All Classes

ABIFChromatogram ABIFParser ABIFParser.DataAccess ABIFParser.TaggedDataRecord ABITools ABITrace AGAVEAltIdsPropHandler AGAVEAnnotFilter AGAVEAnnotFilterFactory AGAVEAnnotationsHandler AGAVEAssemblyHandler AGAVEBioSeqCallbackItf AGAVEBioSeqHandler AGAVEBioSequenceHandler AGAVECallbackItf AGAVECdsHandler AGAVEChromosomeCallbackItf AGAVEChromosomeHandler AGAVEClassificationHandler AGAVECompResultHandler AGAVEComputationHandler AGAVEContigCallbackItf AGAVEContigHandler AGAVEDbId AGAVEDbIdCallbackItf AGAVEDbIdPropCallbackItf AGAVEDbIdPropHandler AGAVEDescPropHandler AGAVEElementIdPropHandler AGAVEEvidenceCallbackItf AGAVEEvidenceHandler AGAVEExonsPropHandler AGAVEFeatureCallbackItf AGAVEFragmentOrderHandler AGAVEFragmentOrientationHandler AGAVEGeneHandler AGAVEHandler AGAVEIdAlias AGAVEIdAliasCallbackItf AGAVEIdAliasPropHandler AGAVEKeywordPropHandler AGAVEMapLocation AGAVEMapLocationPropHandler AGAVEMapPosition AGAVEMapPositionPropHandler AGAVEMatchAlignPropHandler AGAVEMatchDescPropHandler AGAVEMatchRegion AGAVEMatchRegionPropHandler AGAVEMrnaHandler AGAVENotePropHandler AGAVEPredictedProteinHandler AGAVEProperty AGAVEQualifierPropHandler AGAVEQueryRegion AGAVEQueryRegionPropHandler AGAVERelatedAnnot AGAVERelatedAnnotPropHandler AGAVEResultGroupHandler AGAVEResultPropertyPropHandler AGAVESciPropertyPropHandler AGAVESeqFeatureHandler AGAVESeqLocationPropHandler AGAVESeqMapHandler AGAVESeqPropHandler AGAVETranscriptHandler AGAVEUnorderedFragmentsHandler AGAVEViewPropHandler AGAVEXref AGAVEXrefCallbackItf AGAVEXrefPropHandler AGAVEXrefPropPropHandler AGAVEXrefs AGAVEXrefsPropHandler ARAlignment AbiTraceRenderer AbstractAlignmentStyler AbstractAlphabet AbstractAnnotation AbstractBeadRenderer AbstractChangeable AbstractChromatogram AbstractDistribution AbstractFeatureHolder AbstractLocation AbstractLocationDecorator AbstractManyToOneTranslationTable AbstractMatrixPairDPCursor AbstractOrderNDistribution AbstractOrthoPairCollection AbstractOrthoPairSet AbstractOrthologueSet AbstractRangeLocation AbstractReversibleTranslationTable AbstractSVMClassifierModel AbstractSVMTarget AbstractSequenceDB AbstractSymbol AbstractSymbolList AbstractTaxon AbstractTerm AbstractTrainer AbstractULAlignment AbstractWrapper AcnumHitReader AcnumTrgReader ActivityListener Agave2AgaveAnnotFilter AgaveWriter Aggregator AlignIOConstants Alignment Alignment Alignment.SymbolListIterator AlignmentElement AlignmentFormat AlignmentMarker AlignmentRenderer AlignmentStAXHandler AlphaCTools Alphabet AlphabetIndex AlphabetManager AlphabetResolver AlreadyExistsException AminoAcid Annotatable Annotatable.AnnotationForwarder AnnotatedSequenceDB Annotation AnnotationBuilder AnnotationChanger AnnotationDB AnnotationFactory AnnotationRenamer AnnotationTools AnnotationType AnnotationType.Abstract AnnotationType.Impl AppBeanRunner AppEntry AppException ArrayStateMachineToolkit AssembledSymbolList AssertionFailure Atom AtomImpl AtomIterator AtomicSymbol AutomatonException BackMatrixPairDPCursor BackPointer BarLogoPainter BaseXMLWriter BasicFeatureRenderer BasicImapRenderer BasicXFFHelper BasisSymbol BaumWelchSampler BaumWelchTrainer BeadFeatureRenderer BeanAsAnnotation BeanAsMap BetweenLocation BibRef BibRefException BibRefQuery BibRefSupport BiblioArticle BiblioBook BiblioBookArticle BiblioCriterion BiblioDescription BiblioEntryStatus BiblioJournal BiblioJournalArticle BiblioOrganisation BiblioPatent BiblioPerson BiblioProceeding BiblioProvider BiblioScope BiblioService BiblioSubject BiblioTechReport BiblioThesis BiblioWebResource BinarySearch BioError BioException BioFetchSequenceDB BioFetchSequenceDBProvider BioIndex BioMatcher BioPattern BioRuntimeException BioSQLSequenceDB BioSQLSequenceDBProvider BioStore BioStoreFactory Blast2HTMLHandler BlastLikeHomologyBuilder BlastLikeSAXParser BlastLikeSearchBuilder BlastLikeToXMLConverter BlastXMLParser BlastXMLParserFacade BlockPainter BooleanElementHandlerBase BoundaryFinder BumpedRenderer ByteElementHandlerBase Cache CacheMap CacheReference CachingInputStream CachingKernel CachingSequenceDB Calc CandyEntry CandyException CandyFinder CandyVocabulary CardinalityConstraint Cell CellCalculator CellCalculatorFactory CellCalculatorFactoryMaker Chain ChainImpl ChangeAdapter ChangeEvent ChangeForwarder ChangeForwarder.Retyper ChangeHub ChangeListener ChangeListener.AlwaysVetoListener ChangeListener.LoggingListener ChangeSupport ChangeTable ChangeTable.ChainedChanger ChangeTable.Changer ChangeTable.Splitter ChangeType ChangeVetoException Changeable ChangeableCache CharElementHandlerBase CharacterTokenization Chromatogram ChromatogramFactory ChromatogramGraphic ChromatogramGraphic.Option ChromatogramNonlinearScaler ChromatogramNonlinearScaler.Identity ChromatogramTools ChunkedSymbolList ChunkedSymbolListFactory CircularFeatureFilteringRenderer CircularFeatureRenderer CircularFeaturesRenderer CircularLocation CircularMLR CircularPaddedRenderer CircularReferenceException CircularRenderer CircularRendererContext CircularRendererPanel CircularView ClassTools ClassifierExample ClassifierExample.PointClassifier Classify ClustalWAlignmentSAXParser CodonPref CodonPrefFilter CodonPrefFilter.AcceptAll CodonPrefFilter.ByName CodonPrefFilter.EverythingToXML CodonPrefTools CollectionConstraint CollectionConstraint.AllValuesIn CollectionConstraint.And CollectionConstraint.Contains CollectionConstraint.Or ColourCommand CommitFailure Commitable CompactedDataStore CompactedDataStoreFactory ComponentFeature ComponentFeature.Template ComputeObject Constants Count CountedBufferedReader CrossProductTokenization CrosshairRenderer DAS DASAlignmentCall DASAlignmentClient DASAlignmentXMLResponseParser DASException DASLink DASSequence DASSequenceDB DASSequenceDBProvider DASStructureCall DASStructureClient DASStructureXMLResponseParser DBHelper DBHelper.DeleteStyle DBHelper.JoinStyle DNAAmbPack DNANoAmbPack DNAStyle DNATools DP DP.ReverseIterator DPCompiler DPFactory DPFactory.DefaultFactory DPInterpreter DPInterpreter.Maker DPMatrix DataSource DataStore DataStoreFactory DatabaseURLGenerator DefaultOps DefaultURLGeneratorFactory DelegationManager DelegationManager DfaBuilder DiagonalAddKernel DiagonalCachingKernel Digest DistDataSource DistributedSequenceDB Distribution Distribution.NullModelForwarder DistributionFactory DistributionFactory.DefaultDistributionFactory DistributionLogo DistributionTools DistributionTrainer DistributionTrainerContext DivisionLkpReader DotState DoubleAlphabet DoubleAlphabet.DoubleRange DoubleAlphabet.DoubleSymbol DoubleAlphabet.SubDoubleAlphabet DoubleElementHandlerBase DoubleTokenization DummySequence DummySequenceDB DummySequenceDBInstallation DummySymbolList DuplicateTaxonException EbiDatabaseURLGenerator EbiFormat EcNumber EcNumber.Impl Echo Edit EditableAlignment ElementRecognizer ElementRecognizer ElementRecognizer ElementRecognizer.AllElementRecognizer ElementRecognizer.AllElementRecognizer ElementRecognizer.AllElementRecognizer ElementRecognizer.ByLocalName ElementRecognizer.ByLocalName ElementRecognizer.ByLocalName ElementRecognizer.ByNSName ElementRecognizer.ByNSName ElementRecognizer.ByNSName ElementRecognizer.HasAttribute ElementRecognizer.HasAttribute ElementRecognizer.HasAttribute EllipticalBeadRenderer Embl Embl2AgaveAnnotFilter EmblCDROMIndexReader EmblCDROMIndexStore EmblCDROMRandomAccess EmblFileFormer EmblLikeFormat EmblLikeLocationParser EmblProcessor EmblProcessor.Factory EmblReferenceComparator EmissionCache EmissionState EntryNamIdxReader EntryNamRandomAccess Enzyme ExecRunner FastXMLWriter FastaAlignmentFormat FastaDescriptionLineParser FastaDescriptionLineParser.Factory FastaFormat FastaSearchSAXParser FastaSequenceSAXParser Feature Feature.ByLocationComparator Feature.Template FeatureBlockSequenceRenderer FeatureFilter FeatureFilter.And FeatureFilter.AnnotationContains FeatureFilter.ByAncestor FeatureFilter.ByAnnotation FeatureFilter.ByAnnotationType FeatureFilter.ByChild FeatureFilter.ByClass FeatureFilter.ByComponentName FeatureFilter.ByDescendant FeatureFilter.ByFeature FeatureFilter.ByPairwiseScore FeatureFilter.ByParent FeatureFilter.BySequenceName FeatureFilter.BySource FeatureFilter.ByType FeatureFilter.ContainedByLocation FeatureFilter.FrameFilter FeatureFilter.HasAnnotation FeatureFilter.Not FeatureFilter.OnlyChildren FeatureFilter.OnlyDescendants FeatureFilter.Or FeatureFilter.OverlapsLocation FeatureFilter.ShadowContainedByLocation FeatureFilter.ShadowOverlapsLocation FeatureFilter.StrandFilter FeatureHandler FeatureHolder FeatureHolder.EmptyFeatureHolder FeatureImpl FeatureLabelRenderer FeatureLabelRenderer.AnnotationLabelMaker FeatureLabelRenderer.LabelMaker FeatureLabelRenderer.SourceLabelMaker FeatureLabelRenderer.TypeLabelMaker FeatureRealizer FeatureRenderer FeatureTableParser FeatureTree FeatureTypes FeatureTypes.Repository FeatureTypes.RepositoryImpl FeatureTypes.Type FetchURL FileAsList FilterTransformer FilterUtils FilterUtils.FilterTransformer FilteringRenderer FiniteAlphabet FiniteAutomaton FixedBaseWidthScaler FixedSizeCache FixedSizeMap FlatFileUnigeneFactory FlatSequenceDB FlatSequenceDBProvider FlexibleAlignment FloatElementHandlerBase Format FormatTools Formats Frame FramedFeature FramedFeature.ReadingFrame FramedFeature.Template FullHmmerProfileHMM FundamentalAtomicSymbol FuzzyLocation FuzzyLocation.RangeResolver FuzzyPointLocation FuzzyPointLocation.PointResolver GAMEAnnotationHandler GAMEAnnotationHandler GAMEAspectHandler GAMEAspectPropHandler GAMEDbxrefHandler GAMEDbxrefPropHandler GAMEDescriptionPropHandler GAMEFeatureCallbackItf GAMEFeatureSetHandler GAMEFeatureSetHandler GAMEFeatureSetPropHandler GAMEFeatureSpanHandler GAMEFeatureSpanHandler GAMEFormat GAMEGeneHandler GAMEGenePropHandler GAMEHandler GAMEHandler GAMEMapPosPropHandler GAMENameCallbackItf GAMENamePropHandler GAMEPropertyHandler GAMEResiduesPropHandler GAMESeqHandler GAMESeqPropHandler GAMESeqRelHandler GAMESeqRelPropHandler GAMESpanHandler GAMESpanPropHandler GAMETranscriptCallbackItf GAMETypePropHandler GFF3DocumentHandler GFF3Parser GFF3Record GFF3Record.Impl GFFDataSource GFFDocumentHandler GFFEntrySet GFFErrorHandler GFFErrorHandler.AbortErrorHandler GFFErrorHandler.SkipRecordErrorHandler GFFFilterer GFFParser GFFRecord GFFRecordFilter GFFRecordFilter.AcceptAll GFFRecordFilter.FeatureFilter GFFRecordFilter.FrameFilter GFFRecordFilter.NotFilter GFFRecordFilter.SequenceFilter GFFRecordFilter.SourceFilter GFFRecordFilter.StrandFilter GFFTools GFFWriter GOParser GUITools GapDistribution GappedRenderer GappedSequence GappedSymbolList GenEmblFeatureComparator GenEmblPropertyComparator GenbankFileFormer GenbankFormat GenbankProcessor GenbankProcessor.Factory GenbankSequenceDB GeneticCodes GenpeptFormat GenpeptSequenceDB Group GroupIterator HMMTrainer HSPStAXHandler HSPSummaryStAXHandler HTMLRenderer HashSequenceDB HeaderStAXHandler HeadlessRenderContext Hetatom HitMerger HitStAXHandler HmmerProfileHMM HmmerProfileParser HomologeneBuilder HomologeneDB HomologeneTools Homology HomologyDB HomologyFeature HomologyFeature.Template HypersonicDBHelper IDMaker IDMaker.ByName IDMaker.ByURN Identifiable IgnoreCountsTrainer IgnoreRecordException IllegalAlignmentEditException IllegalAlphabetException IllegalIDException IllegalSymbolException IllegalTransitionException ImageMap ImageMap.ClientSide ImageMap.HotSpot ImageMap.ServerSide ImageMapRenderer Index Index2Model IndexStore IndexStore IndexTools IndexedAnnotationDB IndexedAnnotationDB.ParserListenerFactory IndexedAnnotationDB.StaticMethodRPFactory IndexedChangeHub IndexedCount IndexedSequenceDB Indexer Indexer2 Initializable IntElementHandlerBase IntegerAlphabet IntegerAlphabet.IntegerSymbol IntegerAlphabet.SubIntegerAlphabet IntegerOntology IntegerTokenization InvalidTermException IsoelectricPointCalc ItemValue JDBCConnectionPool JDBCPooledDataSource KeyedWeakReference KnuthMorrisPrattSearch LabelRenderer LabelRenderer.RenderNothing LabelledSequenceRenderer LargeBuffer LayeredRenderer LazyFeatureHolder LazyFilterFeatureHolder LazyFilteredAnnotationDB LazySearchedAnnotationDB LifeScienceIdentifier LifeScienceIdentifierParseException Ligand Ligand.Compound Ligand.Enzyme Ligand.Reaction LightPairDPCursor LineInfo LineSplitParser LinearKernel ListSumKernel ListTools ListTools.Doublet ListTools.Mapper ListTools.SeriesList ListTools.Triplet Location LocationHandlerBase LocationTools LocusLinkParser LogoContext LogoPainter LongElementHandlerBase MSDMappingReader MSD_Mapping_ContentHandler MSFAlignmentFormat MagicalState ManyToOneTranslationTable MappedDataStoreFactory MarkovModel MassCalc Matcher MatrixPairDPCursor MaxMissmatchPattern Meme MergeAnnotation MergeFeatureHolder MergeLocation MergingAnnotationDB MergingIterator MergingSet ModelInState ModelTrainer MotifTools MultiLineRenderer MultiTagger MySQLDBHelper NCBISequenceDB NIODataStoreFactory NameTokenization NcbiDatabaseURLGenerator NestedKernel NewAssembledSymbolList NewSimpleAssembly Nfa NfaBuilder NfaSubModel NormalizingKernel Nucleotide NucleotideTools OBDARegistryParser ObdaContext ObdaInitialContextFactory ObdaUriParser ObjectUtil OntoTools Ontology Ontology.Impl OntologyException OntologyFactory OntologyOps OntologyTerm OntologyTerm.Impl OptimizableFilter OracleDBHelper OrderNDistribution OrderNDistributionFactory OrganismParser OrganismParser.Factory OrthoPair OrthoPairCollection OrthoPairCollection.Iterator OrthoPairFilter OrthoPairFilter.AcceptAll OrthoPairFilter.And OrthoPairFilter.ByMaxIdentity OrthoPairFilter.ByMinIdentity OrthoPairFilter.ByRef OrthoPairFilter.BySimilarityType OrthoPairFilter.Not OrthoPairFilter.Or OrthoPairFilter.Xor OrthoPairSet OrthoPairSet.Iterator OrthoPairSetFilter OrthoPairSetFilter.AcceptAll OrthoPairSetFilter.AllPairsInCollection OrthoPairSetFilter.And OrthoPairSetFilter.ByMinIdentity OrthoPairSetFilter.ByTaxon OrthoPairSetFilter.Not OrthoPairSetFilter.Or OrthoPairSetFilter.SomePairsInCollection OrthoPairSetFilter.Xor Orthologue OrthologueFilter OrthologueFilter.AcceptAll OrthologueFilter.And OrthologueFilter.ByAccession OrthologueFilter.ByHomologeneID OrthologueFilter.ByLocusID OrthologueFilter.ByTaxon OrthologueFilter.ByTaxonID OrthologueFilter.ByTitle OrthologueFilter.Not OrthologueFilter.Or OrthologueFilter.Xor OrthologueSet OrthologueSet.Iterator OverlayAnnotation OverlayMap OverlayMarker OverlayRendererWrapper PDBFileReader PDBParseException PDBSRSReader PackedSymbolList PackedSymbolListFactory Packing PackingFactory PaddingRenderer PairDPCursor PairDPMatrix PairDistribution PairwiseDP PairwiseDiagonalRenderer PairwiseFilteringRenderer PairwiseOverlayRenderer PairwiseRenderContext PairwiseSequencePanel PairwiseSequenceRenderer PairwiseSequenceRenderer.PairwiseRendererForwarder ParseErrorEvent ParseErrorListener ParseErrorSource ParseException Parser ParserException ParserListener Pattern PatternBlitz PatternFactory PatternListener PatternMaker PdbSAXParser PdbToXMLConverter PhredFormat PhredSequence PhredTools PlainBlock PlainStyle PointLocation PolynomialKernel PostgreSQLDBHelper PrettyXMLWriter ProcessTimeoutException ProcessTools ProfileEmissionState ProfileHMM ProjectedFeature ProjectedFeatureHolder Projection ProjectionContext ProjectionEngine ProjectionEngine.Instantiator ProjectionEngine.TemplateProjector ProjectionUtils PropDetailHandler PropertyChanger PropertyConstraint PropertyConstraint.And PropertyConstraint.ByAnnotationType PropertyConstraint.ByClass PropertyConstraint.Enumeration PropertyConstraint.ExactValue PropertyConstraint.Or PropertyWriter Protease ProteaseManager ProteinRefSeqFileFormer ProteinRefSeqProcessor ProteinRefSeqProcessor.Factory ProteinTools ProviderNotFoundException Qualitative QualitativeAlignment RAF RNATools RadialBaseKernel RandomAccessReader RangeLocation RealizingFeatureHolder Record Record.Impl RectangularBeadRenderer RectangularImapRenderer ReferenceAnnotation ReferenceServer RegexChanger RegexException RegexFieldFinder RegexParser RegexSplitter Registry RegistryConfiguration RegistryConfiguration.Composite RegistryConfiguration.Impl RegistryException RelabeledAlignment RemoteFeature RemoteFeature.Region RemoteFeature.Resolver RemoteFeature.Template RemoteTerm RemoteTerm.Impl ReparentContext RepeatedCharSequence ResourceEntityResolver RestrictionEnzyme RestrictionEnzymeManager RestrictionMapper RestrictionSite RestrictionSite.Template RevCompSequence ReversibleTranslationTable RoundRectangularBeadRenderer RulerRenderer SAX2StAXAdaptor SAX2StAXAdaptor SCF SMORegressionTrainer SMOTrainer SQLUnigeneFactory SVMClassifierModel SVMKernel SVMRegressionModel SVMTarget SVM_Light SVM_Light.LabelledVector ScoreType ScoreType.NullModel ScoreType.Odds ScoreType.Probability Search Search.Listener SearchBuilder SearchContentAdapter SearchContentFilter SearchContentHandler SearchException SearchListener SearchListener.Echo SearchListener.FilterByLength SearchListener.Tee SearchListener.Wrapper Seekable SeqContentPattern SeqFileFormer SeqIOAdapter SeqIOConstants SeqIOEventEmitter SeqIOFilter SeqIOListener SeqIOTools SeqSimilarityAdapter SeqSimilaritySearchHit SeqSimilaritySearchHit.ByScoreComparator SeqSimilaritySearchHit.BySubHitCountComparator SeqSimilaritySearchResult SeqSimilaritySearchSubHit SeqSimilaritySearchSubHit.ByScoreComparator SeqSimilaritySearchSubHit.BySubjectStartComparator SeqSimilaritySearcher SeqSimilarityStAXAdapter SeqSimilarityStAXHandler Sequence SequenceAlignmentSAXParser SequenceAnnotator SequenceBuilder SequenceBuilderBase SequenceBuilderFactory SequenceBuilderFilter SequenceContentHandlerBase SequenceDB SequenceDBDataSource SequenceDBInstallation SequenceDBLite SequenceDBProvider SequenceDBSearchHit SequenceDBSearchResult SequenceDBSearchSubHit SequenceDBSequenceBuilder SequenceDBWrapper SequenceFactory SequenceFormat SequenceHandler SequenceIterator SequencePanel SequencePoster SequenceRenderContext SequenceRenderContext.Border SequenceRenderer SequenceRenderer.RendererForwarder SequenceRendererWrapper SequenceStreamer SequenceStreamer.FileStreamer SequenceStreamer.SequenceDBStreamer SequenceTools SequenceViewerEvent SequenceViewerListener SequenceViewerMotionListener SequenceViewerMotionSupport SequenceViewerSupport SequencesAsGFF Services SigmoidKernel SimilarityPairBuilder SimilarityPairFeature SimilarityPairFeature.EmptyPairwiseAlignment SimilarityPairFeature.Template SimilarityType SimilarityType.PlaceHolder SimpleAlignment SimpleAlignmentElement SimpleAlignmentStyler SimpleAlphabet SimpleAnnotFilter SimpleAnnotation SimpleAnnotationDB SimpleAssembly SimpleAssemblyBuilder SimpleAtomicSymbol SimpleChromatogram SimpleCodonPref SimpleDistribution SimpleDistributionTrainer SimpleDistributionTrainerContext SimpleDotState SimpleEmissionState SimpleFeature SimpleFeatureHolder SimpleFeatureRealizer SimpleFramedFeature SimpleGFFRecord SimpleGappedSequence SimpleGappedSymbolList SimpleGappedSymbolList.Block SimpleHMMTrainer SimpleHomologeneBuilder SimpleHomologeneDB SimpleHomology SimpleHomologyFeature SimpleIndex SimpleItemValue SimpleLabelRenderer SimpleManyToOneTranslationTable SimpleMarkovModel SimpleModelInState SimpleModelTrainer SimpleOrthoPair SimpleOrthoPairCollection SimpleOrthoPairSet SimpleOrthologue SimpleOrthologueSet SimpleRemoteFeature SimpleRemoteFeature.DBResolver SimpleRestrictionSite SimpleReversibleTranslationTable SimpleSVMClassifierModel SimpleSVMTarget SimpleSeqSimilaritySearchHit SimpleSeqSimilaritySearchResult SimpleSeqSimilaritySearchSubHit SimpleSequence SimpleSequenceBuilder SimpleSequenceDBInstallation SimpleSequenceFactory SimpleSimilarityPairFeature SimpleStatePath SimpleStrandedFeature SimpleSymbolList SimpleSymbolListFactory SimpleSymbolPropertyTable SimpleSymbolStyle SimpleTagValueWrapper SimpleTaxon SimpleTaxonFactory SimpleThreadPool SimpleTranslationTable SimpleWeightMatrix SimpleXMLEmitter SingleDP SingleDPMatrix SingletonAlphabet SingletonList SixFrameRenderer SixFrameZiggyRenderer SmallAnnotation SmallMap SmallSet SmartSequenceBuilder SoftMaskedAlphabet SoftMaskedAlphabet.MaskingDetector SoftMaskedAlphabet.MaskingDetector.DefaultMaskingDetector SoftReferenceCache SparseVector SparseVector.NormalizingKernel StAXContentHandler StAXContentHandler StAXContentHandlerBase StAXContentHandlerBase StAXFeatureHandler StAXFeatureHandler StAXFeatureHandler StAXHandlerBinding StAXHandlerFactory StAXHandlerFactory StAXHandlerFactory StAXHandlerFactory StAXPropertyHandler StAXPropertyHandler StackedFeatureRenderer StackedLogoPainter State StateMachine StateMachine.ExitNotification StateMachine.State StateMachineFactory StateMachineInstance StatePath StaticMemberPlaceHolder StopRenderer StoppingCriteria StrandParser StrandedFeature StrandedFeature.Strand StrandedFeature.Template StrandedFeatureHandler StreamParser StreamReader StreamWriter StringElementHandlerBase Structure StructureException StructureIO StructureIOFile StructureImpl StructureTools SubCircularRendererContext SubPairwiseRenderContext SubSequence SubSequence.SubProjectedFeatureContext SubSequenceDB SubSequenceRenderContext SuffixTree SuffixTree.SuffixNode SuffixTreeKernel SuffixTreeKernel.DepthScaler SuffixTreeKernel.MultipleScalar SuffixTreeKernel.NullModelScaler SuffixTreeKernel.SelectionScalar SuffixTreeKernel.UniformScaler Swissprot SwissprotFileFormer SwissprotProcessor SwissprotProcessor.Factory SwissprotSequenceDB Symbol SymbolList SymbolListCharSequence SymbolListFactory SymbolListViews SymbolPropertyTable SymbolReader SymbolSequenceRenderer SymbolStyle SymbolTokenization SymbolTokenization.TokenType SystemRegistry TabDelimParser TabIndexStore TagDelegator TagDropper TagMapper TagRenamer TagValue TagValueContext TagValueListener TagValueParser TagValueWrapper Taxon Taxon Taxon.TaxonStub TaxonFactory TaxonParser TaxonSQL TemplateUtils Term Term.Impl TextBlock TextLogoPainter ThreadPool TickFeatureRenderer Train TrainRegression Trainable TrainerTransition TrainingAlgorithm TrainingContext TrainingEvent TrainingListener Transition TransitionTrainer TranslateFlipContext TranslatedDistribution TranslatedSequencePanel TranslationTable Triple Triple.Impl TypedProperties URLFactory URLGeneratorFactory UkkonenSuffixTree UkkonenSuffixTree.SuffixNode Unchangeable UnequalLengthAlignment UniformDistribution UnigeneCluster UnigeneDB UnigeneFactory UnigeneTools UnknownDBHelper UnsupportedChromatogramFormatException UntrainableDistribution UtilHelper ValueChanger Variable Variable.Impl ViewSequence ViewSequenceFactory ViewingSequenceDB Visitor WMAsMM Walker WalkerFactory WeakCacheMap WeakTaxon WeakTaxonFactory WeakValueHashMap WebSequenceDB WeightMatrix WeightMatrixAnnotator WobbleDistribution WordTokenization XFFFeatureSetHandler XFFHelper XFFPartHandlerFactory XFFTools XFFWriter XMLAnnotationTypeHandler XMLAnnotationTypeHandler.CollectionConstraintHandler XMLAnnotationTypeHandler.CollectionConstraintHandlerFactory XMLAnnotationTypeHandler.PropertyConstraintHandler XMLAnnotationTypeHandler.PropertyConstraintHandlerFactory XMLAnnotationTypeWriter XMLAnnotationTypeWriter.XMLCollectionConstraintWriter XMLAnnotationTypeWriter.XMLPropertyConstraintWriter XMLBeans XMLDistributionReader XMLDistributionWriter XMLFilterHandler XMLFilterHandler.FilterHandler XMLFilterHandler.FilterHandlerFactory XMLFilterWriter XMLFilterWriter.FilterWriter XMLWritable XMLWriter XmlMarkovModel ZiggyFeatureRenderer ZiggyImapRenderer