Hierarchy For All Packages

Package Hierarchies:

• org.bbop.golr.java,
• org.geneontology.lego.dot,
• org.geneontology.lego.json,
• org.geneontology.lego.model,
• org.geneontology.lego.model2,
• owltools,
• owltools.cli,
• owltools.cli.tools,
• owltools.diff,
• owltools.flex,
• owltools.frame,
• owltools.frame.jsonld,
• owltools.gaf,
• owltools.gaf.bioentities,
• owltools.gaf.eco,
• owltools.gaf.godb,
• owltools.gaf.inference,
• owltools.gaf.io,
• owltools.gaf.metadata,
• owltools.gaf.owl,
• owltools.gaf.owl.mapping,
• owltools.gaf.parser,
• owltools.gaf.rules,
• owltools.gaf.rules.go,
• owltools.gfx,
• owltools.graph,
• owltools.graph.shunt,
• owltools.idmap,
• owltools.io,
• owltools.mooncat,
• owltools.mooncat.ontologymetadata,
• owltools.ncbi,
• owltools.ontologyrelease,
• owltools.ontologyrelease.gui,
• owltools.ontologyrelease.logging,
• owltools.ontologyrelease.reports,
• owltools.ontologyrelease.reports.go,
• owltools.ontologyverification,
• owltools.ontologyverification.impl,
• owltools.panther,
• owltools.phenolog,
• owltools.profile,
• owltools.reasoner,
• owltools.renderer.markdown,
• owltools.sim,
• owltools.sim2,
• owltools.sim2.io,
• owltools.sim2.kb,
• owltools.sim2.preprocessor,
• owltools.sim2.scores,
• owltools.solrj,
• owltools.tr,
• owltools.util,
• owltools.version,
• owltools.vocab,
• owltools.web,
• owltools.yaml.golrconfig

Class Hierarchy

• java.lang.Object
  • owltools.sim2.preprocessor.ABoxUtils
  • owltools.gaf.inference.AbstractAnnotationPredictor (implements owltools.gaf.inference.AnnotationPredictor)
    • owltools.gaf.inference.BasicAnnotationPropagator (implements owltools.gaf.inference.AnnotationPredictor)
    • owltools.gaf.inference.CompositionalClassPredictor (implements owltools.gaf.inference.AnnotationPredictor)
    • owltools.gaf.inference.FoldBasedPredictor (implements owltools.gaf.inference.AnnotationPredictor)
  • owltools.gaf.rules.AbstractAnnotationRule (implements owltools.gaf.rules.AnnotationRule)
    • owltools.gaf.rules.AnnotationRegularExpressionFromXMLRule
    • owltools.gaf.rules.AnnotationTaxonRule
      • owltools.gaf.rules.go.GoAnnotationTaxonRule
    • owltools.gaf.rules.go.BasicChecksRule
    • owltools.gaf.rules.GenericReasonerValidationCheck
    • owltools.gaf.rules.go.GoAnnotationExperimentalPredictionRule
    • owltools.gaf.rules.go.GoAnnotationPredictionRule
    • owltools.gaf.rules.go.GoBindingCheckWithFieldRule
    • owltools.gaf.rules.go.GoClassReferenceAnnotationRule
    • owltools.gaf.rules.go.GoICAnnotationRule
    • owltools.gaf.rules.go.GoIDAAnnotationRule
    • owltools.gaf.rules.go.GoIEPRestrictionsRule
    • owltools.gaf.rules.go.GoIPIAnnotationRule
    • owltools.gaf.rules.go.GoIPICatalyticActivityRestrictionsRule
    • owltools.gaf.rules.go.GoMultipleTaxonRule
    • owltools.gaf.rules.go.GoNDAnnotationRule
    • owltools.gaf.rules.go.GoNoHighLevelTermAnnotationRule
    • owltools.gaf.rules.go.GoNoISSProteinBindingRule
    • owltools.gaf.rules.go.GOReciprocalAnnotationRule
  • owltools.ontologyverification.impl.AbstractCheck (implements owltools.ontologyverification.OntologyCheck)
    • owltools.ontologyverification.impl.AltIdInSignature
    • owltools.ontologyverification.impl.CycleCheck
    • owltools.ontologyverification.impl.DanglingReferenceCheck
    • owltools.ontologyverification.impl.NameRedundancyCheck
    • owltools.ontologyverification.impl.ObsoleteClassInSignature
    • owltools.ontologyverification.impl.SelfReferenceInDefinition
  • owltools.io.AbstractClosureReader (implements owltools.io.GraphReader)
    • owltools.io.CompactGraphClosureReader
  • java.util.AbstractCollection<E> (implements java.util.Collection<E>)
    • java.util.AbstractSet<E> (implements java.util.Set<E>)
      • java.util.HashSet<E> (implements java.lang.Cloneable, java.io.Serializable, java.util.Set<E>)
        • owltools.graph.OWLGraphEdge.OWLGraphEdgeSet
  • owltools.gaf.io.AbstractGafWriter
    • owltools.gaf.io.GafWriter (implements java.io.Closeable)
    • owltools.gaf.io.GafWriter.BufferedGafWriter
  • org.eclipse.jetty.util.component.AbstractLifeCycle (implements org.eclipse.jetty.util.component.LifeCycle)
    • org.eclipse.jetty.util.component.AggregateLifeCycle (implements org.eclipse.jetty.util.component.Destroyable, org.eclipse.jetty.util.component.Dumpable)
      • org.eclipse.jetty.server.handler.AbstractHandler (implements org.eclipse.jetty.server.Handler)
        • owltools.web.OWLServer
  • owltools.idmap.AbstractMappingParser
    • owltools.idmap.IDMappingPIRParser
    • owltools.idmap.UniProtIDMapParser
  • owltools.sim2.AbstractOwlSim (implements owltools.sim2.OwlSim)
    • owltools.sim2.FastOwlSim (implements owltools.sim2.OwlSim)
    • owltools.sim2.SimpleOwlSim (implements owltools.sim2.OwlSim)
  • owltools.io.AbstractRenderer (implements owltools.io.GraphRenderer)
    • owltools.io.AbstractClosureRenderer (implements owltools.io.GraphRenderer)
      • owltools.io.ChadoGraphClosureRenderer (implements owltools.io.GraphRenderer)
      • owltools.io.ClassExpressionGraphClosureRenderer (implements owltools.io.GraphRenderer)
      • owltools.io.CompactGraphClosureRenderer (implements owltools.io.GraphRenderer)
      • owltools.io.GraphClosureRenderer (implements owltools.io.GraphRenderer)
    • owltools.io.EdgeTableRenderer (implements owltools.io.GraphRenderer)
    • owltools.io.InferredParentRenderer (implements owltools.io.GraphRenderer)
    • owltools.io.TableRenderer (implements owltools.io.GraphRenderer)
  • owltools.sim2.io.AbstractRenderer (implements owltools.sim2.io.SimResultRenderer)
    • owltools.sim2.io.DelimitedLineRenderer (implements owltools.sim2.io.SimResultRenderer)
    • owltools.sim2.io.FormattedRenderer (implements owltools.sim2.io.SimResultRenderer)
    • owltools.sim2.io.JSONRenderer (implements owltools.sim2.io.SimResultRenderer)
    • owltools.sim2.io.OWLRenderer (implements owltools.sim2.io.SimResultRenderer)
    • owltools.sim2.io.TabularRenderer (implements owltools.sim2.io.SimResultRenderer)
  • org.bbop.golr.java.AbstractRetrieveGolr
    • org.bbop.golr.java.RetrieveGolrAnnotations
    • org.bbop.golr.java.RetrieveGolrBioentities
  • owltools.sim2.preprocessor.AbstractSimPreProcessor (implements owltools.sim2.preprocessor.SimPreProcessor)
    • owltools.sim2.preprocessor.LCSEnabledSimPreProcessor
      • owltools.sim2.preprocessor.AbstractOBOSimPreProcessor
        • owltools.sim2.preprocessor.ExpressionSimPreProcessor
        • owltools.sim2.preprocessor.GOSimPreProcessor
        • owltools.sim2.preprocessor.PhenoSimHQEPreProcessor
        • owltools.sim2.preprocessor.PropertyViewSimPreProcessor
      • owltools.sim2.preprocessor.AutomaticSimPreProcessor
      • owltools.sim2.preprocessor.BruteForceSimPreProcessor
      • owltools.sim2.preprocessor.NullSimPreProcessor
  • owltools.solrj.AbstractSolrLoader
    • owltools.solrj.ComplexAnnotationSolrDocumentLoader
    • owltools.solrj.FlexSolrDocumentLoader
    • owltools.solrj.GafSolrDocumentLoader
    • owltools.solrj.OntologyGeneralSolrDocumentLoader
    • owltools.solrj.OntologySolrLoader
    • owltools.solrj.OptimizeSolrDocumentLoader
    • owltools.solrj.PANTHERGeneralSolrDocumentLoader
    • owltools.solrj.PANTHERSolrDocumentLoader
  • owltools.util.AbstractTarjan<NODE> (implements owltools.util.Tarjan<NODE>)
    • owltools.util.MappingTarjan<T>
  • owltools.gaf.io.AbstractXmlWriter
    • owltools.gaf.io.PseudoRdfXmlWriter
    • owltools.yaml.golrconfig.SolrSchemaXMLWriter
    • owltools.gaf.io.XgmmlWriter
  • owltools.gaf.metadata.AnnotationDocumentMetadata
  • owltools.gaf.rules.AnnotationRulesEngine
  • owltools.gaf.rules.AnnotationRulesEngine.AnnotationRulesEngineResult
  • owltools.gaf.rules.AnnotationRulesFactoryImpl (implements owltools.gaf.rules.AnnotationRulesFactory)
    • owltools.gaf.rules.go.GoAnnotationRulesFactoryImpl
  • owltools.gaf.rules.AnnotationRulesReportWriter (implements java.io.Closeable)
  • owltools.gaf.rules.AnnotationRuleViolation
  • owltools.gaf.AnnotationSource
  • owltools.cli.AssertInferenceTool
  • owltools.cli.AssertInferredClassExpressions
  • owltools.phenolog.Attribute
  • owltools.sim2.scores.AttributePairScores (implements owltools.sim2.scores.PairScores<T>)
  • owltools.graph.AxiomAnnotationTools
  • owltools.graph.AxiomAnnotationTools.AxiomAnnotationsChanger (implements org.semanticweb.owlapi.model.OWLAxiomVisitorEx<O>)
  • owltools.frame.jsonld.BaseLD (implements owltools.frame.Base)
    • owltools.frame.jsonld.AnnotationLD (implements owltools.frame.Annotation)
    • owltools.frame.jsonld.ExpressionLD (implements owltools.frame.Expression)
      • owltools.frame.jsonld.ClassExpressionLD (implements owltools.frame.ClassExpression)
        • owltools.frame.jsonld.NaryBooleanClassExpressionLD (implements owltools.frame.NaryBooleanClassExpression)
          • owltools.frame.jsonld.IntersectionOfLD (implements owltools.frame.IntersectionOf)
      • owltools.frame.jsonld.RestrictionLD (implements owltools.frame.Restriction)
        • owltools.frame.jsonld.SomeValuesFromLD (implements owltools.frame.SomeValuesFrom)
      • owltools.frame.jsonld.StubLD (implements owltools.frame.Stub)
        • owltools.frame.jsonld.ClassStubLD (implements owltools.frame.ClassStub)
        • owltools.frame.jsonld.FrameLD (implements owltools.frame.Frame)
          • owltools.frame.jsonld.ClassFrameLD (implements owltools.frame.ClassFrame)
          • owltools.frame.jsonld.OntologyFrameLD (implements owltools.frame.OntologyFrame)
        • owltools.frame.jsonld.PropertyStubLD (implements owltools.frame.PropertyStub)
  • owltools.sim2.kb.BasicStatistics
  • owltools.cli.BioChebiGenerator
  • owltools.gaf.Bioentity
  • owltools.gaf.BioentityDocument
  • owltools.util.BloomFilter<E> (implements java.io.Serializable)
  • owltools.mooncat.BridgeExtractor
  • owltools.mooncat.BridgeExtractor.Combo
  • owltools.gaf.parser.BuilderTools
  • owltools.graph.CardinalityContraintsTools
  • owltools.graph.CardinalityContraintsTools.CardinalityReporter
  • owltools.io.CatalogXmlIRIMapper (implements org.semanticweb.owlapi.model.OWLOntologyIRIMapper)
  • org.geneontology.lego.model.CellularLocationTools
  • owltools.ontologyverification.CheckWarning
  • owltools.sim2.ClassDifferentiaLearner
  • owltools.sim2.ClassDifferentiaLearner.InferredClassDefinition (implements java.lang.Comparable<T>)
  • owltools.util.ClassExpressionPair
  • owltools.gaf.inference.ClassTaxonMatrix
  • owltools.cli.CommandLineInterface
  • owltools.cli.CommandRunner
    • owltools.cli.GafCommandRunner
      • owltools.cli.TaxonCommandRunner
        • owltools.cli.SolrCommandRunner
          • owltools.cli.SimCommandRunner
            • owltools.cli.Sim2CommandRunner
              • owltools.cli.JsCommandRunner
  • java.awt.Component (implements java.awt.image.ImageObserver, java.awt.MenuContainer, java.io.Serializable)
    • java.awt.Container
      • javax.swing.JComponent (implements java.io.Serializable)
        • javax.swing.JMenuBar (implements javax.accessibility.Accessible, javax.swing.MenuElement)
          • owltools.ontologyrelease.gui.OortGuiMenuBar
        • javax.swing.JPanel (implements javax.accessibility.Accessible)
          • org.obolibrary.gui.GuiTools.SizedJPanel
            • owltools.ontologyrelease.gui.OortGuiAdvancedPanel
            • owltools.ontologyrelease.gui.OortGuiMainPanel
            • owltools.ontologyrelease.gui.OortGuiQueryOntologyPanel
      • java.awt.Window (implements javax.accessibility.Accessible)
        • java.awt.Frame (implements java.awt.MenuContainer)
          • javax.swing.JFrame (implements javax.accessibility.Accessible, javax.swing.RootPaneContainer, javax.swing.WindowConstants)
            • owltools.ontologyrelease.gui.OortGuiMainFrame
  • owltools.yaml.golrconfig.ConfigManager
  • owltools.gaf.parser.DefaultAspectProvider (implements owltools.gaf.parser.GpadGpiObjectsBuilder.AspectProvider)
  • owltools.mooncat.DLQueryTool
  • owltools.gaf.godb.Dumper
    • owltools.gaf.godb.DatabaseDumper
      • owltools.gaf.godb.GoMySQLDatabaseDumper
  • owltools.gaf.eco.EcoMapperFactory
  • owltools.gaf.eco.EcoMapperFactory.OntologyMapperPair<MAPPER>
  • owltools.gaf.eco.EcoMapperImpl (implements owltools.gaf.eco.EcoMapper)
    • owltools.gaf.eco.TraversingEcoMapperImpl (implements owltools.gaf.eco.TraversingEcoMapper)
  • owltools.gaf.EcoTools
  • owltools.sim2.scores.ElementPairScores (implements java.lang.Comparable<T>, owltools.sim2.scores.PairScores<T>)
  • owltools.sim2.EnrichmentConfig
  • owltools.sim.EnrichmentEngine
  • owltools.sim2.EnrichmentResult (implements java.lang.Comparable<T>)
  • owltools.mooncat.EquivalenceSetMergeUtil
  • owltools.ontologyrelease.logging.ErrorReportFileHandler (implements owltools.ontologyrelease.logging.LogHandler)
  • owltools.ontologyrelease.logging.ExplicitReportFileHandler (implements owltools.ontologyrelease.logging.LogHandler)
  • owltools.gaf.ExtensionExpression
  • owltools.ontologyrelease.reports.go.External2GoReports
  • owltools.sim2.FastOwlSim.ClassCount
  • owltools.sim2.FastOwlSimFactory (implements owltools.sim2.OwlSimFactory)
  • owltools.flex.FlexCollection (implements java.lang.Iterable<T>)
  • owltools.flex.FlexDocument (implements java.lang.Iterable<T>)
  • owltools.flex.FlexLine (implements java.lang.Iterable<T>)
  • owltools.frame.FrameMaker
    • owltools.frame.jsonld.FrameMakerLD
  • owltools.gaf.GafDocument
  • owltools.gaf.parser.GafObjectsBuilder
  • owltools.gaf.owl.GAFOWLBridge
    • owltools.gaf.owl.AnnotationExtensionFolder
    • owltools.gaf.owl.AnnotationExtensionUnfolder
    • owltools.gaf.owl.mapping.BasicABox
  • owltools.gaf.owl.GAFOWLBridge.GAFDescription
  • owltools.gaf.parser.GAFParser
  • owltools.gaf.GeneAnnotation
  • owltools.ontologyrelease.reports.go.GeneOntologyReports
  • owltools.phenolog.GenePheno (implements java.lang.Comparable<T>)
  • owltools.phenolog.GenePhenoTsvParser
  • owltools.io.GeneralObjectDeserializer (implements com.google.gson.JsonDeserializer<T>)
  • owltools.io.GMTParser
  • owltools.yaml.golrconfig.GOlrConfig
  • owltools.yaml.golrconfig.GOlrField
    • owltools.yaml.golrconfig.GOlrDynamicField
    • owltools.yaml.golrconfig.GOlrFixedField
  • owltools.gaf.parser.GpadGpiObjectsBuilder
  • owltools.gaf.parser.GpadParser
  • owltools.gaf.io.GpadWriter
  • owltools.gaf.parser.GpiParser
  • owltools.gaf.io.GpiWriter
  • owltools.gfx.GraphicsConfig
  • owltools.gfx.GraphicsConfig.RelationConfig
  • owltools.reasoner.GraphReasonerFactory (implements org.semanticweb.owlapi.reasoner.OWLReasonerFactory)
  • owltools.gfx.GraphStyle
  • owltools.ontologyrelease.logging.GuiLogHandler (implements owltools.ontologyrelease.logging.LogHandler)
  • owltools.sim2.kb.ICDistribution
  • owltools.sim2.kb.ICDistributionValue
  • owltools.idmap.IDMapHandler
    • owltools.idmap.IDMapPairWriter
  • owltools.gaf.IdMapping
  • owltools.cli.IdTools
  • owltools.gfx.ImageRender
    • owltools.gfx.HierarchyImage
  • owltools.mooncat.ontologymetadata.ImportChainDotWriter
  • owltools.mooncat.ontologymetadata.ImportChainExtractor
  • owltools.io.ImportClosureSlurper
  • owltools.phenolog.Individual (implements java.lang.Comparable<T>)
  • owltools.phenolog.IndividualPair (implements java.lang.Comparable<T>)
  • owltools.InferenceBuilder
  • owltools.InferenceBuilder.ConsistencyReport
  • owltools.InferenceBuilder.PotentialRedundant
  • owltools.gaf.parser.IssueListener.DefaultIssueListener (implements owltools.gaf.parser.IssueListener)
  • owltools.JustifyAssertionsTool
  • owltools.JustifyAssertionsTool.JustifyResult
  • owltools.reasoner.LazyExpressionMaterializingReasonerFactory (implements org.semanticweb.owlapi.reasoner.OWLReasonerFactory)
  • org.geneontology.lego.dot.LegoDotWriter (implements org.geneontology.lego.dot.LegoRenderer)
  • org.geneontology.lego.model2.LegoGraph
  • org.geneontology.lego.model.LegoMetadata
    • org.geneontology.lego.model.LegoLink
    • org.geneontology.lego.model.LegoNode
    • org.geneontology.lego.model2.LegoUnit
  • org.geneontology.lego.json.LegoShuntGraphTool
  • org.geneontology.lego.model.LegoTools
    • org.geneontology.lego.model2.LegoUnitTools
  • owltools.tr.LinkMaker
  • owltools.tr.LinkMaker.LinkMakerResult
  • owltools.tr.LinkMaker.LinkPattern
  • owltools.io.LocalMirrorIRIMapper (implements org.semanticweb.owlapi.model.OWLOntologyIRIMapper)
  • owltools.ontologyrelease.logging.Log4jHandler (implements owltools.ontologyrelease.logging.LogHandler)
  • owltools.phenolog.Main
  • owltools.renderer.markdown.MarkdownRenderer
  • owltools.mooncat.Mooncat
  • owltools.cli.Obo2Obo
  • owltools.ontologyrelease.OboBasicDagCheck
  • org.obolibrary.oboformat.writer.OBOFormatWriter.OBODocNameProvider (implements org.obolibrary.oboformat.writer.OBOFormatWriter.NameProvider)
    • owltools.io.ParserWrapper.OboAndOwlNameProvider
  • owltools.ontologyrelease.OboOntologyReleaseRunnerGui
  • owltools.sim.OldSimpleOwlSim
  • owltools.sim.OldSimpleOwlSim.EnrichmentConfig
  • owltools.sim.OldSimpleOwlSim.EnrichmentResult (implements java.lang.Comparable<T>)
  • owltools.sim.OldSimpleOwlSim.OWLClassExpressionPair
  • owltools.sim.OldSimpleOwlSim.ScoreAttributePair
  • owltools.sim.OldSimpleOwlSim.ScoreAttributesPair
  • owltools.mooncat.ontologymetadata.OntologyAnnotation
  • owltools.ontologyverification.OntologyCheckHandler
  • owltools.ontologyverification.OntologyCheckHandler.CheckSummary
  • owltools.ontologyverification.OntologyCheckRunner
  • owltools.mooncat.ontologymetadata.OntologyMetadata
  • owltools.ontologyrelease.OntologyMetadata
  • owltools.mooncat.ontologymetadata.OntologyMetadataMarkdownWriter
  • owltools.ontologyrelease.reports.OntologyReportGenerator
  • owltools.ontologyrelease.reports.OntologyReportGenerator.AbstractReport (implements owltools.ontologyrelease.reports.OntologyReportGenerator.OntologyReport)
    • owltools.ontologyrelease.reports.go.External2GoReports.External2GoKegg
    • owltools.ontologyrelease.reports.go.External2GoReports.External2GoMetaCyc
    • owltools.ontologyrelease.reports.go.External2GoReports.External2GoReactome
    • owltools.ontologyrelease.reports.go.External2GoReports.External2GoResid
    • owltools.ontologyrelease.reports.go.External2GoReports.External2GoRhea
    • owltools.ontologyrelease.reports.go.External2GoReports.External2GoUmBbdEnzymeId
    • owltools.ontologyrelease.reports.go.External2GoReports.External2GoUmBbdPathwayId
    • owltools.ontologyrelease.reports.go.External2GoReports.External2GoUmBbdReactionId
    • owltools.ontologyrelease.reports.go.External2GoReports.External2GoWikipedia
    • owltools.ontologyrelease.reports.OBOTermsAltIdsReport
    • owltools.ontologyrelease.reports.OBOTermsIdsObsoleteReport
    • owltools.ontologyrelease.reports.OBOTermsIdsReport
    • owltools.ontologyrelease.reports.ObsoletesAllReport
    • owltools.ontologyrelease.reports.ObsoletesExactReport
    • owltools.ontologyrelease.reports.ObsoletesInExactReport
  • owltools.mooncat.ontologymetadata.OntologySetMetadata
  • owltools.ontologyrelease.OntologyVersionTools
  • owltools.ontologyrelease.OortConfiguration
    • owltools.ontologyrelease.gui.OortGuiConfiguration
  • owltools.gaf.io.OpenAnnotationRDFWriter
  • owltools.cli.Opts
  • owltools.sim.OWLClassExpressionPair
  • owltools.ncbi.OWLConverter
    • owltools.ncbi.NCBIConverter
      • owltools.ncbi.NCBI2OWL
      • owltools.ncbi.NCBIOWL
  • owltools.graph.OWLGraphEdge
  • owltools.gfx.OWLGraphLayoutNode (implements uk.ac.ebi.interpro.graphdraw.LayoutNode, uk.ac.ebi.interpro.graphdraw.Node)
  • owltools.gfx.OWLGraphLayoutNode.SVGRectangle
  • owltools.gfx.OWLGraphLayoutRenderer
    • owltools.gfx.OWLGraphvizRenderer
  • owltools.graph.OWLGraphManipulator
  • owltools.gfx.OWLGraphStrokeEdge.SVGEdge
  • owltools.graph.OWLGraphUtil
  • owltools.graph.OWLGraphWrapper.Synonym (implements owltools.graph.OWLGraphWrapper.ISynonym)
  • owltools.graph.OWLGraphWrapperBasic
    • owltools.graph.OWLGraphWrapperExtended
      • owltools.graph.OWLGraphWrapperEdges
        • owltools.graph.OWLGraphWrapperEdgesExtended
          • owltools.graph.OWLGraphWrapperEdgesAdvanced (implements java.io.Closeable)
            • owltools.graph.OWLGraphWrapper
  • owltools.graph.OWLGraphWrapperEdges.Config
  • owltools.io.OWLGsonParser
  • owltools.io.OWLGsonRenderer
  • owltools.web.OWLHandler
  • owltools.web.OWLHandler.ServerMetadata
  • owltools.mooncat.OWLInAboxTranslator
  • owltools.sim.OWLObjectPair
  • org.semanticweb.owlapi.model.OWLOntologyFormat (implements java.io.Serializable)
    • owltools.io.OWLJSONFormat
  • owltools.io.OWLPrettyPrinter
  • owltools.io.OWLPrettyPrinter.LabelProvider (implements org.semanticweb.owlapi.util.ShortFormProvider)
  • owltools.graph.OWLQuantifiedProperty
  • org.semanticweb.owlapi.reasoner.impl.OWLReasonerBase (implements org.semanticweb.owlapi.reasoner.OWLReasoner)
    • owltools.reasoner.GraphReasoner (implements org.geneontology.reasoner.OWLExtendedReasoner)
    • owltools.reasoner.LazyExpressionMaterializingReasoner (implements org.semanticweb.owlapi.reasoner.OWLReasoner)
  • owltools.sim.OWLResultsManager
  • owltools.graph.shunt.OWLShuntEdge
  • owltools.graph.shunt.OWLShuntGraph
  • owltools.graph.shunt.OWLShuntGraphDFIterator (implements java.util.Iterator<E>)
  • owltools.graph.shunt.OWLShuntNode
  • owltools.sim2.OwlSim.ScoreAttributeSetPair (implements java.lang.Comparable<T>)
  • owltools.sim2.OwlSim.StatsPerIndividual
  • owltools.sim2.kb.OwlSimICDistribution
  • owltools.sim2.OwlSimMetadata
  • owltools.sim2.kb.OwlSimPValue
  • owltools.sim2.kb.OWLSimReferenceBasedStatistics
  • owltools.sim2.OwlSimUtil
  • owltools.sim2.kb.OwlSimVariance
  • owltools.panther.PANTHERForest
  • owltools.panther.PANTHERTree
  • owltools.io.ParserWrapper
  • owltools.io.ParserWrapper.OWLGraphWrapperNameProvider (implements org.obolibrary.oboformat.writer.OBOFormatWriter.NameProvider)
  • owltools.phenolog.Pheno (implements java.lang.Comparable<T>)
  • owltools.phenolog.PhenologEngine
  • owltools.phenolog.PhenoTransitiveClosure
  • owltools.reasoner.PlaceholderJcelFactory (implements org.semanticweb.owlapi.reasoner.OWLReasonerFactory)
  • owltools.reasoner.PrecomputingMoreReasonerFactory (implements org.semanticweb.owlapi.reasoner.OWLReasonerFactory)
  • owltools.gaf.inference.Prediction
  • owltools.profile.Profiler
  • org.apache.tools.ant.ProjectComponent (implements java.lang.Cloneable)
    • org.apache.tools.ant.Task
      • owltools.ontologyrelease.BuildVersionId
      • owltools.ontologyrelease.GetOntologyId
      • org.apache.tools.ant.taskdefs.Property
        • owltools.ontologyrelease.OboProperty
  • owltools.mooncat.PropertyExtractor
  • owltools.ontologyrelease.PropertyView
  • owltools.mooncat.PropertyViewOntologyBuilder
  • owltools.gaf.bioentities.ProteinTools
  • owltools.sim2.kb.PValue
  • owltools.mooncat.QuerySubsetGenerator
  • owltools.gaf.bioentities.QuestForOrthologsSeqXMLParser
  • owltools.diff.ReasonerDiff
  • owltools.RedundantInferences
  • owltools.RedundantInferences.RedundantAxiom
  • owltools.graph.RelationSets
  • owltools.ontologyrelease.ReleaseRunnerFileTools
    • owltools.ontologyrelease.OboOntologyReleaseRunner
  • owltools.sim.Reporter
  • owltools.diff.ResonerDiffCommandLine
  • org.bbop.golr.java.RetrieveGolrAnnotations.GolrAnnotationDocument
  • org.bbop.golr.java.RetrieveGolrAnnotations.GolrAnnotationExtension
  • org.bbop.golr.java.RetrieveGolrAnnotations.GolrAnnotationExtension.GolrAnnotationExtensionEntry
  • org.bbop.golr.java.RetrieveGolrAnnotations.GolrAnnotationExtension.GolrAnnotationExtensionEntry.GolrAnnotationExtensionRelation
  • org.bbop.golr.java.RetrieveGolrBioentities.GolrBioentityDocument
  • owltools.sim2.scores.ScoreMatrix<T>
  • owltools.util.ShuntGraphUtils
  • owltools.util.ShuntGraphUtils.ShuntGraphPair
  • owltools.sim.SimEngine
  • owltools.sim.Similarity
    • owltools.sim.AsymmetricJaccardSimilarity
    • owltools.sim.AvgInformationContentBestMatchesSimilarity
    • owltools.sim.AvgInformationContentLCSSimilarity
    • owltools.sim.CombinedJaccardConjunctiveSetSimilarity
    • owltools.sim.CombinedSimilarity
    • owltools.sim.CombinedSimilarity2
    • owltools.sim.ConjunctiveSetInformationContentRatioSimilarity
    • owltools.sim.ConjunctiveSetSimilarity
    • owltools.sim.DescriptionTreeSimilarity
    • owltools.sim.DisjunctiveSetSimilarity
    • owltools.sim.JaccardBloomSimilarity
    • owltools.sim.JaccardSimilarity
    • owltools.sim.MaximumInformationContentSimilarity
    • owltools.sim.MultiSimilarity
    • owltools.sim.OverlapSimilarity
  • owltools.sim2.SimJSONEngine
  • owltools.gaf.owl.SimpleABoxToGAF
  • owltools.gaf.eco.SimpleEcoMapperImpl (implements owltools.gaf.eco.SimpleEcoMapper)
  • owltools.sim2.SimpleOwlSim.ScoreAttributePair (implements java.lang.Comparable<T>)
  • owltools.sim2.SimpleOwlSimFactory (implements owltools.sim2.OwlSimFactory)
  • owltools.sim2.io.SimResultRenderer.AttributesSimScores
  • owltools.sim2.io.SimResultRenderer.IndividualSimScores
  • owltools.sim.SimSearch
  • owltools.sim2.SimStats
  • owltools.mooncat.SpeciesMergeUtil
  • owltools.mooncat.SpeciesSubsetterUtil
  • owltools.io.StanzaToOWLConverter
  • owltools.io.StanzaToOWLConverter.Config
  • owltools.io.StanzaToOWLConverter.Mapping
  • owltools.io.StanzaToOWLConverter.Stanza
  • org.geneontology.lego.dot.StringTools
  • uk.ac.ebi.interpro.graphdraw.StrokeEdge<N> (implements uk.ac.ebi.interpro.graphdraw.LayoutEdge<N>)
    • owltools.gfx.OWLGraphStrokeEdge
  • owltools.sim2.kb.SubclassRetriever
  • owltools.io.TableToAxiomConverter
  • owltools.io.TableToAxiomConverter.Config
  • owltools.gaf.inference.TaxonConstraintsEngine
  • owltools.gaf.TaxonTools
  • owltools.TBoxUnFoldingTool
  • owltools.tr.TemplatedTransformer
  • owltools.tr.TemplatedTransformer.Mapping
  • java.lang.Throwable (implements java.io.Serializable)
    • java.lang.Exception
      • owltools.gaf.rules.AnnotationRulesEngine.AnnotationRuleCheckException
      • owltools.cli.CommandRunner.OptionException
      • owltools.sim2.CutoffException
      • owltools.mooncat.ontologymetadata.ImportChainDotWriter.UnExpectedStructureException
      • org.geneontology.lego.model.LegoTools.UnExpectedStructureException
      • owltools.sim2.NoElementAttributeMapException
      • owltools.ontologyrelease.OboOntologyReleaseRunnerCheckException
      • owltools.sim2.kb.OwlSimVarianceEntityReferenceNotFoundException
      • owltools.gaf.godb.ReferentialIntegrityException
      • owltools.graph.SharedLabelException
      • owltools.sim.SimEngine.SimilarityAlgorithmException
      • owltools.mooncat.SpeciesMergeUtil.UnmergeableOntologyException
      • owltools.TBoxUnFoldingTool.NonDeterministicUnfoldException
      • owltools.sim2.UnknownOWLClassException
  • owltools.ontologyrelease.logging.TraceReportFileHandler (implements owltools.ontologyrelease.logging.LogHandler)
  • owltools.mooncat.TransformationUtils
  • owltools.version.VersionInfo

Interface Hierarchy

• owltools.util.Adjacency<T>
• owltools.gaf.inference.AnnotationPredictor
• owltools.gaf.rules.AnnotationRule
• owltools.gaf.rules.AnnotationRulesFactory
• owltools.cli.AssertInferredClassExpressions.OWLClassFilter
• owltools.frame.Base
  • owltools.frame.Annotation
  • owltools.frame.ClassExpression
    • owltools.frame.IntersectionOf
    • owltools.frame.NaryBooleanClassExpression
      • owltools.frame.IntersectionOf
  • owltools.frame.ClassFrame
  • owltools.frame.ClassStub
  • owltools.frame.Expression
    • owltools.frame.ClassExpression
      • owltools.frame.IntersectionOf
      • owltools.frame.NaryBooleanClassExpression
        • owltools.frame.IntersectionOf
    • owltools.frame.ClassFrame
    • owltools.frame.ClassStub
    • owltools.frame.Frame
      • owltools.frame.ClassFrame
      • owltools.frame.OntologyFrame
    • owltools.frame.IntersectionOf
    • owltools.frame.NaryBooleanClassExpression
      • owltools.frame.IntersectionOf
    • owltools.frame.OntologyFrame
    • owltools.frame.PropertyStub
    • owltools.frame.Restriction
      • owltools.frame.SomeValuesFrom
    • owltools.frame.SomeValuesFrom
    • owltools.frame.Stub
      • owltools.frame.ClassFrame
      • owltools.frame.ClassStub
      • owltools.frame.Frame
        • owltools.frame.ClassFrame
        • owltools.frame.OntologyFrame
      • owltools.frame.OntologyFrame
      • owltools.frame.PropertyStub
  • owltools.frame.Frame
    • owltools.frame.ClassFrame
    • owltools.frame.OntologyFrame
  • owltools.frame.IntersectionOf
  • owltools.frame.NaryBooleanClassExpression
    • owltools.frame.IntersectionOf
  • owltools.frame.OntologyFrame
  • owltools.frame.PropertyStub
  • owltools.frame.Restriction
    • owltools.frame.SomeValuesFrom
  • owltools.frame.SomeValuesFrom
  • owltools.frame.Stub
    • owltools.frame.ClassFrame
    • owltools.frame.ClassStub
    • owltools.frame.Frame
      • owltools.frame.ClassFrame
      • owltools.frame.OntologyFrame
    • owltools.frame.OntologyFrame
    • owltools.frame.PropertyStub
• owltools.gaf.parser.CommentListener
• owltools.gaf.eco.EcoMapper
  • owltools.gaf.eco.TraversingEcoMapper
• owltools.gaf.parser.GpadGpiObjectsBuilder.AspectProvider
• owltools.io.GraphReader
• owltools.io.GraphRenderer
• owltools.InferenceBuilder.OWLClassFilter
• owltools.gaf.parser.IssueListener
• org.geneontology.lego.dot.LegoRenderer
• owltools.gaf.parser.LineFilter<T>
• owltools.ontologyrelease.logging.LogHandler
• owltools.ontologyverification.OntologyCheck
• owltools.ontologyrelease.reports.OntologyReportGenerator.OntologyReport
• owltools.graph.OWLGraphWrapper.ISynonym
• owltools.sim2.OwlSim
• owltools.sim2.OwlSimFactory
• owltools.sim2.scores.PairScores<T>
• owltools.gaf.parser.ParserListener
• owltools.gaf.io.PseudoRdfXmlWriter.ProgressReporter
• owltools.gaf.bioentities.QuestForOrthologsSeqXMLParser.MoreInfoProteinListener
• owltools.gaf.bioentities.QuestForOrthologsSeqXMLParser.MoreInfoProteinListener.MoreInfo
• owltools.gaf.bioentities.QuestForOrthologsSeqXMLParser.ProteinListener
• owltools.sim.SimilarityCalculator
• owltools.gaf.eco.SimpleEcoMapper
• owltools.sim2.preprocessor.SimPreProcessor
• owltools.sim2.io.SimResultRenderer
• owltools.util.Tarjan<NODE>

Annotation Type Hierarchy

• owltools.cli.tools.CLIMethod (implements java.lang.annotation.Annotation)

Enum Hierarchy

• java.lang.Object
  • java.lang.Enum<E> (implements java.lang.Comparable<T>, java.io.Serializable)
    • owltools.gfx.RelationType
    • owltools.gfx.RelationType.Polarity
    • owltools.graph.OWLQuantifiedProperty.Quantifier
    • owltools.idmap.IDMappingPIRParser.Types
    • owltools.vocab.OBOUpperVocabulary
    • owltools.vocab.OBONamespaces
    • owltools.gaf.godb.GoMySQLDatabaseDumper.GOMySQLTable
    • owltools.gaf.owl.GAFOWLBridge.BioentityMapping
    • owltools.gaf.owl.GAFOWLBridge.Vocab
    • owltools.gaf.rules.AnnotationRuleViolation.ViolationType
    • owltools.ontologyrelease.OortConfiguration.MacroStrategy
    • owltools.ontologyrelease.OntologyMetadata.MetadataField
    • owltools.ontologyrelease.OntologyMetadata.MetadataQualifier
    • owltools.ontologyverification.OntologyCheckRunner.TimePoint
    • owltools.sim.OldSimpleOwlSim.Stage
    • owltools.sim2.SimpleOwlSim.Metric
    • owltools.sim2.SimpleOwlSim.Direction
    • owltools.sim2.SimpleOwlSim.OutputFormat
    • owltools.sim2.SimpleOwlSim.SimConfigurationProperty
    • owltools.sim2.OwlSim.Stat
    • owltools.web.OWLHandler.ResultType
    • owltools.web.OWLHandler.Param