All Classes
ABoxUtils
AbstractAnnotationPredictor
AbstractAnnotationRule
AbstractCheck
AbstractClosureReader
AbstractClosureRenderer
AbstractGafWriter
AbstractMappingParser
AbstractOBOSimPreProcessor
AbstractOwlSim
AbstractRenderer
AbstractRenderer
AbstractRetrieveGolr
AbstractSimPreProcessor
AbstractSolrLoader
AbstractTarjan
AbstractXmlWriter
Adjacency
AltIdInSignature
Annotation
AnnotationDocumentMetadata
AnnotationExtensionFolder
AnnotationExtensionUnfolder
AnnotationLD
AnnotationPredictor
AnnotationRegularExpressionFromXMLRule
AnnotationRule
AnnotationRulesEngine
AnnotationRulesEngine.AnnotationRuleCheckException
AnnotationRulesEngine.AnnotationRulesEngineResult
AnnotationRulesFactory
AnnotationRulesFactoryImpl
AnnotationRulesReportWriter
AnnotationRuleViolation
AnnotationRuleViolation.ViolationType
AnnotationSource
AnnotationTaxonRule
AssertInferenceTool
AssertInferredClassExpressions
AssertInferredClassExpressions.OWLClassFilter
AsymmetricJaccardSimilarity
Attribute
AttributePairScores
AutomaticSimPreProcessor
AvgInformationContentBestMatchesSimilarity
AvgInformationContentLCSSimilarity
AxiomAnnotationTools
AxiomAnnotationTools.AxiomAnnotationsChanger
Base
BaseLD
BasicABox
BasicAnnotationPropagator
BasicChecksRule
BasicStatistics
BioChebiGenerator
Bioentity
BioentityDocument
BloomFilter
BridgeExtractor
BruteForceSimPreProcessor
BuilderTools
BuildVersionId
CardinalityContraintsTools
CardinalityContraintsTools.CardinalityReporter
CatalogXmlIRIMapper
CellularLocationTools
ChadoGraphClosureRenderer
CheckWarning
ClassDifferentiaLearner
ClassExpression
ClassExpressionGraphClosureRenderer
ClassExpressionLD
ClassExpressionPair
ClassFrame
ClassFrameLD
ClassStub
ClassStubLD
ClassTaxonMatrix
CLIMethod
CombinedJaccardConjunctiveSetSimilarity
CombinedSimilarity
CombinedSimilarity2
CommandLineInterface
CommandRunner
CommentListener
CompactGraphClosureReader
CompactGraphClosureRenderer
ComplexAnnotationSolrDocumentLoader
CompositionalClassPredictor
ConfigManager
ConjunctiveSetInformationContentRatioSimilarity
ConjunctiveSetSimilarity
CutoffException
CycleCheck
DanglingReferenceCheck
DatabaseDumper
DefaultAspectProvider
DelimitedLineRenderer
DescriptionTreeSimilarity
DisjunctiveSetSimilarity
DLQueryTool
Dumper
EcoMapper
EcoMapperFactory
EcoMapperFactory.OntologyMapperPair
EcoMapperImpl
EcoTools
EdgeTableRenderer
ElementPairScores
EnrichmentConfig
EnrichmentEngine
EnrichmentResult
EquivalenceSetMergeUtil
ErrorReportFileHandler
ExplicitReportFileHandler
Expression
ExpressionLD
ExpressionSimPreProcessor
ExtensionExpression
External2GoReports
External2GoReports.External2GoKegg
External2GoReports.External2GoMetaCyc
External2GoReports.External2GoReactome
External2GoReports.External2GoResid
External2GoReports.External2GoRhea
External2GoReports.External2GoUmBbdEnzymeId
External2GoReports.External2GoUmBbdPathwayId
External2GoReports.External2GoUmBbdReactionId
External2GoReports.External2GoWikipedia
FastOwlSim
FastOwlSimFactory
FlexCollection
FlexDocument
FlexLine
FlexSolrDocumentLoader
FoldBasedPredictor
FormattedRenderer
Frame
FrameLD
FrameMaker
FrameMakerLD
GafCommandRunner
GafDocument
GafObjectsBuilder
GAFOWLBridge
GAFOWLBridge.BioentityMapping
GAFOWLBridge.Vocab
GAFParser
GafSolrDocumentLoader
GafWriter
GafWriter.BufferedGafWriter
GeneAnnotation
GeneOntologyReports
GenePheno
GenePhenoTsvParser
GeneralObjectDeserializer
GenericReasonerValidationCheck
GetOntologyId
GMTParser
GoAnnotationExperimentalPredictionRule
GoAnnotationPredictionRule
GoAnnotationRulesFactoryImpl
GoAnnotationTaxonRule
GoBindingCheckWithFieldRule
GoClassReferenceAnnotationRule
GoICAnnotationRule
GoIDAAnnotationRule
GoIEPRestrictionsRule
GoIPIAnnotationRule
GoIPICatalyticActivityRestrictionsRule
GOlrConfig
GOlrDynamicField
GOlrField
GOlrFixedField
GoMultipleTaxonRule
GoMySQLDatabaseDumper
GoMySQLDatabaseDumper.GOMySQLTable
GoNDAnnotationRule
GoNoHighLevelTermAnnotationRule
GoNoISSProteinBindingRule
GOReciprocalAnnotationRule
GOSimPreProcessor
GpadGpiObjectsBuilder
GpadGpiObjectsBuilder.AspectProvider
GpadParser
GpadWriter
GpiParser
GpiWriter
GraphClosureRenderer
GraphicsConfig
GraphReader
GraphReasoner
GraphReasonerFactory
GraphRenderer
GraphStyle
GuiLogHandler
HierarchyImage
ICDistribution
ICDistributionValue
IDMapHandler
IDMapPairWriter
IdMapping
IDMappingPIRParser
IDMappingPIRParser.Types
IdTools
ImageRender
ImportChainDotWriter
ImportChainDotWriter.UnExpectedStructureException
ImportChainExtractor
ImportClosureSlurper
Individual
IndividualPair
InferenceBuilder
InferenceBuilder.ConsistencyReport
InferenceBuilder.OWLClassFilter
InferenceBuilder.PotentialRedundant
InferredParentRenderer
IntersectionOf
IntersectionOfLD
IssueListener
IssueListener.DefaultIssueListener
JaccardBloomSimilarity
JaccardSimilarity
JsCommandRunner
JSONRenderer
JustifyAssertionsTool
JustifyAssertionsTool.JustifyResult
LazyExpressionMaterializingReasoner
LazyExpressionMaterializingReasonerFactory
LCSEnabledSimPreProcessor
LegoDotWriter
LegoGraph
LegoLink
LegoMetadata
LegoNode
LegoRenderer
LegoShuntGraphTool
LegoTools
LegoTools.UnExpectedStructureException
LegoUnit
LegoUnitTools
LineFilter
LinkMaker
LinkMaker.LinkPattern
LocalMirrorIRIMapper
Log4jHandler
LogHandler
Main
MappingTarjan
MarkdownRenderer
MaximumInformationContentSimilarity
Mooncat
MultiSimilarity
NameRedundancyCheck
NaryBooleanClassExpression
NaryBooleanClassExpressionLD
NCBI2OWL
NCBIConverter
NCBIOWL
NoElementAttributeMapException
NullSimPreProcessor
Obo2Obo
OboBasicDagCheck
OBONamespaces
OboOntologyReleaseRunner
OboOntologyReleaseRunnerCheckException
OboOntologyReleaseRunnerGui
OboProperty
OBOTermsAltIdsReport
OBOTermsIdsObsoleteReport
OBOTermsIdsReport
OBOUpperVocabulary
ObsoleteClassInSignature
ObsoletesAllReport
ObsoletesExactReport
ObsoletesInExactReport
OldSimpleOwlSim
OldSimpleOwlSim.EnrichmentConfig
OldSimpleOwlSim.Stage
OntologyAnnotation
OntologyCheck
OntologyCheckHandler
OntologyCheckHandler.CheckSummary
OntologyCheckRunner
OntologyCheckRunner.TimePoint
OntologyFrame
OntologyFrameLD
OntologyGeneralSolrDocumentLoader
OntologyMetadata
OntologyMetadata
OntologyMetadata.MetadataField
OntologyMetadata.MetadataQualifier
OntologyMetadataMarkdownWriter
OntologyReportGenerator
OntologyReportGenerator.AbstractReport
OntologyReportGenerator.OntologyReport
OntologySetMetadata
OntologySolrLoader
OntologyVersionTools
OortConfiguration
OortConfiguration.MacroStrategy
OortGuiAdvancedPanel
OortGuiConfiguration
OortGuiMainFrame
OortGuiMainPanel
OortGuiMenuBar
OortGuiQueryOntologyPanel
OpenAnnotationRDFWriter
OptimizeSolrDocumentLoader
Opts
OverlapSimilarity
OWLClassExpressionPair
OWLConverter
OWLGraphEdge
OWLGraphEdge.OWLGraphEdgeSet
OWLGraphLayoutNode
OWLGraphLayoutRenderer
OWLGraphManipulator
OWLGraphStrokeEdge
OWLGraphStrokeEdge.SVGEdge
OWLGraphUtil
OWLGraphvizRenderer
OWLGraphWrapper
OWLGraphWrapper.ISynonym
OWLGraphWrapper.Synonym
OWLGraphWrapperBasic
OWLGraphWrapperEdges
OWLGraphWrapperEdgesAdvanced
OWLGraphWrapperEdgesExtended
OWLGraphWrapperExtended
OWLGsonParser
OWLGsonRenderer
OWLHandler
OWLHandler.Param
OWLHandler.ResultType
OWLInAboxTranslator
OWLJSONFormat
OWLObjectPair
OWLPrettyPrinter
OWLQuantifiedProperty
OWLQuantifiedProperty.Quantifier
OWLRenderer
OWLResultsManager
OWLServer
OWLShuntEdge
OWLShuntGraph
OWLShuntGraphDFIterator
OWLShuntNode
OwlSim
OwlSim.ScoreAttributeSetPair
OwlSim.Stat
OwlSim.StatsPerIndividual
OwlSimFactory
OwlSimICDistribution
OwlSimMetadata
OwlSimPValue
OWLSimReferenceBasedStatistics
OwlSimUtil
OwlSimVariance
OwlSimVarianceEntityReferenceNotFoundException
PairScores
PANTHERForest
PANTHERGeneralSolrDocumentLoader
PANTHERSolrDocumentLoader
PANTHERTree
ParserListener
ParserWrapper
ParserWrapper.OboAndOwlNameProvider
ParserWrapper.OWLGraphWrapperNameProvider
Pheno
PhenologEngine
PhenoSimHQEPreProcessor
PhenoTransitiveClosure
PlaceholderJcelFactory
PrecomputingMoreReasonerFactory
Prediction
Profiler
PropertyExtractor
PropertyStub
PropertyStubLD
PropertyView
PropertyViewOntologyBuilder
PropertyViewSimPreProcessor
ProteinTools
PseudoRdfXmlWriter
PseudoRdfXmlWriter.ProgressReporter
PValue
QuerySubsetGenerator
QuestForOrthologsSeqXMLParser
QuestForOrthologsSeqXMLParser.MoreInfoProteinListener
QuestForOrthologsSeqXMLParser.MoreInfoProteinListener.MoreInfo
QuestForOrthologsSeqXMLParser.ProteinListener
ReasonerDiff
RedundantInferences
RedundantInferences.RedundantAxiom
ReferentialIntegrityException
RelationSets
RelationType
RelationType.Polarity
ReleaseRunnerFileTools
Reporter
ResonerDiffCommandLine
Restriction
RestrictionLD
RetrieveGolrAnnotations
RetrieveGolrAnnotations.GolrAnnotationDocument
RetrieveGolrAnnotations.GolrAnnotationExtension
RetrieveGolrAnnotations.GolrAnnotationExtension.GolrAnnotationExtensionEntry
RetrieveGolrAnnotations.GolrAnnotationExtension.GolrAnnotationExtensionEntry.GolrAnnotationExtensionRelation
RetrieveGolrBioentities
RetrieveGolrBioentities.GolrBioentityDocument
ScoreMatrix
SelfReferenceInDefinition
SharedLabelException
ShuntGraphUtils
ShuntGraphUtils.ShuntGraphPair
Sim2CommandRunner
SimCommandRunner
SimEngine
Similarity
SimilarityCalculator
SimJSONEngine
SimpleABoxToGAF
SimpleEcoMapper
SimpleEcoMapperImpl
SimpleOwlSim
SimpleOwlSim.Direction
SimpleOwlSim.Metric
SimpleOwlSim.OutputFormat
SimpleOwlSim.SimConfigurationProperty
SimpleOwlSimFactory
SimPreProcessor
SimResultRenderer
SimResultRenderer.AttributesSimScores
SimResultRenderer.IndividualSimScores
SimSearch
SimStats
SolrCommandRunner
SolrSchemaXMLWriter
SomeValuesFrom
SomeValuesFromLD
SpeciesMergeUtil
SpeciesSubsetterUtil
StanzaToOWLConverter
StringTools
Stub
StubLD
SubclassRetriever
TableRenderer
TableToAxiomConverter
TabularRenderer
Tarjan
TaxonCommandRunner
TaxonConstraintsEngine
TaxonTools
TBoxUnFoldingTool
TBoxUnFoldingTool.NonDeterministicUnfoldException
TemplatedTransformer
TraceReportFileHandler
TransformationUtils
TraversingEcoMapper
TraversingEcoMapperImpl
UniProtIDMapParser
UnknownOWLClassException
VersionInfo
XgmmlWriter