
getRedundantAxioms() - Method in class owltools.InferenceBuilder
getRedundantAxioms(OWLOntology, OWLReasoner, OWLDataFactory) - Method in class owltools.InferenceBuilder: Search for redundant axioms.
getReference() - Method in class owltools.gaf.parser.GAFParser
getReferenceBasicStatistics() - Method in class owltools.sim2.kb.ICDistribution
getReferenceDistribution() - Method in class owltools.sim2.kb.ICDistribution
getReferencedOntologies() - Method in class owltools.mooncat.Mooncat: delegates to OWLGraphWrapper support ontologies
getReferenceIds() - Method in class owltools.gaf.GeneAnnotation
getReferenceStats() - Method in class owltools.sim2.kb.OWLSimReferenceBasedStatistics
getReflexiveSubClasses(OWLClassExpression) - Method in class owltools.sim2.preprocessor.AbstractSimPreProcessor
getRegex() - Method in class owltools.gaf.rules.AnnotationRegularExpressionFromXMLRule
getRelation() - Method in class owltools.gaf.ExtensionExpression
getRelation() - Method in class owltools.gaf.GeneAnnotation
getRelationClosureMap(OWLObject, List<String>) - Method in class owltools.graph.OWLGraphWrapperEdgesAdvanced: Return a map of id to label for the closure of the ontology using the supplied relation id list and .isSubClassOf().
getRelationClosureMapEngine(OWLObject, List<String>) - Method in class owltools.graph.OWLGraphWrapperEdgesAdvanced: Generator for the cache in OWLGraphWrapperEdgesAdvanced.getRelationClosureMap(OWLObject, List).
getRelationIDClosure(OWLObject, List<String>) - Method in class owltools.graph.OWLGraphWrapperEdgesAdvanced: Return a overlaps with getIsaPartofLabelClosure and stuff in GafSolrDocumentLoader.
getRelationLabelClosure(OWLObject, List<String>) - Method in class owltools.graph.OWLGraphWrapperEdgesAdvanced: Return a overlaps with getIsaPartofIDClosure and stuff in GafSolrDocumentLoader.
getRelationOrChain(String) - Method in class owltools.graph.OWLGraphWrapperEdges: If available, return the elements of the equivalent property chain.
getRelationSet(String) - Static method in class owltools.graph.RelationSets
getRelationship() - Method in class owltools.gaf.IdMapping
getRelationType(OWLGraphEdge, OWLGraphWrapper) - Static method in class owltools.gfx.OWLGraphStrokeEdge: Sets the value of relType based on OWLGraphEdge properties TODO : this is too hacky.
getRelevantFields() - Method in class org.bbop.golr.java.AbstractRetrieveGolr
getRelevantFields() - Method in class org.bbop.golr.java.RetrieveGolrAnnotations
getRelevantFields() - Method in class org.bbop.golr.java.RetrieveGolrBioentities
getRemoved() - Method in class owltools.graph.CardinalityContraintsTools.CardinalityReporter
getRemovedInferredAxioms() - Method in class owltools.diff.ReasonerDiff
getReplacedBy(OWLObject) - Method in class owltools.graph.OWLGraphWrapperExtended: It returns the values of the replaced_by tag or IAO_0100001 annotation.
getReportFileName() - Method in class owltools.ontologyrelease.reports.OBOTermsAltIdsReport
getReportFileName() - Method in class owltools.ontologyrelease.reports.OBOTermsIdsObsoleteReport
getReportFileName() - Method in class owltools.ontologyrelease.reports.OBOTermsIdsReport
getReportFileName() - Method in class owltools.ontologyrelease.reports.ObsoletesAllReport
getReportFileName() - Method in class owltools.ontologyrelease.reports.ObsoletesExactReport
getReportFileName() - Method in class owltools.ontologyrelease.reports.ObsoletesInExactReport
getReportFileName() - Method in interface owltools.ontologyrelease.reports.OntologyReportGenerator.OntologyReport: Get the target file name for this report.
getReports() - Static method in class owltools.ontologyrelease.reports.go.External2GoReports: Get all external reports.
getReportSubFolderName() - Method in class owltools.ontologyrelease.reports.OntologyReportGenerator.AbstractReport
getReportSubFolderName() - Method in interface owltools.ontologyrelease.reports.OntologyReportGenerator.OntologyReport: Get the sub folder name for the report
getResultOutStream() - Method in class owltools.sim2.io.AbstractRenderer
getResultOutStream() - Method in interface owltools.sim2.io.SimResultRenderer
getRewriteIRIMap() - Method in class owltools.ontologyrelease.OortConfiguration
getRootOntology() - Method in class owltools.reasoner.LazyExpressionMaterializingReasoner: Deprecated.
getRoots() - Method in class owltools.graph.shunt.OWLShuntGraph: Return the set of graph roots (no parents) as IDs.
getRow() - Method in class owltools.gaf.AnnotationSource
getRule(String) - Method in class owltools.gaf.rules.AnnotationRulesEngine: Retrieve the corresponding rule for a given rule id.
getRuleId() - Method in class owltools.gaf.rules.AbstractAnnotationRule
getRuleId() - Method in interface owltools.gaf.rules.AnnotationRule: Get the ruleId.
getRuleId() - Method in class owltools.gaf.rules.AnnotationRuleViolation
getRules() - Method in class owltools.gaf.rules.AnnotationRulesEngine.AnnotationRulesEngineResult
getRuleViolations(GeneAnnotation) - Method in class owltools.gaf.rules.AbstractAnnotationRule
getRuleViolations(GafDocument) - Method in class owltools.gaf.rules.AbstractAnnotationRule
getRuleViolations(GafDocument, OWLGraphWrapper) - Method in class owltools.gaf.rules.AbstractAnnotationRule
getRuleViolations(GeneAnnotation) - Method in class owltools.gaf.rules.AnnotationRegularExpressionFromXMLRule
getRuleViolations(GeneAnnotation) - Method in interface owltools.gaf.rules.AnnotationRule: Given an annotation, find the set of violations using the rule
getRuleViolations(GafDocument) - Method in interface owltools.gaf.rules.AnnotationRule: Given a whole GafDocument , find the set of violations using the rule
getRuleViolations(GafDocument, OWLGraphWrapper) - Method in interface owltools.gaf.rules.AnnotationRule: Given a whole GafDocument in OWL, find the set of violations using the rule
getRuleViolations(GeneAnnotation) - Method in class owltools.gaf.rules.AnnotationTaxonRule
getRuleViolations(GafDocument, OWLGraphWrapper) - Method in class owltools.gaf.rules.AnnotationTaxonRule
getRuleViolations(GeneAnnotation) - Method in class owltools.gaf.rules.GenericReasonerValidationCheck
getRuleViolations(GafDocument, OWLGraphWrapper) - Method in class owltools.gaf.rules.GenericReasonerValidationCheck
getRuleViolations(GeneAnnotation) - Method in class owltools.gaf.rules.go.BasicChecksRule
getRuleViolations(GeneAnnotation) - Method in class owltools.gaf.rules.go.GoAnnotationExperimentalPredictionRule
getRuleViolations(GeneAnnotation) - Method in class owltools.gaf.rules.go.GoAnnotationPredictionRule
getRuleViolations(GeneAnnotation) - Method in class owltools.gaf.rules.go.GoBindingCheckWithFieldRule
getRuleViolations(GeneAnnotation) - Method in class owltools.gaf.rules.go.GoClassReferenceAnnotationRule
getRuleViolations(GeneAnnotation) - Method in class owltools.gaf.rules.go.GoICAnnotationRule
getRuleViolations(GeneAnnotation) - Method in class owltools.gaf.rules.go.GoIDAAnnotationRule
getRuleViolations(GeneAnnotation) - Method in class owltools.gaf.rules.go.GoIEPRestrictionsRule
getRuleViolations(GeneAnnotation) - Method in class owltools.gaf.rules.go.GoIPIAnnotationRule
getRuleViolations(GeneAnnotation) - Method in class owltools.gaf.rules.go.GoIPICatalyticActivityRestrictionsRule
getRuleViolations(GeneAnnotation) - Method in class owltools.gaf.rules.go.GoMultipleTaxonRule
getRuleViolations(GeneAnnotation) - Method in class owltools.gaf.rules.go.GoNDAnnotationRule
getRuleViolations(GeneAnnotation) - Method in class owltools.gaf.rules.go.GoNoHighLevelTermAnnotationRule
getRuleViolations(GeneAnnotation) - Method in class owltools.gaf.rules.go.GoNoISSProteinBindingRule
getRuleViolations(GeneAnnotation) - Method in class owltools.gaf.rules.go.GOReciprocalAnnotationRule
getRuleViolations(GafDocument) - Method in class owltools.gaf.rules.go.GOReciprocalAnnotationRule
getSameIndividuals(OWLNamedIndividual) - Method in class owltools.reasoner.GraphReasoner
getSameIndividuals(OWLNamedIndividual) - Method in class owltools.reasoner.LazyExpressionMaterializingReasoner: Deprecated.
getScope() - Method in interface owltools.graph.OWLGraphWrapper.ISynonym
getScope() - Method in class owltools.graph.OWLGraphWrapper.Synonym
getScore() - Method in class owltools.sim.Similarity
getScoredAttributesForElement(OWLNamedIndividual) - Method in class owltools.sim2.SimpleOwlSim: Given an individual element, return all direct attribute classes that the individual instantiates, combined with IC.
getSegmentShuntGraph(OWLObject, List<String>) - Method in class owltools.graph.OWLGraphWrapperEdgesAdvanced: Gets all ancestors and direct descendants (distance == 1) that are OWLNamedObjects.
getSegmentShuntGraphJSON(OWLObject, List<String>) - Method in class owltools.graph.OWLGraphWrapperEdgesAdvanced: Return a JSONized version of the output of getSegmentShuntGraph Defaults to is_a/part_of and regulates.
getSeqDb() - Method in class owltools.gaf.Bioentity
getSeqId() - Method in class owltools.gaf.Bioentity
getSequence() - Method in interface owltools.gaf.bioentities.QuestForOrthologsSeqXMLParser.MoreInfoProteinListener.MoreInfo
getSharedElements(OWLClass, OWLClass) - Method in class owltools.sim2.AbstractOwlSim
getShortEvidence() - Method in class owltools.gaf.GeneAnnotation
getShortForm(OWLEntity) - Method in class owltools.io.OWLPrettyPrinter.LabelProvider
getShortId(OWLClass) - Method in class owltools.sim2.AbstractOwlSim
getShortId(OWLClass) - Method in interface owltools.sim2.OwlSim
getSimEngine() - Method in class owltools.sim.SimSearch
getSimilarClassesCommand() - Method in class owltools.web.OWLHandler
getSimilarIndividualsCommand() - Method in class owltools.web.OWLHandler
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
getSimilarityBestMatchAverage(OWLNamedIndividual, OWLNamedIndividual, SimpleOwlSim.Metric, SimpleOwlSim.Direction) - Method in class owltools.sim2.FastOwlSim
getSimilarityBestMatchAverage(OWLNamedIndividual, OWLNamedIndividual, SimpleOwlSim.Metric, SimpleOwlSim.Direction) - Method in interface owltools.sim2.OwlSim: Deprecated.
getSimilarityBestMatchAverage(OWLNamedIndividual, OWLNamedIndividual, SimpleOwlSim.Metric, SimpleOwlSim.Direction) - Method in class owltools.sim2.SimpleOwlSim
getSimilarityBestMatchAverageAsym(OWLNamedIndividual, OWLNamedIndividual) - Method in class owltools.sim.OldSimpleOwlSim: Pesquita et al
getSimilarityBestMatchAverageAsym(OWLNamedIndividual, OWLNamedIndividual) - Method in class owltools.sim2.FastOwlSim
getSimilarityBestMatchAverageAsym(OWLNamedIndividual, OWLNamedIndividual, SimpleOwlSim.Metric) - Method in class owltools.sim2.FastOwlSim
getSimilarityBestMatchAverageAsym(OWLNamedIndividual, OWLNamedIndividual) - Method in interface owltools.sim2.OwlSim: Deprecated.
getSimilarityBestMatchAverageAsym(OWLNamedIndividual, OWLNamedIndividual, SimpleOwlSim.Metric) - Method in interface owltools.sim2.OwlSim: See: Pesquita et al
getSimilarityBestMatchAverageAsym(OWLNamedIndividual, OWLNamedIndividual) - Method in class owltools.sim2.SimpleOwlSim
getSimilarityBestMatchAverageAsym(OWLNamedIndividual, OWLNamedIndividual, SimpleOwlSim.Metric) - Method in class owltools.sim2.SimpleOwlSim
getSimilarityMaxIC(OWLNamedIndividual, OWLNamedIndividual) - Method in class owltools.sim.OldSimpleOwlSim
getSimilarityMaxIC(OWLNamedIndividual, OWLNamedIndividual) - Method in class owltools.sim2.FastOwlSim
getSimilarityMaxIC(OWLNamedIndividual, OWLNamedIndividual) - Method in interface owltools.sim2.OwlSim: Find the inferred attribute shared by both i and j that has highest IC.
getSimilarityMaxIC(OWLNamedIndividual, OWLNamedIndividual) - Method in class owltools.sim2.SimpleOwlSim
getSimplePValue() - Method in class owltools.sim2.kb.PValue
getSimPreProcessor() - Method in class owltools.sim.OldSimpleOwlSim
getSimPreProcessor() - Method in class owltools.sim2.SimpleOwlSim
getSimProperties() - Method in class owltools.sim2.AbstractOwlSim
getSimProperties() - Method in interface owltools.sim2.OwlSim
getSimProperties() - Method in class owltools.sim2.preprocessor.AbstractSimPreProcessor
getSimStatistics() - Method in class owltools.sim2.AbstractOwlSim
getSimStatistics(String) - Method in class owltools.sim2.FastOwlSim
getSimStatistics(String) - Method in interface owltools.sim2.OwlSim
getSimStatistics(String) - Method in class owltools.sim2.SimpleOwlSim
getSimStats() - Method in class owltools.sim2.AbstractOwlSim
getSimStats() - Method in interface owltools.sim2.OwlSim
getSingleQuantifiedProperty() - Method in class owltools.graph.OWLGraphEdge
getSkewness() - Method in class owltools.sim2.kb.BasicStatistics
getSkipFormatSet() - Method in class owltools.ontologyrelease.OortConfiguration
getSkolemIRI(OWLEntity...) - Static method in class owltools.mooncat.TransformationUtils
getSkolemIRI(List<OWLEntity>) - Static method in class owltools.mooncat.TransformationUtils
getSource() - Method in class org.geneontology.lego.model.LegoLink: Deprecated.
getSource() - Method in class owltools.gaf.GeneAnnotation
getSource() - Method in class owltools.graph.OWLGraphEdge
getSourceAnnotation() - Method in class owltools.gaf.rules.AnnotationRuleViolation
getSourceId() - Method in class owltools.gaf.IdMapping
getSourceId() - Method in class owltools.graph.OWLGraphEdge
getSourceOntology() - Method in class owltools.graph.OWLGraphWrapperBasic: Every OWLGraphWrapper objects wraps zero or one source ontologies.
getSourceOntology() - Method in class owltools.sim2.AbstractOwlSim
getSourceOntology() - Method in interface owltools.sim2.OwlSim
getSourceOntology() - Method in class owltools.sim2.SimpleOwlSim
getSourceOntologyPrefixes() - Method in class owltools.mooncat.Mooncat: E.g.
getSourceOntologyPrefixes() - Method in class owltools.ontologyrelease.OortConfiguration
getSources() - Method in class org.geneontology.lego.model.LegoMetadata: Deprecated.
getSources() - Method in interface owltools.util.Adjacency
getSourceViewProperties() - Method in class owltools.sim.OldSimpleOwlSim: Deprecated.
getSpeciesLabel() - Method in class owltools.gaf.Bioentity
getSplitSize() - Method in class owltools.gaf.parser.GafObjectsBuilder
getStandardDeviation() - Method in class owltools.sim2.kb.BasicStatistics
getStatus() - Method in class owltools.gaf.rules.AbstractAnnotationRule
getStatus() - Method in interface owltools.gaf.rules.AnnotationRule: Get the status of this rule.
getStream() - Method in class owltools.gaf.io.GafWriter
getStream() - Method in class owltools.io.AbstractClosureReader
getStream() - Method in class owltools.io.AbstractRenderer
getSubAnnotationPropertiesOf(OWLAnnotationProperty) - Method in class owltools.graph.OWLGraphWrapperEdgesExtended: Returns the direct child properties of prop in all ontologies.
getSubAnnotationPropertyClosureOf(OWLAnnotationProperty) - Method in class owltools.graph.OWLGraphWrapperEdgesExtended: Returns all child properties of prop in all ontologies, ordered from the more general (closer from prop) to the more precise.
getSubAnnotationPropertyReflexiveClosureOf(OWLAnnotationProperty) - Method in class owltools.graph.OWLGraphWrapperEdgesExtended: Returns all sub-properties of prop in all ontologies, and prop itself as the first element (reflexive).
getSubClasses(OWLClassExpression, boolean) - Method in class owltools.reasoner.GraphReasoner
getSubClasses(OWLClassExpression, boolean) - Method in class owltools.reasoner.LazyExpressionMaterializingReasoner: Deprecated.
getSubClasses() - Method in class owltools.sim2.kb.SubclassRetriever
getSubClassesCommand() - Method in class owltools.web.OWLHandler: Params: direct, (id | expression)
getSubClassesNames(OWLClass) - Method in class owltools.graph.OWLGraphWrapperEdgesAdvanced: Deprecated.
getSubClassOfAxioms() - Method in class owltools.graph.OWLGraphEdge: Returns only the OWLSubClassOfAxioms among the OWLAxioms returned by OWLGraphEdge.getAxioms().
getSubDataProperties(OWLDataProperty, boolean) - Method in class owltools.reasoner.GraphReasoner
getSubDataProperties(OWLDataProperty, boolean) - Method in class owltools.reasoner.LazyExpressionMaterializingReasoner: Deprecated.
getSubGenus() - Method in class owltools.tr.LinkMaker.LinkPattern
getSubObjectProperties(OWLObjectPropertyExpression, boolean) - Method in class owltools.reasoner.GraphReasoner
getSubObjectProperties(OWLObjectPropertyExpression, boolean) - Method in class owltools.reasoner.LazyExpressionMaterializingReasoner: Deprecated.
getSubOntology(OWLClass) - Method in class owltools.gaf.inference.BasicAnnotationPropagator
getSubPropertiesOf(OWLObjectPropertyExpression) - Method in class owltools.graph.OWLGraphWrapperEdgesExtended: Returns the direct child properties of prop in all ontologies.
getSubPropertyClosureOf(OWLObjectPropertyExpression) - Method in class owltools.graph.OWLGraphWrapperEdgesExtended: Returns all child properties of prop in all ontologies, ordered from the more general (closer from prop) to the more precise (e.g., for the "overlaps" property, return "part_of" then "in_deep_part_of").
getSubPropertyReflexiveClosureOf(OWLObjectPropertyExpression) - Method in class owltools.graph.OWLGraphWrapperEdgesExtended: Returns all sub-properties of prop in all ontologies, and prop itself as the first element (reflexive).
getSubsetCoannotationMatrix(Set<OWLNamedIndividual>) - Method in class owltools.sim2.FastOwlSim
getSubsetCoannotationMatrix(Set<OWLNamedIndividual>) - Method in interface owltools.sim2.OwlSim
getSubsetCoannotationMatrix(Set<OWLNamedIndividual>) - Method in class owltools.sim2.SimpleOwlSim
getSubsets(OWLObject) - Method in class owltools.graph.OWLGraphWrapperExtended: Returns the values of the subset tag for a given OWLObject
getSubsets(OWLObject, List<String>) - Method in class owltools.graph.OWLGraphWrapperExtended: It returns the value of the subset tag.
getSubSimMethod() - Method in class owltools.sim.MultiSimilarity
getSubsumersFromClosure(OWLObject) - Method in class owltools.graph.OWLGraphWrapperEdges: find the set of classes or class expressions subsuming source, using the graph closure.
getSuggestedReplacements() - Method in class owltools.gaf.rules.AnnotationRuleViolation
getSummaryStatistics() - Method in class owltools.sim2.AbstractOwlSim
getSummaryStatistics(OWLClass) - Method in class owltools.sim2.AbstractOwlSim
getSummaryStatistics() - Method in interface owltools.sim2.OwlSim: Fetch the pre-computed summary values
getSummaryStatistics(OWLClass) - Method in interface owltools.sim2.OwlSim: OwlSim.StatsPerIndividual summary statistic calculations using OWLClass c as the root node
getSummaryStatistics() - Method in class owltools.sim2.SimpleOwlSim
getSummaryStatisticsForCollection(Collection<SummaryStatistics>, OwlSim.Stat) - Method in class owltools.sim2.AbstractOwlSim: This function will take an aggregated collection of Summary Statistics and will generate a derived SummaryStatistic based on a flag for the desired summation.
getSuperClasses(OWLClassExpression, boolean) - Method in class owltools.reasoner.GraphReasoner
getSuperClasses(OWLClassExpression, boolean) - Method in class owltools.reasoner.LazyExpressionMaterializingReasoner: Deprecated.
getSuperClassesCommand() - Method in class owltools.web.OWLHandler: Params: direct, (id | expression)
getSuperClassesOver(OWLClassExpression, OWLObjectProperty, boolean) - Method in class owltools.reasoner.GraphReasoner
getSuperClassExpressions(OWLClassExpression, boolean) - Method in class owltools.reasoner.GraphReasoner: note that this is not a standard reasoner method
getSuperDataProperties(OWLDataProperty, boolean) - Method in class owltools.reasoner.GraphReasoner
getSuperDataProperties(OWLDataProperty, boolean) - Method in class owltools.reasoner.LazyExpressionMaterializingReasoner: Deprecated.
getSuperGenus() - Method in class owltools.tr.LinkMaker.LinkPattern
getSuperObjectProperties(OWLObjectPropertyExpression, boolean) - Method in class owltools.reasoner.GraphReasoner
getSuperObjectProperties(OWLObjectPropertyExpression, boolean) - Method in class owltools.reasoner.LazyExpressionMaterializingReasoner: Deprecated.
getSuperPropertiesOf(OWLObjectPropertyExpression) - Method in class owltools.graph.OWLGraphWrapperEdges: returns parent properties of p in all ontologies
getSuperPropertyClosureOf(OWLObjectPropertyExpression) - Method in class owltools.graph.OWLGraphWrapperEdges
getSuperPropertyReflexiveClosureOf(OWLObjectPropertyExpression) - Method in class owltools.graph.OWLGraphWrapperEdges
getSuperPropertyReflexiveClosureOf(OWLObjectPropertyExpression) - Method in class owltools.graph.OWLGraphWrapperEdgesExtended: Returns all parent properties of prop in all ontologies, and prop itself as the first element (reflexive).
getSupportOntologySet() - Method in class owltools.graph.OWLGraphWrapperBasic: all operations are over a set of ontologies - the source ontology plus any number of supporting ontologies.
getSymbol() - Method in class owltools.gaf.Bioentity
getSynonyms() - Method in class owltools.gaf.Bioentity
getSynonymStrings(OWLObject) - Method in class owltools.graph.OWLGraphWrapper: Deprecated.
getSystemStats() - Method in class owltools.sim2.AbstractOwlSim
getSystemStats() - Method in interface owltools.sim2.OwlSim
getTarget() - Method in class owltools.graph.OWLGraphEdge
getTargetDirectory() - Method in class owltools.gaf.godb.Dumper
getTargetId() - Method in class owltools.gaf.IdMapping
getTargetId() - Method in class owltools.graph.OWLGraphEdge
getTargetOntology() - Method in class owltools.gaf.owl.GAFOWLBridge
getTaxon() - Method in class owltools.gaf.parser.GAFParser
getTaxon() - Method in class owltools.gaf.parser.GpiParser
getTaxonID(OWLClass) - Static method in class owltools.ncbi.NCBIConverter: Get the NCBI Taxonomy ID of an OWL Class.
getThreads() - Method in class owltools.ontologyrelease.OortConfiguration
getTimeOut() - Method in class owltools.reasoner.LazyExpressionMaterializingReasoner: Deprecated.
getTimePoint() - Method in class owltools.ontologyverification.impl.AbstractCheck
getTimePoint() - Method in interface owltools.ontologyverification.OntologyCheck: Get the OntologyCheckRunner.TimePoint for this check.
If the check is to be run on multiple time points, create multiple instance.
getTitle(Iterable<OWLAnnotation>) - Static method in class org.geneontology.lego.model.LegoMetadata: Deprecated.
getTitle() - Method in class org.geneontology.lego.model2.LegoGraph: Deprecated.
getTopClassNode() - Method in class owltools.reasoner.GraphReasoner
getTopClassNode() - Method in class owltools.reasoner.LazyExpressionMaterializingReasoner: Deprecated.
getTopDataPropertyNode() - Method in class owltools.reasoner.GraphReasoner
getTopDataPropertyNode() - Method in class owltools.reasoner.LazyExpressionMaterializingReasoner: Deprecated.
getTopNVariances(Set<OWLClass>, int) - Method in class owltools.sim2.kb.OWLSimReferenceBasedStatistics
getTopNVarianceValues(Set<OWLClass>, int) - Method in class owltools.sim2.kb.OwlSimVariance: This implementation can be heavily optimized
getTopObjectPropertyNode() - Method in class owltools.reasoner.GraphReasoner
getTopObjectPropertyNode() - Method in class owltools.reasoner.LazyExpressionMaterializingReasoner: Deprecated.
getTopologyGraph() - Method in class owltools.util.ShuntGraphUtils.ShuntGraphPair
getTraceReportFile() - Method in class owltools.ontologyrelease.OortConfiguration
getTreeByID(String) - Method in class owltools.panther.PANTHERForest: Return the tree for the tree unique identifier, If nothing was found, return null.
getTreeID() - Method in class owltools.panther.PANTHERTree: Return the tree internal identifier.
getTreeIDSet() - Method in class owltools.panther.PANTHERForest: Return the unique tree identifiers found in the forest.
getTreeLabel() - Method in class owltools.panther.PANTHERTree: Return the tree label.
getTruncatedId(OWLEntity) - Method in class owltools.io.OWLPrettyPrinter.LabelProvider
getType() - Method in class org.geneontology.lego.model.LegoNode: Deprecated.
getType() - Method in class owltools.frame.jsonld.BaseLD
getType() - Method in class owltools.frame.jsonld.ClassExpressionLD
getType() - Method in class owltools.frame.jsonld.ClassFrameLD
getType() - Method in class owltools.frame.jsonld.ClassStubLD
getType() - Method in class owltools.frame.jsonld.PropertyStubLD
getType() - Method in class owltools.frame.jsonld.RestrictionLD
getType() - Method in class owltools.gaf.rules.AnnotationRuleViolation
getType() - Method in class owltools.graph.shunt.OWLShuntNode
getTypeCls() - Method in class owltools.gaf.Bioentity
getTypes() - Method in class owltools.gaf.rules.AnnotationRulesEngine.AnnotationRulesEngineResult
getTypes(OWLNamedIndividual, boolean) - Method in class owltools.reasoner.GraphReasoner
getTypes(OWLNamedIndividual, boolean) - Method in class owltools.reasoner.LazyExpressionMaterializingReasoner: Deprecated.
getUnionSubsumers(OWLObject, OWLObject) - Method in class owltools.sim.SimEngine
getUnionSubsumersSize(OWLObject, OWLObject) - Method in class owltools.sim.SimEngine
getUnits() - Method in class org.geneontology.lego.model2.LegoGraph: Deprecated.

The units are for display purposes only.
For the full model use nodes and links.
getUnknowns() - Method in class org.geneontology.lego.model.LegoNode: Deprecated.
getUnsatisfiableClasses() - Method in class owltools.reasoner.GraphReasoner
getUnsatisfiableClasses() - Method in class owltools.reasoner.LazyExpressionMaterializingReasoner: Deprecated.
getVariance(Set<OWLClass>, IRI) - Method in class owltools.sim2.kb.OWLSimReferenceBasedStatistics
getVariance(Set<OWLClass>, IRI, Set<OWLClass>) - Method in class owltools.sim2.kb.OWLSimReferenceBasedStatistics
getVarianceValue(Set<OWLClass>, IRI) - Method in class owltools.sim2.kb.OwlSimVariance
getVarianceValue(Set<OWLClass>, IRI, Set<OWLClass>) - Method in class owltools.sim2.kb.OwlSimVariance
getVersions() - Method in class owltools.graph.OWLGraphWrapperExtended: Retrieve the version information of all ontologies.
getVersionSubdirectory() - Method in class owltools.ontologyrelease.OortConfiguration
getViewClasses(OWLClass) - Method in class owltools.sim2.preprocessor.AbstractSimPreProcessor
getViewClasses(OWLClass) - Method in interface owltools.sim2.preprocessor.SimPreProcessor: The pre-processor may generate view classes.
getViewEntities() - Method in class owltools.mooncat.PropertyViewOntologyBuilder
getViewLabelPrefix() - Method in class owltools.mooncat.PropertyViewOntologyBuilder
getViewLabelSuffix() - Method in class owltools.mooncat.PropertyViewOntologyBuilder
getViewProperties() - Method in class owltools.sim.OldSimpleOwlSim
getViewRootClass() - Method in class owltools.mooncat.PropertyViewOntologyBuilder: As the we treat Thing as belonging to O, O(P) will contain "P some Thing", and this will be the root of O(P)
getViolations(AnnotationRuleViolation.ViolationType) - Method in class owltools.gaf.rules.AnnotationRulesEngine.AnnotationRulesEngineResult: Retrieve all violations for a given AnnotationRuleViolation.ViolationType.
getWarningCount() - Method in class owltools.gaf.rules.AnnotationRulesEngine.AnnotationRulesEngineResult
getWarnings() - Method in class owltools.gaf.parser.IssueListener.DefaultIssueListener
getWidth() - Method in class owltools.gfx.OWLGraphLayoutNode
getWith() - Method in class owltools.gaf.parser.GAFParser
getWith() - Method in class owltools.gaf.parser.GpadParser
getWithInfos() - Method in class owltools.gaf.GeneAnnotation
getWrappedReasoner() - Method in class owltools.reasoner.LazyExpressionMaterializingReasoner: Deprecated.
getWrappedReasonerFactory() - Method in class owltools.reasoner.LazyExpressionMaterializingReasoner: Deprecated.
getX() - Method in class owltools.sim2.kb.ICDistributionValue
getXref(OWLObject) - Method in class owltools.graph.OWLGraphWrapperExtended: get the values of of the obo xref tag
getXref(OWLObject, List<String>) - Method in class owltools.graph.OWLGraphWrapperExtended: get the values of of the obo xref tag
getXrefs() - Method in interface owltools.graph.OWLGraphWrapper.ISynonym
getXrefs() - Method in class owltools.graph.OWLGraphWrapper.Synonym
getY() - Method in class owltools.sim2.kb.ICDistributionValue
GMTParser - Class in owltools.io: reads in a table (e.g.
GMTParser(OWLGraphWrapper) - Constructor for class owltools.io.GMTParser
GoAnnotationExperimentalPredictionRule - Class in owltools.gaf.rules.go
GoAnnotationExperimentalPredictionRule(OWLGraphWrapper) - Constructor for class owltools.gaf.rules.go.GoAnnotationExperimentalPredictionRule
GoAnnotationPredictionRule - Class in owltools.gaf.rules.go
GoAnnotationPredictionRule(OWLGraphWrapper) - Constructor for class owltools.gaf.rules.go.GoAnnotationPredictionRule
GoAnnotationRulesFactoryImpl - Class in owltools.gaf.rules.go
GoAnnotationRulesFactoryImpl(ParserWrapper, String) - Constructor for class owltools.gaf.rules.go.GoAnnotationRulesFactoryImpl
GoAnnotationRulesFactoryImpl(String, String, ParserWrapper, String, String, String) - Constructor for class owltools.gaf.rules.go.GoAnnotationRulesFactoryImpl: Deprecated.
GoAnnotationRulesFactoryImpl(String, String, ParserWrapper, List<String>, String, String) - Constructor for class owltools.gaf.rules.go.GoAnnotationRulesFactoryImpl
GoAnnotationRulesFactoryImpl(OWLGraphWrapper, TraversingEcoMapper, String) - Constructor for class owltools.gaf.rules.go.GoAnnotationRulesFactoryImpl
GoAnnotationRulesFactoryImpl(String, String, OWLGraphWrapper, TraversingEcoMapper, String) - Constructor for class owltools.gaf.rules.go.GoAnnotationRulesFactoryImpl
GoAnnotationTaxonRule - Class in owltools.gaf.rules.go: Checks if an annotation is valid according to GO taxon constraints.
GoAnnotationTaxonRule(OWLGraphWrapper, String) - Constructor for class owltools.gaf.rules.go.GoAnnotationTaxonRule
GoBindingCheckWithFieldRule - Class in owltools.gaf.rules.go: GO_AR:0000003
GoBindingCheckWithFieldRule(TraversingEcoMapper) - Constructor for class owltools.gaf.rules.go.GoBindingCheckWithFieldRule
GoClassReferenceAnnotationRule - Class in owltools.gaf.rules.go: Checks to see if an annotation uses a class that is not in the current ontology, and that the class has not been obsoleted
GoClassReferenceAnnotationRule(OWLGraphWrapper, String...) - Constructor for class owltools.gaf.rules.go.GoClassReferenceAnnotationRule
GoICAnnotationRule - Class in owltools.gaf.rules.go: GO_AR:0000016
GoICAnnotationRule(TraversingEcoMapper) - Constructor for class owltools.gaf.rules.go.GoICAnnotationRule
GOID - Static variable in class owltools.gaf.parser.GAFParser
GoIDAAnnotationRule - Class in owltools.gaf.rules.go: GO_AR:0000017
GoIDAAnnotationRule(TraversingEcoMapper) - Constructor for class owltools.gaf.rules.go.GoIDAAnnotationRule
GoIEPRestrictionsRule - Class in owltools.gaf.rules.go: GO_AR:0000006
GoIEPRestrictionsRule(OWLGraphWrapper, TraversingEcoMapper) - Constructor for class owltools.gaf.rules.go.GoIEPRestrictionsRule
GoIPIAnnotationRule - Class in owltools.gaf.rules.go: GO_AR:0000018
GoIPIAnnotationRule(TraversingEcoMapper) - Constructor for class owltools.gaf.rules.go.GoIPIAnnotationRule
GoIPICatalyticActivityRestrictionsRule - Class in owltools.gaf.rules.go: GO_AR:0000007
GoIPICatalyticActivityRestrictionsRule(OWLGraphWrapper, TraversingEcoMapper) - Constructor for class owltools.gaf.rules.go.GoIPICatalyticActivityRestrictionsRule
GOlrConfig - Class in owltools.yaml.golrconfig
GOlrConfig() - Constructor for class owltools.yaml.golrconfig.GOlrConfig
GOlrDynamicField - Class in owltools.yaml.golrconfig: Deprecated.
GOlrDynamicField() - Constructor for class owltools.yaml.golrconfig.GOlrDynamicField: Deprecated.
GOlrField - Class in owltools.yaml.golrconfig
GOlrField() - Constructor for class owltools.yaml.golrconfig.GOlrField
GOlrFixedField - Class in owltools.yaml.golrconfig: Deprecated.
GOlrFixedField() - Constructor for class owltools.yaml.golrconfig.GOlrFixedField: Deprecated.
GoMultipleTaxonRule - Class in owltools.gaf.rules.go: GO_AR:0000015
GoMultipleTaxonRule(OWLGraphWrapper) - Constructor for class owltools.gaf.rules.go.GoMultipleTaxonRule
GoMySQLDatabaseDumper - Class in owltools.gaf.godb: implements DatabaseDumper for GO MySQL db
GoMySQLDatabaseDumper(OWLGraphWrapper) - Constructor for class owltools.gaf.godb.GoMySQLDatabaseDumper
GoMySQLDatabaseDumper.GOMySQLTable - Enum in owltools.gaf.godb
GoNDAnnotationRule - Class in owltools.gaf.rules.go: GO_AR:0000011
GoNDAnnotationRule(TraversingEcoMapper) - Constructor for class owltools.gaf.rules.go.GoNDAnnotationRule
GoNoHighLevelTermAnnotationRule - Class in owltools.gaf.rules.go: GO_AR:0000008
GoNoHighLevelTermAnnotationRule(OWLGraphWrapper, TraversingEcoMapper) - Constructor for class owltools.gaf.rules.go.GoNoHighLevelTermAnnotationRule
GoNoISSProteinBindingRule - Class in owltools.gaf.rules.go: GO_AR:0000005
GoNoISSProteinBindingRule(TraversingEcoMapper, AnnotationRuleViolation.ViolationType) - Constructor for class owltools.gaf.rules.go.GoNoISSProteinBindingRule
GoNoISSProteinBindingRule(TraversingEcoMapper) - Constructor for class owltools.gaf.rules.go.GoNoISSProteinBindingRule
GOReciprocalAnnotationRule - Class in owltools.gaf.rules.go: GO_AR:0000004
GOReciprocalAnnotationRule(OWLGraphWrapper, TraversingEcoMapper) - Constructor for class owltools.gaf.rules.go.GOReciprocalAnnotationRule
GOSimPreProcessor - Class in owltools.sim2.preprocessor
GOSimPreProcessor() - Constructor for class owltools.sim2.preprocessor.GOSimPreProcessor
GpadGpiObjectsBuilder - Class in owltools.gaf.parser
GpadGpiObjectsBuilder(SimpleEcoMapper) - Constructor for class owltools.gaf.parser.GpadGpiObjectsBuilder
GpadGpiObjectsBuilder.AspectProvider - Interface in owltools.gaf.parser
GpadParser - Class in owltools.gaf.parser
GpadParser() - Constructor for class owltools.gaf.parser.GpadParser
GpadWriter - Class in owltools.gaf.io
GpadWriter(PrintWriter, double) - Constructor for class owltools.gaf.io.GpadWriter
GpiParser - Class in owltools.gaf.parser
GpiParser() - Constructor for class owltools.gaf.parser.GpiParser
GpiWriter - Class in owltools.gaf.io
GpiWriter(PrintWriter, double) - Constructor for class owltools.gaf.io.GpiWriter
graph - Variable in class org.geneontology.lego.model.LegoTools: Deprecated.
graph - Variable in class owltools.flex.FlexCollection
graph - Variable in class owltools.gaf.godb.Dumper
graph - Variable in class owltools.gaf.owl.GAFOWLBridge
graph - Variable in class owltools.io.AbstractRenderer
graph - Variable in class owltools.io.StanzaToOWLConverter
graph - Variable in class owltools.io.TableToAxiomConverter
graph - Variable in class owltools.sim.SimEngine
graph - Variable in class owltools.sim2.io.AbstractRenderer
graph - Variable in class owltools.solrj.AbstractSolrLoader
GraphClosureRenderer - Class in owltools.io
GraphClosureRenderer(PrintStream) - Constructor for class owltools.io.GraphClosureRenderer
GraphClosureRenderer(String) - Constructor for class owltools.io.GraphClosureRenderer
graphEdgeExcludeSet - Variable in class owltools.graph.OWLGraphWrapperEdges.Config
graphEdgeIncludeSet - Variable in class owltools.graph.OWLGraphWrapperEdges.Config
GraphicsConfig - Class in owltools.gfx
GraphicsConfig() - Constructor for class owltools.gfx.GraphicsConfig
graphicsConfig - Variable in class owltools.gfx.OWLGraphLayoutRenderer
GraphicsConfig.RelationConfig - Class in owltools.gfx
GraphicsConfig.RelationConfig() - Constructor for class owltools.gfx.GraphicsConfig.RelationConfig
GraphReader - Interface in owltools.io
GraphReasoner - Class in owltools.reasoner: incomplete.
GraphReasoner(OWLOntology, OWLReasonerConfiguration, BufferingMode) - Constructor for class owltools.reasoner.GraphReasoner
GraphReasonerFactory - Class in owltools.reasoner
GraphReasonerFactory() - Constructor for class owltools.reasoner.GraphReasonerFactory
GraphRenderer - Interface in owltools.io
GraphStyle - Class in owltools.gfx: hacked crudely from QuickGO
GraphStyle() - Constructor for class owltools.gfx.GraphStyle: Create default style.
GraphStyle(Map<String, String>) - Constructor for class owltools.gfx.GraphStyle: Create a custom style TODO implement configuration options.
GSON - Static variable in class org.bbop.golr.java.AbstractRetrieveGolr
gson - Variable in class owltools.solrj.AbstractSolrLoader
GuiLogHandler - Class in owltools.ontologyrelease.logging
GuiLogHandler(BlockingQueue<String>) - Constructor for class owltools.ontologyrelease.logging.GuiLogHandler

H

handle(String, Request, HttpServletRequest, HttpServletResponse) - Method in class owltools.web.OWLServer
handleAdditionalRules(List<AnnotationRule>, List<AnnotationRule>, List<AnnotationRule>, List<AnnotationRule>, List<AnnotationRule>) - Method in class owltools.gaf.rules.AnnotationRulesFactoryImpl
handleAdditionalRules(List<AnnotationRule>, List<AnnotationRule>, List<AnnotationRule>, List<AnnotationRule>, List<AnnotationRule>) - Method in class owltools.gaf.rules.go.GoAnnotationRulesFactoryImpl
handleAnnotationExtension(GeneAnnotation, RetrieveGolrAnnotations.GolrAnnotationDocument) - Method in class org.bbop.golr.java.RetrieveGolrAnnotations
handleChanges(Set<OWLAxiom>, Set<OWLAxiom>) - Method in class owltools.reasoner.GraphReasoner
handleChanges(Set<OWLAxiom>, Set<OWLAxiom>) - Method in class owltools.reasoner.LazyExpressionMaterializingReasoner: Deprecated.
handleHeaderMetaData(String) - Method in class owltools.gaf.parser.GpiParser
handleLine(OWLOntology, Map<String, List<OWLClass>>, OWLClass, String, int) - Static method in class owltools.ncbi.NCBI2OWL: Handle one line of the data file.
handlePrettyPrinter(Opts) - Method in class owltools.cli.CommandRunner
handleProtein(String, String, String, String, String, String, QuestForOrthologsSeqXMLParser.MoreInfoProteinListener.MoreInfo) - Method in interface owltools.gaf.bioentities.QuestForOrthologsSeqXMLParser.MoreInfoProteinListener
handleProtein(String, String, String, String, String, String) - Method in interface owltools.gaf.bioentities.QuestForOrthologsSeqXMLParser.ProteinListener
handler - Variable in class owltools.idmap.IDMappingPIRParser
handleTerm(PrintWriter, OWLClass, OWLGraphWrapper) - Method in class owltools.ontologyrelease.reports.OBOTermsAltIdsReport
handleTerm(PrintWriter, OWLClass, OWLGraphWrapper) - Method in class owltools.ontologyrelease.reports.OBOTermsIdsObsoleteReport
handleTerm(PrintWriter, OWLClass, OWLGraphWrapper) - Method in class owltools.ontologyrelease.reports.OBOTermsIdsReport
handleTerm(PrintWriter, OWLClass, OWLGraphWrapper) - Method in class owltools.ontologyrelease.reports.ObsoletesAllReport
handleTerm(PrintWriter, OWLClass, OWLGraphWrapper) - Method in class owltools.ontologyrelease.reports.ObsoletesExactReport
handleTerm(PrintWriter, OWLClass, OWLGraphWrapper) - Method in class owltools.ontologyrelease.reports.ObsoletesInExactReport
handleTerm(PrintWriter, OWLClass, OWLGraphWrapper) - Method in interface owltools.ontologyrelease.reports.OntologyReportGenerator.OntologyReport: Handle an OWLObject during the report.
handleUnsatisfiable(Set<OWLClass>, OWLOntology) - Method in class owltools.gaf.rules.AnnotationTaxonRule
handleUnsatisfiable(Set<OWLClass>, OWLOntology) - Method in class owltools.gaf.rules.go.GoAnnotationTaxonRule
HAS_PART - Variable in class owltools.sim2.preprocessor.AbstractOBOSimPreProcessor
HAS_PHENOTYPE - Variable in class owltools.sim2.preprocessor.AbstractOBOSimPreProcessor
hasArgs() - Method in class owltools.cli.Opts
hasAssertedSubClassAxiom(OWLClass, OWLClassExpression, OWLOntology) - Method in class owltools.InferenceBuilder: Check the ontology for an existing subClassOf axiom with the given sub- and superclass.
hasEdge(OWLShuntEdge) - Method in class owltools.graph.shunt.OWLShuntGraph: Check to see if an edge is in the graph.
hasErrors() - Method in class owltools.gaf.rules.AnnotationRulesEngine.AnnotationRulesEngineResult
hasFirstEdgeMoreGeneralGCIParams(OWLGraphEdge, OWLGraphEdge) - Method in class owltools.graph.OWLGraphWrapperEdgesExtended: Determines whether the GCI parameters of the GCI relation firstEdge are more general than the GCI parameters of the GCI relation otherEdge.
hasGrandFathering() - Method in class owltools.gaf.rules.AbstractAnnotationRule
hasGrandFathering() - Method in interface owltools.gaf.rules.AnnotationRule: Indicate the use of grand fathering, meaning do not report violations for this rule for annotations older than the given grand fathering date cut-off.
hashCode() - Method in class owltools.gaf.ExtensionExpression
hashCode() - Method in class owltools.gaf.inference.Prediction
hashCode() - Method in class owltools.gfx.OWLGraphStrokeEdge
hashCode() - Method in class owltools.graph.OWLGraphEdge
hashCode() - Method in class owltools.graph.OWLGraphWrapper.Synonym
hashCode() - Method in class owltools.graph.OWLQuantifiedProperty
hashCode() - Method in class owltools.graph.shunt.OWLShuntEdge
hashCode() - Method in class owltools.graph.shunt.OWLShuntNode
hashCode() - Method in class owltools.ontologyverification.CheckWarning
hashCode() - Method in class owltools.ontologyverification.impl.AbstractCheck
hashCode() - Method in class owltools.phenolog.GenePheno
hashCode() - Method in class owltools.phenolog.Individual
hashCode() - Method in class owltools.phenolog.IndividualPair
hashCode() - Method in class owltools.phenolog.Pheno
hashCode() - Method in class owltools.RedundantInferences.RedundantAxiom
hashCode() - Method in class owltools.sim.OldSimpleOwlSim.OWLClassExpressionPair
hashCode() - Method in class owltools.sim.OWLClassExpressionPair
hashCode() - Method in class owltools.sim.OWLObjectPair
hashCode() - Method in class owltools.sim2.EnrichmentResult
hashCode() - Method in class owltools.sim2.io.SimResultRenderer.AttributesSimScores
hashCode() - Method in class owltools.sim2.scores.ElementPairScores
hashCode() - Method in class owltools.util.BloomFilter: Calculates a hash code for this class.
hashCode() - Method in class owltools.util.ClassExpressionPair
hasInformationContent(OWLObject) - Method in class owltools.sim.SimEngine
hasNext() - Method in class owltools.graph.shunt.OWLShuntGraphDFIterator
hasNode(OWLShuntNode) - Method in class owltools.graph.shunt.OWLShuntGraph: Check to see if a node is in the graph.
hasOpt(String) - Method in class owltools.cli.Opts: Check if the option flag is in the remaining parameters
hasOpts() - Method in class owltools.cli.Opts
hasProperty() - Method in class owltools.graph.OWLQuantifiedProperty
hasQualifiers() - Method in class owltools.gaf.GeneAnnotation
hasRecommendations() - Method in class owltools.gaf.rules.AnnotationRulesEngine.AnnotationRulesEngineResult
hasType(AnnotationRuleViolation.ViolationType) - Method in class owltools.gaf.rules.AnnotationRulesEngine.AnnotationRulesEngineResult
hasWarnings() - Method in class owltools.gaf.rules.AnnotationRulesEngine.AnnotationRulesEngineResult
headerHTML() - Method in class owltools.web.OWLHandler
headerImage(String) - Method in class owltools.web.OWLHandler
headerOWL() - Method in class owltools.web.OWLHandler
headerText() - Method in class owltools.web.OWLHandler
height - Variable in class owltools.gfx.GraphStyle
height - Variable in class owltools.gfx.ImageRender
height - Variable in class owltools.gfx.OWLGraphLayoutNode
help() - Method in class owltools.cli.CommandRunner
helpCommand() - Method in class owltools.web.OWLHandler
helpFooter() - Method in class owltools.cli.CommandRunner
hideIds() - Method in class owltools.io.OWLPrettyPrinter
HierarchyImage - Class in owltools.gfx: Adapted from QuickGO
HierarchyImage(String) - Constructor for class owltools.gfx.HierarchyImage
HierarchyImage(int, int, Collection<OWLGraphLayoutNode>, Collection<OWLGraphStrokeEdge>, GraphStyle, Set<RelationType>) - Constructor for class owltools.gfx.HierarchyImage

I

i - Variable in class owltools.sim2.io.SimResultRenderer.IndividualSimScores
i - Variable in class owltools.sim2.scores.ElementPairScores
IAO - Static variable in class owltools.ncbi.OWLConverter: Define the base IRI for Information Artifact Ontology (IAO) terms.
ICDistribution - Class in owltools.sim2.kb
ICDistribution(double[], DescriptiveStatistics, double) - Constructor for class owltools.sim2.kb.ICDistribution
ICDistributionValue - Class in owltools.sim2.kb
ICDistributionValue(double, double) - Constructor for class owltools.sim2.kb.ICDistributionValue
icIRIString - Variable in class owltools.sim2.AbstractOwlSim
iclcsMatrix - Variable in class owltools.sim2.scores.ElementPairScores
id - Variable in class org.bbop.golr.java.RetrieveGolrBioentities.GolrBioentityDocument
id() - Method in class owltools.gfx.HierarchyImage
id - Variable in class owltools.gfx.OWLGraphLayoutNode
id - Variable in class owltools.graph.shunt.OWLShuntGraph
id - Variable in class owltools.graph.shunt.OWLShuntNode
id - Variable in class owltools.yaml.golrconfig.GOlrConfig
id - Variable in class owltools.yaml.golrconfig.GOlrField
idColour - Variable in class owltools.gfx.OWLGraphLayoutNode
idField - Variable in class owltools.io.StanzaToOWLConverter.Config
idMap - Variable in class owltools.idmap.UniProtIDMapParser
IDMapHandler - Class in owltools.idmap
IDMapHandler() - Constructor for class owltools.idmap.IDMapHandler
IDMapPairWriter - Class in owltools.idmap
IDMapPairWriter() - Constructor for class owltools.idmap.IDMapPairWriter
IdMapping - Class in owltools.gaf
IdMapping() - Constructor for class owltools.gaf.IdMapping
IdMapping(String, String, String, String) - Constructor for class owltools.gaf.IdMapping
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
IdTools - Class in owltools.cli: Convenience tool to convert IRI style Id suffixes into OBO style identifier.
IdTools() - Constructor for class owltools.cli.IdTools
idTypes - Variable in class owltools.idmap.UniProtIDMapParser
ignoreClasses(Set<String>) - Method in class owltools.sim2.preprocessor.AbstractSimPreProcessor
ignoreUnknownTypes - Variable in class org.geneontology.lego.model.LegoTools: Deprecated.
ImageRender - Class in owltools.gfx: Adapted from QuickGO
ImageRender(int, int) - Constructor for class owltools.gfx.ImageRender
ImportChainDotWriter - Class in owltools.mooncat.ontologymetadata: Rudimentary implementation of a DOT writer for the LEGO annotations in OWL.
ImportChainDotWriter(OWLGraphWrapper) - Constructor for class owltools.mooncat.ontologymetadata.ImportChainDotWriter: Create a new writer for the given ontology and reasoner.
ImportChainDotWriter.UnExpectedStructureException - Exception in owltools.mooncat.ontologymetadata
ImportChainDotWriter.UnExpectedStructureException(String, Throwable) - Constructor for exception owltools.mooncat.ontologymetadata.ImportChainDotWriter.UnExpectedStructureException
ImportChainDotWriter.UnExpectedStructureException(String) - Constructor for exception owltools.mooncat.ontologymetadata.ImportChainDotWriter.UnExpectedStructureException
ImportChainExtractor - Class in owltools.mooncat.ontologymetadata
ImportChainExtractor() - Constructor for class owltools.mooncat.ontologymetadata.ImportChainExtractor
ImportClosureSlurper - Class in owltools.io
ImportClosureSlurper(OWLOntology) - Constructor for class owltools.io.ImportClosureSlurper
includeAllWith(OWLAnnotationProperty, OWLOntology) - Method in class owltools.graph.OWLGraphWrapperEdges.Config
includedProperties - Variable in class owltools.mooncat.SpeciesMergeUtil
includeProperty(OWLObjectProperty) - Method in class owltools.graph.OWLGraphWrapperEdges.Config
includeProperty(OWLObjectProperty, OWLQuantifiedProperty.Quantifier) - Method in class owltools.graph.OWLGraphWrapperEdges.Config
incrementalAddAndCommit() - Method in class owltools.solrj.AbstractSolrLoader
incrementallyLoadedTables - Variable in class owltools.gaf.godb.DatabaseDumper
incrementClassPairCount(int) - Method in class owltools.sim2.SimStats
incrementIndividualPairCount() - Method in class owltools.sim2.SimStats
incrementUniqueClassPairCount() - Method in class owltools.sim2.SimStats
index() - Method in class owltools.gaf.GafDocument: Index all current annotations of this document.
indexed - Variable in class owltools.yaml.golrconfig.GOlrField
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
individualCount - Variable in class owltools.sim2.OwlSimMetadata
IndividualPair - Class in owltools.phenolog
IndividualPair() - Constructor for class owltools.phenolog.IndividualPair
IndividualPair(Individual, Individual) - Constructor for class owltools.phenolog.IndividualPair
individualPairCount - Variable in class owltools.sim2.SimStats
individualsIC - Variable in class owltools.sim2.SimStats
individualsType - Variable in class owltools.io.TableToAxiomConverter.Config
InferenceBuilder - Class in owltools: This class build inferred axioms of an ontology.
InferenceBuilder(OWLGraphWrapper) - Constructor for class owltools.InferenceBuilder
InferenceBuilder(OWLGraphWrapper, String) - Constructor for class owltools.InferenceBuilder
InferenceBuilder(OWLGraphWrapper, String, boolean) - Constructor for class owltools.InferenceBuilder
InferenceBuilder(OWLGraphWrapper, OWLReasonerFactory, boolean) - Constructor for class owltools.InferenceBuilder
InferenceBuilder.ConsistencyReport - Class in owltools
InferenceBuilder.OWLClassFilter - Interface in owltools: Filter for relevant OWLClasses during the inference Building process.
InferenceBuilder.PotentialRedundant - Class in owltools
InferenceBuilder.PotentialRedundant(OWLAxiom, OWLAxiom, OWLClass, OWLObjectProperty, OWLClass) - Constructor for class owltools.InferenceBuilder.PotentialRedundant
inferredEdgeBySource - Variable in class owltools.graph.OWLGraphWrapperEdges
InferredParentRenderer - Class in owltools.io: Renders the most specific parent over a set of Objectproperties using an extended reasoner.
InferredParentRenderer(PrintStream) - Constructor for class owltools.io.InferredParentRenderer
InferredParentRenderer(String) - Constructor for class owltools.io.InferredParentRenderer
info(String, String) - Method in class owltools.cli.Opts: Write an info.
info(String) - Method in class owltools.web.OWLHandler
infoFontName - Variable in class owltools.gfx.GraphStyle
infoFontSize - Variable in class owltools.gfx.GraphStyle
INHERES_IN - Variable in class owltools.sim2.preprocessor.AbstractOBOSimPreProcessor
INHERES_IN_PART_OF - Variable in class owltools.sim2.preprocessor.AbstractOBOSimPreProcessor
init() - Method in class owltools.gaf.inference.FoldBasedPredictor
init() - Method in class owltools.gaf.parser.GAFParser
init() - Method in interface owltools.gaf.rules.AnnotationRulesFactory: Initialize the factory.
init() - Method in class owltools.gaf.rules.AnnotationRulesFactoryImpl
init() - Method in class owltools.idmap.IDMapHandler
init() - Method in class owltools.idmap.IDMapPairWriter
init() - Method in class owltools.sim2.SimStats
initCoannotationMatrix(int[][]) - Method in class owltools.sim2.FastOwlSim
initCoannotationMatrix(int[][]) - Method in interface owltools.sim2.OwlSim
initCoannotationMatrix(int[][]) - Method in class owltools.sim2.SimpleOwlSim
initializeFormat() - Static method in class owltools.ncbi.OWLConverter: Initialize the format with standard default prefixes (rdf, rdfs, xsd, owl) and with the prefixes we will use (obo, oio, iao).
instanceICValues(Opts) - Method in class owltools.cli.Sim2CommandRunner: Prints a tab-delimited report of the IC measures for each annotation (class) made to each instance.
instanceStats(Opts) - Method in class owltools.cli.Sim2CommandRunner: Computes & reports on some summary statistics on the loaded data set.
INTEGRAL_TO_MASK - Static variable in class owltools.gaf.GeneAnnotation
interrupt() - Method in class owltools.reasoner.GraphReasoner
interrupt() - Method in class owltools.reasoner.LazyExpressionMaterializingReasoner: Deprecated.
intersection(Collection<E>) - Method in class owltools.util.BloomFilter
IntersectionOf - Interface in owltools.frame
IntersectionOfLD - Class in owltools.frame.jsonld
IntersectionOfLD(Set<ExpressionLD>) - Constructor for class owltools.frame.jsonld.IntersectionOfLD
inverseAsymmetricSimGIC - Variable in class owltools.sim2.scores.ElementPairScores
inverseAsymmetricSimjScore - Variable in class owltools.sim2.scores.AttributePairScores
inverseAsymmetricSimjScore - Variable in class owltools.sim2.scores.ElementPairScores
iriPrefixMap - Variable in class owltools.io.TableToAxiomConverter.Config
ISA_PARTOF - Static variable in class owltools.graph.RelationSets
isAboveMinScore() - Method in class owltools.sim.Similarity
isAddImportsFromSupports() - Method in class owltools.ontologyrelease.OortConfiguration
isAddSupportFromImports() - Method in class owltools.ontologyrelease.OortConfiguration
isAllowEquivalentNamedClassPairs() - Method in class owltools.ontologyrelease.OortConfiguration
isAllowFileOverWrite() - Method in class owltools.ontologyrelease.OortConfiguration
isAllValuesFrom() - Method in class owltools.graph.OWLQuantifiedProperty
isAnnotation - Variable in class owltools.io.StanzaToOWLConverter.Mapping
isAnnotationLevel() - Method in class owltools.gaf.rules.AbstractAnnotationRule
isAnnotationLevel() - Method in interface owltools.gaf.rules.AnnotationRule
isAnnotationLevel() - Method in class owltools.gaf.rules.GenericReasonerValidationCheck
isAnnotationLevel() - Method in class owltools.gaf.rules.go.GoAnnotationExperimentalPredictionRule
isAnnotationLevel() - Method in class owltools.gaf.rules.go.GoAnnotationPredictionRule
isAnnotationLevel() - Method in class owltools.gaf.rules.go.GOReciprocalAnnotationRule
isAPartOfEdge(OWLGraphEdge) - Method in class owltools.graph.OWLGraphManipulator: Determine if edge represents a part_of relation or one of its sub-relations (e.g., "deep_part_of").
isAsserted() - Method in class owltools.ontologyrelease.OortConfiguration
isAssumeOBOStyleIRIs() - Method in class owltools.mooncat.PropertyViewOntologyBuilder
isASubClassOfEdge(OWLGraphEdge) - Method in class owltools.graph.OWLGraphManipulator: Determine if edge represents an is_a relation.
isAutoDetectBridgingOntology() - Method in class owltools.ontologyrelease.OortConfiguration
isBasicAboxMapping() - Method in class owltools.gaf.owl.GAFOWLBridge
isBestMatch - Variable in class owltools.sim2.io.SimResultRenderer.AttributesSimScores
isBestMatchForI - Variable in class owltools.sim2.scores.AttributePairScores
isBp() - Method in class org.geneontology.lego.model.LegoNode: Deprecated.
isCacheClosure - Variable in class owltools.graph.OWLGraphWrapperEdges.Config
isCardinality() - Method in class owltools.graph.OWLQuantifiedProperty
isChain - Variable in class owltools.io.ChadoGraphClosureRenderer
isCheckConsistency() - Method in class owltools.ontologyrelease.OortConfiguration
isCheckOboDoc() - Method in class owltools.io.ParserWrapper
isCheckPotentialRedundant() - Method in class owltools.ontologyrelease.OortConfiguration
isClassApplicable(String, String) - Method in class owltools.gaf.inference.TaxonConstraintsEngine: Deprecated.
isClassApplicable(OWLClass, OWLClass) - Method in class owltools.gaf.inference.TaxonConstraintsEngine: Deprecated.

returns true if testOntologyCls is applicable for testTax
isClassApplicable(OWLClass, OWLClass, Set<OWLGraphEdge>, Set<OWLObject>) - Method in class owltools.gaf.inference.TaxonConstraintsEngine: Deprecated.
isClassApplicableForTaxonCommand() - Method in class owltools.web.OWLHandler: tests which of a set of input classes (specified using id) is applicable for a set of taxa (specified using taxid)
isClassifyIndividuals() - Method in class owltools.mooncat.PropertyViewOntologyBuilder
isCmf() - Method in class org.geneontology.lego.model.LegoNode: Deprecated.
isColocatesWith() - Method in class owltools.gaf.GeneAnnotation
isConsistent() - Method in class owltools.reasoner.GraphReasoner
isConsistent() - Method in class owltools.reasoner.LazyExpressionMaterializingReasoner: Deprecated.
isContributesTo() - Method in class owltools.gaf.GeneAnnotation
isCreateErrorModules() - Method in class owltools.ontologyrelease.OortConfiguration
isCreateReflexiveClasses() - Method in class owltools.mooncat.PropertyViewOntologyBuilder
isCreateShorthand - Variable in class owltools.mooncat.PropertyExtractor
isCut() - Method in class owltools.gaf.GeneAnnotation
isDangling(OWLOntology, OWLEntity) - Method in class owltools.mooncat.Mooncat: Here a dangling entity is one that has no annotation assertions; this is not a perfect test, as conceivable a class could lack assertions; however, this would not be the case for any ontology following obo library principles.
isDebug() - Method in class owltools.InferenceBuilder
isDeprecated(OWLClass, OWLOntology, OWLAnnotationProperty) - Method in class owltools.ontologyrelease.OntologyMetadata
isDirectNot() - Method in class owltools.gaf.GeneAnnotation
isDisableLCSCache - Variable in class owltools.sim2.AbstractOwlSim
isDisableLCSCache() - Method in class owltools.sim2.AbstractOwlSim
isDisposeReasonerOnExit - Variable in class owltools.cli.CommandRunner
isDocumentLevel() - Method in class owltools.gaf.rules.AbstractAnnotationRule
isDocumentLevel() - Method in interface owltools.gaf.rules.AnnotationRule
isDocumentLevel() - Method in class owltools.gaf.rules.go.GOReciprocalAnnotationRule
isDocumentSplitted() - Method in class owltools.gaf.parser.GafObjectsBuilder
isEmpty() - Method in class owltools.gaf.rules.AnnotationRulesEngine.AnnotationRulesEngineResult
isEnforceEL() - Method in class owltools.ontologyrelease.OortConfiguration
isEntailed(OWLAxiom) - Method in class owltools.reasoner.GraphReasoner
isEntailed(Set<? extends OWLAxiom>) - Method in class owltools.reasoner.GraphReasoner
isEntailed(OWLAxiom) - Method in class owltools.reasoner.LazyExpressionMaterializingReasoner: Deprecated.
isEntailed(Set<? extends OWLAxiom>) - Method in class owltools.reasoner.LazyExpressionMaterializingReasoner: Deprecated.
isEntailmentCheckingSupported(AxiomType<?>) - Method in class owltools.reasoner.GraphReasoner
isEntailmentCheckingSupported(AxiomType<?>) - Method in class owltools.reasoner.LazyExpressionMaterializingReasoner: Deprecated.
isExcluded(OWLQuantifiedProperty) - Method in class owltools.graph.OWLGraphWrapperEdges
isExcludedFromAnalysis(OWLObject) - Method in class owltools.sim.SimEngine: A class is excluded from the analysis if: it is a named entity, and the label for that entity matches the exclude labels list OR: it is a class expression, and the signature contains an excluded class
isExcludeEdge(OWLGraphEdge) - Method in class owltools.graph.OWLGraphWrapperEdges
isExecuteOntologyChecks() - Method in class owltools.ontologyrelease.OortConfiguration
isExpandMacros() - Method in class owltools.ontologyrelease.OortConfiguration
isExpandShortcutRelations() - Method in class owltools.ontologyrelease.OortConfiguration
isExpandXrefs() - Method in class owltools.ontologyrelease.OortConfiguration
isFatal() - Method in class owltools.ontologyverification.CheckWarning
isFatal() - Method in class owltools.ontologyverification.impl.AbstractCheck
isFatal() - Method in interface owltools.ontologyverification.OntologyCheck
isFiltered - Variable in class owltools.sim2.io.SimResultRenderer.AttributesSimScores
isFilterUnused() - Method in class owltools.mooncat.PropertyViewOntologyBuilder
isFollowComplementOfInClosure - Variable in class owltools.graph.OWLGraphWrapperEdges.Config
isForceRelease() - Method in class owltools.ontologyrelease.OortConfiguration
isFormatDeclaration(String) - Method in class owltools.gaf.parser.GpadParser
isFormatDeclaration(String) - Method in class owltools.gaf.parser.GpiParser
isGafToOwl() - Method in class owltools.ontologyrelease.OortConfiguration
isGCI() - Method in class owltools.graph.OWLGraphEdge: Determines whether this OWLGraphEdge corresponds to an OBO gci_relation.
isGenerateIndividuals() - Method in class owltools.gaf.owl.GAFOWLBridge
isGoEvidenceCode(String) - Method in interface owltools.gaf.eco.EcoMapper: Check that the given GO code is a valid code with an existing mapping to ECO
isGoEvidenceCode(String) - Method in class owltools.gaf.eco.EcoMapperImpl
isGpadIncludeUnknowBioentities() - Method in class owltools.gaf.parser.GpadGpiObjectsBuilder
isGpadIncludeUnmappedECO() - Method in class owltools.gaf.parser.GpadGpiObjectsBuilder
isHasValue() - Method in class owltools.graph.OWLQuantifiedProperty
isHeaderMetaData(String) - Method in class owltools.gaf.parser.GpadParser
isHeaderMetaData(String) - Method in class owltools.gaf.parser.GpiParser
isHelpMode() - Method in class owltools.cli.Opts
isICmetric(String) - Static method in enum owltools.sim2.SimpleOwlSim.Metric
isIdentity() - Method in class owltools.graph.OWLQuantifiedProperty
isIgnoreLockFile() - Method in class owltools.ontologyrelease.OortConfiguration
isIgnoreObsolete() - Method in class owltools.ontologyverification.impl.NameRedundancyCheck
isImportMarkedEntity(OWLNamedObject, OWLOntology) - Static method in class owltools.mooncat.Mooncat: Check, if the named object has the annotation property IAO:0000412, declaring the object as imported.
isIncludeClassExpressionsInClosure - Variable in class owltools.graph.OWLGraphWrapperEdges.Config
isIndentJson() - Method in class org.bbop.golr.java.AbstractRetrieveGolr
isIndentJson() - Method in class org.bbop.golr.java.RetrieveGolrAnnotations
isIndentJson() - Method in class org.bbop.golr.java.RetrieveGolrBioentities
isInferred() - Method in class owltools.graph.OWLQuantifiedProperty
isInferringAnnotations() - Method in class owltools.gaf.rules.AbstractAnnotationRule
isInferringAnnotations() - Method in interface owltools.gaf.rules.AnnotationRule
isInferringAnnotations() - Method in class owltools.gaf.rules.go.GoAnnotationExperimentalPredictionRule
isInferringAnnotations() - Method in class owltools.gaf.rules.go.GoAnnotationPredictionRule
isInitialized() - Method in interface owltools.gaf.inference.AnnotationPredictor
isInitialized() - Method in class owltools.gaf.inference.BasicAnnotationPropagator
isInitialized() - Method in class owltools.gaf.inference.CompositionalClassPredictor: Deprecated.
isInitialized() - Method in class owltools.gaf.inference.FoldBasedPredictor
isInStack(Stack<NODE>, NODE) - Method in class owltools.util.AbstractTarjan: Check: is the NODE n in the given stack

WARNING: This is currently an inefficient implementation.
isInstanceOf() - Method in class owltools.graph.OWLQuantifiedProperty
isIntegralTo() - Method in class owltools.gaf.GeneAnnotation
isInverseOf() - Method in class owltools.graph.OWLQuantifiedProperty
isJmetric(String) - Static method in enum owltools.sim2.SimpleOwlSim.Metric
isJustifyAssertedSubclasses() - Method in class owltools.ontologyrelease.OortConfiguration
isLCSCacheFullyPopulated - Variable in class owltools.sim2.AbstractOwlSim
isLeaf() - Method in class owltools.gaf.Bioentity
isMarkedAsInferredAxiom(OWLAxiom) - Static method in class owltools.graph.AxiomAnnotationTools: Check if there as an annotation with is_inferred="true" for the given axiom.
isMf() - Method in class org.geneontology.lego.model.LegoNode: Deprecated.
isMonitorMemory - Variable in class owltools.graph.OWLGraphWrapperEdges.Config
isMRC() - Method in class owltools.gaf.GeneAnnotation
isMulti() - Method in class owltools.flex.FlexLine: Return whether or not the line has a single value or multiple values.
isMultiSpecies - Variable in class owltools.sim2.preprocessor.PhenoSimHQEPreProcessor
isNegated() - Method in class owltools.gaf.GeneAnnotation
isNoLookupForLCSCache - Variable in class owltools.sim2.AbstractOwlSim
isNoLookupForLCSCache() - Method in class owltools.sim2.AbstractOwlSim
isObjectLiteral - Variable in class owltools.io.TableToAxiomConverter.Config
isOboIdentifiers - Variable in class owltools.io.StanzaToOWLConverter.Config
isOboIdentifiers - Variable in class owltools.io.TableToAxiomConverter.Config
isObsolete(OWLObject) - Method in class owltools.graph.OWLGraphWrapperExtended: tests if an OWLObject has been declared obsolete in the graph.
isOwlDocumentLevel() - Method in class owltools.gaf.rules.AbstractAnnotationRule
isOwlDocumentLevel() - Method in interface owltools.gaf.rules.AnnotationRule
isOwlDocumentLevel() - Method in class owltools.gaf.rules.AnnotationTaxonRule
isOwlDocumentLevel() - Method in class owltools.gaf.rules.GenericReasonerValidationCheck
isOWLObjectInSubsets(OWLObject, Collection<String>) - Method in class owltools.graph.OWLGraphWrapperEdgesExtended: Determine if testObject belongs to at least one of the subsets in subsets.
isPrecomputed(InferenceType) - Method in class owltools.reasoner.GraphReasoner
isPrecomputed(InferenceType) - Method in class owltools.reasoner.LazyExpressionMaterializingReasoner: Deprecated.
isPreserveObjectPropertyIRIs() - Method in class owltools.mooncat.OWLInAboxTranslator
isPropertyAssertion() - Method in class owltools.graph.OWLQuantifiedProperty
isPruned() - Method in class owltools.gaf.Bioentity
isQuantified() - Method in class owltools.graph.OWLQuantifiedProperty
isQueryOntologyReferenceIsIRI() - Method in class owltools.ontologyrelease.OortConfiguration
isRealClass(OWLObject) - Method in class owltools.graph.OWLGraphWrapperEdgesExtended: Determines that object is an OWLClass that is neither owl:thing, nor owl:nothing, and that it is not deprecated (OWLGraphWrapperExtended.isObsolete(OWLObject) returns false).
isRecreateMireot() - Method in class owltools.ontologyrelease.OortConfiguration
isRedundantWithExistingAnnotations() - Method in class owltools.gaf.inference.Prediction
isRedundantWithOtherPredictions() - Method in class owltools.gaf.inference.Prediction
isRelaxed() - Method in class owltools.ontologyrelease.OortConfiguration
isRemoveDanglingBeforeReasoning() - Method in class owltools.ontologyrelease.OortConfiguration
isRemoveQueryOntologyReference() - Method in class owltools.ontologyrelease.OortConfiguration
isRemoveRedunantAxioms() - Method in class owltools.ontologyrelease.OortConfiguration
isRemoveTrailingQualifiers() - Method in class owltools.ontologyrelease.OortConfiguration
isRepairAnnotationCardinality() - Method in class owltools.ontologyrelease.OortConfiguration
isReplace - Variable in class owltools.tr.TemplatedTransformer.Mapping
isReplaceGenus - Variable in class owltools.gaf.owl.AnnotationExtensionUnfolder
isRunOboBasicDagCheck() - Method in class owltools.ontologyrelease.OortConfiguration
isSatisfiable(OWLClassExpression) - Method in class owltools.reasoner.GraphReasoner
isSatisfiable(OWLClassExpression) - Method in class owltools.reasoner.LazyExpressionMaterializingReasoner: Deprecated.
isSimple() - Method in class owltools.ontologyrelease.OortConfiguration
isSingle() - Method in class owltools.flex.FlexLine: Return whether or not the line has a single value or multiple values.
isSkipFormat(String) - Method in class owltools.ontologyrelease.OortConfiguration
isSkipNotAnnotations() - Method in class owltools.gaf.owl.GAFOWLBridge
isSkippable(OWLClass) - Method in class owltools.mooncat.SpeciesMergeUtil
isSomeValuesFrom() - Method in class owltools.graph.OWLQuantifiedProperty
isSourceNamedObject() - Method in class owltools.graph.OWLGraphEdge
isStrict - Variable in class owltools.gaf.godb.DatabaseDumper
isStrict - Variable in class owltools.io.StanzaToOWLConverter.Config
isSubClassOf() - Method in class owltools.graph.OWLQuantifiedProperty
IssueListener - Interface in owltools.gaf.parser
IssueListener.DefaultIssueListener - Class in owltools.gaf.parser
IssueListener.DefaultIssueListener() - Constructor for class owltools.gaf.parser.IssueListener.DefaultIssueListener
isSwitchSubjectObject - Variable in class owltools.io.TableToAxiomConverter.Config
isTargetNamedObject() - Method in class owltools.graph.OWLGraphEdge
isTerminus() - Method in class owltools.gaf.Bioentity
isThrowOnMultipleExpressions - Variable in class owltools.gaf.owl.AnnotationExtensionUnfolder
isToObject - Variable in class owltools.io.StanzaToOWLConverter.Mapping
isTranslateDisjointsToEquivalents() - Method in class owltools.ontologyrelease.OortConfiguration
isUpperLevel(OWLClass) - Method in class owltools.sim2.preprocessor.AbstractSimPreProcessor
isUseIsInferred() - Method in class owltools.ontologyrelease.OortConfiguration
isUseOriginalClassIRIs() - Method in class owltools.mooncat.PropertyViewOntologyBuilder
isUseQueryOntology() - Method in class owltools.ontologyrelease.OortConfiguration
isUseReleaseFolder() - Method in class owltools.ontologyrelease.OortConfiguration
isUseSubProperties - Variable in class owltools.mooncat.PropertyExtractor
isVerbotenEntity(OWLClass) - Method in class owltools.sim2.preprocessor.PhenoSimHQEPreProcessor
isVersionReportFiles() - Method in class owltools.ontologyrelease.OortConfiguration
isWriteELOntology() - Method in class owltools.ontologyrelease.OortConfiguration
isWriteLabelOWL() - Method in class owltools.ontologyrelease.OortConfiguration
isWriteMetadata() - Method in class owltools.ontologyrelease.OortConfiguration
isWriteSubsets() - Method in class owltools.ontologyrelease.OortConfiguration
iterator() - Method in class owltools.flex.FlexCollection
iterator() - Method in class owltools.flex.FlexDocument
iterator() - Method in class owltools.flex.FlexLine
iteratorDF() - Method in class owltools.graph.shunt.OWLShuntGraph: Get a depth-first iterator for the graph.

J

j - Variable in class owltools.sim2.io.SimResultRenderer.IndividualSimScores
j - Variable in class owltools.sim2.scores.ElementPairScores
JaccardBloomSimilarity - Class in owltools.sim
JaccardBloomSimilarity() - Constructor for class owltools.sim.JaccardBloomSimilarity
JaccardSimilarity - Class in owltools.sim
JaccardSimilarity() - Constructor for class owltools.sim.JaccardSimilarity
join(List<String>, String) - Static method in class owltools.io.InferredParentRenderer
JsCommandRunner - Class in owltools.cli: Provide a JavaScript interpreter for OWLTools.
JsCommandRunner() - Constructor for class owltools.cli.JsCommandRunner
jsonLdToRdf(Opts) - Method in class owltools.cli.CommandRunner
JSONRenderer - Class in owltools.sim2.io
JSONRenderer(PrintStream, String, String) - Constructor for class owltools.sim2.io.JSONRenderer
JSONRenderer(PrintStream) - Constructor for class owltools.sim2.io.JSONRenderer
JustifyAssertionsTool - Class in owltools: Methods to test/justify, whether certain axioms can be inferred from the ontology.
JustifyAssertionsTool() - Constructor for class owltools.JustifyAssertionsTool
JustifyAssertionsTool.JustifyResult - Class in owltools: Generic result for a justify.
JustifyAssertionsTool.JustifyResult() - Constructor for class owltools.JustifyAssertionsTool.JustifyResult
justifySubClasses(OWLOntology, OWLReasoner, Set<OWLSubClassOfAxiom>) - Static method in class owltools.JustifyAssertionsTool: Justify the given set of subClass axioms from the given ontology.
justifySubClasses(OWLOntology, InferenceBuilder, Set<OWLSubClassOfAxiom>) - Static method in class owltools.JustifyAssertionsTool: Justify the given set of subClass axioms from the given ontology.
justifySubClasses(OWLOntology, OWLReasoner, Set<OWLSubClassOfAxiom>, Collection<OWLAxiom>) - Static method in class owltools.JustifyAssertionsTool: Justify the given set of subClass axioms from the given ontology.

K

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

L

label - Variable in class owltools.gfx.OWLGraphLayoutNode
label(OWLObject) - Method in class owltools.sim.SimEngine
labelFontName - Variable in class owltools.gfx.GraphStyle
labelFontSize - Variable in class owltools.gfx.GraphStyle
LazyExpressionMaterializingReasoner - Class in owltools.reasoner: Deprecated.
This is no longer necessary as ELK 0.4 supports queries using class expressions.
LazyExpressionMaterializingReasoner(OWLOntology, OWLReasonerConfiguration, BufferingMode) - Constructor for class owltools.reasoner.LazyExpressionMaterializingReasoner: Deprecated.
LazyExpressionMaterializingReasoner(OWLOntology) - Constructor for class owltools.reasoner.LazyExpressionMaterializingReasoner: Deprecated.
LazyExpressionMaterializingReasonerFactory - Class in owltools.reasoner: Deprecated.
LazyExpressionMaterializingReasonerFactory() - Constructor for class owltools.reasoner.LazyExpressionMaterializingReasonerFactory: Deprecated.
lbl - Variable in class owltools.graph.shunt.OWLShuntNode
lcsCache - Variable in class owltools.sim2.preprocessor.LCSEnabledSimPreProcessor
lcsCacheWidth - Variable in class owltools.sim2.OwlSimMetadata
LCSEnabledSimPreProcessor - Class in owltools.sim2.preprocessor
LCSEnabledSimPreProcessor() - Constructor for class owltools.sim2.preprocessor.LCSEnabledSimPreProcessor
lcsIC - Variable in class owltools.sim2.scores.AttributePairScores
lcsIntersectionSet - Variable in class owltools.sim.ConjunctiveSetInformationContentRatioSimilarity
lcsScore - Variable in class owltools.sim2.io.SimResultRenderer.AttributesSimScores
lcsScorePrefix - Variable in class owltools.sim2.io.SimResultRenderer.AttributesSimScores
lcsSet - Variable in class owltools.sim2.scores.AttributePairScores
lcsx(Opts) - Method in class owltools.cli.SimCommandRunner
lcsxAll(Opts) - Method in class owltools.cli.SimCommandRunner
learnClassDifferentia(Opts) - Method in class owltools.cli.Sim2CommandRunner
left() - Method in class owltools.gfx.OWLGraphLayoutNode
left - Variable in class owltools.gfx.OWLGraphLayoutNode.SVGRectangle
legend - Variable in class owltools.gfx.HierarchyImage
LegoDotWriter - Class in org.geneontology.lego.dot: Deprecated.
LegoDotWriter(OWLGraphWrapper, OWLReasoner) - Constructor for class org.geneontology.lego.dot.LegoDotWriter: Deprecated.

Create a new writer for the given ontology and reasoner.
LegoGraph - Class in org.geneontology.lego.model2: Deprecated.
LegoGraph(List<LegoUnit>, List<LegoNode>, String) - Constructor for class org.geneontology.lego.model2.LegoGraph: Deprecated.
LegoLink - Class in org.geneontology.lego.model: Deprecated.
LegoLink(OWLNamedIndividual, OWLNamedIndividual, OWLObjectPropertyExpression) - Constructor for class org.geneontology.lego.model.LegoLink: Deprecated.
LegoMetadata - Class in org.geneontology.lego.model: Deprecated.
LegoMetadata() - Constructor for class org.geneontology.lego.model.LegoMetadata: Deprecated.
LegoNode - Class in org.geneontology.lego.model: Deprecated.
LegoNode(OWLNamedIndividual, OWLClassExpression) - Constructor for class org.geneontology.lego.model.LegoNode: Deprecated.
LegoRenderer - Interface in org.geneontology.lego.dot: Deprecated.
LegoShuntGraphTool - Class in org.geneontology.lego.json: Deprecated.
LegoShuntGraphTool() - Constructor for class org.geneontology.lego.json.LegoShuntGraphTool: Deprecated.
LegoTools - Class in org.geneontology.lego.model: Deprecated.
LegoTools(OWLGraphWrapper, OWLReasoner) - Constructor for class org.geneontology.lego.model.LegoTools: Deprecated.
LegoTools(OWLGraphWrapper, OWLReasoner, boolean) - Constructor for class org.geneontology.lego.model.LegoTools: Deprecated.
LegoTools(OWLGraphWrapper, OWLReasoner, Set<OWLObjectProperty>, Set<OWLObjectProperty>, Set<OWLObjectProperty>, OWLClass, OWLClass, boolean) - Constructor for class org.geneontology.lego.model.LegoTools: Deprecated.
LegoTools.UnExpectedStructureException - Exception in org.geneontology.lego.model: Deprecated.
LegoTools.UnExpectedStructureException(String, Throwable) - Constructor for exception org.geneontology.lego.model.LegoTools.UnExpectedStructureException: Deprecated.
LegoTools.UnExpectedStructureException(String) - Constructor for exception org.geneontology.lego.model.LegoTools.UnExpectedStructureException: Deprecated.
LegoUnit - Class in org.geneontology.lego.model2: Deprecated.
LegoUnit(IRI, OWLClass, OWLClass, OWLClass, List<OWLClass>) - Constructor for class org.geneontology.lego.model2.LegoUnit: Deprecated.
LegoUnitTools - Class in org.geneontology.lego.model2: Deprecated.
LegoUnitTools(OWLGraphWrapper, OWLReasoner) - Constructor for class org.geneontology.lego.model2.LegoUnitTools: Deprecated.
line - Variable in class owltools.gfx.OWLGraphLayoutNode
LineFilter<T> - Interface in owltools.gaf.parser
lineNumber - Variable in class owltools.idmap.AbstractMappingParser
lines - Variable in class owltools.flex.FlexDocument
LinkMaker - Class in owltools.tr: Hard coded version to create relationships based on matching genus differentia patterns, such as:
LinkMaker(OWLGraphWrapper, OWLReasoner) - Constructor for class owltools.tr.LinkMaker
LinkMaker.LinkMakerResult - Class in owltools.tr
LinkMaker.LinkMakerResult(Set<OWLAxiom>, Set<OWLAxiom>, Set<OWLAxiom>) - Constructor for class owltools.tr.LinkMaker.LinkMakerResult
LinkMaker.LinkPattern - Class in owltools.tr: Set of variables for a pattern.
LinkMaker.LinkPattern(OWLClass, OWLClass, OWLObjectProperty, OWLObjectProperty) - Constructor for class owltools.tr.LinkMaker.LinkPattern
literalPrototype - Variable in class owltools.io.StanzaToOWLConverter.Mapping
load() - Method in class owltools.solrj.AbstractSolrLoader
load() - Method in class owltools.solrj.ComplexAnnotationSolrDocumentLoader
load() - Method in class owltools.solrj.FlexSolrDocumentLoader
load() - Method in class owltools.solrj.GafSolrDocumentLoader
load() - Method in class owltools.solrj.OntologyGeneralSolrDocumentLoader
load() - Method in class owltools.solrj.OntologySolrLoader: Deprecated.
load() - Method in class owltools.solrj.OptimizeSolrDocumentLoader
load() - Method in class owltools.solrj.PANTHERGeneralSolrDocumentLoader
load() - Method in class owltools.solrj.PANTHERSolrDocumentLoader
loadComplexAnnotationSolr(Opts) - Method in class owltools.cli.SolrCommandRunner: Experimental method for trying out the loading of complex_annotation doc type.
loadConfig(File, OortConfiguration) - Static method in class owltools.ontologyrelease.OortConfiguration: Load the configuration from a property file into the given OortConfiguration.
loadECO(ParserWrapper) - Static method in class owltools.gaf.EcoTools: Deprecated.

Load the evidence code ontology (ECO) from its default PURL.
loadGAFsSolr(Opts) - Method in class owltools.cli.SolrCommandRunner: Used for loading a list of GAFs into GOlr.
loadGpadGpi(Opts) - Method in class owltools.cli.GafCommandRunner
loadGpadGpi(File, File) - Method in class owltools.gaf.parser.GpadGpiObjectsBuilder
loadGPADsSolr(Opts) - Method in class owltools.cli.SolrCommandRunner: Used for loading a list of GPAD pairs into GOlr.
loadLCSCache(String) - Method in class owltools.sim2.FastOwlSim
loadLCSCache(String) - Method in interface owltools.sim2.OwlSim: Loads a pregenerated IC cache.
loadLCSCache(String) - Method in class owltools.sim2.SimpleOwlSim
loadOortConfig(Properties, OortConfiguration) - Static method in class owltools.ontologyrelease.OortConfiguration: Load the given Properties into the OortConfiguration.
loadOWLOntology(File) - Static method in class owltools.ncbi.NCBIOWL: Load an ontology from a file.
loadPANTHERGeneralSolr(Opts) - Method in class owltools.cli.SolrCommandRunner: Requires the --read-panther argument (or something else that fills the pSet object).
loadPANTHERSolr(Opts) - Method in class owltools.cli.SolrCommandRunner: Requires the --read-panther argument (or something else that fills the pSet object).
loadProperties(Opts) - Method in class owltools.cli.Sim2CommandRunner
loadProperties(Opts) - Method in class owltools.cli.SimCommandRunner
LocalMirrorIRIMapper - Class in owltools.io: This mapper allows for IRI resolution based on matching *parts* of URIs.
LocalMirrorIRIMapper(String) - Constructor for class owltools.io.LocalMirrorIRIMapper: Create an instance from the given directory file.
LocalMirrorIRIMapper(File) - Constructor for class owltools.io.LocalMirrorIRIMapper: Create an mappingXmlIRIMapper from the given mapping.xml file.
LocalMirrorIRIMapper(File, File) - Constructor for class owltools.io.LocalMirrorIRIMapper: Create an mappingXmlIRIMapper from the given mapping.xml file.
LocalMirrorIRIMapper(URL) - Constructor for class owltools.io.LocalMirrorIRIMapper: Create an instance from the given mapping URL.
LocalMirrorIRIMapper(URL, File) - Constructor for class owltools.io.LocalMirrorIRIMapper: Create an instance from the given mapping URL.
LOG - Static variable in class owltools.gaf.inference.BasicAnnotationPropagator
LOG - Static variable in class owltools.gaf.inference.CompositionalClassPredictor: Deprecated.
LOG - Static variable in class owltools.gaf.parser.GAFParser
LOG - Variable in class owltools.sim2.preprocessor.AbstractSimPreProcessor
Log4jHandler - Class in owltools.ontologyrelease.logging
Log4jHandler(Logger, boolean) - Constructor for class owltools.ontologyrelease.logging.Log4jHandler
logCountMatrix(int[][]) - Method in class owltools.sim2.FastOwlSim
logDebug(String) - Method in class owltools.InferenceBuilder
logError(String, Throwable) - Method in class owltools.ontologyrelease.logging.ErrorReportFileHandler
logError(String, Throwable) - Method in class owltools.ontologyrelease.logging.ExplicitReportFileHandler
logError(String, Throwable) - Method in class owltools.ontologyrelease.logging.GuiLogHandler
logError(String, Throwable) - Method in class owltools.ontologyrelease.logging.Log4jHandler
logError(String, Throwable) - Method in interface owltools.ontologyrelease.logging.LogHandler
logError(String, Throwable) - Method in class owltools.ontologyrelease.logging.TraceReportFileHandler
logError(String) - Method in class owltools.ontologyrelease.ReleaseRunnerFileTools
logError(String, Exception) - Method in class owltools.ontologyrelease.ReleaseRunnerFileTools
logger - Static variable in class owltools.InferenceBuilder
logger - Static variable in class owltools.ncbi.NCBI2OWL: Create a logger.
logger - Static variable in class owltools.ncbi.NCBIConverter: Create a logger.
logger - Static variable in class owltools.ncbi.NCBIOWL: Create a logger.
logger - Static variable in class owltools.ncbi.OWLConverter: Create a logger.
LogHandler - Interface in owltools.ontologyrelease.logging
logInfo(String) - Method in class owltools.InferenceBuilder
logInfo(String) - Method in class owltools.ontologyrelease.logging.ErrorReportFileHandler
logInfo(String) - Method in class owltools.ontologyrelease.logging.ExplicitReportFileHandler
logInfo(String) - Method in class owltools.ontologyrelease.logging.GuiLogHandler
logInfo(String) - Method in class owltools.ontologyrelease.logging.Log4jHandler
logInfo(String) - Method in interface owltools.ontologyrelease.logging.LogHandler
logInfo(String) - Method in class owltools.ontologyrelease.logging.TraceReportFileHandler
logInfo(String) - Method in class owltools.ontologyrelease.ReleaseRunnerFileTools
logRequest(URI) - Method in class org.bbop.golr.java.AbstractRetrieveGolr
logRequestError(URI, IOException) - Method in class org.bbop.golr.java.AbstractRetrieveGolr
logRetry(URI, IOException, int) - Method in class org.bbop.golr.java.AbstractRetrieveGolr
logWarn(String, Throwable) - Method in class owltools.ontologyrelease.logging.ErrorReportFileHandler
logWarn(String, Throwable) - Method in class owltools.ontologyrelease.logging.ExplicitReportFileHandler
logWarn(String, Throwable) - Method in class owltools.ontologyrelease.logging.GuiLogHandler
logWarn(String, Throwable) - Method in class owltools.ontologyrelease.logging.Log4jHandler
logWarn(String, Throwable) - Method in interface owltools.ontologyrelease.logging.LogHandler
logWarn(String, Throwable) - Method in class owltools.ontologyrelease.logging.TraceReportFileHandler
logWarn(String) - Method in class owltools.ontologyrelease.ReleaseRunnerFileTools
logWarn(String, Exception) - Method in class owltools.ontologyrelease.ReleaseRunnerFileTools

M

main(String[]) - Static method in class owltools.cli.AssertInferenceTool
main(String[]) - Static method in class owltools.cli.AssertInferredClassExpressions
main(String[]) - Static method in class owltools.cli.BioChebiGenerator: Main method.
main(String[]) - Static method in class owltools.cli.CommandLineInterface
main(String[]) - Static method in class owltools.cli.Obo2Obo
main(String[]) - Static method in class owltools.diff.ResonerDiffCommandLine
main(String[]) - Static method in class owltools.gfx.GraphStyle: Deprecated.
main(String[]) - Static method in class owltools.io.OWLGsonParser
main(String[]) - Static method in class owltools.io.OWLGsonRenderer
main(String[]) - Static method in class owltools.ncbi.NCBI2OWL: Handle command-line arguments when this class is used in an executable Jar file.
main(String[]) - Static method in class owltools.ontologyrelease.OboOntologyReleaseRunner
main(String[]) - Static method in class owltools.ontologyrelease.OboOntologyReleaseRunnerGui
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
makeAllByAllLowestCommonSubsumer() - Method in class owltools.sim.OldSimpleOwlSim
makeAnnotationValue(OWLAnnotationValue) - Method in class owltools.frame.jsonld.FrameMakerLD
makeClass(OWLObjectIntersectionOf) - Method in class owltools.sim.OldSimpleOwlSim: given a CE of the form A1 and A2 and ...
makeClass(OWLObjectIntersectionOf) - Method in class owltools.sim2.preprocessor.LCSEnabledSimPreProcessor: given a CE of the form A1 and A2 and ...
makeClassFrame(OWLClass) - Method in class owltools.frame.FrameMaker
makeClassFrame(OWLClass) - Method in class owltools.frame.jsonld.FrameMakerLD
makeClassStub(OWLObject) - Method in class owltools.frame.FrameMaker
makeClassStub(OWLObject) - Method in class owltools.frame.jsonld.FrameMakerLD
makeClassTaxonMatrix(Opts) - Method in class owltools.cli.TaxonCommandRunner
makeClosureSubsetOntology(Set<OWLClass>, IRI) - Method in class owltools.mooncat.Mooncat
makeDefaultIndividuals(OWLOntology) - Static method in class owltools.sim2.preprocessor.ABoxUtils: Creates a "fake" individual for every class.
makeDefaultIndividuals(OWLOntology, String) - Static method in class owltools.sim2.preprocessor.ABoxUtils: Creates a "fake" individual for every class.
makeDevelopmentMorphologyLinks() - Method in class owltools.sim2.preprocessor.PhenoSimHQEPreProcessor: In MP we have + abn.
makeEdge(OWLGraphEdge) - Method in class owltools.gfx.OWLGraphLayoutRenderer: Make a layout edge from a OWLGraphEdge make private?
makeExpression(OWLClassExpression) - Method in class owltools.frame.FrameMaker
makeExpression(OWLClassExpression) - Method in class owltools.frame.jsonld.FrameMakerLD
makeHasPhenotypeInstancesDirect() - Method in class owltools.sim2.preprocessor.PhenoSimHQEPreProcessor
makeIndividualSummaryStatistics(SummaryStatistics) - Method in class owltools.sim2.SimJSONEngine
makeIntersectionOf(OWLObjectIntersectionOf) - Method in class owltools.frame.FrameMaker
makeIntersectionOf(OWLObjectIntersectionOf) - Method in class owltools.frame.jsonld.FrameMakerLD
makeIntersectionPair(OWLClassExpression, OWLClassExpression) - Method in class owltools.sim.SimEngine
makeLCSTriple(OWLObject, OWLObject, OWLObject) - Method in class owltools.sim2.SimJSONEngine
makeLinks(List<LinkMaker.LinkPattern>, OWLAnnotation, boolean) - Method in class owltools.tr.LinkMaker: Start search for matches of the given patterns.
makeMinimalSubsetOntology(Set<OWLClass>, IRI) - Method in class owltools.mooncat.Mooncat
makeMinimalSubsetOntology(Set<OWLClass>, IRI, boolean) - Method in class owltools.mooncat.Mooncat
makeMinimalSubsetOntology(Set<OWLClass>, IRI, boolean, Boolean) - Method in class owltools.mooncat.Mooncat: Given a set of classes (e.g.
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 y
makeNonRedundant(Set<OWLObject>, boolean) - Method in class owltools.sim.SimEngine
makeObj(OWLObject) - Method in class owltools.sim2.SimJSONEngine
makeObjAndSet(Map<String, Object>, String, OWLObject) - Method in class owltools.sim2.SimJSONEngine
makeOntologyFrame(Set<OWLClass>) - Method in class owltools.frame.jsonld.FrameMakerLD
makeOntologyFrame(String, Set<OWLClass>) - Method in class owltools.frame.jsonld.FrameMakerLD
makePartOfReflexive() - Method in class owltools.sim2.preprocessor.AbstractOBOSimPreProcessor
makePropertyStub(OWLObject) - Method in class owltools.frame.FrameMaker
makePropertyStub(OWLObject) - Method in class owltools.frame.jsonld.FrameMakerLD
makeReflexive(String) - Method in class owltools.sim2.preprocessor.AbstractOBOSimPreProcessor
makeReflexive(OWLObjectProperty) - Method in class owltools.sim2.preprocessor.AbstractSimPreProcessor
makeReflexive(OWLObjectProperty, OWLClass) - Method in class owltools.sim2.preprocessor.AbstractSimPreProcessor: makes class and all subclasses reflexive
makeSimpleOntology() - Method in class owltools.graph.OWLGraphManipulator: Make a basic ontology, with only is_a, part_of, and develops_from relations, and redundant relations removed, and redundant relations over is_a/part_of removed.
makeSomeValuesFrom(OWLObjectSomeValuesFrom) - Method in class owltools.frame.FrameMaker
makeSomeValuesFrom(OWLObjectSomeValuesFrom) - Method in class owltools.frame.jsonld.FrameMakerLD
makeStub(OWLObject) - Method in class owltools.frame.FrameMaker
makeStub(OWLObject) - Method in class owltools.frame.jsonld.FrameMakerLD
makeSubsetOntologyCommand() - Method in class owltools.web.OWLHandler: generates a sub-ontology consisting only of classes specified using the id param.
makeSummaryStatistics(OwlSim.StatsPerIndividual) - Method in class owltools.sim2.SimJSONEngine
makeSummaryStatistics(OWLClass) - Method in class owltools.sim2.SimJSONEngine
makeSummaryStatistics() - Method in class owltools.sim2.SimJSONEngine
makeTaxonSet(Opts) - Method in class owltools.cli.TaxonCommandRunner
makeUnionPair(OWLClassExpression, OWLClassExpression) - Method in class owltools.sim.SimEngine
makeUniqAttSet(List<Map>) - Method in class owltools.sim2.SimJSONEngine
makeViewClassIRI(IRI, IRI, String) - Method in class owltools.mooncat.PropertyViewOntologyBuilder
makeViewClassIRI(IRI, IRI) - Method in class owltools.sim2.preprocessor.AbstractSimPreProcessor
makeViewClassIRI(IRI, IRI, String, boolean, boolean) - Method in class owltools.sim2.preprocessor.AbstractSimPreProcessor
manager - Static variable in class owltools.ncbi.NCBIOWL: Create OWLAPI utilities: An ontology manager.
mapClassAssertionsUp(OWLOntology, OWLReasoner, Set<OWLClass>, Set<OWLClass>) - Static method in class owltools.sim2.preprocessor.ABoxUtils
mapExt(OWLClass, List<ExtensionExpression>) - Method in class owltools.gaf.owl.AnnotationExtensionFolder
mappingSource - Variable in class owltools.gaf.IdMapping
MappingTarjan<T> - Class in owltools.util: Extension of the AbstractTarjan implementation to use internal map for handling the required information for a node.
MappingTarjan(boolean) - Constructor for class owltools.util.MappingTarjan
mapRelationsToParent(Collection<String>) - Method in class owltools.graph.OWLGraphManipulator: Replace the sub-relations of parentRelations by these parent relations.
mapRelationsToParent(Collection<String>, Collection<String>) - Method in class owltools.graph.OWLGraphManipulator: Identical to OWLGraphManipulator.mapRelationsToParent(Collection), except that this method allows to filter relations not to be mapped to parents:
mapToSlim(Opts) - Method in class owltools.cli.GafCommandRunner
markAsInferredAxiom(OWLAxiom, OWLOntology) - Static method in class owltools.graph.AxiomAnnotationTools: Mark the given axiom as inferred.
Side effect: Removes the axiom in the given ontology and creates a new axiom with the changed annotations.
markAsInferredAxiom(OWLAxiom, OWLDataFactory) - Static method in class owltools.graph.AxiomAnnotationTools: Mark the given axiom as inferred.
markAsInferredAxiom(Set<OWLAxiom>, OWLOntology) - Static method in class owltools.graph.AxiomAnnotationTools: Mark the given axioms as inferred.
Side effect: Removes the axiom in the given ontology and creates a new axiom with the changed annotations.
markAsInferredAxiom(Set<OWLAxiom>, OWLDataFactory) - Static method in class owltools.graph.AxiomAnnotationTools: Mark the given axioms as inferred.
MarkdownRenderer - Class in owltools.renderer.markdown: Fairly hacky md renderer, geared towards storing md in github.
MarkdownRenderer() - Constructor for class owltools.renderer.markdown.MarkdownRenderer
materializeClassExpression(OWLClassExpression) - Method in class owltools.sim2.preprocessor.AbstractSimPreProcessor
materializeClassExpressions(Set<OWLClassExpression>) - Method in class owltools.sim2.preprocessor.AbstractSimPreProcessor: Note: does not flush
materializeClassExpressionsReferencedBy(OWLObjectProperty) - Method in class owltools.sim2.preprocessor.AbstractSimPreProcessor
materializedClassExpressionMap - Variable in class owltools.sim2.preprocessor.AbstractSimPreProcessor
matrix - Variable in class owltools.sim2.scores.ScoreMatrix
max - Variable in class owltools.sim2.OwlSim.StatsPerIndividual
MAX_REFERENCING_AXIOMS - Variable in class owltools.renderer.markdown.MarkdownRenderer
maxDepthChain - Variable in class owltools.gfx.GraphicsConfig.RelationConfig
maxDepthTotal - Variable in class owltools.gfx.GraphicsConfig.RelationConfig
maxHits - Variable in class owltools.sim.SimSearch
maxIC - Variable in class owltools.sim2.io.SimResultRenderer.IndividualSimScores
maxIC - Variable in class owltools.sim2.scores.ElementPairScores
maxICLabel - Variable in class owltools.sim2.io.SimResultRenderer.IndividualSimScores
maxICwitness - Variable in class owltools.sim2.scores.ElementPairScores
maximumClassSize - Variable in class owltools.sim2.EnrichmentConfig
MaximumInformationContentSimilarity - Class in owltools.sim: MaximumInformationContentSimilarity(a,b) = max { IC(LCA_1(a,b)) ...
MaximumInformationContentSimilarity() - Constructor for class owltools.sim.MaximumInformationContentSimilarity
MD5(String) - Method in class owltools.sim2.preprocessor.AbstractSimPreProcessor
mean - Variable in class owltools.sim2.OwlSim.StatsPerIndividual
memCommand() - Method in class owltools.web.OWLHandler
merge(OWLGraphEdge) - Method in class owltools.graph.OWLGraphEdge: Merges this OWLGraphEdge and edge into a new one, containing the union of their underlying OWLAxioms, as returned by getAxioms().
merge() - Method in class owltools.mooncat.EquivalenceSetMergeUtil
merge() - Method in class owltools.mooncat.SpeciesMergeUtil
mergeImportClosure() - Method in class owltools.graph.OWLGraphWrapperBasic: note: may move to mooncat
mergeImportClosure(boolean) - Method in class owltools.graph.OWLGraphWrapperBasic
mergeIntoReferenceOntology(OWLOntology) - Method in class owltools.mooncat.Mooncat
mergeOntologies() - Method in class owltools.mooncat.Mooncat: merge minimal subset of referenced ontologies into the source ontology.
mergeOntology(OWLOntology) - Method in class owltools.graph.OWLGraphWrapperBasic: Adds all axioms from extOnt into source ontology
mergeOntology(OWLOntology, boolean) - Method in class owltools.graph.OWLGraphWrapperBasic
mergeSim(Opts) - Method in class owltools.cli.Sim2CommandRunner
mergeSim(Opts) - Method in class owltools.cli.SimCommandRunner
mergeSupportOntology(String, boolean) - Method in class owltools.graph.OWLGraphWrapperBasic
mergeSupportOntology(String) - Method in class owltools.graph.OWLGraphWrapperBasic
message - Variable in class owltools.ontologyverification.OntologyCheckHandler.CheckSummary
meta - Variable in class owltools.graph.shunt.OWLShuntEdge
meta - Variable in class owltools.graph.shunt.OWLShuntNode
metrics - Static variable in interface owltools.sim2.OwlSim
metricStatMaxes - Variable in class owltools.sim2.AbstractOwlSim
metricStatMeans - Variable in class owltools.sim2.AbstractOwlSim
metricStatMins - Variable in class owltools.sim2.AbstractOwlSim
mf - Variable in class org.geneontology.lego.model.LegoTools: Deprecated.
min - Variable in class owltools.sim2.OwlSim.StatsPerIndividual
minIC - Variable in class owltools.sim.SimSearch
minimumIC - Variable in class owltools.sim.SimEngine
minScore - Variable in class owltools.sim.Similarity
minScore - Variable in class owltools.sim.SimSearch
minWidth - Static variable in class owltools.gfx.HierarchyImage
Mooncat - Class in owltools.mooncat: Given one source ontology referencing one or more referenced ontologies (e.g.
Mooncat(OWLOntologyManager, OWLDataFactory, OWLOntology) - Constructor for class owltools.mooncat.Mooncat
Mooncat(OWLGraphWrapper) - Constructor for class owltools.mooncat.Mooncat
MultiSimilarity - Class in owltools.sim: This is the standard method to use when comparing entities with multiple attributes.
MultiSimilarity() - Constructor for class owltools.sim.MultiSimilarity

N

n - Variable in class owltools.sim2.OwlSim.StatsPerIndividual
nameObjectSomeValuesFrom(OWLOntology, OWLOntology, Map<OWLClass, OWLClassExpression>, boolean) - Static method in class owltools.mooncat.TransformationUtils: Names all inner ObjectSomeValuesFrom expressions
NameRedundancyCheck - Class in owltools.ontologyverification.impl: Check for redundant names in labels and synonyms (scope EXACT).
By default all obsoleted objects are ignored.
NameRedundancyCheck() - Constructor for class owltools.ontologyverification.impl.NameRedundancyCheck
NaryBooleanClassExpression - Interface in owltools.frame
NaryBooleanClassExpressionLD - Class in owltools.frame.jsonld
NaryBooleanClassExpressionLD() - Constructor for class owltools.frame.jsonld.NaryBooleanClassExpressionLD
NCBI - Static variable in class owltools.gaf.TaxonTools
NCBI - Static variable in class owltools.ncbi.OWLConverter: Define the base IRI for NCBI Taxonomy terms.
NCBI2OWL - Class in owltools.ncbi: Provides static methods for converting NCBI Taxonomy data files into OWL format.
NCBI2OWL() - Constructor for class owltools.ncbi.NCBI2OWL
NCBIConverter - Class in owltools.ncbi: Provides common methods for working with NCBI.
NCBIConverter() - Constructor for class owltools.ncbi.NCBIConverter
NCBIOWL - Class in owltools.ncbi: Provides static methods for creating and initializing an OWLOntology into which taxa can be inserted.
NCBIOWL() - Constructor for class owltools.ncbi.NCBIOWL
next() - Method in class owltools.gaf.parser.GAFParser: Try to parse a next line, may skip lines until a line is parsed successfully or the file ends.
next() - Method in class owltools.graph.shunt.OWLShuntGraphDFIterator
next() - Method in class owltools.idmap.IDMappingPIRParser
nextArgIsHelp() - Method in class owltools.cli.Opts
nextEq(String) - Method in class owltools.cli.Opts
nextEq(Collection<String>) - Method in class owltools.cli.Opts
nextFile() - Method in class owltools.cli.Opts
nextList() - Method in class owltools.cli.Opts
nextOpt() - Method in class owltools.cli.Opts
nl() - Method in class owltools.gaf.io.AbstractGafWriter: Append the separator between rows.
nl() - Method in class owltools.gaf.io.GafWriter.BufferedGafWriter
nl() - Method in class owltools.gaf.io.GpadWriter: Append the separator between rows.
nl() - Method in class owltools.gaf.io.GpiWriter: Append the separator between rows.
nl() - Method in class owltools.io.AbstractRenderer
nodes - Variable in class owltools.graph.shunt.OWLShuntGraph
NoElementAttributeMapException - Exception in owltools.sim2
NoElementAttributeMapException() - Constructor for exception owltools.sim2.NoElementAttributeMapException
nonSignificantObjects() - Method in class owltools.sim.SimEngine
noQuoteLabels() - Method in class owltools.io.OWLPrettyPrinter
NOT_MASK - Static variable in class owltools.gaf.GeneAnnotation
notEquals(NODE, NODE) - Method in class owltools.util.AbstractTarjan
notEquals(T, T) - Method in class owltools.util.MappingTarjan
NullSimPreProcessor - Class in owltools.sim2.preprocessor: uses ClassAssertions to determine view property
NullSimPreProcessor() - Constructor for class owltools.sim2.preprocessor.NullSimPreProcessor
numberOfElementsI - Variable in class owltools.sim2.io.SimResultRenderer.IndividualSimScores
numberOfElementsJ - Variable in class owltools.sim2.io.SimResultRenderer.IndividualSimScores

O

obj - Variable in class owltools.graph.shunt.OWLShuntEdge
objLastIdMap - Variable in class owltools.gaf.godb.DatabaseDumper
OBO - Static variable in class owltools.ncbi.OWLConverter: Define the base IRI for Open Biomedical Ontologies (OBO).
OBO - Static variable in enum owltools.vocab.OBOUpperVocabulary
Obo2Obo - Class in owltools.cli: Read an OBO file and write it back out as OBO, useful for sorting hand-edited OBO files.
Obo2Obo() - Constructor for class owltools.cli.Obo2Obo
OboBasicDagCheck - Class in owltools.ontologyrelease
OboBasicDagCheck() - Constructor for class owltools.ontologyrelease.OboBasicDagCheck
OBONamespaces - Enum in owltools.vocab
OboOntologyReleaseRunner - Class in owltools.ontologyrelease: This class is a command line utility which builds an ontology release.
OboOntologyReleaseRunner(OortConfiguration, File, List<LogHandler>) - Constructor for class owltools.ontologyrelease.OboOntologyReleaseRunner
OboOntologyReleaseRunnerCheckException - Exception in owltools.ontologyrelease: OORT Exception indicating a failed check during the release process.
OboOntologyReleaseRunnerCheckException(String) - Constructor for exception owltools.ontologyrelease.OboOntologyReleaseRunnerCheckException
OboOntologyReleaseRunnerCheckException(String, List<String>) - Constructor for exception owltools.ontologyrelease.OboOntologyReleaseRunnerCheckException
OboOntologyReleaseRunnerCheckException(String, List<String>, String) - Constructor for exception owltools.ontologyrelease.OboOntologyReleaseRunnerCheckException
OboOntologyReleaseRunnerGui - Class in owltools.ontologyrelease: GUI access for ontology release runner.
OboOntologyReleaseRunnerGui() - Constructor for class owltools.ontologyrelease.OboOntologyReleaseRunnerGui
OboProperty - Class in owltools.ontologyrelease: Deprecated.
OboProperty() - Constructor for class owltools.ontologyrelease.OboProperty: Deprecated.
OboProperty(boolean, Project) - Constructor for class owltools.ontologyrelease.OboProperty: Deprecated.
OboProperty(boolean) - Constructor for class owltools.ontologyrelease.OboProperty: Deprecated.
OBOTermsAltIdsReport - Class in owltools.ontologyrelease.reports: OntologyReportGenerator.OntologyReport for GeneOntology terms with alternative identifiers.
OBOTermsAltIdsReport(OWLGraphWrapper) - Constructor for class owltools.ontologyrelease.reports.OBOTermsAltIdsReport
OBOTermsAltIdsReport(String) - Constructor for class owltools.ontologyrelease.reports.OBOTermsAltIdsReport
OBOTermsAltIdsReport(String, String) - Constructor for class owltools.ontologyrelease.reports.OBOTermsAltIdsReport
OBOTermsIdsObsoleteReport - Class in owltools.ontologyrelease.reports: OntologyReportGenerator.OntologyReport for obsolete GeneOntology terms.
OBOTermsIdsObsoleteReport(OWLGraphWrapper) - Constructor for class owltools.ontologyrelease.reports.OBOTermsIdsObsoleteReport
OBOTermsIdsObsoleteReport(String) - Constructor for class owltools.ontologyrelease.reports.OBOTermsIdsObsoleteReport
OBOTermsIdsObsoleteReport(String, String) - Constructor for class owltools.ontologyrelease.reports.OBOTermsIdsObsoleteReport
OBOTermsIdsReport - Class in owltools.ontologyrelease.reports: OntologyReportGenerator.OntologyReport for identifiers and labels of all GeneOntology terms.
OBOTermsIdsReport(OWLGraphWrapper) - Constructor for class owltools.ontologyrelease.reports.OBOTermsIdsReport
OBOTermsIdsReport(String) - Constructor for class owltools.ontologyrelease.reports.OBOTermsIdsReport
OBOTermsIdsReport(String, String) - Constructor for class owltools.ontologyrelease.reports.OBOTermsIdsReport
OBOUpperVocabulary - Enum in owltools.vocab
ObsoleteClassInSignature - Class in owltools.ontologyverification.impl
ObsoleteClassInSignature() - Constructor for class owltools.ontologyverification.impl.ObsoleteClassInSignature
ObsoletesAllReport - Class in owltools.ontologyrelease.reports: OntologyReportGenerator.OntologyReport for obsolete terms with a direct or possible replacement
ObsoletesAllReport(OWLGraphWrapper) - Constructor for class owltools.ontologyrelease.reports.ObsoletesAllReport
ObsoletesAllReport(String) - Constructor for class owltools.ontologyrelease.reports.ObsoletesAllReport
ObsoletesExactReport - Class in owltools.ontologyrelease.reports: OntologyReportGenerator.OntologyReport for obsolete terms with a direct replacement
ObsoletesExactReport(OWLGraphWrapper) - Constructor for class owltools.ontologyrelease.reports.ObsoletesExactReport
ObsoletesExactReport(String) - Constructor for class owltools.ontologyrelease.reports.ObsoletesExactReport
ObsoletesInExactReport - Class in owltools.ontologyrelease.reports: OntologyReportGenerator.OntologyReport for obsolete terms with possible replacements (consider)
ObsoletesInExactReport(OWLGraphWrapper) - Constructor for class owltools.ontologyrelease.reports.ObsoletesInExactReport
ObsoletesInExactReport(String) - Constructor for class owltools.ontologyrelease.reports.ObsoletesInExactReport
occurs_in - Variable in class org.geneontology.lego.model.LegoTools: Deprecated.
OIO - Static variable in class owltools.ncbi.OWLConverter: Define the base IRI for OboInOwl terms.
OLDinstanceICValues(Opts) - Method in class owltools.cli.Sim2CommandRunner: Deprecated.
OldSimpleOwlSim - Class in owltools.sim: Inputs
OldSimpleOwlSim(OWLOntology) - Constructor for class owltools.sim.OldSimpleOwlSim
OldSimpleOwlSim.EnrichmentConfig - Class in owltools.sim
OldSimpleOwlSim.EnrichmentConfig() - Constructor for class owltools.sim.OldSimpleOwlSim.EnrichmentConfig
OldSimpleOwlSim.EnrichmentResult - Class in owltools.sim
OldSimpleOwlSim.EnrichmentResult(OWLClass, OWLClass, double, double) - Constructor for class owltools.sim.OldSimpleOwlSim.EnrichmentResult
OldSimpleOwlSim.OWLClassExpressionPair - Class in owltools.sim
OldSimpleOwlSim.OWLClassExpressionPair(OWLClassExpression, OWLClassExpression) - Constructor for class owltools.sim.OldSimpleOwlSim.OWLClassExpressionPair
OldSimpleOwlSim.ScoreAttributePair - Class in owltools.sim
OldSimpleOwlSim.ScoreAttributePair(Double, OWLClassExpression) - Constructor for class owltools.sim.OldSimpleOwlSim.ScoreAttributePair
OldSimpleOwlSim.ScoreAttributesPair - Class in owltools.sim
OldSimpleOwlSim.ScoreAttributesPair(Double, OWLClassExpression) - Constructor for class owltools.sim.OldSimpleOwlSim.ScoreAttributesPair
OldSimpleOwlSim.ScoreAttributesPair(Double, Set<OWLClassExpression>) - Constructor for class owltools.sim.OldSimpleOwlSim.ScoreAttributesPair
OldSimpleOwlSim.ScoreAttributesPair(double) - Constructor for class owltools.sim.OldSimpleOwlSim.ScoreAttributesPair
OldSimpleOwlSim.Stage - Enum in owltools.sim
ontologies - Variable in class owltools.mooncat.ontologymetadata.OntologySetMetadata
OntologyAnnotation - Class in owltools.mooncat.ontologymetadata
OntologyAnnotation(OWLAnnotation) - Constructor for class owltools.mooncat.ontologymetadata.OntologyAnnotation
OntologyCheck - Interface in owltools.ontologyverification: Methods for executing and describing an ontology check.
OntologyCheckHandler - Class in owltools.ontologyverification: Handle the ontology checks for an ontology and its reporting to the LogHandler.
OntologyCheckHandler(boolean, List<OntologyCheck>, List<LogHandler>) - Constructor for class owltools.ontologyverification.OntologyCheckHandler: Create a new instance.
OntologyCheckHandler.CheckSummary - Class in owltools.ontologyverification
OntologyCheckHandler.CheckSummary(boolean, int, String) - Constructor for class owltools.ontologyverification.OntologyCheckHandler.CheckSummary
OntologyCheckRunner - Class in owltools.ontologyverification: Identify and run ontology checks for an ontology (OWLGraphWrapper) via the OntologyCheck interface.
OntologyCheckRunner.TimePoint - Enum in owltools.ontologyverification
OntologyFrame - Interface in owltools.frame
OntologyFrameLD - Class in owltools.frame.jsonld
OntologyFrameLD() - Constructor for class owltools.frame.jsonld.OntologyFrameLD
OntologyGeneralSolrDocumentLoader - Class in owltools.solrj: A highly hard-wired class to specifically load the ontology graph into a set of hard-wired fields for the AmiGO 2/GOlr general-config.yaml schema.
OntologyGeneralSolrDocumentLoader(String, OWLGraphWrapper) - Constructor for class owltools.solrj.OntologyGeneralSolrDocumentLoader
OntologyMetadata - Class in owltools.mooncat.ontologymetadata
OntologyMetadata(OWLOntology) - Constructor for class owltools.mooncat.ontologymetadata.OntologyMetadata
OntologyMetadata - Class in owltools.ontologyrelease
OntologyMetadata(PrintWriter) - Constructor for class owltools.ontologyrelease.OntologyMetadata
OntologyMetadata() - Constructor for class owltools.ontologyrelease.OntologyMetadata
OntologyMetadata.MetadataField - Enum in owltools.ontologyrelease
OntologyMetadata.MetadataQualifier - Enum in owltools.ontologyrelease
OntologyMetadataMarkdownWriter - Class in owltools.mooncat.ontologymetadata
OntologyMetadataMarkdownWriter() - Constructor for class owltools.mooncat.ontologymetadata.OntologyMetadataMarkdownWriter
OntologyReportGenerator - Class in owltools.ontologyrelease.reports: Basic tool for generating ontology reports on a term basis.
OntologyReportGenerator(List<OntologyReportGenerator.OntologyReport>, File) - Constructor for class owltools.ontologyrelease.reports.OntologyReportGenerator
OntologyReportGenerator.AbstractReport - Class in owltools.ontologyrelease.reports: Abstract helper class for OntologyReportGenerator.OntologyReport.
OntologyReportGenerator.AbstractReport() - Constructor for class owltools.ontologyrelease.reports.OntologyReportGenerator.AbstractReport
OntologyReportGenerator.OntologyReport - Interface in owltools.ontologyrelease.reports: Ontology report to be run with the OntologyReportGenerator.
OntologySetMetadata - Class in owltools.mooncat.ontologymetadata
OntologySetMetadata(OWLOntology) - Constructor for class owltools.mooncat.ontologymetadata.OntologySetMetadata
OntologySolrLoader - Class in owltools.solrj: Deprecated.
OntologySolrLoader(String, OWLGraphWrapper) - Constructor for class owltools.solrj.OntologySolrLoader: Deprecated.
OntologyVersionTools - Class in owltools.ontologyrelease: Tools to handle the writing and reading of version information of owl ontology files.
OortConfiguration - Class in owltools.ontologyrelease: Parameters for OboOntologyReleaseRunner.
OortConfiguration() - Constructor for class owltools.ontologyrelease.OortConfiguration
OortConfiguration.MacroStrategy - Enum in owltools.ontologyrelease
OortGuiAdvancedPanel - Class in owltools.ontologyrelease.gui: Panel containing advanced options for the release manager.
OortGuiAdvancedPanel(Frame, OortConfiguration) - Constructor for class owltools.ontologyrelease.gui.OortGuiAdvancedPanel: Create the panel with the given default values.
OortGuiConfiguration - Class in owltools.ontologyrelease.gui: Parameters for OboOntologyReleaseRunnerGui with different default values.
OortGuiConfiguration() - Constructor for class owltools.ontologyrelease.gui.OortGuiConfiguration
OortGuiMainFrame - Class in owltools.ontologyrelease.gui: GUI main frame, calls all constructors for the sub components.
OortGuiMainFrame(OortGuiConfiguration) - Constructor for class owltools.ontologyrelease.gui.OortGuiMainFrame
OortGuiMainFrame(BlockingQueue<String>, OortGuiConfiguration) - Constructor for class owltools.ontologyrelease.gui.OortGuiMainFrame: Main constructor.
OortGuiMainPanel - Class in owltools.ontologyrelease.gui: GUI component for the minimum number of configurations required for the release manager.
OortGuiMainPanel(Frame, OortConfiguration) - Constructor for class owltools.ontologyrelease.gui.OortGuiMainPanel: Constructor allows to build a panel with default values.
OortGuiMenuBar - Class in owltools.ontologyrelease.gui: Menu bar for OORT.
OortGuiMenuBar(OortGuiMainFrame, OortConfiguration) - Constructor for class owltools.ontologyrelease.gui.OortGuiMenuBar: Create a new menu instance.
OortGuiQueryOntologyPanel - Class in owltools.ontologyrelease.gui
OortGuiQueryOntologyPanel(Frame, OortConfiguration) - Constructor for class owltools.ontologyrelease.gui.OortGuiQueryOntologyPanel
open() - Method in class org.geneontology.lego.dot.LegoDotWriter: Deprecated.

Overwrite this method to implement a custom open() routine for the writer.
open(String) - Method in class owltools.mooncat.ontologymetadata.ImportChainDotWriter
OpenAnnotationRDFWriter - Class in owltools.gaf.io: Generates and writes RDF Models conforming to http://www.openannotation.org/spec/core/core.html from GeneAnnotation objects.
OpenAnnotationRDFWriter() - Constructor for class owltools.gaf.io.OpenAnnotationRDFWriter: Creates a new writer, using the default output format (turtle)
OpenAnnotationRDFWriter(String) - Constructor for class owltools.gaf.io.OpenAnnotationRDFWriter
optimizeSolr(Opts) - Method in class owltools.cli.SolrCommandRunner: Requires the --solr-url argument.
OptimizeSolrDocumentLoader - Class in owltools.solrj: A hard-wired optimize command for after we've done everything that we wanted to load.
OptimizeSolrDocumentLoader(String) - Constructor for class owltools.solrj.OptimizeSolrDocumentLoader
Opts - Class in owltools.cli: Helper for easy handling of command line parameters and input.
Opts(String[]) - Constructor for class owltools.cli.Opts: Create a new instance for the given command-line parameters.
Opts(List<String>) - Constructor for class owltools.cli.Opts: Create a new instance for the given command-line parameters.
org.bbop.golr.java - package org.bbop.golr.java
org.geneontology.lego.dot - package org.geneontology.lego.dot
org.geneontology.lego.json - package org.geneontology.lego.json
org.geneontology.lego.model - package org.geneontology.lego.model
org.geneontology.lego.model2 - package org.geneontology.lego.model2
overallStats - Variable in class owltools.sim2.AbstractOwlSim
overallSummaryStatsPerIndividual - Variable in class owltools.sim2.AbstractOwlSim
OverlapSimilarity - Class in owltools.sim
OverlapSimilarity() - Constructor for class owltools.sim.OverlapSimilarity
OWLClassExpressionPair - Class in owltools.sim
OWLClassExpressionPair(OWLClassExpression, OWLClassExpression) - Constructor for class owltools.sim.OWLClassExpressionPair
OWLConverter - Class in owltools.ncbi: Provides common methods for converting data into Web Ontology Language (OWL) format using OWLAPI.
OWLConverter() - Constructor for class owltools.ncbi.OWLConverter
OWLGraphEdge - Class in owltools.graph: Note that when storing OWLGraphEdges in a Set, an OWLGraphEdge.OWLGraphEdgeSet should be used.
OWLGraphEdge(OWLObject, OWLObject, OWLOntology, OWLQuantifiedProperty) - Constructor for class owltools.graph.OWLGraphEdge
OWLGraphEdge(OWLRestriction<?, ?, ?>, OWLObject, OWLQuantifiedProperty, OWLOntology) - Constructor for class owltools.graph.OWLGraphEdge
OWLGraphEdge(OWLObject, OWLObject, List<OWLQuantifiedProperty>, OWLOntology) - Constructor for class owltools.graph.OWLGraphEdge
OWLGraphEdge(OWLObject, OWLObject, List<OWLQuantifiedProperty>, OWLOntology, Set<OWLAxiom>, OWLClass, OWLObjectPropertyExpression) - Constructor for class owltools.graph.OWLGraphEdge
OWLGraphEdge(OWLObject, OWLObject, OWLOntology) - Constructor for class owltools.graph.OWLGraphEdge
OWLGraphEdge(OWLObject, OWLObject, OWLOntology, Set<OWLAxiom>, OWLClass, OWLObjectPropertyExpression) - Constructor for class owltools.graph.OWLGraphEdge
OWLGraphEdge(OWLObject, OWLObject) - Constructor for class owltools.graph.OWLGraphEdge
OWLGraphEdge(OWLObject, OWLObject, OWLObjectPropertyExpression, OWLQuantifiedProperty.Quantifier, OWLOntology) - Constructor for class owltools.graph.OWLGraphEdge
OWLGraphEdge(OWLObject, OWLObject, OWLObjectPropertyExpression, OWLQuantifiedProperty.Quantifier, OWLOntology, OWLAxiom) - Constructor for class owltools.graph.OWLGraphEdge
OWLGraphEdge(OWLObject, OWLObject, OWLObjectPropertyExpression, OWLQuantifiedProperty.Quantifier, OWLOntology, OWLAxiom, OWLClass, OWLObjectPropertyExpression) - Constructor for class owltools.graph.OWLGraphEdge
OWLGraphEdge(OWLObject, OWLObject, OWLQuantifiedProperty.Quantifier) - Constructor for class owltools.graph.OWLGraphEdge
OWLGraphEdge(OWLGraphEdge) - Constructor for class owltools.graph.OWLGraphEdge: Copy constructor.
OWLGraphEdge.OWLGraphEdgeSet - Class in owltools.graph: Represents a Set of OWLGraphEdges.
OWLGraphEdge.OWLGraphEdgeSet() - Constructor for class owltools.graph.OWLGraphEdge.OWLGraphEdgeSet
OWLGraphEdge.OWLGraphEdgeSet(OWLGraphEdge.OWLGraphEdgeSet) - Constructor for class owltools.graph.OWLGraphEdge.OWLGraphEdgeSet
OWLGraphEdge.OWLGraphEdgeSet(Set<OWLGraphEdge>) - Constructor for class owltools.graph.OWLGraphEdge.OWLGraphEdgeSet
OWLGraphLayoutNode - Class in owltools.gfx
OWLGraphLayoutNode(OWLGraphWrapper, OWLObject) - Constructor for class owltools.gfx.OWLGraphLayoutNode
OWLGraphLayoutNode(OWLGraphWrapper, OWLObject, GraphStyle) - Constructor for class owltools.gfx.OWLGraphLayoutNode
OWLGraphLayoutNode.SVGRectangle - Class in owltools.gfx
OWLGraphLayoutNode.SVGRectangle() - Constructor for class owltools.gfx.OWLGraphLayoutNode.SVGRectangle
OWLGraphLayoutRenderer - Class in owltools.gfx: Render a portion of an ontology using the QuickGO graphics code This should be capable of rendering relationships between any OWLObjects - as well as class hierarchies, also object property hierarchies.
OWLGraphLayoutRenderer(OWLGraphWrapper) - Constructor for class owltools.gfx.OWLGraphLayoutRenderer: Create a new renderer with default graph style.
OWLGraphLayoutRenderer(OWLGraphWrapper, GraphStyle) - Constructor for class owltools.gfx.OWLGraphLayoutRenderer
OWLGraphManipulator - Class in owltools.graph: This class provides functionalities to modify an ontology to simplify its graph structure.
OWLGraphManipulator(OWLOntology) - Constructor for class owltools.graph.OWLGraphManipulator: Constructor providing the OWLOntology on which modifications will be performed, that will be wrapped in a OWLGraphWrapper.
OWLGraphManipulator(OWLGraphWrapper) - Constructor for class owltools.graph.OWLGraphManipulator: Constructor providing the OWLGraphWrapper wrapping the ontology on which modifications will be performed.
OWLGraphStrokeEdge - Class in owltools.gfx: Represents an edge in a layout graph Adapted from QuickGO
OWLGraphStrokeEdge(OWLGraphLayoutNode, OWLGraphLayoutNode, OWLGraphEdge, OWLGraphWrapper) - Constructor for class owltools.gfx.OWLGraphStrokeEdge
OWLGraphStrokeEdge.SVGEdge - Class in owltools.gfx
OWLGraphUtil - Class in owltools.graph: general static methods for additional graph operations
OWLGraphUtil() - Constructor for class owltools.graph.OWLGraphUtil
OWLGraphvizRenderer - Class in owltools.gfx: IN-PROGRESS GraphViz renderer TODO - make a common abstract class for all renderers
OWLGraphvizRenderer(OWLGraphWrapper) - Constructor for class owltools.gfx.OWLGraphvizRenderer
owlGraphWrapper - Variable in class owltools.gfx.OWLGraphLayoutRenderer
OWLGraphWrapper - Class in owltools.graph: Wraps one or more OWLOntology objects providing convenient OBO-like operations
OWLGraphWrapper(OWLOntology) - Constructor for class owltools.graph.OWLGraphWrapper: Create a new wrapper for an OWLOntology
OWLGraphWrapper(OWLOntology, boolean) - Constructor for class owltools.graph.OWLGraphWrapper: Deprecated.
OWLGraphWrapper(String) - Constructor for class owltools.graph.OWLGraphWrapper: creates a new OWLOntology as the source ontology
OWLGraphWrapper.ISynonym - Interface in owltools.graph
OWLGraphWrapper.Synonym - Class in owltools.graph
OWLGraphWrapper.Synonym(String, String, String, Set<String>) - Constructor for class owltools.graph.OWLGraphWrapper.Synonym
OWLGraphWrapperBasic - Class in owltools.graph: Basic methods for handling multiple OWLOntology objects as one graph.
OWLGraphWrapperBasic(OWLOntology) - Constructor for class owltools.graph.OWLGraphWrapperBasic
OWLGraphWrapperBasic(String) - Constructor for class owltools.graph.OWLGraphWrapperBasic
OWLGraphWrapperEdges - Class in owltools.graph: Methods to extract and traverse relation in the graph.
OWLGraphWrapperEdges(OWLOntology) - Constructor for class owltools.graph.OWLGraphWrapperEdges
OWLGraphWrapperEdges(String) - Constructor for class owltools.graph.OWLGraphWrapperEdges
OWLGraphWrapperEdges.Config - Class in owltools.graph: Configuration options.
OWLGraphWrapperEdges.Config() - Constructor for class owltools.graph.OWLGraphWrapperEdges.Config
OWLGraphWrapperEdgesAdvanced - Class in owltools.graph
OWLGraphWrapperEdgesAdvanced(OWLOntology) - Constructor for class owltools.graph.OWLGraphWrapperEdgesAdvanced
OWLGraphWrapperEdgesAdvanced(String) - Constructor for class owltools.graph.OWLGraphWrapperEdgesAdvanced
OWLGraphWrapperEdgesExtended - Class in owltools.graph: This class groups methods that could be modified, or added to OWLGraphWrapper and parent classes.
OWLGraphWrapperEdgesExtended(OWLOntology) - Constructor for class owltools.graph.OWLGraphWrapperEdgesExtended: Default constructor.
OWLGraphWrapperEdgesExtended(String) - Constructor for class owltools.graph.OWLGraphWrapperEdgesExtended
OWLGraphWrapperExtended - Class in owltools.graph: Methods to extract values from entities in the graph with potential multiple OWLOntology objects.
OWLGraphWrapperExtended(OWLOntology) - Constructor for class owltools.graph.OWLGraphWrapperExtended
OWLGraphWrapperExtended(String) - Constructor for class owltools.graph.OWLGraphWrapperExtended
OWLGsonParser - Class in owltools.io: Counterpart to OWLGsonRenderer UNTESTED
OWLGsonParser() - Constructor for class owltools.io.OWLGsonParser
OWLGsonRenderer - Class in owltools.io
OWLGsonRenderer(PrintWriter) - Constructor for class owltools.io.OWLGsonRenderer
OWLHandler - Class in owltools.web: See http://code.google.com/p/owltools/wiki/WebServices
OWLHandler(OWLServer, OWLGraphWrapper, HttpServletRequest, HttpServletResponse) - Constructor for class owltools.web.OWLHandler
OWLHandler.Param - Enum in owltools.web
OWLHandler.ResultType - Enum in owltools.web
OWLHandler.ServerMetadata - Class in owltools.web
OWLHandler.ServerMetadata() - Constructor for class owltools.web.OWLHandler.ServerMetadata
OWLInAboxTranslator - Class in owltools.mooncat: Translates an OWL TBox into a "shadow" representation in the ABox.
OWLInAboxTranslator(OWLOntology) - Constructor for class owltools.mooncat.OWLInAboxTranslator
OWLJSONFormat - Class in owltools.io
OWLJSONFormat() - Constructor for class owltools.io.OWLJSONFormat
OWLJSONFormat(IDSpaceManager) - Constructor for class owltools.io.OWLJSONFormat: Constructs an OBOOntologyFormat object.
owlObjectCachedSet - Variable in class owltools.cli.CommandRunner
OWLObjectPair - Class in owltools.sim
OWLObjectPair(OWLObject, OWLObject) - Constructor for class owltools.sim.OWLObjectPair
OWLObjectPair(OWLObject, OWLObject, boolean) - Constructor for class owltools.sim.OWLObjectPair
owlpp - Variable in class owltools.sim.OldSimpleOwlSim
owlpp - Variable in class owltools.sim2.io.AbstractRenderer
OWLPrettyPrinter - Class in owltools.io: Use a OWLGraphWrapper or OWLGraphWrapperExtended to render OWLAxiom, OWLGraphEdge, or OWLQuantifiedProperty in better human readable form.

Hint: Every OWLGraphWrapper is also a OWLGraphWrapperExtended.
OWLPrettyPrinter(OWLGraphWrapperExtended, OWLObjectRenderer) - Constructor for class owltools.io.OWLPrettyPrinter
OWLPrettyPrinter(OWLGraphWrapperExtended) - Constructor for class owltools.io.OWLPrettyPrinter
OWLPrettyPrinter.LabelProvider - Class in owltools.io
OWLPrettyPrinter.LabelProvider(OWLGraphWrapperExtended) - 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
OWLRenderer - Class in owltools.sim2.io
OWLRenderer(PrintStream) - Constructor for class owltools.sim2.io.OWLRenderer
OWLResultsManager - Class in owltools.sim
OWLResultsManager() - Constructor for class owltools.sim.OWLResultsManager
OWLServer - Class in owltools.web: See http://code.google.com/p/owltools/wiki/WebServices This is the core of the existing OWLTools services implementation It takes web API calls, creates an OWLHandler object and calls the appropriate method see OWLHandler for details
OWLServer(OWLGraphWrapper) - Constructor for class owltools.web.OWLServer
OWLServer(OWLGraphWrapper, OwlSim) - Constructor for class owltools.web.OWLServer
OWLShuntEdge - Class in owltools.graph.shunt: An edge reduced to nothing; for use with OWLShuntGraph.
OWLShuntEdge(String, String) - Constructor for class owltools.graph.shunt.OWLShuntEdge
OWLShuntEdge(String, String, String) - Constructor for class owltools.graph.shunt.OWLShuntEdge
OWLShuntEdge(OWLObject, OWLObject, String, OWLGraphWrapper) - Constructor for class owltools.graph.shunt.OWLShuntEdge
OWLShuntGraph - Class in owltools.graph.shunt: A simple (and easily serializable through GSON) graph model to move data from the OWL model out to more standard graph resources.
OWLShuntGraph() - Constructor for class owltools.graph.shunt.OWLShuntGraph: Empty constructor.
OWLShuntGraphDFIterator - Class in owltools.graph.shunt: Iterate over an OWLShuntGraph.
OWLShuntGraphDFIterator(OWLShuntGraph) - Constructor for class owltools.graph.shunt.OWLShuntGraphDFIterator: Constructor.
OWLShuntNode - Class in owltools.graph.shunt: A node reduced to nothing; for use with OWLShuntGraph.
OWLShuntNode(String) - Constructor for class owltools.graph.shunt.OWLShuntNode
OWLShuntNode(String, String) - Constructor for class owltools.graph.shunt.OWLShuntNode
OWLShuntNode(OWLGraphWrapper, OWLObject) - Constructor for class owltools.graph.shunt.OWLShuntNode
OwlSim - Interface in owltools.sim2: Semantic Similarity
OwlSim.ScoreAttributeSetPair - Class in owltools.sim2: A pair consisting of a set of equal-scoring attributes, and a score
OwlSim.ScoreAttributeSetPair(double, OWLClass) - Constructor for class owltools.sim2.OwlSim.ScoreAttributeSetPair
OwlSim.ScoreAttributeSetPair(double, Set<OWLClass>) - Constructor for class owltools.sim2.OwlSim.ScoreAttributeSetPair
OwlSim.ScoreAttributeSetPair(double) - Constructor for class owltools.sim2.OwlSim.ScoreAttributeSetPair: Combined/Summary score May vary depending on the method used
OwlSim.Stat - Enum in owltools.sim2
OwlSim.StatsPerIndividual - Class in owltools.sim2
OwlSim.StatsPerIndividual() - Constructor for class owltools.sim2.OwlSim.StatsPerIndividual
owlsimEnrichmentAnalysis(Opts) - Method in class owltools.cli.Sim2CommandRunner
owlsimEnrichmentAnalysis(Opts) - Method in class owltools.cli.SimCommandRunner
owlsimEnrichmentAnalysisAllByAll(Opts) - Method in class owltools.cli.Sim2CommandRunner
OwlSimFactory - Interface in owltools.sim2: Factory for creating OwlSim engines
OwlSimICDistribution - Class in owltools.sim2.kb
OwlSimICDistribution(OWLSimReferenceBasedStatistics, double[], IRI, Set<OWLClass>, double) - Constructor for class owltools.sim2.kb.OwlSimICDistribution
OwlSimMetadata - Class in owltools.sim2
OwlSimMetadata() - Constructor for class owltools.sim2.OwlSimMetadata
OwlSimPValue - Class in owltools.sim2.kb
OwlSimPValue(OWLSimReferenceBasedStatistics) - Constructor for class owltools.sim2.kb.OwlSimPValue
OWLSimReferenceBasedStatistics - Class in owltools.sim2.kb
OWLSimReferenceBasedStatistics(OwlSim, OWLOntology, OWLGraphWrapper) - Constructor for class owltools.sim2.kb.OWLSimReferenceBasedStatistics: Assuming owlsim, ontologyGraph and sourceOntology objects already initialized
OwlSimUtil - Class in owltools.sim2: Utility methods wrapping OwlSim Most of this functionality duplicates code found elsewhere in OWLTools, but using these static methods may be more straightforward.
OwlSimUtil() - Constructor for class owltools.sim2.OwlSimUtil
OwlSimVariance - Class in owltools.sim2.kb
OwlSimVariance(OWLSimReferenceBasedStatistics) - Constructor for class owltools.sim2.kb.OwlSimVariance
OwlSimVarianceEntityReferenceNotFoundException - Exception in owltools.sim2.kb
OwlSimVarianceEntityReferenceNotFoundException(IRI) - Constructor for exception owltools.sim2.kb.OwlSimVarianceEntityReferenceNotFoundException
owlThing() - Method in class owltools.sim2.FastOwlSim: Convenience method.
owlThingNode() - Method in class owltools.sim2.FastOwlSim: Convenience method.
owltools - package owltools: OWLTools - an OWL API wrapper
owltools.cli - package owltools.cli: CLI - Command Line Interface
owltools.cli.tools - package owltools.cli.tools
owltools.diff - package owltools.diff
owltools.flex - package owltools.flex: Flex Document
owltools.frame - package owltools.frame
owltools.frame.jsonld - package owltools.frame.jsonld
owltools.gaf - package owltools.gaf: Processing of GO Gene Association Files
owltools.gaf.bioentities - package owltools.gaf.bioentities
owltools.gaf.eco - package owltools.gaf.eco
owltools.gaf.godb - package owltools.gaf.godb: This will replace go-db-perl MySQL loader
owltools.gaf.inference - package owltools.gaf.inference: Perform inference on Gene Associations
owltools.gaf.io - package owltools.gaf.io
owltools.gaf.metadata - package owltools.gaf.metadata
owltools.gaf.owl - package owltools.gaf.owl
owltools.gaf.owl.mapping - package owltools.gaf.owl.mapping
owltools.gaf.parser - package owltools.gaf.parser
owltools.gaf.rules - package owltools.gaf.rules
owltools.gaf.rules.go - package owltools.gaf.rules.go
owltools.gfx - package owltools.gfx: GFX - OWL Graphics and Visualization
owltools.graph - package owltools.graph: OWLGraph -- OBO-like Graph Wrapper for OWL Ontologies
owltools.graph.shunt - package owltools.graph.shunt: OWL Shunt
owltools.idmap - package owltools.idmap
owltools.io - package owltools.io: IO - Input/Output
owltools.mooncat - package owltools.mooncat: Mooncat -- Multiple OWL ONtology Catenation
owltools.mooncat.ontologymetadata - package owltools.mooncat.ontologymetadata: OntologyMetadata
owltools.ncbi - package owltools.ncbi
owltools.ontologyrelease - package owltools.ontologyrelease: Oort - OBO Ontology Release Tool (OORT)
owltools.ontologyrelease.gui - package owltools.ontologyrelease.gui
owltools.ontologyrelease.logging - package owltools.ontologyrelease.logging
owltools.ontologyrelease.reports - package owltools.ontologyrelease.reports
owltools.ontologyrelease.reports.go - package owltools.ontologyrelease.reports.go
owltools.ontologyverification - package owltools.ontologyverification
owltools.ontologyverification.impl - package owltools.ontologyverification.impl
owltools.panther - package owltools.panther: PANTHER Tree Tools
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.renderer.markdown - package owltools.renderer.markdown
owltools.sim - package owltools.sim: OWLSim -- Semantic Similarity over OWL ontologies
owltools.sim2 - package owltools.sim2
owltools.sim2.io - package owltools.sim2.io
owltools.sim2.kb - package owltools.sim2.kb
owltools.sim2.preprocessor - package owltools.sim2.preprocessor
owltools.sim2.scores - package owltools.sim2.scores
owltools.solrj - package owltools.solrj: OWLTools and Solr
owltools.tr - package owltools.tr
owltools.util - package owltools.util
owltools.version - package owltools.version
owltools.vocab - package owltools.vocab
owltools.web - package owltools.web: OWLTools Web Services
owltools.yaml.golrconfig - package owltools.yaml.golrconfig: YAML GOlr Configuration

P

PairScores<T> - Interface in owltools.sim2.scores: A set of scores for any pair of objects
PANTHERForest - Class in owltools.panther: Methods to simplify the work with sets of PANTHER trees.
PANTHERForest(File) - Constructor for class owltools.panther.PANTHERForest: Create an instance for the given privitve array of files.
PANTHERGeneralSolrDocumentLoader - Class in owltools.solrj: A hard-wired loader for the general-config.yaml profile.
PANTHERGeneralSolrDocumentLoader(String) - Constructor for class owltools.solrj.PANTHERGeneralSolrDocumentLoader
PANTHERSolrDocumentLoader - Class in owltools.solrj: A hard-wired loader for the family-config.yaml profile.
PANTHERSolrDocumentLoader(String) - Constructor for class owltools.solrj.PANTHERSolrDocumentLoader
PANTHERTree - Class in owltools.panther: Methods to simplify the work with the Newick-ish output we get from PANTHER.
PANTHERTree(File) - Constructor for class owltools.panther.PANTHERTree: Create an instance for the given path
parentArrowShape - Variable in class owltools.gfx.GraphicsConfig.RelationConfig
parse(InputStream) - Method in class owltools.gaf.bioentities.QuestForOrthologsSeqXMLParser: Parse the content of the stream with an event-based XML parser.
Content is only provided to registered listeners.
parse(Reader) - Method in class owltools.gaf.parser.GAFParser
parse(String) - Method in class owltools.gaf.parser.GAFParser
parse(File) - Method in class owltools.gaf.parser.GAFParser
parse(String) - Method in class owltools.idmap.AbstractMappingParser
parse(Reader) - Method in class owltools.idmap.AbstractMappingParser
parse(File) - Method in class owltools.idmap.AbstractMappingParser
parse(Reader) - Method in class owltools.idmap.IDMappingPIRParser
parse(Reader) - Method in class owltools.idmap.UniProtIDMapParser
parse(String) - Method in class owltools.io.GMTParser
parse(String) - Method in class owltools.io.ParserWrapper
parse(String) - Method in class owltools.io.StanzaToOWLConverter: parses a stanza file and generates axioms in targetOntology
parse(File) - Method in class owltools.io.StanzaToOWLConverter
parse(String) - Method in class owltools.io.TableToAxiomConverter
parse(File) - Method in class owltools.io.TableToAxiomConverter
parse(String) - Method in class owltools.phenolog.GenePhenoTsvParser
parseArgString(String) - Method in class owltools.cli.CommandRunner
parseCompositeQualifier(String) - Static method in class owltools.gaf.parser.BuilderTools: Parse the string into a list of qualifier strings
parseExtensionExpression(String) - Static method in class owltools.gaf.parser.BuilderTools
parseGolrResponse(String, Class<T>) - Method in class org.bbop.golr.java.AbstractRetrieveGolr
parseLine(String, int) - Static method in class owltools.ncbi.NCBI2OWL: Parse a line of the data file into a pair of strings: the field name and the field value.
parseOBO(String) - Method in class owltools.io.ParserWrapper
parseOWL(String) - Method in class owltools.io.ParserWrapper
parseOWL(IRI) - Method in class owltools.io.ParserWrapper
parserError(String, String, int) - Method in interface owltools.gaf.parser.ParserListener: Report a parser error.
ParserListener - Interface in owltools.gaf.parser
parserWarning(String, String, int) - Method in interface owltools.gaf.parser.ParserListener: Report a parser warning.
ParserWrapper - Class in owltools.io: Convenience class wrapping org.oboformat that abstracts away underlying details of ontology format or location
ParserWrapper() - Constructor for class owltools.io.ParserWrapper
ParserWrapper.OboAndOwlNameProvider - Class in owltools.io: Provide names for the OBOFormatWriter using an OBODoc first and an OWLGraphWrapper as secondary.
ParserWrapper.OboAndOwlNameProvider(OBODoc, OWLGraphWrapper) - Constructor for class owltools.io.ParserWrapper.OboAndOwlNameProvider
ParserWrapper.OWLGraphWrapperNameProvider - Class in owltools.io: Provide names for the OBOFormatWriter using an OWLGraphWrapper.
ParserWrapper.OWLGraphWrapperNameProvider(OWLGraphWrapper) - Constructor for class owltools.io.ParserWrapper.OWLGraphWrapperNameProvider
ParserWrapper.OWLGraphWrapperNameProvider(OWLGraphWrapper, String) - Constructor for class owltools.io.ParserWrapper.OWLGraphWrapperNameProvider
ParserWrapper.OWLGraphWrapperNameProvider(OWLGraphWrapper, OBODoc) - Constructor for class owltools.io.ParserWrapper.OWLGraphWrapperNameProvider: Deprecated.
parseTaxonRelationshipPair(String) - Static method in class owltools.gaf.parser.BuilderTools
parseToOWLGraph(String) - Method in class owltools.io.ParserWrapper
parseToOWLGraph(String, boolean) - Method in class owltools.io.ParserWrapper
parseVersion(String) - Method in class owltools.gaf.parser.GpadParser
parseVersion(String) - Method in class owltools.gaf.parser.GpiParser
parseVersion(String) - Static method in class owltools.ontologyrelease.OntologyVersionTools: Try to parse the IRI as a version IRI using the both patterns for version IRI and OboInOwl.
parseWithInfo(String) - Static method in class owltools.gaf.parser.BuilderTools: Parse the string into a collection of with strings
parsing(String, int) - Method in interface owltools.gaf.parser.ParserListener: The current line is parsed.
part_of - Variable in class org.geneontology.lego.model.LegoTools: Deprecated.
PART_OF - Variable in class owltools.sim2.preprocessor.AbstractOBOSimPreProcessor
peekArg() - Method in class owltools.cli.Opts
performConsistencyChecks() - Method in class owltools.InferenceBuilder
performtransiviteclosure() - Method in class owltools.phenolog.PhenoTransitiveClosure
performtransiviteclosure(String, String, HashSet<Pheno>, HashMap<String, Pheno>, HashMap<String, IndividualPair>) - Method in class owltools.phenolog.PhenoTransitiveClosure
PERMANENT_JAVA_ID - Static variable in class owltools.gaf.rules.GenericReasonerValidationCheck: The string to identify this class in the annotation_qc.xml and related factories.
PERMANENT_JAVA_ID - Static variable in class owltools.gaf.rules.go.BasicChecksRule: The string to identify this class in the annotation_qc.xml and related factories.
PERMANENT_JAVA_ID - Static variable in class owltools.gaf.rules.go.GoAnnotationExperimentalPredictionRule: The string to identify this class in the annotation_qc.xml and related factories.
PERMANENT_JAVA_ID - Static variable in class owltools.gaf.rules.go.GoAnnotationPredictionRule: The string to identify this class in the annotation_qc.xml and related factories.
PERMANENT_JAVA_ID - Static variable in class owltools.gaf.rules.go.GoAnnotationTaxonRule: The string to identify this class in the annotation_qc.xml and related factories.
PERMANENT_JAVA_ID - Static variable in class owltools.gaf.rules.go.GoBindingCheckWithFieldRule: The string to identify this class in the annotation_qc.xml and related factories.
PERMANENT_JAVA_ID - Static variable in class owltools.gaf.rules.go.GoClassReferenceAnnotationRule: The string to identify this class in the annotation_qc.xml and related factories.
PERMANENT_JAVA_ID - Static variable in class owltools.gaf.rules.go.GoICAnnotationRule: The string to identify this class in the annotation_qc.xml and related factories.
PERMANENT_JAVA_ID - Static variable in class owltools.gaf.rules.go.GoIDAAnnotationRule: The string to identify this class in the annotation_qc.xml and related factories.
PERMANENT_JAVA_ID - Static variable in class owltools.gaf.rules.go.GoIEPRestrictionsRule: The string to identify this class in the annotation_qc.xml and related factories.
PERMANENT_JAVA_ID - Static variable in class owltools.gaf.rules.go.GoIPIAnnotationRule: The string to identify this class in the annotation_qc.xml and related factories.
PERMANENT_JAVA_ID - Static variable in class owltools.gaf.rules.go.GoIPICatalyticActivityRestrictionsRule: The string to identify this class in the annotation_qc.xml and related factories.
PERMANENT_JAVA_ID - Static variable in class owltools.gaf.rules.go.GoMultipleTaxonRule: The string to identify this class in the annotation_qc.xml and related factories.
PERMANENT_JAVA_ID - Static variable in class owltools.gaf.rules.go.GoNDAnnotationRule: The string to identify this class in the annotation_qc.xml and related factories.
PERMANENT_JAVA_ID - Static variable in class owltools.gaf.rules.go.GoNoHighLevelTermAnnotationRule: The string to identify this class in the annotation_qc.xml and related factories.
PERMANENT_JAVA_ID - Static variable in class owltools.gaf.rules.go.GoNoISSProteinBindingRule: The string to identify this class in the annotation_qc.xml and related factories.
PERMANENT_JAVA_ID - Static variable in class owltools.gaf.rules.go.GOReciprocalAnnotationRule: The string to identify this class in the annotation_qc.xml and related factories.
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
phenoSim(Opts) - Method in class owltools.cli.SimCommandRunner
PhenoSimHQEPreProcessor - Class in owltools.sim2.preprocessor
PhenoSimHQEPreProcessor() - Constructor for class owltools.sim2.preprocessor.PhenoSimHQEPreProcessor
PhenoTransitiveClosure - Class in owltools.phenolog
PhenoTransitiveClosure() - Constructor for class owltools.phenolog.PhenoTransitiveClosure
PlaceholderJcelFactory - Class in owltools.reasoner
PlaceholderJcelFactory() - Constructor for class owltools.reasoner.PlaceholderJcelFactory
polarity - Variable in enum owltools.gfx.RelationType
populateFullCoannotationMatrix() - Method in class owltools.sim2.FastOwlSim
populateFullCoannotationMatrix() - Method in interface owltools.sim2.OwlSim
populateFullCoannotationMatrix() - Method in class owltools.sim2.SimpleOwlSim
populateSimilarityMatrix(OWLNamedIndividual, OWLNamedIndividual, ElementPairScores) - Method in class owltools.sim2.FastOwlSim
populationClassSize - Variable in class owltools.sim2.EnrichmentResult
preCheckOntology(String, String) - Method in class owltools.cli.GafCommandRunner
precomputeAttributeAllByAll() - Method in class owltools.sim2.AbstractOwlSim
precomputeAttributeAllByAll() - Method in interface owltools.sim2.OwlSim: For implementations that use a cache, this performs an all by all comparison of all attributes and caches the results.
precomputeAttributeElementCount() - Method in class owltools.sim.OldSimpleOwlSim
precomputeAttributeElementCount() - Method in class owltools.sim2.SimpleOwlSim: Mapping between an attribute (e.g.
precomputeInferences(InferenceType...) - Method in class owltools.reasoner.GraphReasoner
precomputeInferences(InferenceType...) - Method in class owltools.reasoner.LazyExpressionMaterializingReasoner: Deprecated.
PrecomputingMoreReasonerFactory - Class in owltools.reasoner
pred - Variable in class owltools.graph.shunt.OWLShuntEdge
predict(String) - Method in class owltools.gaf.inference.AbstractAnnotationPredictor
predict(String) - Method in interface owltools.gaf.inference.AnnotationPredictor
predictForBioEntity(Bioentity, Collection<GeneAnnotation>) - Method in interface owltools.gaf.inference.AnnotationPredictor
predictForBioEntity(Bioentity, Collection<GeneAnnotation>) - Method in class owltools.gaf.inference.BasicAnnotationPropagator
predictForBioEntity(Bioentity, Collection<GeneAnnotation>) - Method in class owltools.gaf.inference.CompositionalClassPredictor: Deprecated.
predictForBioEntity(Bioentity, Collection<GeneAnnotation>) - Method in class owltools.gaf.inference.FoldBasedPredictor
Prediction - Class in owltools.gaf.inference
Prediction(GeneAnnotation) - Constructor for class owltools.gaf.inference.Prediction
predictionReportWriter - Variable in class owltools.gaf.rules.AnnotationRulesReportWriter
predictionWriter - Variable in class owltools.gaf.rules.AnnotationRulesReportWriter
prefix - Variable in class owltools.io.GMTParser
prepare() - Method in class owltools.gfx.ImageRender
preprocess() - Method in class owltools.sim.OldSimpleOwlSim: NEW: externalize preprocessing to separate class
preprocess() - Method in class owltools.sim2.preprocessor.AbstractSimPreProcessor
preprocess() - Method in class owltools.sim2.preprocessor.AutomaticSimPreProcessor
preprocess() - Method in class owltools.sim2.preprocessor.BruteForceSimPreProcessor
preprocess() - Method in class owltools.sim2.preprocessor.ExpressionSimPreProcessor
preprocess() - Method in class owltools.sim2.preprocessor.GOSimPreProcessor
preprocess() - Method in class owltools.sim2.preprocessor.NullSimPreProcessor
preprocess() - Method in class owltools.sim2.preprocessor.PhenoSimHQEPreProcessor
preprocess() - Method in class owltools.sim2.preprocessor.PropertyViewSimPreProcessor
preprocess() - Method in interface owltools.sim2.preprocessor.SimPreProcessor: Generate output ontology
preSimMethod - Variable in class owltools.sim.MultiSimilarity
prettyPrinter - Variable in class owltools.io.AbstractRenderer
primitiveEdgeToFullEdges(OWLGraphEdge) - Method in class owltools.graph.OWLGraphWrapperEdges
print(String) - Method in class owltools.gaf.io.AbstractGafWriter: Append an arbitrary string.
print(String) - Method in class owltools.gaf.io.GafWriter.BufferedGafWriter
print(String) - Method in class owltools.gaf.io.GafWriter
print(String) - Method in class owltools.gaf.io.GpadWriter: Append an arbitrary string.
print(String) - Method in class owltools.gaf.io.GpiWriter: Append an arbitrary string.
print(OWLObject) - Method in class owltools.io.AbstractRenderer
print(String) - Method in class owltools.io.AbstractRenderer
print(OWLObject) - Method in class owltools.io.OWLPrettyPrinter
print(Set<OWLAxiom>) - Method in class owltools.io.OWLPrettyPrinter
print(String) - Method in class owltools.io.OWLPrettyPrinter
print(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
PRINT_COMPARATOR - Static variable in class owltools.InferenceBuilder.PotentialRedundant
printAttributeSim(SimResultRenderer.AttributesSimScores, OWLGraphWrapper, OWLPrettyPrinter) - Method in class owltools.sim2.io.DelimitedLineRenderer
printAttributeSim(SimResultRenderer.AttributesSimScores, OWLGraphWrapper) - Method in class owltools.sim2.io.DelimitedLineRenderer
printAttributeSim(SimResultRenderer.AttributesSimScores, OWLGraphWrapper, OWLPrettyPrinter) - Method in class owltools.sim2.io.FormattedRenderer
printAttributeSim(SimResultRenderer.AttributesSimScores, OWLGraphWrapper) - Method in class owltools.sim2.io.FormattedRenderer
printAttributeSim(SimResultRenderer.AttributesSimScores, OWLGraphWrapper) - Method in class owltools.sim2.io.JSONRenderer
printAttributeSim(SimResultRenderer.AttributesSimScores, OWLGraphWrapper, OWLPrettyPrinter) - Method in class owltools.sim2.io.JSONRenderer
printAttributeSim(SimResultRenderer.AttributesSimScores, OWLGraphWrapper) - Method in class owltools.sim2.io.OWLRenderer: Deprecated.
printAttributeSim(SimResultRenderer.AttributesSimScores, OWLGraphWrapper, OWLPrettyPrinter) - Method in class owltools.sim2.io.OWLRenderer
printAttributeSim(SimResultRenderer.AttributesSimScores, OWLGraphWrapper) - Method in interface owltools.sim2.io.SimResultRenderer
printAttributeSim(SimResultRenderer.AttributesSimScores, OWLGraphWrapper, OWLPrettyPrinter) - Method in interface owltools.sim2.io.SimResultRenderer
printAttributeSim(SimResultRenderer.AttributesSimScores, OWLGraphWrapper) - Method in class owltools.sim2.io.TabularRenderer
printAttributeSim(SimResultRenderer.AttributesSimScores, OWLGraphWrapper, OWLPrettyPrinter) - Method in class owltools.sim2.io.TabularRenderer
printAttributeSimWithIndividuals(SimResultRenderer.AttributesSimScores, OWLPrettyPrinter, OWLGraphWrapper, OWLNamedIndividual, OWLNamedIndividual) - Method in class owltools.sim2.io.DelimitedLineRenderer
printAttributeSimWithIndividuals(SimResultRenderer.AttributesSimScores, OWLPrettyPrinter, OWLGraphWrapper, OWLNamedIndividual, OWLNamedIndividual) - Method in class owltools.sim2.io.FormattedRenderer
printAttributeSimWithIndividuals(SimResultRenderer.AttributesSimScores, OWLPrettyPrinter, OWLGraphWrapper, OWLNamedIndividual, OWLNamedIndividual) - Method in class owltools.sim2.io.JSONRenderer
printAttributeSimWithIndividuals(SimResultRenderer.AttributesSimScores, OWLPrettyPrinter, OWLGraphWrapper, OWLNamedIndividual, OWLNamedIndividual) - Method in class owltools.sim2.io.OWLRenderer
printAttributeSimWithIndividuals(SimResultRenderer.AttributesSimScores, OWLPrettyPrinter, OWLGraphWrapper, OWLNamedIndividual, OWLNamedIndividual) - Method in interface owltools.sim2.io.SimResultRenderer
printAttributeSimWithIndividuals(SimResultRenderer.AttributesSimScores, OWLPrettyPrinter, OWLGraphWrapper, OWLNamedIndividual, OWLNamedIndividual) - Method in class owltools.sim2.io.TabularRenderer
printAxioms(OWLOntology, String) - Static method in class owltools.ncbi.NCBI2OWL: Print string representations of all the axioms in an ontology, one axiom statement per line.
printCachedObjects() - Method in class owltools.web.OWLHandler
printComment(CharSequence) - Method in class owltools.sim2.io.DelimitedLineRenderer
printComment(CharSequence) - Method in class owltools.sim2.io.FormattedRenderer
printComment(CharSequence) - Method in class owltools.sim2.io.JSONRenderer
printComment(CharSequence) - Method in class owltools.sim2.io.OWLRenderer
printComment(CharSequence) - Method in interface owltools.sim2.io.SimResultRenderer
printComment(CharSequence) - Method in class owltools.sim2.io.TabularRenderer
printDescription(PrintStream, OWLObject) - Method in class owltools.sim.Similarity
printDescription(PrintStream, OWLObject, int) - Method in class owltools.sim.Similarity
printIndividualPairSim(SimResultRenderer.IndividualSimScores, OWLPrettyPrinter, OWLGraphWrapper) - Method in class owltools.sim2.io.DelimitedLineRenderer
printIndividualPairSim(SimResultRenderer.IndividualSimScores, OWLPrettyPrinter, OWLGraphWrapper) - Method in class owltools.sim2.io.FormattedRenderer
printIndividualPairSim(SimResultRenderer.IndividualSimScores, OWLPrettyPrinter, OWLGraphWrapper) - Method in class owltools.sim2.io.JSONRenderer
printIndividualPairSim(SimResultRenderer.IndividualSimScores, OWLPrettyPrinter, OWLGraphWrapper) - Method in class owltools.sim2.io.OWLRenderer
printIndividualPairSim(SimResultRenderer.IndividualSimScores, OWLPrettyPrinter, OWLGraphWrapper) - Method in interface owltools.sim2.io.SimResultRenderer
printIndividualPairSim(SimResultRenderer.IndividualSimScores, OWLPrettyPrinter, OWLGraphWrapper) - Method in class owltools.sim2.io.TabularRenderer
printPairScores(ElementPairScores) - Method in class owltools.sim2.io.DelimitedLineRenderer
printPairScores(AttributePairScores) - Method in class owltools.sim2.io.DelimitedLineRenderer
printPairScores(ElementPairScores) - Method in class owltools.sim2.io.FormattedRenderer
printPairScores(AttributePairScores) - Method in class owltools.sim2.io.FormattedRenderer
printPairScores(ElementPairScores) - Method in class owltools.sim2.io.JSONRenderer
printPairScores(AttributePairScores) - Method in class owltools.sim2.io.JSONRenderer
printPairScores(ElementPairScores) - Method in class owltools.sim2.io.OWLRenderer
printPairScores(AttributePairScores) - Method in class owltools.sim2.io.OWLRenderer
printPairScores(ElementPairScores) - Method in interface owltools.sim2.io.SimResultRenderer
printPairScores(AttributePairScores) - Method in interface owltools.sim2.io.SimResultRenderer
printPairScores(ElementPairScores) - Method in class owltools.sim2.io.TabularRenderer
printPairScores(AttributePairScores) - Method in class owltools.sim2.io.TabularRenderer
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
problems - Variable in class owltools.gaf.godb.Dumper
process(String[]) - Method in class owltools.idmap.IDMapHandler
process(String[]) - Method in class owltools.idmap.IDMapPairWriter
process(String[]) - Method in class owltools.idmap.IDMappingPIRParser
processCAFiles(Opts) - Method in class owltools.cli.SolrCommandRunner: Used for reading the lego files to be used for loading complex annotations.
processLegoCatalogs(Opts) - Method in class owltools.cli.SolrCommandRunner: Used for reading the ontology catalogs to be used for loading complex annotations.
processLegoFiles(Opts) - Method in class owltools.cli.SolrCommandRunner: Used for reading the lego files to be used for loading complex annotations.
processPantherTrees(Opts) - Method in class owltools.cli.SolrCommandRunner: Used for applying the panther trees to the currently data run.
profiler - Variable in class owltools.graph.OWLGraphWrapperEdges
Profiler - Class in owltools.profile
Profiler() - Constructor for class owltools.profile.Profiler
property - Variable in class owltools.gfx.GraphicsConfig.RelationConfig
property - Variable in class owltools.io.StanzaToOWLConverter.Mapping
property - Variable in class owltools.io.TableToAxiomConverter.Config
property - Variable in class owltools.yaml.golrconfig.GOlrField
property_config - Variable in class owltools.yaml.golrconfig.GOlrField
PropertyExtractor - Class in owltools.mooncat
PropertyExtractor(OWLOntology) - Constructor for class owltools.mooncat.PropertyExtractor: Creates a new PE object
PropertyExtractor(OWLOntology, OWLOntology) - Constructor for class owltools.mooncat.PropertyExtractor
PropertyStub - Interface in owltools.frame
PropertyStubLD - Class in owltools.frame.jsonld
PropertyStubLD() - Constructor for class owltools.frame.jsonld.PropertyStubLD
PropertyStubLD(String, String) - Constructor for class owltools.frame.jsonld.PropertyStubLD
PropertyView - Class in owltools.ontologyrelease
PropertyView() - Constructor for class owltools.ontologyrelease.PropertyView
PropertyViewOntologyBuilder - Class in owltools.mooncat: This class will create a property view or *faceted* view over an ontology using a specified property (relation).
PropertyViewOntologyBuilder(OWLOntology, OWLOntology, OWLObjectProperty) - Constructor for class owltools.mooncat.PropertyViewOntologyBuilder
PropertyViewOntologyBuilder(OWLOntology, OWLObjectProperty) - Constructor for class owltools.mooncat.PropertyViewOntologyBuilder
PropertyViewOntologyBuilder(OWLDataFactory, OWLOntologyManager, OWLOntology, OWLOntology, OWLObjectProperty) - Constructor for class owltools.mooncat.PropertyViewOntologyBuilder
PropertyViewSimPreProcessor - Class in owltools.sim2.preprocessor
PropertyViewSimPreProcessor() - Constructor for class owltools.sim2.preprocessor.PropertyViewSimPreProcessor
ProteinTools - Class in owltools.gaf.bioentities
ProteinTools() - Constructor for class owltools.gaf.bioentities.ProteinTools
PseudoRdfXmlWriter - Class in owltools.gaf.io: Java implementation to create a legacy pseudo RDF XML file for GO terms and gene annotations.
PseudoRdfXmlWriter() - Constructor for class owltools.gaf.io.PseudoRdfXmlWriter
PseudoRdfXmlWriter.ProgressReporter - Interface in owltools.gaf.io
purgeSolr(Opts) - Method in class owltools.cli.SolrCommandRunner: Manually purge the index to try again.
pValue - Variable in class owltools.sim.OldSimpleOwlSim.EnrichmentResult
pValue - Variable in class owltools.sim2.EnrichmentResult
PValue - Class in owltools.sim2.kb
PValue(double, double, double) - Constructor for class owltools.sim2.kb.PValue
pValueCorrected - Variable in class owltools.sim.OldSimpleOwlSim.EnrichmentResult
pValueCorrected - Variable in class owltools.sim2.EnrichmentResult
pValueCorrectedCutoff - Variable in class owltools.sim.OldSimpleOwlSim.EnrichmentConfig
pValueCorrectedCutoff - Variable in class owltools.sim2.EnrichmentConfig
pw - Variable in class owltools.cli.CommandRunner

Q

QUALIFIER - Static variable in class owltools.gaf.parser.GAFParser
QUALIFIER - Variable in class owltools.sim2.preprocessor.AbstractOBOSimPreProcessor
QUALITY - Variable in class owltools.sim2.preprocessor.PhenoSimHQEPreProcessor
queryDescendants(OWLGraphEdge) - Method in class owltools.graph.OWLGraphWrapperEdges: Treats an edge as a path and performs a query.
queryDescendants(OWLClassExpression) - Method in class owltools.graph.OWLGraphWrapperEdges: Performs a closed-world query using a DL expression as a set of boolean database-style constraints.
queryDescendants(OWLClassExpression, boolean, boolean) - Method in class owltools.graph.OWLGraphWrapperEdges
queryOntology - Variable in class owltools.cli.CommandRunner
QuerySubsetGenerator - Class in owltools.mooncat: Tools for creating a sub ontology spanning multiple ontologies.
QuerySubsetGenerator() - Constructor for class owltools.mooncat.QuerySubsetGenerator
QuestForOrthologsSeqXMLParser - Class in owltools.gaf.bioentities: This is an event based parser for the seq XML produced by the Quest for Orthologs project.

Add listeners to retrieve the information.
QuestForOrthologsSeqXMLParser() - Constructor for class owltools.gaf.bioentities.QuestForOrthologsSeqXMLParser
QuestForOrthologsSeqXMLParser.MoreInfoProteinListener - Interface in owltools.gaf.bioentities: Listener of QuestForOrthologsSeqXMLParser.
QuestForOrthologsSeqXMLParser.MoreInfoProteinListener.MoreInfo - Interface in owltools.gaf.bioentities: Additional data about a protein.
QuestForOrthologsSeqXMLParser.ProteinListener - Interface in owltools.gaf.bioentities: Listener for QuestForOrthologsSeqXMLParser.
quickScore(Set<OWLObject>, Set<OWLObject>) - Method in class owltools.sim.DescriptionTreeSimilarity
qvizCommand() - Method in class owltools.web.OWLHandler: visualize using QuickGO graphdraw.

R

randomizeClassAssertions(OWLOntology, int) - Static method in class owltools.sim2.preprocessor.ABoxUtils
randomWait(int, int) - Method in class org.bbop.golr.java.AbstractRetrieveGolr
rank - Variable in class owltools.sim2.scores.ElementPairScores
ranks - Static variable in class owltools.ncbi.NCBIOWL: Names of the NCBI ranks.
rdfToJsonLd(Opts) - Method in class owltools.cli.CommandRunner
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
readConfig(File) - Static method in class owltools.ontologyrelease.OortConfiguration: Read from a configuration property file and load it into a new OortConfiguration object.
reader - Variable in class owltools.idmap.AbstractMappingParser
readingComment(String, String, int) - Method in interface owltools.gaf.parser.CommentListener
reason() - Method in class owltools.sim.OldSimpleOwlSim
reasoner - Variable in class org.geneontology.lego.model.LegoTools: Deprecated.
reasoner - Variable in class owltools.cli.CommandRunner
reasoner - Variable in class owltools.mooncat.EquivalenceSetMergeUtil
reasoner - Variable in class owltools.mooncat.SpeciesMergeUtil
reasoner - Variable in class owltools.mooncat.SpeciesSubsetterUtil
reasoner - Variable in class owltools.sim2.AbstractOwlSim
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_JFACT - Static variable in class owltools.InferenceBuilder
REASONER_MORE - Static variable in class owltools.InferenceBuilder
REASONER_MORE_HERMIT - Static variable in class owltools.InferenceBuilder
REASONER_MORE_JFACT - Static variable in class owltools.InferenceBuilder
reasonerClass - Variable in class owltools.sim2.OwlSimMetadata
ReasonerDiff - Class in owltools.diff
ReasonerDiff(List<OWLAxiom>, List<OWLAxiom>) - Constructor for class owltools.diff.ReasonerDiff
reasonerName - Variable in class owltools.cli.CommandRunner
reduce(List<String>) - Method in class owltools.mooncat.BridgeExtractor.Combo: if srcOntIds is a subset of xOntIds, then replace that subset with tgtOntId
reduceAxiomAnnotationsToOboBasic(OWLOntology) - Static method in class owltools.graph.AxiomAnnotationTools: Remove axiom annotations, which do not comply with the OBO-Basic level, i.e.
reduceAxiomAnnotationsToOboBasic(OWLAxiom, OWLOntology) - Static method in class owltools.graph.AxiomAnnotationTools: Remove axiom annotations, which do not comply with the OBO-Basic level, i.e.
reducePartOfIsARelations() - Method in class owltools.graph.OWLGraphManipulator: Remove redundant relations by considering is_a (SubClassOf) and part_of relations equivalent.
reduceRelations() - Method in class owltools.graph.OWLGraphManipulator: Remove redundant relations.
reduceToNonRedundant(Set<OWLClass>, OWLReasoner) - Static method in class owltools.gaf.inference.BasicAnnotationPropagator: Given a set of classes, create a new non-redundant set with respect to the inferred super class hierarchy.
RedundantInferences - Class in owltools
RedundantInferences.RedundantAxiom - Class in owltools
RedundantInferences.RedundantAxiom(OWLSubClassOfAxiom, Set<OWLClass>) - Constructor for class owltools.RedundantInferences.RedundantAxiom
REFERENCE - Static variable in class owltools.gaf.parser.GAFParser
ReferentialIntegrityException - Exception in owltools.gaf.godb
ReferentialIntegrityException(String, Object) - Constructor for exception owltools.gaf.godb.ReferentialIntegrityException
reformatName(String) - Static method in class owltools.ncbi.OWLConverter: Reformat names for use in IRIs.
REGULATES - Static variable in class owltools.graph.RelationSets
relation - Variable in class owltools.gaf.ExtensionExpression
relationConfigMap - Variable in class owltools.gfx.GraphicsConfig
relations - Variable in class owltools.gfx.HierarchyImage
RelationSets - Class in owltools.graph
RelationSets() - Constructor for class owltools.graph.RelationSets
relationship - Variable in class owltools.gaf.IdMapping
relationshipIDsToPropertySet(List<String>) - Method in class owltools.graph.OWLGraphWrapperEdgesAdvanced: Convert a list of relationship IDs to a hash set of OWLObjectProperties.
RelationType - Enum in owltools.gfx: hacked crudely from QuickGO TODO: use config object to map relationship types to colors
RelationType.Polarity - Enum in owltools.gfx
ReleaseRunnerFileTools - Class in owltools.ontologyrelease: Provide a staging directory for the release runners.
remakeOntologiesFromImportsClosure() - Method in class owltools.graph.OWLGraphWrapperBasic
remakeOntologiesFromImportsClosure(IRI) - Method in class owltools.graph.OWLGraphWrapperBasic
remoteParserListener(ParserListener) - Method in class owltools.gaf.parser.GAFParser
remove(OWLOntology, OWLAxiom) - Method in class owltools.graph.CardinalityContraintsTools.CardinalityReporter
remove() - Method in class owltools.graph.shunt.OWLShuntGraphDFIterator
removeAxiomsFromOutput(Set<OWLAxiom>, boolean) - Method in class owltools.sim2.preprocessor.AbstractSimPreProcessor
removeCardinalityConstraints(OWLOntology) - Static method in class owltools.graph.CardinalityContraintsTools: Remove the cardinality constraints, by removing the axioms and replacing them with the weaker axioms without the constraints.
removeClass(OWLClass) - Method in class owltools.graph.OWLGraphManipulator: Remove from all ontologies the OWLClass classToDel, and then update the OWLGraphWrapper container.
removeClassAndPropagateEdges(String) - Method in class owltools.graph.OWLGraphManipulator: Remove the OWLClass with the OBO-style ID classToRemoveId from the ontology, and propagate its incoming edges to the targets of its outgoing edges.
removeClasses(Set<OWLClass>) - Method in class owltools.graph.OWLGraphManipulator: Remove from all ontologies all OWLClasses present in classesToDel, and then update the OWLGraphWrapper container.
removeCommentListener(CommentListener) - Method in class owltools.gaf.parser.GAFParser
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
removeDangningAnnotations(Opts) - Method in class owltools.cli.Sim2CommandRunner
removeDirectEdgesBetween(String, String) - Method in class owltools.graph.OWLGraphManipulator: Remove direct edges between the OWLObjects with the OBO-like IDs sourceId and targetId.
removeDisjointClassesAxioms() - Method in class owltools.sim2.preprocessor.AbstractSimPreProcessor
removeEdge(OWLGraphEdge) - Method in class owltools.graph.OWLGraphManipulator: Remove edge from its ontology.
removeEdges(Collection<OWLGraphEdge>) - Method in class owltools.graph.OWLGraphManipulator: Remove edges from their related ontology.
removeExternalEntities() - Method in class owltools.mooncat.Mooncat
removeExternalEntities(OWLOntology) - Method in class owltools.mooncat.Mooncat: Removes all classes, individuals and object properties that are marked with IAO_0000412
removeExternalEntities(boolean, OWLOntology) - Method in class owltools.mooncat.Mooncat: removes external entities: - anything marked with IAO_0000412 is removed - if isMain is true then anything that is also present in an external ontology is removed
removeExternalOntologyClasses(boolean) - Method in class owltools.mooncat.Mooncat: Removes all classes that have IAO_0000412 'imported from' set to another ontology.
removeFilter(InferenceBuilder.OWLClassFilter) - Method in class owltools.InferenceBuilder
removeFromSkipFormatSet(String) - Method in class owltools.ontologyrelease.OortConfiguration
removeIRIMapper(OWLOntologyIRIMapper) - Method in class owltools.io.ParserWrapper
removeMarkAsInferredAxiom(OWLAxiom, OWLOntology) - Static method in class owltools.graph.AxiomAnnotationTools: Remove the inferred mark from the axiom.
Side effect: Removes the axiom in the given ontology and creates a new axiom with the changed annotations.
removeOldOwlApiObo(OWLOntologyManager) - Static method in class owltools.io.ParserWrapper: This will try to remove the old OBO parser from the OWL-API.
removeOtherSpecies() - Method in class owltools.mooncat.SpeciesSubsetterUtil
removePrefix(String, char) - Static method in class owltools.gaf.parser.BuilderTools
removeRedundant(Set<OWLObject>) - Method in class owltools.mooncat.Mooncat
removeRedundantInferredSuperClassAxioms(Opts) - Method in class owltools.cli.CommandRunner
removeRedundantSubClassAxioms(OWLOntology, OWLReasoner) - Static method in class owltools.RedundantInferences: Remove the redundant and marked as inferred super class assertions for each class in the ontology signature.
removeRelations(Collection<String>, boolean) - Method in class owltools.graph.OWLGraphManipulator: Remove the OWLAxioms in the ontologies corresponding to the OWLObjectPropertys listed in forbiddenRels, as OBO-style IDs.
removeRelsToSubsets(Collection<String>) - Method in class owltools.graph.OWLGraphManipulator: Delegates method call to OWLGraphManipulator.removeRelsToSubsets(Collection, Collection), with no OWLClasses excluded specified.
removeRelsToSubsets(Collection<String>, Collection<String>) - Method in class owltools.graph.OWLGraphManipulator: Remove is_a and part_of incoming edges to OWLClasses in subsets, only if the source of the incoming edge will not be left orphan of other is_a/part_of relations to OWLClasses not in subsets.
removeSubgraphs(Collection<String>, boolean) - Method in class owltools.graph.OWLGraphManipulator: Delegates to OWLGraphManipulator.removeSubgraphs(Collection, boolean, Collection), with the last Collection argument being null.
removeSubgraphs(Collection<String>, boolean, Collection<String>) - Method in class owltools.graph.OWLGraphManipulator: Remove from the ontology the subgraphs starting from the OWLClasses with their ID in subgraphRootIds.
removeSubsetClasses(Set<OWLClass>, boolean) - Method in class owltools.mooncat.Mooncat: Remove a set of classes from the ontology
removeSubsetComplementClasses(Set<OWLClass>, boolean) - Method in class owltools.mooncat.Mooncat: Remove all classes *not* in subset.
removeSubsetEntities(Opts) - Method in class owltools.cli.CommandRunner
removeSupportOntology(OWLOntology) - Method in class owltools.graph.OWLGraphWrapperBasic
removeUnreachableAxioms() - Method in class owltools.sim.OldSimpleOwlSim: If a node cannot be reached on the existential graph, then remove it.
removeUnreachableAxioms() - Method in class owltools.sim2.preprocessor.AbstractSimPreProcessor: note: approximation used, may end up removing too many.
removeUnrelatedRelations(Collection<String>) - Method in class owltools.graph.OWLGraphManipulator: Remove from all OWLOntologies wrapped by this object the OWLObjectPropertys not related to the provided allowedRels.
render(Collection<OWLNamedIndividual>, String, boolean) - Method in class org.geneontology.lego.dot.LegoDotWriter: Deprecated.
render(Collection<OWLNamedIndividual>, String, boolean) - Method in interface org.geneontology.lego.dot.LegoRenderer: Deprecated.

Render the given individuals (aka set of annotations).
render(OWLPrettyPrinter) - Method in class owltools.gaf.inference.Prediction
render(Graphics2D) - Method in class owltools.gfx.HierarchyImage
render() - Method in class owltools.gfx.ImageRender
render(Graphics2D) - Method in class owltools.gfx.ImageRender
render(Graphics2D) - Method in class owltools.gfx.OWLGraphLayoutNode
render(OWLGraphWrapper) - Method in class owltools.io.AbstractClosureRenderer
render(OWLGraphEdge) - Method in class owltools.io.AbstractClosureRenderer
render(OWLGraphEdge) - Method in class owltools.io.ChadoGraphClosureRenderer
render(OWLGraphEdge) - Method in class owltools.io.ClassExpressionGraphClosureRenderer
render(OWLGraphEdge) - Method in class owltools.io.CompactGraphClosureRenderer
render(OWLGraphWrapper) - Method in class owltools.io.EdgeTableRenderer
render(OWLGraphEdge) - Method in class owltools.io.GraphClosureRenderer
render(OWLGraphWrapper) - Method in interface owltools.io.GraphRenderer
render(OWLGraphWrapper) - Method in class owltools.io.InferredParentRenderer
render(OWLAxiom) - Method in class owltools.io.OWLGsonParser
render(OWLGraphEdge) - Method in class owltools.io.OWLGsonParser
render(OWLOntology) - Method in class owltools.io.OWLGsonParser
render(Set) - Method in class owltools.io.OWLGsonParser
render(OWLAxiom) - Method in class owltools.io.OWLGsonRenderer
render(OWLGraphEdge) - Method in class owltools.io.OWLGsonRenderer
render(OWLOntology) - Method in class owltools.io.OWLGsonRenderer
render(Set) - Method in class owltools.io.OWLGsonRenderer
render(OWLObject) - Method in class owltools.io.OWLPrettyPrinter
render(OWLAxiom) - Method in class owltools.io.OWLPrettyPrinter
render(OWLGraphEdge) - Method in class owltools.io.OWLPrettyPrinter
render(OWLGraphWrapper) - Method in class owltools.io.TableRenderer
render(OWLOntology, String) - Method in class owltools.renderer.markdown.MarkdownRenderer
render(OWLOntology) - Method in class owltools.renderer.markdown.MarkdownRenderer
render(OWLClass) - Method in class owltools.renderer.markdown.MarkdownRenderer
render(OWLObjectProperty) - Method in class owltools.renderer.markdown.MarkdownRenderer
render(OWLAnnotationProperty) - Method in class owltools.renderer.markdown.MarkdownRenderer
render(OWLPrettyPrinter) - Method in class owltools.sim2.ClassDifferentiaLearner
render(Set<OWLClass>) - Method in class owltools.sim2.io.FormattedRenderer
render(OWLClass) - Method in class owltools.sim2.io.FormattedRenderer
render(OWLNamedIndividual) - Method in class owltools.sim2.io.FormattedRenderer
renderAbout(OWLClass) - Method in class owltools.renderer.markdown.MarkdownRenderer
renderAttScore(String, double, OWLClass, OWLClass, OWLGraphWrapper, OWLPrettyPrinter) - Method in class owltools.sim2.io.DelimitedLineRenderer
renderAttScoreWithIndividuals(String, double, OWLClass, OWLClass, OWLNamedIndividual, OWLNamedIndividual, OWLGraphWrapper, OWLPrettyPrinter) - Method in class owltools.sim2.io.DelimitedLineRenderer
renderDot() - Method in class owltools.gfx.OWLGraphvizRenderer
renderDot(OWLOntology, String, String, boolean) - Method in class owltools.mooncat.ontologymetadata.ImportChainDotWriter
renderDot(Collection<OWLOntology>, String, String, boolean) - Method in class owltools.mooncat.ontologymetadata.ImportChainDotWriter
renderDot(OWLOntology, Collection<OWLOntology>, String, String, boolean) - Method in class owltools.mooncat.ontologymetadata.ImportChainDotWriter: Render a dot file for the given ontologies (aka set of annotations).
renderEngineResult(AnnotationRulesEngine.AnnotationRulesEngineResult, AnnotationRulesEngine) - Method in class owltools.gaf.rules.AnnotationRulesReportWriter: A print-out of the results, summaries, and preditions.
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
renderIndividualScore(String, double, Set<OWLClass>, OWLNamedIndividual, OWLNamedIndividual, OWLPrettyPrinter) - Method in class owltools.sim2.io.DelimitedLineRenderer
renderIRI(String) - Method in class owltools.io.OWLPrettyPrinter
renderLego(Collection<LegoNode>, String, boolean) - Method in class org.geneontology.lego.dot.LegoDotWriter: Deprecated.

Render the given collection of nodes (LegoNode)
renderLego(Collection<LegoNode>, OWLGraphWrapper) - Method in class org.geneontology.lego.json.LegoShuntGraphTool: Deprecated.

Render the given collection of nodes (LegoNode)
renderMarkdown(OWLGraphWrapper, String, boolean) - Static method in class owltools.mooncat.ontologymetadata.OntologyMetadataMarkdownWriter
renderMessageString() - Method in exception owltools.ontologyrelease.OboOntologyReleaseRunnerCheckException: Render the exception in an human readable form and suitable for appending to a logger.
renderPair(OWLNamedIndividual, OWLNamedIndividual, OWLPrettyPrinter) - Method in class owltools.sim2.io.DelimitedLineRenderer
renderPair(OWLNamedIndividual, OWLNamedIndividual, OWLPrettyPrinter) - Method in class owltools.sim2.io.JSONRenderer
renderPair(OWLNamedIndividual, OWLNamedIndividual, OWLPrettyPrinter) - Method in class owltools.sim2.io.TabularRenderer
renderViolations(AnnotationRulesEngine.AnnotationRulesEngineResult, AnnotationRulesEngine, PrintWriter) - Static method in class owltools.gaf.rules.AnnotationRulesReportWriter: A simple tab delimited print-out of the validation results.
report(int, int) - Method in interface owltools.gaf.io.PseudoRdfXmlWriter.ProgressReporter
report(String, CharSequence) - Method in class owltools.ontologyrelease.logging.ErrorReportFileHandler
report(String, CharSequence) - Method in class owltools.ontologyrelease.logging.ExplicitReportFileHandler
report(String, CharSequence) - Method in class owltools.ontologyrelease.logging.GuiLogHandler
report(String, CharSequence) - Method in class owltools.ontologyrelease.logging.Log4jHandler
report(String, CharSequence) - Method in interface owltools.ontologyrelease.logging.LogHandler
report(String, CharSequence) - Method in class owltools.ontologyrelease.logging.TraceReportFileHandler
report(String, CharSequence) - Method in class owltools.ontologyrelease.ReleaseRunnerFileTools
report(StringBuilder, OntologyCheckRunner.TimePoint) - Method in class owltools.ontologyverification.OntologyCheckHandler
report(StringBuilder, OntologyCheck, Collection<CheckWarning>, String) - Method in class owltools.ontologyverification.OntologyCheckHandler
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
reportEvidenceIssue(String, String, boolean) - Method in class owltools.gaf.parser.GpadGpiObjectsBuilder
reportHeader(StringBuilder) - Method in class owltools.ontologyverification.OntologyCheckHandler
reportIssue(String, String, boolean) - Method in class owltools.gaf.parser.IssueListener.DefaultIssueListener
reportIssue(String, String, boolean) - Method in interface owltools.gaf.parser.IssueListener
reportProblems() - Method in class owltools.gaf.godb.Dumper
reportUnknowBioentityId(String, boolean) - Method in class owltools.gaf.parser.GpadGpiObjectsBuilder
reportWarnings() - Method in interface owltools.gaf.parser.ParserListener
required - Variable in class owltools.yaml.golrconfig.GOlrField
resolveClass(String) - Method in class owltools.cli.CommandRunner
resolveClassList(Opts) - Method in class owltools.cli.CommandRunner
resolveEntity(Opts) - Method in class owltools.cli.CommandRunner
resolveEntity(String) - Method in class owltools.cli.CommandRunner
resolveEntityList(Opts) - Method in class owltools.cli.CommandRunner
resolveObjectProperty(String) - Method in class owltools.cli.CommandRunner
resolveObjectPropertyList(Opts) - Method in class owltools.cli.CommandRunner
resolveObjectPropertyListAsList(Opts) - Method in class owltools.cli.CommandRunner
ResonerDiffCommandLine - Class in owltools.diff: Wrapper for ReasonerDiff as command-line tool.
ResonerDiffCommandLine() - Constructor for class owltools.diff.ResonerDiffCommandLine
Restriction - Interface in owltools.frame
RestrictionLD - Class in owltools.frame.jsonld
RestrictionLD() - Constructor for class owltools.frame.jsonld.RestrictionLD
result_weights - Variable in class owltools.yaml.golrconfig.GOlrConfig
result_weights - Variable in class owltools.yaml.golrconfig.GOlrField
resultOutStream - Variable in class owltools.cli.Sim2CommandRunner
resultOutStream - Variable in class owltools.sim2.io.AbstractRenderer
RESULTS_IN_DEVELOPMENT_OF - Variable in class owltools.sim2.preprocessor.AbstractOBOSimPreProcessor
RESULTS_IN_MORPHOGENESIS_OF - Variable in class owltools.sim2.preprocessor.AbstractOBOSimPreProcessor
retainAxiomsInPropertySubset(Set<OWLObjectProperty>) - Method in class owltools.mooncat.Mooncat
retainAxiomsInPropertySubset(OWLOntology, Set<OWLObjectProperty>) - Static method in class owltools.mooncat.Mooncat
retainAxiomsInPropertySubset(OWLOntology, Set<OWLObjectProperty>, OWLReasoner) - Static method in class owltools.mooncat.Mooncat: given an ontology *ont* and a set of object properties *filterProps*, remove all axioms from ontology that have an object property P in their signature where P is not in *filterProps*
retrieveCandidatesIC(Set<OWLClass>) - Method in class owltools.sim2.kb.OWLSimReferenceBasedStatistics
RetrieveGolrAnnotations - Class in org.bbop.golr.java
RetrieveGolrAnnotations(String) - Constructor for class org.bbop.golr.java.RetrieveGolrAnnotations
RetrieveGolrAnnotations(String, int, boolean) - Constructor for class org.bbop.golr.java.RetrieveGolrAnnotations
RetrieveGolrAnnotations.GolrAnnotationDocument - Class in org.bbop.golr.java
RetrieveGolrAnnotations.GolrAnnotationDocument() - Constructor for class org.bbop.golr.java.RetrieveGolrAnnotations.GolrAnnotationDocument
RetrieveGolrAnnotations.GolrAnnotationExtension - Class in org.bbop.golr.java
RetrieveGolrAnnotations.GolrAnnotationExtension() - Constructor for class org.bbop.golr.java.RetrieveGolrAnnotations.GolrAnnotationExtension
RetrieveGolrAnnotations.GolrAnnotationExtension.GolrAnnotationExtensionEntry - Class in org.bbop.golr.java
RetrieveGolrAnnotations.GolrAnnotationExtension.GolrAnnotationExtensionEntry() - Constructor for class org.bbop.golr.java.RetrieveGolrAnnotations.GolrAnnotationExtension.GolrAnnotationExtensionEntry
RetrieveGolrAnnotations.GolrAnnotationExtension.GolrAnnotationExtensionEntry.GolrAnnotationExtensionRelation - Class in org.bbop.golr.java
RetrieveGolrAnnotations.GolrAnnotationExtension.GolrAnnotationExtensionEntry.GolrAnnotationExtensionRelation() - Constructor for class org.bbop.golr.java.RetrieveGolrAnnotations.GolrAnnotationExtension.GolrAnnotationExtensionEntry.GolrAnnotationExtensionRelation
RetrieveGolrBioentities - Class in org.bbop.golr.java
RetrieveGolrBioentities(String, int) - Constructor for class org.bbop.golr.java.RetrieveGolrBioentities
RetrieveGolrBioentities.GolrBioentityDocument - Class in org.bbop.golr.java
RetrieveGolrBioentities.GolrBioentityDocument() - Constructor for class org.bbop.golr.java.RetrieveGolrBioentities.GolrBioentityDocument
retryRequest(URI, IOException, int) - Method in class org.bbop.golr.java.AbstractRetrieveGolr
returnJSON(Object) - Method in class owltools.web.OWLHandler
right() - Method in class owltools.gfx.OWLGraphLayoutNode
right - Variable in class owltools.gfx.OWLGraphLayoutNode.SVGRectangle
rightMargin - Static variable in class owltools.gfx.HierarchyImage
rootClass - Variable in class owltools.mooncat.SpeciesSubsetterUtil
rowToAxioms(String[]) - Method in class owltools.io.TableToAxiomConverter
run(String[]) - Method in class owltools.cli.CommandRunner
run(Opts) - Method in class owltools.cli.CommandRunner
run(Opts) - Method in class owltools.cli.Obo2Obo
runDAGCheck(Opts) - Method in class owltools.cli.CommandRunner
runGAFChecks(Opts) - Method in class owltools.cli.GafCommandRunner
runJavaScript(Opts) - Method in class owltools.cli.JsCommandRunner: Run the given js with the current graph (and reasoner).
runOntologyPreCheck(Opts) - Method in class owltools.cli.GafCommandRunner: Similar method to '--run-reasoner', but not only checks for unsatisfiable classes, but also checks first for a consistent ontology.
runOwlSim(Opts) - Method in class owltools.cli.Sim2CommandRunner: Deprecated.
runOwlSim(OwlSim, Opts) - Method in class owltools.cli.Sim2CommandRunner
runOwlSim(Opts) - Method in class owltools.cli.SimCommandRunner: performs all by all individual comparison
runSingleIteration(String[]) - Method in class owltools.cli.CommandRunner
runSingleIteration(Opts) - Method in class owltools.cli.CommandRunner

S

sampleSetClass - Variable in class owltools.sim.OldSimpleOwlSim.EnrichmentResult
sampleSetClass - Variable in class owltools.sim2.EnrichmentResult
sampleSetClassSize - Variable in class owltools.sim2.EnrichmentResult
save() - Method in class owltools.io.ImportClosureSlurper
save(String) - Method in class owltools.io.ImportClosureSlurper
save(String, String) - Method in class owltools.io.ImportClosureSlurper
save(File, OutputStream) - Method in class owltools.io.ImportClosureSlurper
save(File, BufferedWriter) - Method in class owltools.io.ImportClosureSlurper
save(String, OWLOntologyFormat, OWLOntology) - Method in class owltools.mooncat.BridgeExtractor
saveBridgeOntologies(String) - Method in class owltools.mooncat.BridgeExtractor
saveBridgeOntologies(String, OWLOntologyFormat) - Method in class owltools.mooncat.BridgeExtractor
saveIntermediateStates - Variable in class owltools.sim2.preprocessor.AbstractSimPreProcessor
saveLCSCache(String) - Method in class owltools.sim2.AbstractOwlSim
saveLCSCache(String, Double) - Method in class owltools.sim2.FastOwlSim
saveLCSCache(String) - Method in interface owltools.sim2.OwlSim: Saves the contents of the LCS-IC cache Assumes that this has already been filled by comparing all classes by all classes.
saveLCSCache(String, Double) - Method in interface owltools.sim2.OwlSim: As OwlSim.saveLCSCache(String), but do not write a line for any LCS whose IC falls below the threshold.
saveLCSCache(String, Double) - Method in class owltools.sim2.SimpleOwlSim
saveOntology(OldSimpleOwlSim.Stage) - Method in class owltools.sim.OldSimpleOwlSim
saveOntology(String) - Method in class owltools.sim.OldSimpleOwlSim
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
saveSim(Opts) - Method in class owltools.cli.Sim2CommandRunner
saveSim(Opts) - Method in class owltools.cli.SimCommandRunner
saveState(String) - Method in class owltools.sim2.AbstractOwlSim
saveState(String) - Method in class owltools.sim2.FastOwlSim
saveState(String) - Method in interface owltools.sim2.OwlSim: Experimental: save internal state of object
saveState(String) - Method in class owltools.sim2.preprocessor.AbstractSimPreProcessor
scaleFactor - Variable in class owltools.sim2.OwlSimMetadata
schema() - Method in class owltools.yaml.golrconfig.SolrSchemaXMLWriter: Dump the necessary Solr schema as a String.
schema_generating - Variable in class owltools.yaml.golrconfig.GOlrConfig
score - Variable in class owltools.sim.OldSimpleOwlSim.ScoreAttributePair
score - Variable in class owltools.sim.OldSimpleOwlSim.ScoreAttributesPair
score - Variable in class owltools.sim2.FastOwlSim.ClassCount
score - Variable in class owltools.sim2.OwlSim.ScoreAttributeSetPair: Score shared by all attributes in attribute set
score - Variable in class owltools.sim2.SimpleOwlSim.ScoreAttributePair
ScoreMatrix<T> - Class in owltools.sim2.scores: A matrix of scores or scored entities for two groups of attributes
ScoreMatrix() - Constructor for class owltools.sim2.scores.ScoreMatrix
search(OWLObject) - Method in class owltools.sim.SimSearch: Given a query object (e.g.
search(Set<OWLClass>, String, boolean) - Method in class owltools.sim2.SimJSONEngine
search(Set<OWLClass>, String, boolean, boolean) - Method in class owltools.sim2.SimJSONEngine
search(Set<OWLClass>, String, boolean, Integer) - Method in class owltools.sim2.SimJSONEngine
search(Set<OWLClass>, String, boolean, Integer, boolean) - Method in class owltools.sim2.SimJSONEngine
search(Set<OWLClass>, SimpleOwlSim.Metric) - Method in class owltools.sim2.SimpleOwlSim
searchable - Variable in class owltools.yaml.golrconfig.GOlrField
searchByAttributeSetCommand() - Method in class owltools.web.OWLHandler
searchCellularLocation(OWLClassExpression, OWLGraphWrapper, Set<OWLObjectProperty>) - Static method in class org.geneontology.lego.model.CellularLocationTools: Deprecated.
selected - Variable in class owltools.gfx.HierarchyImage
SelfReferenceInDefinition - Class in owltools.ontologyverification.impl: Check, whether the class is defined using the class itself.
SelfReferenceInDefinition() - Constructor for class owltools.ontologyverification.impl.SelfReferenceInDefinition
sep() - Method in class owltools.gaf.io.AbstractGafWriter: Append a the separator between columns.
sep() - Method in class owltools.gaf.io.GpadWriter: Append a the separator between columns.
sep() - Method in class owltools.gaf.io.GpiWriter: Append a the separator between columns.
sep() - Method in class owltools.io.AbstractRenderer
serialise() - Method in class owltools.gfx.OWLGraphLayoutNode
serialise() - Method in class owltools.gfx.OWLGraphStrokeEdge
server - Variable in class owltools.solrj.AbstractSolrLoader
serverManifestVersion - Variable in class owltools.mooncat.ontologymetadata.OntologySetMetadata
setActiveEntity(OWLClass) - Method in class org.geneontology.lego.model.LegoNode: Deprecated.
setActsOnTaxonId(String) - Method in class owltools.gaf.GeneAnnotation
setActsOnTaxonId(Pair<String, String>) - Method in class owltools.gaf.GeneAnnotation
setAddImportsFromSupports(boolean) - Method in class owltools.ontologyrelease.OortConfiguration
setAddSupportFromImports(boolean) - Method in class owltools.ontologyrelease.OortConfiguration
setAllowEquivalentNamedClassPairs(boolean) - Method in class owltools.ontologyrelease.OortConfiguration
setAllowFileOverWrite(boolean) - Method in class owltools.ontologyrelease.OortConfiguration: Set allowFileOverWrite
setAllowOverwrite(boolean) - Method in class owltools.ontologyrelease.gui.OortGuiAdvancedPanel
setancestors(HashSet<Pheno>) - Method in class owltools.phenolog.Pheno
setAndFilterRedundantPredictions(Set<Prediction>, Set<OWLClass>) - Method in class owltools.gaf.inference.AbstractAnnotationPredictor: side-effects: removes redundant predictions over all relationships
setAndFilterRedundantPredictions(Set<Prediction>, Set<OWLClass>, Set<OWLPropertyExpression>) - Method in class owltools.gaf.inference.AbstractAnnotationPredictor: side-effects: removes redundant predictions over a set of relationships.
setAnnotationCount(int) - Method in class owltools.gaf.rules.AnnotationRulesEngine.AnnotationRulesEngineResult
setAnnotationRow(String) - Method in class owltools.gaf.rules.AnnotationRuleViolation
setAnnotations(List<GeneAnnotation>) - Method in class owltools.gaf.Bioentity
setAspect(String) - Method in class owltools.gaf.GeneAnnotation
setAspectProvider(GpadGpiObjectsBuilder.AspectProvider) - Method in class owltools.gaf.parser.GpadGpiObjectsBuilder
setAsserted(boolean) - Method in class owltools.ontologyrelease.OortConfiguration: Set asserted
setAssertedViewOntology(OWLOntology) - Method in class owltools.mooncat.PropertyViewOntologyBuilder
setAssignedBy(String) - Method in class owltools.gaf.GeneAnnotation
setAssumeOBOStyleIRIs(boolean) - Method in class owltools.mooncat.PropertyViewOntologyBuilder: set to false if IRIs are not OBO purls.
setAttributeClassSet(Set<OWLClass>) - Method in class owltools.sim2.OwlSim.ScoreAttributeSetPair: Setter
setAttributes(Set<Attribute>) - Method in class owltools.phenolog.Individual
setAttributesFromOntology(OWLOntology) - Method in class owltools.sim.OldSimpleOwlSim: Deprecated.
setAutoDetectBridgingOntology(boolean) - Method in class owltools.ontologyrelease.OortConfiguration
setAxiomType(String) - Method in class owltools.io.TableToAxiomConverter.Config
setBase(File) - Method in class owltools.ontologyrelease.OortConfiguration
setBaseFileName(String) - Method in class owltools.sim.OldSimpleOwlSim
setBasicAboxMapping(boolean) - Method in class owltools.gaf.owl.GAFOWLBridge
setBioentity(String) - Method in class owltools.gaf.GeneAnnotation
setBioentityMapping(GAFOWLBridge.BioentityMapping) - Method in class owltools.gaf.owl.GAFOWLBridge
setBioentityObject(Bioentity) - Method in class owltools.gaf.GeneAnnotation
setBit(int, boolean) - Method in class owltools.util.BloomFilter: Set a single bit in the Bloom filter.
setBp(boolean) - Method in class org.geneontology.lego.model.LegoNode: Deprecated.
setBridgeOntologies(List<String>) - Method in class owltools.ontologyrelease.OortConfiguration
setCandidates(Set<OWLObject>) - Method in class owltools.sim.SimSearch
setCatalogXML(String) - Method in class owltools.ontologyrelease.OortConfiguration
setCellularLocation(Collection<OWLClassExpression>) - Method in class org.geneontology.lego.model.LegoNode: Deprecated.
setCheckConsistency(boolean) - Method in class owltools.ontologyrelease.OortConfiguration
setCheckOboDoc(boolean) - Method in class owltools.io.ParserWrapper
setCheckPotentialRedundant(boolean) - Method in class owltools.ontologyrelease.OortConfiguration
setChildren(List<Bioentity>) - Method in class owltools.gaf.Bioentity
setClassifyIndividuals(boolean) - Method in class owltools.mooncat.PropertyViewOntologyBuilder
setClosest(Pheno) - Method in class owltools.phenolog.Pheno
setClosestDistance(double) - Method in class owltools.phenolog.Pheno
setClosestOverlap(int) - Method in class owltools.phenolog.Pheno
setClosestOverlapPairs(HashSet<IndividualPair>) - Method in class owltools.phenolog.Pheno
setCls(String) - Method in class owltools.gaf.ExtensionExpression
setCls(String) - Method in class owltools.gaf.GeneAnnotation
setCmf(boolean) - Method in class org.geneontology.lego.model.LegoNode: Deprecated.
setCommandName(String) - Method in class owltools.web.OWLHandler
setConfig(OWLGraphWrapperEdges.Config) - Method in class owltools.graph.OWLGraphWrapperEdges
setConfigForFlyMine() - Method in class owltools.phenolog.GenePhenoTsvParser
setConfigForMGIPhenoGeno() - Method in class owltools.phenolog.GenePhenoTsvParser
setContributors(Set<String>) - Method in class org.geneontology.lego.model.LegoMetadata: Deprecated.
setCorpusSize(int) - Method in class owltools.sim.OldSimpleOwlSim
setCorpusSize(int) - Method in class owltools.sim2.AbstractOwlSim
setCorpusSize(int) - Method in interface owltools.sim2.OwlSim: Sets the number of entities in domain.
setCorpusSize(int) - Method in class owltools.sim2.SimpleOwlSim
setCreateErrorModules(boolean) - Method in class owltools.ontologyrelease.OortConfiguration
setCreateReflexiveClasses(boolean) - Method in class owltools.mooncat.PropertyViewOntologyBuilder
setDate(Date) - Method in class owltools.gaf.rules.AbstractAnnotationRule
setDate(Date) - Method in interface owltools.gaf.rules.AnnotationRule: Set the status date for this rule.
setDates(Set<String>) - Method in class org.geneontology.lego.model.LegoMetadata: Deprecated.
setDb(String) - Method in class owltools.gaf.Bioentity
setDefaults() - Method in class owltools.io.StanzaToOWLConverter
setDescription(String) - Method in class owltools.gaf.rules.AbstractAnnotationRule
setDescription(String) - Method in interface owltools.gaf.rules.AnnotationRule: Set the description for this rule.
setDirectMRC(boolean) - Method in class owltools.gaf.GeneAnnotation
setDirectNot(boolean) - Method in class owltools.gaf.GeneAnnotation
setDisableLCSCache(boolean) - Method in class owltools.sim2.AbstractOwlSim
setDisableLCSCache(boolean) - Method in interface owltools.sim2.OwlSim: if set, the cache is neither read nor written to.
setDistance(int) - Method in class owltools.graph.OWLGraphEdge
setDistanceFromParent(float) - Method in class owltools.gaf.Bioentity
setEcoTools(EcoTools) - Method in class owltools.solrj.GafSolrDocumentLoader
setEdgesAdvancedCacheSize(int) - Method in class owltools.graph.OWLGraphWrapperEdgesAdvanced
setElementsOntology(OWLOntology) - Method in class owltools.mooncat.PropertyViewOntologyBuilder
setEnforceEL(boolean) - Method in class owltools.ontologyrelease.OortConfiguration
setEnrichmentConfig(OldSimpleOwlSim.EnrichmentConfig) - Method in class owltools.sim.OldSimpleOwlSim
setEnrichmentConfig(EnrichmentConfig) - Method in class owltools.sim2.AbstractOwlSim
setEnrichmentConfig(EnrichmentConfig) - Method in interface owltools.sim2.OwlSim
setErrorMessage(String) - Method in class owltools.gaf.rules.AnnotationRegularExpressionFromXMLRule
setErrorReportFile(String) - Method in class owltools.ontologyrelease.OortConfiguration
setEvidence(Set<String>) - Method in class org.geneontology.lego.model.LegoMetadata: Deprecated.
setEvidence(String, String) - Method in class owltools.gaf.GeneAnnotation
setExcludedClasses(Set<OWLClass>) - Method in class owltools.mooncat.PropertyViewOntologyBuilder
setExecuteOntologyChecks(boolean) - Method in class owltools.ontologyrelease.OortConfiguration
setExpandMacros(boolean) - Method in class owltools.ontologyrelease.OortConfiguration
setExpandShortcutRelations(boolean) - Method in class owltools.ontologyrelease.OortConfiguration
setExpandXrefs(boolean) - Method in class owltools.ontologyrelease.OortConfiguration: Set export bridges
setExperimentalGAFPredictionFile(Opts) - Method in class owltools.cli.GafCommandRunner
setExperimentalGAFPredictionReportFile(Opts) - Method in class owltools.cli.GafCommandRunner
setExtensionExpressions(List<List<ExtensionExpression>>) - Method in class owltools.gaf.GeneAnnotation
setFatal(boolean) - Method in class owltools.ontologyverification.impl.AbstractCheck
setFatal(boolean) - Method in interface owltools.ontologyverification.OntologyCheck: Set the fatal parameter of the check.
setFile(File) - Method in class owltools.ontologyrelease.BuildVersionId: Deprecated.

The file in which the build number is stored.
setFile(String) - Method in class owltools.ontologyrelease.GetOntologyId: Deprecated.
setFilterSimpleProperties(List<String>) - Method in class owltools.ontologyrelease.OortConfiguration
setFilterUnused(boolean) - Method in class owltools.mooncat.PropertyViewOntologyBuilder
setFoldedClassMap(Map<OWLClass, OWLClassExpression>) - Method in class owltools.gaf.owl.AnnotationExtensionFolder
setForceRelease(boolean) - Method in class owltools.ontologyrelease.OortConfiguration
setFormat(String) - Method in class owltools.web.OWLHandler
setFullName(String) - Method in class owltools.gaf.Bioentity
setGafdocs(Set<GafDocument>) - Method in class owltools.gaf.godb.Dumper
setGafDocument(GafDocument) - Method in class owltools.gaf.inference.AbstractAnnotationPredictor
setGafDocument(GafDocument) - Method in class owltools.solrj.GafSolrDocumentLoader
setGafMode() - Method in class owltools.gaf.io.OpenAnnotationRDFWriter: If set, calling {OpenAnnotationRDFWriter.write(GafDocument, File) generates bioentities plus annotations (as in a GAF file)
setGAFPredictionFile(Opts) - Method in class owltools.cli.GafCommandRunner
setGAFPredictionReportFile(Opts) - Method in class owltools.cli.GafCommandRunner
setGAFReportFile(Opts) - Method in class owltools.cli.GafCommandRunner
setGAFReportSummaryFile(Opts) - Method in class owltools.cli.GafCommandRunner
setGAFTaxonModule(Opts) - Method in class owltools.cli.GafCommandRunner
setGafToOwl(boolean) - Method in class owltools.ontologyrelease.OortConfiguration
setGciFillers(List<OWLClass>) - Method in class owltools.io.InferredParentRenderer
setGciProperty(OWLObjectProperty) - Method in class owltools.io.InferredParentRenderer
setGeneAnnotations(List<GeneAnnotation>) - Method in class owltools.gaf.GafDocument: Replace the current set of annotations with the given list.
setGeneId(String) - Method in class owltools.gaf.Bioentity
setGeneProductForm(String) - Method in class owltools.gaf.GeneAnnotation
setGenerateIndividuals(boolean) - Method in class owltools.gaf.owl.GAFOWLBridge
setGpadfMode() - Method in class owltools.gaf.io.OpenAnnotationRDFWriter: If set, calling {OpenAnnotationRDFWriter.write(GafDocument, File) generates annotations only (as in a GPAD file) This is the default
setGpadIncludeUnknowBioentities(boolean) - Method in class owltools.gaf.parser.GpadGpiObjectsBuilder
setGpadIncludeUnmappedECO(boolean) - Method in class owltools.gaf.parser.GpadGpiObjectsBuilder
setGpifMode() - Method in class owltools.gaf.io.OpenAnnotationRDFWriter: If set, calling {OpenAnnotationRDFWriter.write(GafDocument, File) generates bioentities only (as in a GPI file)
setGrandFatheringDate(Date) - Method in class owltools.gaf.rules.AbstractAnnotationRule
setGrandFatheringDate(Date) - Method in interface owltools.gaf.rules.AnnotationRule: Set the cut-off date for grand fathering the rule.
setGraph(OWLGraphWrapper) - Method in class owltools.gaf.inference.AbstractAnnotationPredictor
setGraph(OWLGraphWrapper) - Method in class owltools.mooncat.Mooncat
setGraph(OWLGraphWrapper) - Method in class owltools.sim.SimEngine
setGraph(OWLGraphWrapper) - Method in interface owltools.sim.SimilarityCalculator
setGraph(OWLGraphWrapper) - Method in class owltools.sim2.io.AbstractRenderer
setGraph(OWLGraphWrapper) - Method in interface owltools.sim2.io.SimResultRenderer
setGraph(OWLGraphWrapper) - Method in class owltools.solrj.AbstractSolrLoader
setHelpMode(boolean) - Method in class owltools.cli.Opts
sethmp(HashMap<String, Pheno>) - Method in class owltools.phenolog.PhenoTransitiveClosure
sethmpair(HashMap<String, IndividualPair>) - Method in class owltools.phenolog.PhenoTransitiveClosure
sethsp(HashSet<Pheno>) - Method in class owltools.phenolog.PhenoTransitiveClosure
setId(String) - Method in class owltools.gaf.Bioentity
setId(String) - Method in class owltools.graph.shunt.OWLShuntNode
setId(String) - Method in class owltools.phenolog.Attribute
setid(String) - Method in class owltools.phenolog.GenePheno
setId(String) - Method in class owltools.phenolog.Individual
setId(String) - Method in class owltools.phenolog.Pheno
setIgnoreLockFile(boolean) - Method in class owltools.ontologyrelease.OortConfiguration
setIgnoreObsolete(boolean) - Method in class owltools.ontologyverification.impl.NameRedundancyCheck
setIgnoreSelectedEquivalentPairSet(Set<String>) - Method in class owltools.ontologyrelease.OortConfiguration
setIgnoreSubClassesOf(Set<OWLClass>) - Method in class owltools.sim.OldSimpleOwlSim
setIgnoreSubClassesOf(Set<OWLClass>) - Method in class owltools.sim2.SimpleOwlSim
setIndex(NODE, int) - Method in class owltools.util.AbstractTarjan
setIndex(T, int) - Method in class owltools.util.MappingTarjan
setIndividualPairs(Set<IndividualPair>) - Method in class owltools.phenolog.PhenologEngine
setIndividuals(HashSet<Individual>) - Method in class owltools.phenolog.Pheno
setInferred(boolean) - Method in class owltools.graph.OWLQuantifiedProperty
setInferredViewOntology(OWLOntology) - Method in class owltools.mooncat.PropertyViewOntologyBuilder
setInformationContentFromOntology(OWLOntology) - Method in class owltools.sim2.AbstractOwlSim
setInformationContentFromOntology(OWLOntology) - Method in interface owltools.sim2.OwlSim: Populate the IC cache from an ontology of class-IC mappings.
setInformtionContectForAttribute(OWLClass, Double) - Method in class owltools.sim2.AbstractOwlSim
setInformtionContectForAttribute(OWLClass, Double) - Method in class owltools.sim2.FastOwlSim
setInformtionContectForAttribute(OWLClass, Double) - Method in class owltools.sim2.SimpleOwlSim
setInputOntology(OWLOntology) - Method in class owltools.sim2.preprocessor.AbstractSimPreProcessor
setInputOntology(OWLOntology) - Method in interface owltools.sim2.preprocessor.SimPreProcessor: sets the input ontology.
setInverseOf(boolean) - Method in class owltools.graph.OWLQuantifiedProperty
setIsColocatesWith(boolean) - Method in class owltools.gaf.GeneAnnotation
setIsContributesTo(boolean) - Method in class owltools.gaf.GeneAnnotation
setIsCut(boolean) - Method in class owltools.gaf.GeneAnnotation
setisFromTC(boolean) - Method in class owltools.phenolog.Pheno
setIsIntegralTo(boolean) - Method in class owltools.gaf.GeneAnnotation
setIsNegated(boolean) - Method in class owltools.gaf.GeneAnnotation
setJustifyAssertedSubclasses(boolean) - Method in class owltools.ontologyrelease.OortConfiguration
setJustifyAssertedSubclassesFrom(String) - Method in class owltools.ontologyrelease.OortConfiguration
setLabel(String) - Method in class owltools.graph.shunt.OWLShuntNode
setLabel(String) - Method in class owltools.phenolog.Attribute
setlabel(String) - Method in class owltools.phenolog.GenePheno
setLabel(String) - Method in class owltools.phenolog.Individual
setLabel(String) - Method in class owltools.phenolog.Pheno
setLastUpdateDate(Date) - Method in class owltools.gaf.GeneAnnotation
setLastUpdateDate(String) - Method in class owltools.gaf.GeneAnnotation
setLeafClasses(Set<OWLClass>) - Method in class owltools.mooncat.PropertyViewOntologyBuilder
setLineNumber(int) - Method in class owltools.gaf.rules.AnnotationRuleViolation
setLinks(Collection<LegoLink>) - Method in class org.geneontology.lego.model.LegoNode: Deprecated.
setLocation(int, int) - Method in class owltools.gfx.OWLGraphLayoutNode
setLowlink(NODE, int) - Method in class owltools.util.AbstractTarjan
setLowlink(T, int) - Method in class owltools.util.MappingTarjan
setMacroStrategy(OortConfiguration.MacroStrategy) - Method in class owltools.ontologyrelease.OortConfiguration: Set the OortConfiguration.MacroStrategy
setManager(OWLOntologyManager) - Method in class owltools.io.ParserWrapper
setManager(OWLOntologyManager) - Method in class owltools.mooncat.Mooncat
setMappingSource(String) - Method in class owltools.gaf.IdMapping
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
setMemoryUsage() - Method in class owltools.web.OWLHandler.ServerMetadata
setMetadata(Map<String, String>) - Method in class owltools.graph.shunt.OWLShuntEdge
setMetadata(Map<String, Object>) - Method in class owltools.graph.shunt.OWLShuntNode
setMf(boolean) - Method in class org.geneontology.lego.model.LegoNode: Deprecated.
setMinCardinality(Integer) - Method in class owltools.graph.OWLQuantifiedProperty
setName(String) - Method in class owltools.gaf.rules.AbstractAnnotationRule
setName(String) - Method in interface owltools.gaf.rules.AnnotationRule: Set the name for the rule.
setNcbiTaxonId(String) - Method in class owltools.gaf.Bioentity
setNoLookupForLCSCache(boolean) - Method in class owltools.sim2.AbstractOwlSim
setNoLookupForLCSCache(boolean) - Method in interface owltools.sim2.OwlSim: Ff set, the cache is written to but not read from.
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
setOntologyChecks(List<OntologyCheck>) - Method in class owltools.ontologyrelease.OortConfiguration
setOriginalChildrenToCurrentChildren() - Method in class owltools.gaf.Bioentity
setOrthologs(int) - Method in class owltools.phenolog.Individual
setOutputOntology(OWLOntology) - Method in class owltools.sim2.preprocessor.AbstractSimPreProcessor
setOutputOntology(OWLOntology) - Method in interface owltools.sim2.preprocessor.SimPreProcessor: sets the output ontology.
setOWLGraphWrapper(OWLGraphWrapper) - Method in class owltools.InferenceBuilder
setOWLPrettyPrinter(OWLPrettyPrinter) - Method in class owltools.sim2.preprocessor.AbstractSimPreProcessor
setOWLPrettyPrinter(OWLPrettyPrinter) - Method in interface owltools.sim2.preprocessor.SimPreProcessor
setOwlSim(OwlSim) - Method in class owltools.web.OWLHandler
setOwlSimFactory(OwlSimFactory) - Method in class owltools.cli.Sim2CommandRunner
setPaintId(String) - Method in class owltools.gaf.Bioentity
setPair(String, String) - Method in class owltools.idmap.IDMapPairWriter
setPANTHERSet(PANTHERForest) - Method in class owltools.solrj.GafSolrDocumentLoader
setPANTHERSet(PANTHERForest) - Method in class owltools.solrj.PANTHERGeneralSolrDocumentLoader
setPANTHERSet(PANTHERForest) - Method in class owltools.solrj.PANTHERSolrDocumentLoader
setParent(Bioentity) - Method in class owltools.gaf.Bioentity
setPattern(Pattern) - Method in class owltools.gaf.rules.AnnotationRegularExpressionFromXMLRule
setPersistantNodeID(String, String) - Method in class owltools.gaf.Bioentity
setphenoid(String) - Method in class owltools.phenolog.GenePheno
setphenolabel(String) - Method in class owltools.phenolog.GenePheno
setprefix(String) - Method in class owltools.phenolog.PhenoTransitiveClosure
setPrefixScore(Map<String, Double>, String, Double) - Method in class owltools.mooncat.EquivalenceSetMergeUtil
setPrefixScore(String, Double) - Method in class owltools.mooncat.EquivalenceSetMergeUtil
setPreserveObjectPropertyIRIs(boolean) - Method in class owltools.mooncat.OWLInAboxTranslator
setPreSimMethod(String) - Method in class owltools.sim.MultiSimilarity
setProfiler(Profiler) - Method in class owltools.graph.OWLGraphWrapperEdges
setProgressReporter(PseudoRdfXmlWriter.ProgressReporter) - Method in class owltools.gaf.io.PseudoRdfXmlWriter
setProperties(List<OWLObjectProperty>) - Method in class owltools.io.InferredParentRenderer
setProperty(OWLObjectProperty) - Method in class owltools.graph.OWLQuantifiedProperty
setPropertyPrefixScore(OWLAnnotationProperty, String, Double) - Method in class owltools.mooncat.EquivalenceSetMergeUtil
setPropertyToComment() - Method in class owltools.io.TableToAxiomConverter.Config
setPropertyToLabel() - Method in class owltools.io.TableToAxiomConverter.Config
setPropertyViews(Set<PropertyView>) - Method in class owltools.ontologyrelease.OortConfiguration
setPrune(boolean) - Method in class owltools.gaf.Bioentity
setQualifiers(int) - Method in class owltools.gaf.GeneAnnotation
setQuantifiedPropertyList(List<OWLQuantifiedProperty>) - Method in class owltools.graph.OWLGraphEdge
setQuantifier(OWLQuantifiedProperty.Quantifier) - Method in class owltools.graph.OWLQuantifiedProperty
setQueryOntology(String) - Method in class owltools.ontologyrelease.OortConfiguration
setQueryOntologyReference(String) - Method in class owltools.ontologyrelease.OortConfiguration
setQueryOntologyReferenceIsIRI(boolean) - Method in class owltools.ontologyrelease.OortConfiguration
setReason(String) - Method in class owltools.gaf.inference.Prediction
setReasoner(OWLReasoner) - Method in class owltools.graph.OWLGraphWrapperEdges
setReasoner(OWLReasoner) - Method in class owltools.InferenceBuilder
setReasoner(OWLExtendedReasoner) - Method in class owltools.io.InferredParentRenderer
setReasoner(OWLReasoner) - Method in class owltools.sim.OldSimpleOwlSim
setReasoner(OWLReasoner) - Method in class owltools.sim2.preprocessor.AbstractSimPreProcessor
setReasoner(OWLReasoner) - Method in interface owltools.sim2.preprocessor.SimPreProcessor: Sets the reasoner.
setReasoner(OWLReasoner) - Method in class owltools.sim2.SimpleOwlSim
setReasonerFactory(OWLReasonerFactory) - Method in class owltools.sim.OldSimpleOwlSim
setReasonerFactory(OWLReasonerFactory) - Method in class owltools.sim2.preprocessor.AbstractSimPreProcessor
setReasonerFactory(OWLReasonerFactory) - Method in interface owltools.sim2.preprocessor.SimPreProcessor: Sets the reasoner factory.
setReasonerName(String) - Method in class owltools.ontologyrelease.OortConfiguration: Set the reasoner name
setRecreateMireot(boolean) - Method in class owltools.ontologyrelease.OortConfiguration: Set recreateMireot
setRedundantWithExistingAnnotations(boolean) - Method in class owltools.gaf.inference.Prediction
setRedundantWithOtherPredictions(boolean) - Method in class owltools.gaf.inference.Prediction
setReferencedOntologies(Set<OWLOntology>) - Method in class owltools.mooncat.Mooncat: Deprecated.
setRegex(String) - Method in class owltools.gaf.rules.AnnotationRegularExpressionFromXMLRule
setRelation(String) - Method in class owltools.gaf.ExtensionExpression
setRelation(String) - Method in class owltools.gaf.GeneAnnotation
setRelationship(String) - Method in class owltools.gaf.IdMapping
setRelaxed(boolean) - Method in class owltools.ontologyrelease.OortConfiguration
setRemoveDanglingBeforeReasoning(boolean) - Method in class owltools.ontologyrelease.OortConfiguration
setRemoveQueryOntologyReference(boolean) - Method in class owltools.ontologyrelease.OortConfiguration
setRemoveRedunantAxioms(boolean) - Method in class owltools.ontologyrelease.OortConfiguration
setRemoveTrailingQualifiers(boolean) - Method in class owltools.ontologyrelease.OortConfiguration
setRepairAnnotationCardinality(boolean) - Method in class owltools.ontologyrelease.OortConfiguration
setResultOutStream(PrintStream) - Method in class owltools.sim2.io.AbstractRenderer
setRewriteIRIMap(Map<IRI, IRI>) - Method in class owltools.ontologyrelease.OortConfiguration
setRuleId(String) - Method in class owltools.gaf.rules.AbstractAnnotationRule
setRuleId(String) - Method in interface owltools.gaf.rules.AnnotationRule: Set the rule id
setRunOboBasicDagCheck(boolean) - Method in class owltools.ontologyrelease.OortConfiguration
setScore(Double) - Method in class owltools.sim.Similarity
setScore(int) - Method in class owltools.sim.Similarity
setSeqId(String, String) - Method in class owltools.gaf.Bioentity
setSimEngine(SimEngine) - Method in class owltools.sim.SimSearch
setSimMethod(Opts) - Method in class owltools.cli.SimCommandRunner
setSimple(boolean) - Method in class owltools.ontologyrelease.OortConfiguration: Set simple.
setSimPreProcessor(SimPreProcessor) - Method in class owltools.sim.OldSimpleOwlSim
setSimPreProcessor(SimPreProcessor) - Method in class owltools.sim2.SimpleOwlSim
setSimProperties(Properties) - Method in class owltools.sim2.AbstractOwlSim
setSimProperties(Properties) - Method in interface owltools.sim2.OwlSim
setSimProperties(Properties) - Method in class owltools.sim2.preprocessor.AbstractSimPreProcessor
setSimProperties(Properties) - Method in interface owltools.sim2.preprocessor.SimPreProcessor
setSimProperty(Opts) - Method in class owltools.cli.Sim2CommandRunner
setSimStats(SimStats) - Method in class owltools.sim2.AbstractOwlSim
setSingleQuantifiedProperty(OWLQuantifiedProperty) - Method in class owltools.graph.OWLGraphEdge
setSkipFormatSet(Set<String>) - Method in class owltools.ontologyrelease.OortConfiguration
setSkipNotAnnotations(boolean) - Method in class owltools.gaf.owl.GAFOWLBridge
setSolrLogFile(Opts) - Method in class owltools.cli.SolrCommandRunner: Set an optional file to use for logging load data (can be consumed by AmiGO 2).
setSolrUrl(Opts) - Method in class owltools.cli.SolrCommandRunner: Set an optional Solr URL to use with Solr options so they don't have to be specified separately for every option.
setSource(AnnotationSource) - Method in class owltools.gaf.GeneAnnotation
setSource(OWLObject) - Method in class owltools.graph.OWLGraphEdge
setSourceAnnotation(GeneAnnotation) - Method in class owltools.gaf.rules.AnnotationRuleViolation
setSourceId(String) - Method in class owltools.gaf.IdMapping
setSourceOntology(OWLOntology) - Method in class owltools.graph.OWLGraphWrapperBasic
setSourceOntology(OWLOntology) - Method in class owltools.sim2.SimpleOwlSim
setSourceOntologyPrefixes(Set<String>) - Method in class owltools.mooncat.Mooncat: Set the source ontology prefixes.
setSourceOntologyPrefixes(Set<String>) - Method in class owltools.ontologyrelease.OortConfiguration
setSources(Set<String>) - Method in class org.geneontology.lego.model.LegoMetadata: Deprecated.
setSourceViewProperties(List<OWLObjectProperty>) - Method in class owltools.sim.OldSimpleOwlSim: Deprecated.
setStatus(String) - Method in class owltools.gaf.rules.AbstractAnnotationRule
setStatus(String) - Method in interface owltools.gaf.rules.AnnotationRule: Set the status for this rule.
setStream(PrintStream) - Method in class owltools.gaf.io.GafWriter
setStream(String) - Method in class owltools.gaf.io.GafWriter
setStream(File) - Method in class owltools.gaf.io.GafWriter
setStream(InputStream) - Method in class owltools.io.AbstractClosureReader
setStream(String) - Method in class owltools.io.AbstractClosureReader
setStream(PrintStream) - Method in class owltools.io.AbstractRenderer
setStream(String) - Method in class owltools.io.AbstractRenderer
setSubSimMethod(String) - Method in class owltools.sim.MultiSimilarity
setSuggestedReplacements(Set<GeneAnnotation>) - Method in class owltools.gaf.rules.AnnotationRuleViolation
setSupportOntologySet(Set<OWLOntology>) - Method in class owltools.graph.OWLGraphWrapperBasic
setSymbol(String) - Method in class owltools.gaf.Bioentity
setSynonyms(List<String>) - Method in class owltools.gaf.Bioentity
setTarget(OWLObject) - Method in class owltools.graph.OWLGraphEdge
setTargetDirectory(String) - Method in class owltools.gaf.godb.Dumper
setTargetId(String) - Method in class owltools.gaf.IdMapping
setTargetOntology(OWLOntology) - Method in class owltools.gaf.owl.GAFOWLBridge
setTaxonSubsetName(String) - Method in class owltools.solrj.GafSolrDocumentLoader
setTaxonTools(TaxonTools) - Method in class owltools.solrj.GafSolrDocumentLoader
setThreads(int) - Method in class owltools.ontologyrelease.OortConfiguration
setTimePoint(OntologyCheckRunner.TimePoint) - Method in class owltools.ontologyverification.impl.AbstractCheck
setTimePoint(OntologyCheckRunner.TimePoint) - Method in interface owltools.ontologyverification.OntologyCheck: Set the OntologyCheckRunner.TimePoint for this ontology check instance.
setTraceReportFile(String) - Method in class owltools.ontologyrelease.OortConfiguration
setTranslateDisjointsToEquivalents(boolean) - Method in class owltools.ontologyrelease.OortConfiguration
setType(String) - Method in class owltools.gaf.Bioentity
setType(AnnotationRuleViolation.ViolationType) - Method in class owltools.gaf.rules.AnnotationRuleViolation
setType(String) - Method in class owltools.graph.shunt.OWLShuntNode
setTypeCls(String) - Method in class owltools.gaf.Bioentity
setUnknowns(Collection<OWLClassExpression>) - Method in class org.geneontology.lego.model.LegoNode: Deprecated.
setupAltIdProperty(OWLOntology) - Static method in class owltools.ncbi.NCBIOWL: Setup the alternative identifier annotation property.
setUseIsInferred(boolean) - Method in class owltools.ontologyrelease.OortConfiguration
setUseOriginalClassIRIs(boolean) - Method in class owltools.mooncat.PropertyViewOntologyBuilder
setUseQueryOntology(boolean) - Method in class owltools.ontologyrelease.OortConfiguration
setUseReleaseFolder(boolean) - Method in class owltools.ontologyrelease.OortConfiguration
setValue(SimpleOwlSim.Metric, double) - Method in class owltools.sim2.SimStats
setVersionReportFiles(boolean) - Method in class owltools.ontologyrelease.OortConfiguration
setVersionSubdirectory(String) - Method in class owltools.ontologyrelease.OortConfiguration
setViewEntities(Set<OWLEntity>) - Method in class owltools.mooncat.PropertyViewOntologyBuilder
setViewLabelPrefix(String) - Method in class owltools.mooncat.PropertyViewOntologyBuilder: Set this to prefix all class labels in O(P)
setViewLabelPrefixAndSuffix(String, String) - Method in class owltools.mooncat.PropertyViewOntologyBuilder
setViewLabelSuffix(String) - Method in class owltools.mooncat.PropertyViewOntologyBuilder: Set this to suffix all class labels in O(P)
setViewProperties(Set<OWLObjectProperty>) - Method in class owltools.sim.OldSimpleOwlSim: Deprecated.
setWithInfos(Collection<String>) - Method in class owltools.gaf.GeneAnnotation
setWrappedReasoner(OWLReasoner) - Method in class owltools.reasoner.LazyExpressionMaterializingReasoner: Deprecated.
setWrappedReasonerFactory(OWLReasonerFactory) - Method in class owltools.reasoner.LazyExpressionMaterializingReasoner: Deprecated.
setWriteELOntology(boolean) - Method in class owltools.ontologyrelease.OortConfiguration
setWriteLabelOWL(boolean) - Method in class owltools.ontologyrelease.OortConfiguration
setWriteMetadata(boolean) - Method in class owltools.ontologyrelease.OortConfiguration
setWriteSubsets(boolean) - Method in class owltools.ontologyrelease.OortConfiguration
SharedLabelException - Exception in owltools.graph
SharedLabelException(String, IRI, IRI) - Constructor for exception owltools.graph.SharedLabelException
SHORT_HAND - Static variable in class owltools.ontologyverification.impl.AltIdInSignature
SHORT_HAND - Static variable in class owltools.ontologyverification.impl.CycleCheck
SHORT_HAND - Static variable in class owltools.ontologyverification.impl.DanglingReferenceCheck
SHORT_HAND - Static variable in class owltools.ontologyverification.impl.NameRedundancyCheck
SHORT_HAND - Static variable in class owltools.ontologyverification.impl.ObsoleteClassInSignature
SHORT_HAND - Static variable in class owltools.ontologyverification.impl.SelfReferenceInDefinition
show(Set<OWLClassExpression>, OWLPrettyPrinter) - Method in class owltools.sim2.io.JSONRenderer
show(Set<OWLClass>, OWLPrettyPrinter) - Method in class owltools.sim2.io.TabularRenderer
showAttributeGroupings(Opts) - Method in class owltools.cli.Sim2CommandRunner
showAttributeGroupingsAsList(Opts) - Method in class owltools.cli.Sim2CommandRunner: Given a set of classes, will print the grouping class(es) for each annotation in a comma-separated list.
showAttributeGroupingsInTable(Opts) - Method in class owltools.cli.Sim2CommandRunner: Given a set of classes, will print a table of grouping class(es) for each annotation, and show a binary flag if the given annotation belongs to that class.
showSimProperties(Opts) - Method in class owltools.cli.Sim2CommandRunner
showStats() - Method in class owltools.gaf.godb.DatabaseDumper
showTimings() - Method in class owltools.sim2.AbstractOwlSim
showTimings() - Method in interface owltools.sim2.OwlSim: Writes timing information using log4j.
showTimingsAndReset() - Method in class owltools.sim2.AbstractOwlSim
ShuntGraphUtils - Class in owltools.util: Alternative method for generating ShuntGraphs - experimental
ShuntGraphUtils() - Constructor for class owltools.util.ShuntGraphUtils
ShuntGraphUtils.ShuntGraphPair - Class in owltools.util: Result object containing two corresponding shunt graphs.
ShuntGraphUtils.ShuntGraphPair(OWLShuntGraph, OWLShuntGraph) - Constructor for class owltools.util.ShuntGraphUtils.ShuntGraphPair
sim(Opts) - Method in class owltools.cli.SimCommandRunner
Sim2CommandRunner - Class in owltools.cli: Semantic similarity and information content.
Sim2CommandRunner() - Constructor for class owltools.cli.Sim2CommandRunner
simAll(Opts) - Method in class owltools.cli.SimCommandRunner
simAttMatchOld(Opts) - Method in class owltools.cli.Sim2CommandRunner: Deprecated.
simBasic(Opts) - Method in class owltools.cli.Sim2CommandRunner: Deprecated.
simBasic(Opts) - Method in class owltools.cli.SimCommandRunner
simBasicStats(Opts) - Method in class owltools.cli.Sim2CommandRunner: This method will report to the user some metadata about the previous similarity run.
SimCommandRunner - Class in owltools.cli: Semantic similarity and information content.
SimCommandRunner() - Constructor for class owltools.cli.SimCommandRunner
simDlQuery(Opts) - Method in class owltools.cli.Sim2CommandRunner
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
simGIC - Variable in class owltools.sim2.io.SimResultRenderer.IndividualSimScores
simGIC - Variable in class owltools.sim2.scores.AttributePairScores
simGIC - Variable in class owltools.sim2.scores.ElementPairScores
simGICLabel - Variable in class owltools.sim2.io.SimResultRenderer.IndividualSimScores
Similarity - Class in owltools.sim: Represents a pairwise similarity between two OWLObjects.
Similarity() - Constructor for class owltools.sim.Similarity
SimilarityCalculator - Interface in owltools.sim
simJScore - Variable in class owltools.sim2.io.SimResultRenderer.AttributesSimScores
simjScore - Variable in class owltools.sim2.io.SimResultRenderer.IndividualSimScores
simjScore - Variable in class owltools.sim2.scores.AttributePairScores
simjScore - Variable in class owltools.sim2.scores.ElementPairScores
simjScoreLabel - Variable in class owltools.sim2.io.SimResultRenderer.AttributesSimScores
simjScoreLabel - Variable in class owltools.sim2.io.SimResultRenderer.IndividualSimScores
SimJSONEngine - Class in owltools.sim2
SimJSONEngine(OWLGraphWrapper, OwlSim) - Constructor for class owltools.sim2.SimJSONEngine
simLCS(Opts) - Method in class owltools.cli.Sim2CommandRunner
simLoadICCache(Opts) - Method in class owltools.cli.Sim2CommandRunner
simLoadLCSCache(Opts) - Method in class owltools.cli.Sim2CommandRunner
simPairwiseAttMatch(Opts) - Method in class owltools.cli.Sim2CommandRunner
SimpleABoxToGAF - Class in owltools.gaf.owl: Translates a set of ClassAssertion axioms to a minimal GAF
SimpleABoxToGAF() - Constructor for class owltools.gaf.owl.SimpleABoxToGAF
SimpleEcoMapper - Interface in owltools.gaf.eco
SimpleEcoMapperImpl - Class in owltools.gaf.eco
SimpleOwlSim - Class in owltools.sim2: Soon to be deprecated implementation of OwlSim
SimpleOwlSim(OWLOntology) - Constructor for class owltools.sim2.SimpleOwlSim
SimpleOwlSim.Direction - Enum in owltools.sim2: Asymmetric metrics can be applied in either of two directions, or both can be aggregated
SimpleOwlSim.Metric - Enum in owltools.sim2: Base similarity metric - may be applied at individual or class level
SimpleOwlSim.OutputFormat - Enum in owltools.sim2: The OutputFormat enumerates the different styles of output for sim results, and maps 1:1 with different renderers.
SimpleOwlSim.ScoreAttributePair - Class in owltools.sim2: A pair consisting of an attribute class, and a score for that class
SimpleOwlSim.ScoreAttributePair(double, OWLClass) - Constructor for class owltools.sim2.SimpleOwlSim.ScoreAttributePair
SimpleOwlSim.SimConfigurationProperty - Enum in owltools.sim2: Set of tags that can be used in configuration
SimpleOwlSimFactory - Class in owltools.sim2
SimpleOwlSimFactory() - Constructor for class owltools.sim2.SimpleOwlSimFactory
simplifies(Collection<String>, Collection<String>, Collection<String>, Collection<String>, Collection<String>) - Method in class owltools.graph.OWLGraphManipulator: Helper method to perform standard simplifications.
SimPreProcessor - Interface in owltools.sim2.preprocessor: An ontology pre-processor will take an input ontology, apply a series of transforms, and generate an output ontology The output ontology may in many cases be the same as the input ontology
simProperties - Variable in class owltools.sim2.preprocessor.AbstractSimPreProcessor
SimResultRenderer - Interface in owltools.sim2.io
SimResultRenderer.AttributesSimScores - Class in owltools.sim2.io
SimResultRenderer.AttributesSimScores(OWLClass, OWLClass) - Constructor for class owltools.sim2.io.SimResultRenderer.AttributesSimScores
SimResultRenderer.IndividualSimScores - Class in owltools.sim2.io
SimResultRenderer.IndividualSimScores(OWLNamedIndividual, OWLNamedIndividual) - Constructor for class owltools.sim2.io.SimResultRenderer.IndividualSimScores
simResume(Opts) - Method in class owltools.cli.SimCommandRunner
simSaveICCache(Opts) - Method in class owltools.cli.Sim2CommandRunner
simSaveLCSCache(Opts) - Method in class owltools.cli.Sim2CommandRunner
simSavePhenodigmClassScores(Opts) - Method in class owltools.cli.Sim2CommandRunner
simSaveState(Opts) - Method in class owltools.cli.Sim2CommandRunner
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
simStats - Variable in class owltools.sim2.AbstractOwlSim
SimStats - Class in owltools.sim2: Will keep track of the overall stats of analysis in data sets.
SimStats() - Constructor for class owltools.sim2.SimStats
simStatsPerIndividual - Variable in class owltools.sim2.AbstractOwlSim
simTest(Opts) - Method in class owltools.cli.Sim2CommandRunner
size() - Method in class owltools.util.BloomFilter: Returns the number of bits in the Bloom filter.
SKIP_IEA - Static variable in class owltools.gaf.inference.BasicAnnotationPropagator
SolrCommandRunner - Class in owltools.cli: Solr/GOlr loading.
SolrCommandRunner() - Constructor for class owltools.cli.SolrCommandRunner
solrSchemaDump(Opts) - Method in class owltools.cli.SolrCommandRunner: Output (STDOUT) XML segment to put into the Solr schema file after reading the YAML configuration file(s).
SolrSchemaXMLWriter - Class in owltools.yaml.golrconfig
SolrSchemaXMLWriter(ConfigManager) - Constructor for class owltools.yaml.golrconfig.SolrSchemaXMLWriter
SomeValuesFrom - Interface in owltools.frame
SomeValuesFromLD - Class in owltools.frame.jsonld
SomeValuesFromLD(StubLD, StubLD) - Constructor for class owltools.frame.jsonld.SomeValuesFromLD
sortMapByScore(Map<OWLObject, Similarity>) - Method in class owltools.sim.MultiSimilarity
source - Variable in class org.bbop.golr.java.RetrieveGolrBioentities.GolrBioentityDocument
sourceId - Variable in class owltools.gaf.IdMapping
sourceOntology - Variable in class owltools.graph.OWLGraphWrapperBasic
SpeciesMergeUtil - Class in owltools.mooncat: This utility is for making "composite" ontologies from the combination of a species-specific ontology (e.g.
SpeciesMergeUtil(OWLGraphWrapper) - Constructor for class owltools.mooncat.SpeciesMergeUtil
SpeciesMergeUtil.UnmergeableOntologyException - Exception in owltools.mooncat
SpeciesMergeUtil.UnmergeableOntologyException(String) - Constructor for exception owltools.mooncat.SpeciesMergeUtil.UnmergeableOntologyException
SpeciesSubsetterUtil - Class in owltools.mooncat: This implements species subsetting (module generation) using OWL reasoning.
SpeciesSubsetterUtil(OWLGraphWrapper) - Constructor for class owltools.mooncat.SpeciesSubsetterUtil: Constructor providing the OWLGraphWrapper wrapping the OWLOntology used for species subsetting.
split(String) - Method in class owltools.idmap.IDMapHandler
splitIRI(IRI) - Method in class owltools.sim.Similarity
STAGING_DIRECTORY_NAME - Static variable in class owltools.ontologyrelease.ReleaseRunnerFileTools
StanzaToOWLConverter - Class in owltools.io: reads in a stanza-formatted file (e.g.
StanzaToOWLConverter(OWLGraphWrapper) - Constructor for class owltools.io.StanzaToOWLConverter
StanzaToOWLConverter.Config - Class in owltools.io
StanzaToOWLConverter.Config() - Constructor for class owltools.io.StanzaToOWLConverter.Config
StanzaToOWLConverter.Mapping - Class in owltools.io: incomplete.
StanzaToOWLConverter.Mapping() - Constructor for class owltools.io.StanzaToOWLConverter.Mapping
StanzaToOWLConverter.Stanza - Class in owltools.io: A stanza is set of key-value pairs E.g
StanzaToOWLConverter.Stanza() - Constructor for class owltools.io.StanzaToOWLConverter.Stanza
start(PrintWriter, OWLGraphWrapper) - Method in class owltools.ontologyrelease.reports.OntologyReportGenerator.AbstractReport
start(PrintWriter, OWLGraphWrapper) - Method in interface owltools.ontologyrelease.reports.OntologyReportGenerator.OntologyReport: Start the report.
startSimServer(Opts) - Method in class owltools.cli.Sim2CommandRunner
startTaskNotify(String) - Method in class owltools.profile.Profiler
status_df - Static variable in class owltools.gaf.rules.AnnotationRulesFactoryImpl
storeResult(OWLNamedIndividual, OWLNamedIndividual, OwlSim.ScoreAttributeSetPair, String) - Method in class owltools.sim.OWLResultsManager
stream - Variable in class owltools.gaf.io.GafWriter
stream - Variable in class owltools.io.AbstractClosureReader
stream - Variable in class owltools.io.AbstractRenderer
StringTools - Class in org.geneontology.lego.dot: Deprecated.
StringTools() - Constructor for class org.geneontology.lego.dot.StringTools: Deprecated.
Stub - Interface in owltools.frame
StubLD - Class in owltools.frame.jsonld
StubLD() - Constructor for class owltools.frame.jsonld.StubLD
StubLD(String, String) - Constructor for class owltools.frame.jsonld.StubLD
sub - Variable in class owltools.graph.shunt.OWLShuntEdge
SubclassRetriever - Class in owltools.sim2.kb
SubclassRetriever(OWLClass, OWLOntology) - Constructor for class owltools.sim2.kb.SubclassRetriever
subDir - Variable in class owltools.mooncat.BridgeExtractor
subgraphSummaryStatsPerIndividual - Variable in class owltools.sim2.AbstractOwlSim
submissionDate - Variable in class owltools.gaf.metadata.AnnotationDocumentMetadata
subSimMethod - Variable in class owltools.sim.MultiSimilarity
subsumes(OWLQuantifiedProperty) - Method in class owltools.graph.OWLQuantifiedProperty: true if this is equal to other.
success - Variable in class owltools.ontologyverification.OntologyCheckHandler.CheckSummary
suffix - Variable in class owltools.mooncat.SpeciesMergeUtil
sum - Variable in class owltools.sim2.OwlSim.StatsPerIndividual
summarizeOntology(OWLOntology) - Method in class owltools.cli.CommandRunner
summary(int, int, int, int, int) - Method in class owltools.ontologyverification.OntologyCheckHandler
summaryWriter - Variable in class owltools.gaf.rules.AnnotationRulesReportWriter
supportOntologySet - Variable in class owltools.graph.OWLGraphWrapperBasic
svgPath - Variable in class owltools.gfx.OWLGraphStrokeEdge.SVGEdge
synonym - Variable in class org.bbop.golr.java.RetrieveGolrBioentities.GolrBioentityDocument
synonym(OWLOntology, OWLEntity, OWLAnnotationValue, OWLAnnotationProperty, OWLAnnotationValue) - Static method in class owltools.ncbi.OWLConverter: Add an synonym annotation, plus an annotation on that annotation that specified the type of synonym.
synonym(OWLOntology, OWLEntity, String, String, String) - Static method in class owltools.ncbi.OWLConverter: Add an synonym annotation, plus an annotation on that annotation that specified the type of synonym.
synonymTypes - Static variable in class owltools.ncbi.NCBIOWL: A map from NCBI synonym types to OboInOwl annotation properties.

T

t1 - Variable in class owltools.idmap.IDMapPairWriter
t2 - Variable in class owltools.idmap.IDMapPairWriter
tableObjIdMap - Variable in class owltools.gaf.godb.DatabaseDumper
TableRenderer - Class in owltools.io: Renders the graph closure - i.e.
TableRenderer(PrintStream) - Constructor for class owltools.io.TableRenderer
TableRenderer(String) - Constructor for class owltools.io.TableRenderer
TableToAxiomConverter - Class in owltools.io: reads in a table (e.g.
TableToAxiomConverter(OWLGraphWrapper) - Constructor for class owltools.io.TableToAxiomConverter
TableToAxiomConverter.Config - Class in owltools.io: If AxiomType is ClassAssertion, then axioms will be of form ClassAssertion(sub obj) If AxiomType is SubClassOf, then axioms will be of form SubClassOf(sub obj) if a property P is specified, then obj is transformed to a class expression "P some obj'" where obj' is the original value for obj
TableToAxiomConverter.Config() - Constructor for class owltools.io.TableToAxiomConverter.Config
TabularRenderer - Class in owltools.sim2.io
TabularRenderer(PrintStream, String, String) - Constructor for class owltools.sim2.io.TabularRenderer
TabularRenderer(PrintStream) - Constructor for class owltools.sim2.io.TabularRenderer
targetDirectory - Variable in class owltools.gaf.godb.Dumper
targetId - Variable in class owltools.gaf.IdMapping
targetOntology - Variable in class owltools.io.StanzaToOWLConverter.Config
Tarjan<NODE> - Interface in owltools.util: Interface for the Tarjan's strongly connected components algorithm.
taxClass - Variable in class owltools.mooncat.SpeciesMergeUtil
taxClass - Variable in class owltools.mooncat.SpeciesSubsetterUtil
taxon - Variable in class org.bbop.golr.java.RetrieveGolrBioentities.GolrBioentityDocument
TAXON - Static variable in class owltools.gaf.parser.GAFParser
taxon_label - Variable in class org.bbop.golr.java.RetrieveGolrBioentities.GolrBioentityDocument
TAXON_PREFIX - Static variable in class owltools.gaf.TaxonTools
TAXON_PURL - Static variable in class owltools.gaf.TaxonTools
TaxonCommandRunner - Class in owltools.cli: Command-line module for taxon constraints.
TaxonCommandRunner() - Constructor for class owltools.cli.TaxonCommandRunner
TaxonConstraintsEngine - Class in owltools.gaf.inference: Deprecated.
There is now a taxon checks using an OWL resoner. This implementation may over-report violations, i.e. taxon constrains should not be propagated over regulates relations.
TaxonConstraintsEngine(OWLGraphWrapper) - Constructor for class owltools.gaf.inference.TaxonConstraintsEngine: Deprecated.
TaxonTools - Class in owltools.gaf: Methods to simplify the work with the taxons.
TaxonTools(OWLReasoner, boolean) - Constructor for class owltools.gaf.TaxonTools: Create an instance for the given reasoner.
TBoxUnFoldingTool - Class in owltools: Provide TBox unfolding methods.
TBoxUnFoldingTool(OWLGraphWrapper, Set<String>, String) - Constructor for class owltools.TBoxUnFoldingTool: Create a new instance for the given ontology graph.
TBoxUnFoldingTool.NonDeterministicUnfoldException - Exception in owltools: Exception indication, that the unfold operation is not deterministic.
TBoxUnFoldingTool.NonDeterministicUnfoldException(String) - Constructor for exception owltools.TBoxUnFoldingTool.NonDeterministicUnfoldException
tdelta(long) - Method in class owltools.sim2.AbstractOwlSim
TemplatedTransformer - Class in owltools.tr: Examples:
TemplatedTransformer(OWLOntology) - Constructor for class owltools.tr.TemplatedTransformer
TemplatedTransformer.Mapping - Class in owltools.tr
TemplatedTransformer.Mapping() - Constructor for class owltools.tr.TemplatedTransformer.Mapping
termIds - Variable in class owltools.gfx.GraphStyle
terms - Variable in class owltools.gfx.HierarchyImage
threadDumpCommand() - Method in class owltools.web.OWLHandler
toJSON() - Method in class owltools.graph.shunt.OWLShuntGraph
top - Variable in class owltools.gfx.OWLGraphLayoutNode.SVGRectangle
top() - Method in class owltools.gfx.OWLGraphLayoutNode
topCommand() - Method in class owltools.web.OWLHandler
topLine - Variable in class owltools.gfx.OWLGraphLayoutNode
toString() - Method in class org.geneontology.lego.model2.LegoUnit: Deprecated.
toString() - Method in class owltools.gaf.Bioentity
toString() - Method in class owltools.gaf.ExtensionExpression
toString() - Method in class owltools.gaf.GeneAnnotation
toString() - Method in class owltools.gaf.inference.Prediction
toString() - Method in class owltools.gaf.rules.AnnotationRuleViolation
toString() - Method in class owltools.graph.OWLGraphEdge
toString() - Method in class owltools.graph.OWLGraphWrapper.Synonym
toString() - Method in class owltools.graph.OWLQuantifiedProperty
toString() - Method in class owltools.io.OWLJSONFormat: Returns a string representation of the object.
toString() - Method in class owltools.io.StanzaToOWLConverter.Mapping
toString() - Method in class owltools.ontologyrelease.OortConfiguration
toString() - Method in class owltools.ontologyverification.CheckWarning
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.OldSimpleOwlSim.EnrichmentResult
toString() - Method in class owltools.sim.OWLObjectPair
toString() - Method in class owltools.sim.Similarity
toString() - Method in class owltools.sim2.ClassDifferentiaLearner.InferredClassDefinition
toString() - Method in class owltools.sim2.ClassDifferentiaLearner
toString() - Method in class owltools.sim2.EnrichmentResult
toString() - Method in class owltools.sim2.OwlSim.StatsPerIndividual
toString() - Method in class owltools.sim2.scores.ElementPairScores
toString() - Method in class owltools.tr.TemplatedTransformer.Mapping
toString() - Method in enum owltools.vocab.OBOUpperVocabulary
tr(OWLSubClassOfAxiom) - Method in class owltools.mooncat.SpeciesMergeUtil
tr(OWLEquivalentClassesAxiom) - Method in class owltools.mooncat.SpeciesMergeUtil
tr() - Method in class owltools.tr.TemplatedTransformer
tr(TemplatedTransformer.Mapping) - Method in class owltools.tr.TemplatedTransformer
tr(OWLOntology, TemplatedTransformer.Mapping) - Method in class owltools.tr.TemplatedTransformer
tr(OWLAxiom, TemplatedTransformer.Mapping) - Method in class owltools.tr.TemplatedTransformer
TraceReportFileHandler - Class in owltools.ontologyrelease.logging
TraceReportFileHandler(File, String) - Constructor for class owltools.ontologyrelease.logging.TraceReportFileHandler
transferAxiomsUsingIdSpace(String, OWLOntology) - Method in class owltools.mooncat.Mooncat: Assumes OBO-style IDspaces; specifically URI contains "..../IDSPACE_..."
transform - Variable in class owltools.yaml.golrconfig.GOlrDynamicField: Deprecated.
transform - Variable in class owltools.yaml.golrconfig.GOlrField
TransformationUtils - Class in owltools.mooncat: Static methods for performing common logical transforms and view creation on OWL ontologies
TransformationUtils() - Constructor for class owltools.mooncat.TransformationUtils
translate(GafDocument) - Method in class owltools.gaf.owl.GAFOWLBridge
translate(StanzaToOWLConverter.Stanza) - Method in class owltools.io.StanzaToOWLConverter: Translates a stanza to axioms (triples) and adds these to the targetOntology
translate() - Method in class owltools.mooncat.OWLInAboxTranslator
translateABoxToTBox(OWLOntology) - Method in class owltools.mooncat.PropertyViewOntologyBuilder: Deprecated.
translateABoxToTBox() - Method in class owltools.mooncat.PropertyViewOntologyBuilder: Deprecated.
translateABoxToTBox(OWLOntology) - Static method in class owltools.sim2.preprocessor.ABoxUtils: generates SubClassOf axioms from ClassAssertion axioms Note that property assertions are currently ignored
translateBioentity(Bioentity) - Method in class owltools.gaf.owl.GAFOWLBridge
translateBioentity(Bioentity) - Method in class owltools.gaf.owl.mapping.BasicABox
translateDisjointsToEquivalents() - Method in class owltools.mooncat.Mooncat: For every pair X DisjointWith Y, generate an axiom A and Y = Nothing (may become deprecated after Elk supports disjoints)
translateDisjointsToEquivalents(OWLOntology, OWLOntologyManager, OWLDataFactory) - Static method in class owltools.mooncat.Mooncat: For every pair X DisjointWith Y, generate an axiom A and Y = Nothing (may become deprecated after Elk supports disjoints)
translateGeneAnnotation(GeneAnnotation) - Method in class owltools.gaf.owl.GAFOWLBridge
translateGeneAnnotation(GeneAnnotation) - Method in class owltools.gaf.owl.mapping.BasicABox
translateInto(OWLOntology) - Method in class owltools.mooncat.OWLInAboxTranslator: Adds all shadow axioms of original ontology to target
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
translateToJson(Frame) - Method in class owltools.frame.FrameMaker
TraversingEcoMapper - Interface in owltools.gaf.eco
TraversingEcoMapperImpl - Class in owltools.gaf.eco
trim() - Method in class owltools.sim2.preprocessor.AbstractSimPreProcessor
type - Variable in class org.bbop.golr.java.RetrieveGolrBioentities.GolrBioentityDocument
type - Variable in class owltools.graph.shunt.OWLShuntNode
type - Variable in class owltools.yaml.golrconfig.GOlrField
typeIxMap - Variable in class owltools.idmap.IDMappingPIRParser
typeMap - Variable in class owltools.idmap.IDMapHandler

U

unescape(String) - Static method in class owltools.ontologyrelease.OortConfiguration: Only public for testing purposes.
unfold(GafDocument) - Method in class owltools.gaf.owl.AnnotationExtensionUnfolder
unfold(GafDocument, GeneAnnotation) - Method in class owltools.gaf.owl.AnnotationExtensionUnfolder: given an annotation to a pre-existing term, this will return a set of zero or more annotations to new terms that are generated from folding the annotation extensions into newly created term
unfold(String) - Method in class owltools.TBoxUnFoldingTool: Unfold the equivalence axiom of the OWLClass for the given id.
unfold(OWLClass) - Method in class owltools.TBoxUnFoldingTool: Unfold the equivalence axiom of the OWLClass
unfold(OWLEquivalentClassesAxiom, OWLClass) - Method in class owltools.TBoxUnFoldingTool: Unfold the OWLEquivalentClassesAxiom of the OWLClass.
unfoldGafExtensions(Opts) - Method in class owltools.cli.GafCommandRunner
unfoldToString(String) - Method in class owltools.TBoxUnFoldingTool: Unfold the equivalence axiom of the OWLClass for the given id.
unfoldToString(OWLClass) - Method in class owltools.TBoxUnFoldingTool: Unfold the equivalence axiom of the OWLClass
unify(OWLClassExpression, OWLClassExpression, Set<IRI>) - Method in class owltools.tr.TemplatedTransformer
unifyAll(OWLClassExpression, OWLClassExpression, Set<IRI>) - Method in class owltools.tr.TemplatedTransformer
UniProtIDMapParser - Class in owltools.idmap
UniProtIDMapParser() - Constructor for class owltools.idmap.UniProtIDMapParser
uniqueClassCount - Variable in class owltools.sim2.SimStats
uniqueClassPairCount - Variable in class owltools.sim2.SimStats
UnknownOWLClassException - Exception in owltools.sim2
UnknownOWLClassException(OWLClass) - Constructor for exception owltools.sim2.UnknownOWLClassException
unsafeToJSON() - Method in class owltools.graph.shunt.OWLShuntGraph
unsatisfiable - Variable in class owltools.InferenceBuilder.ConsistencyReport
updateAnnotation(OWLOntology, OWLEntity, String, String) - Static method in class owltools.ncbi.OWLConverter
updateRedundant(OWLClass, OWLOntology, Set<OWLAxiom>, OWLReasoner, OWLDataFactory) - Static method in class owltools.InferenceBuilder: Update the set of redundant axioms for the given OWLClass cls.
usage - Static variable in class owltools.ncbi.NCBI2OWL: Command line usage information.
use(OWLClass) - Method in interface owltools.cli.AssertInferredClassExpressions.OWLClassFilter
useFastOwlSim(Opts) - Method in class owltools.cli.Sim2CommandRunner
useImportClosureForQueries() - Method in class owltools.graph.OWLGraphWrapper: Deprecated.
useOWLClass(OWLClass, OWLOntology) - Method in interface owltools.InferenceBuilder.OWLClassFilter: Return true, if the inferences are to made for the given OWLClass and OWLOntology; otherwise false.
useSimpleOwlSim(Opts) - Method in class owltools.cli.Sim2CommandRunner

V

validateAnnotations(GafDocument) - Method in class owltools.gaf.rules.AnnotationRulesEngine: Validate the given GafDocument.
value - Variable in class owltools.flex.FlexLine
value() - Method in class owltools.flex.FlexLine: Return the first/only value.
valueOf(String) - Static method in enum owltools.gaf.godb.GoMySQLDatabaseDumper.GOMySQLTable: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum owltools.gaf.owl.GAFOWLBridge.BioentityMapping: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum owltools.gaf.owl.GAFOWLBridge.Vocab: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum owltools.gaf.rules.AnnotationRuleViolation.ViolationType: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum owltools.gfx.RelationType.Polarity: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum owltools.gfx.RelationType: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum owltools.graph.OWLQuantifiedProperty.Quantifier: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum owltools.idmap.IDMappingPIRParser.Types: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum owltools.ontologyrelease.OntologyMetadata.MetadataField: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum owltools.ontologyrelease.OntologyMetadata.MetadataQualifier: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum owltools.ontologyrelease.OortConfiguration.MacroStrategy: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum owltools.ontologyverification.OntologyCheckRunner.TimePoint: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum owltools.sim.OldSimpleOwlSim.Stage: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum owltools.sim2.OwlSim.Stat: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum owltools.sim2.SimpleOwlSim.Direction: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum owltools.sim2.SimpleOwlSim.Metric: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum owltools.sim2.SimpleOwlSim.OutputFormat: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum owltools.sim2.SimpleOwlSim.SimConfigurationProperty: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum owltools.vocab.OBONamespaces: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum owltools.vocab.OBOUpperVocabulary: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum owltools.web.OWLHandler.Param: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum owltools.web.OWLHandler.ResultType: Returns the enum constant of this type with the specified name.
values() - Method in class owltools.flex.FlexLine: Return all the values.
values() - Static method in enum owltools.gaf.godb.GoMySQLDatabaseDumper.GOMySQLTable: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum owltools.gaf.owl.GAFOWLBridge.BioentityMapping: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum owltools.gaf.owl.GAFOWLBridge.Vocab: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum owltools.gaf.rules.AnnotationRuleViolation.ViolationType: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum owltools.gfx.RelationType.Polarity: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum owltools.gfx.RelationType: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum owltools.graph.OWLQuantifiedProperty.Quantifier: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum owltools.idmap.IDMappingPIRParser.Types: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum owltools.ontologyrelease.OntologyMetadata.MetadataField: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum owltools.ontologyrelease.OntologyMetadata.MetadataQualifier: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum owltools.ontologyrelease.OortConfiguration.MacroStrategy: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum owltools.ontologyverification.OntologyCheckRunner.TimePoint: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum owltools.sim.OldSimpleOwlSim.Stage: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum owltools.sim2.OwlSim.Stat: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum owltools.sim2.SimpleOwlSim.Direction: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum owltools.sim2.SimpleOwlSim.Metric: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum owltools.sim2.SimpleOwlSim.OutputFormat: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum owltools.sim2.SimpleOwlSim.SimConfigurationProperty: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum owltools.vocab.OBONamespaces: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum owltools.vocab.OBOUpperVocabulary: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum owltools.web.OWLHandler.Param: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum owltools.web.OWLHandler.ResultType: Returns an array containing the constants of this enum type, in the order they are declared.
verifyChanges(Opts) - Method in class owltools.cli.CommandRunner
verifyExistingInferences(OWLGraphWrapper, BufferedWriter, boolean, boolean) - Static method in class owltools.cli.AssertInferenceTool
VersionInfo - Class in owltools.version
viewProperty - Variable in class owltools.mooncat.SpeciesMergeUtil
viewProperty - Variable in class owltools.mooncat.SpeciesSubsetterUtil
visit(OWLSubAnnotationPropertyOfAxiom) - Method in class owltools.graph.AxiomAnnotationTools.AxiomAnnotationsChanger
visit(OWLAnnotationPropertyDomainAxiom) - Method in class owltools.graph.AxiomAnnotationTools.AxiomAnnotationsChanger
visit(OWLAnnotationPropertyRangeAxiom) - Method in class owltools.graph.AxiomAnnotationTools.AxiomAnnotationsChanger
visit(OWLSubClassOfAxiom) - Method in class owltools.graph.AxiomAnnotationTools.AxiomAnnotationsChanger
visit(OWLNegativeObjectPropertyAssertionAxiom) - Method in class owltools.graph.AxiomAnnotationTools.AxiomAnnotationsChanger
visit(OWLAsymmetricObjectPropertyAxiom) - Method in class owltools.graph.AxiomAnnotationTools.AxiomAnnotationsChanger
visit(OWLReflexiveObjectPropertyAxiom) - Method in class owltools.graph.AxiomAnnotationTools.AxiomAnnotationsChanger
visit(OWLDisjointClassesAxiom) - Method in class owltools.graph.AxiomAnnotationTools.AxiomAnnotationsChanger
visit(OWLDataPropertyDomainAxiom) - Method in class owltools.graph.AxiomAnnotationTools.AxiomAnnotationsChanger
visit(OWLObjectPropertyDomainAxiom) - Method in class owltools.graph.AxiomAnnotationTools.AxiomAnnotationsChanger
visit(OWLEquivalentObjectPropertiesAxiom) - Method in class owltools.graph.AxiomAnnotationTools.AxiomAnnotationsChanger
visit(OWLNegativeDataPropertyAssertionAxiom) - Method in class owltools.graph.AxiomAnnotationTools.AxiomAnnotationsChanger
visit(OWLDifferentIndividualsAxiom) - Method in class owltools.graph.AxiomAnnotationTools.AxiomAnnotationsChanger
visit(OWLDisjointDataPropertiesAxiom) - Method in class owltools.graph.AxiomAnnotationTools.AxiomAnnotationsChanger
visit(OWLDisjointObjectPropertiesAxiom) - Method in class owltools.graph.AxiomAnnotationTools.AxiomAnnotationsChanger
visit(OWLObjectPropertyRangeAxiom) - Method in class owltools.graph.AxiomAnnotationTools.AxiomAnnotationsChanger
visit(OWLObjectPropertyAssertionAxiom) - Method in class owltools.graph.AxiomAnnotationTools.AxiomAnnotationsChanger
visit(OWLFunctionalObjectPropertyAxiom) - Method in class owltools.graph.AxiomAnnotationTools.AxiomAnnotationsChanger
visit(OWLSubObjectPropertyOfAxiom) - Method in class owltools.graph.AxiomAnnotationTools.AxiomAnnotationsChanger
visit(OWLDisjointUnionAxiom) - Method in class owltools.graph.AxiomAnnotationTools.AxiomAnnotationsChanger
visit(OWLDeclarationAxiom) - Method in class owltools.graph.AxiomAnnotationTools.AxiomAnnotationsChanger
visit(OWLAnnotationAssertionAxiom) - Method in class owltools.graph.AxiomAnnotationTools.AxiomAnnotationsChanger
visit(OWLSymmetricObjectPropertyAxiom) - Method in class owltools.graph.AxiomAnnotationTools.AxiomAnnotationsChanger
visit(OWLDataPropertyRangeAxiom) - Method in class owltools.graph.AxiomAnnotationTools.AxiomAnnotationsChanger
visit(OWLFunctionalDataPropertyAxiom) - Method in class owltools.graph.AxiomAnnotationTools.AxiomAnnotationsChanger
visit(OWLEquivalentDataPropertiesAxiom) - Method in class owltools.graph.AxiomAnnotationTools.AxiomAnnotationsChanger
visit(OWLClassAssertionAxiom) - Method in class owltools.graph.AxiomAnnotationTools.AxiomAnnotationsChanger
visit(OWLEquivalentClassesAxiom) - Method in class owltools.graph.AxiomAnnotationTools.AxiomAnnotationsChanger
visit(OWLDataPropertyAssertionAxiom) - Method in class owltools.graph.AxiomAnnotationTools.AxiomAnnotationsChanger
visit(OWLTransitiveObjectPropertyAxiom) - Method in class owltools.graph.AxiomAnnotationTools.AxiomAnnotationsChanger
visit(OWLIrreflexiveObjectPropertyAxiom) - Method in class owltools.graph.AxiomAnnotationTools.AxiomAnnotationsChanger
visit(OWLSubDataPropertyOfAxiom) - Method in class owltools.graph.AxiomAnnotationTools.AxiomAnnotationsChanger
visit(OWLInverseFunctionalObjectPropertyAxiom) - Method in class owltools.graph.AxiomAnnotationTools.AxiomAnnotationsChanger
visit(OWLSameIndividualAxiom) - Method in class owltools.graph.AxiomAnnotationTools.AxiomAnnotationsChanger
visit(OWLSubPropertyChainOfAxiom) - Method in class owltools.graph.AxiomAnnotationTools.AxiomAnnotationsChanger
visit(OWLInverseObjectPropertiesAxiom) - Method in class owltools.graph.AxiomAnnotationTools.AxiomAnnotationsChanger
visit(OWLHasKeyAxiom) - Method in class owltools.graph.AxiomAnnotationTools.AxiomAnnotationsChanger
visit(OWLDatatypeDefinitionAxiom) - Method in class owltools.graph.AxiomAnnotationTools.AxiomAnnotationsChanger
visit(SWRLRule) - Method in class owltools.graph.AxiomAnnotationTools.AxiomAnnotationsChanger

W

weight - Variable in class owltools.yaml.golrconfig.GOlrConfig
width - Variable in class owltools.gfx.GraphStyle
width - Variable in class owltools.gfx.ImageRender
width - Variable in class owltools.gfx.OWLGraphLayoutNode
WITH - Static variable in class owltools.gaf.parser.GAFParser
wring(OWLObject, ConfigManager) - Method in class owltools.flex.FlexCollection: Main wrapping for adding ontology documents to GOlr.
write(ClassTaxonMatrix, OWLGraphWrapper, BufferedWriter) - Static method in class owltools.gaf.inference.ClassTaxonMatrix: Write a ClassTaxonMatrix using the default delimiter.
write(ClassTaxonMatrix, OWLGraphWrapper, char, BufferedWriter) - Static method in class owltools.gaf.inference.ClassTaxonMatrix: Write a ClassTaxonMatrix using the specified delimiter.
write(GafDocument) - Method in class owltools.gaf.io.AbstractGafWriter: Write a full GAF.
write(GeneAnnotation) - Method in class owltools.gaf.io.AbstractGafWriter: Write a single GeneAnnotation.
write(GafDocument) - Method in class owltools.gaf.io.GpadWriter: Write a full GAF.
write(GeneAnnotation) - Method in class owltools.gaf.io.GpadWriter: Write a single GeneAnnotation.
write(BioentityDocument) - Method in class owltools.gaf.io.GpiWriter
write(Collection<Bioentity>) - Method in class owltools.gaf.io.GpiWriter: Write a full GAF.
write(Bioentity) - Method in class owltools.gaf.io.GpiWriter: Write a single Bioentity.
write(GafDocument, PrintStream) - Method in class owltools.gaf.io.OpenAnnotationRDFWriter: Writes associations from GAF document as RDF on out
write(GafDocument, File) - Method in class owltools.gaf.io.OpenAnnotationRDFWriter
write(GafDocument, String) - Method in class owltools.gaf.io.OpenAnnotationRDFWriter
write(OutputStream, OWLGraphWrapper, List<GafDocument>) - Method in class owltools.gaf.io.PseudoRdfXmlWriter: Write a pseudo RDF XML for the given ontology and gene annotations.
write(OutputStream, OWLGraphWrapper, List<GafDocument>) - Method in class owltools.gaf.io.XgmmlWriter: Write a pseudo RDF XML for the given ontology and gene annotations.
writeConfig(File, OortConfiguration) - Static method in class owltools.ontologyrelease.OortConfiguration: Write the given OortConfiguration into the file as properties.
writeGaf(Opts) - Method in class owltools.cli.GafCommandRunner
writeGpad(Opts) - Method in class owltools.cli.GafCommandRunner
writeGpi(Opts) - Method in class owltools.cli.GafCommandRunner
writeHeader(GafDocument) - Method in class owltools.gaf.io.AbstractGafWriter: Write a header of a GAF, use the comments from the GafDocument.
writeHeader(List<String>) - Method in class owltools.gaf.io.AbstractGafWriter: Write a header for a GAF, header comments are optional.
writeHeader(List<String>) - Method in class owltools.gaf.io.GafWriter.BufferedGafWriter
writeHeader(GafDocument) - Method in class owltools.gaf.io.GpadWriter: Write a header of a GAF, use the comments from the GafDocument.
writeHeader(List<String>) - Method in class owltools.gaf.io.GpadWriter: Write a header for a GAF, header comments are optional.
writeHeader(Collection<Bioentity>) - Method in class owltools.gaf.io.GpiWriter: Write a header of a GPI.
writeHeader(List<String>, Collection<Bioentity>) - Method in class owltools.gaf.io.GpiWriter: Write a header for a GAF, header comments are optional.
writer - Variable in class owltools.gaf.rules.AnnotationRulesReportWriter
writeTabs(PrintWriter, CharSequence...) - Method in class owltools.ontologyrelease.reports.OntologyReportGenerator.AbstractReport
writeXgmml(Opts) - Method in class owltools.cli.GafCommandRunner

X

x - Variable in class owltools.gfx.OWLGraphLayoutNode
XgmmlWriter - Class in owltools.gaf.io: Generates Xgmml for import into Cytoscape
XgmmlWriter() - Constructor for class owltools.gaf.io.XgmmlWriter

Y

y - Variable in class owltools.gfx.OWLGraphLayoutNode

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