AbstractAnnotationPredictor
AbstractAnnotationRule
AbstractGafWriter
AbstractXmlWriter
AnnotationDocumentMetadata
AnnotationExtensionFolder
AnnotationExtensionUnfolder
AnnotationPredictor
AnnotationRegularExpressionFromXMLRule
AnnotationRule
AnnotationRulesEngine
AnnotationRulesEngine.AnnotationRuleCheckException
AnnotationRulesEngine.AnnotationRulesEngineResult
AnnotationRulesFactory
AnnotationRulesFactoryImpl
AnnotationRulesReportWriter
AnnotationRuleViolation
AnnotationRuleViolation.ViolationType
AnnotationSource
AnnotationTaxonRule
BasicABox
BasicAnnotationPropagator
BasicChecksRule
Bioentity
BuilderTools
ClassTaxonMatrix
CommentListener
CompositionalClassPredictor
DatabaseDumper
Dumper
EcoMapper
EcoMapperFactory
EcoMapperFactory.OntologyMapperPair
EcoMapperImpl
EcoTools
ExtensionExpression
FoldBasedPredictor
GafDocument
GafObjectsBuilder
GAFOWLBridge
GAFOWLBridge.BioentityMapping
GAFOWLBridge.Vocab
GAFParser
GafToLegoTranslator
GafWriter
GafWriter.BufferedGafWriter
GeneAnnotation
GenericReasonerValidationCheck
GoAnnotationExperimentalPredictionRule
GoAnnotationPredictionRule
GoAnnotationRulesFactoryImpl
GoAnnotationTaxonRule
GoBindingCheckWithFieldRule
GoClassReferenceAnnotationRule
GoICAnnotationRule
GoIDAAnnotationRule
GoIEPRestrictionsRule
GoIPIAnnotationRule
GoIPICatalyticActivityRestrictionsRule
GoMultipleTaxonRule
GoMySQLDatabaseDumper
GoMySQLDatabaseDumper.GOMySQLTable
GoNDAnnotationRule
GoNoHighLevelTermAnnotationRule
GoNoISSProteinBindingRule
GOReciprocalAnnotationRule
GpadGpiObjectsBuilder
GpadGpiObjectsBuilder.AspectProvider
GpadParser
GpadWriter
GpiParser
GpiWriter
IdMapping
LegoModelGenerator
LineFilter
ManchesterSyntaxTool
MolecularModelJsonRenderer
MolecularModelJsonRenderer.KEY
MolecularModelJsonRenderer.VAL
MolecularModelManager
MolecularModelManager.LegoAnnotationType
MolecularModelManager.UnknownIdentifierException
NetworkInferenceEngine
ParserListener
Prediction
ProteinTools
PseudoRdfXmlWriter
PseudoRdfXmlWriter.ProgressReporter
QuestForOrthologsSeqXMLParser
QuestForOrthologsSeqXMLParser.MoreInfoProteinListener
QuestForOrthologsSeqXMLParser.MoreInfoProteinListener.MoreInfo
QuestForOrthologsSeqXMLParser.ProteinListener
ReferentialIntegrityException
SimpleABoxToGAF
SimpleEcoMapper
SimpleEcoMapperImpl
TaxonConstraintsEngine
TaxonTools
TraversingEcoMapper
TraversingEcoMapperImpl
XgmmlWriter
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