All Classes

AAindex AAindexStreamReader ABIFChromatogram ABIFParser ABIFParser.DataAccess ABIFParser.TaggedDataRecord ABITools ABITrace AbiTraceRenderer AbstractAlignmentStyler AbstractAlphabet AbstractAnnotation AbstractBeadRenderer AbstractBean AbstractBioEntryDB AbstractChangeable AbstractChromatogram AbstractCrossOverFunction AbstractDistribution AbstractFeatureHolder AbstractGeneticAlgorithm AbstractLocation AbstractLocationDecorator AbstractManyToOneTranslationTable AbstractMatrixPairDPCursor AbstractMutationFunction AbstractOrderNDistribution AbstractOrganism AbstractOrthologueSet AbstractOrthoPairCollection AbstractOrthoPairSet AbstractPeptideDigestRenderer AbstractPopulation AbstractRangeLocation AbstractReversibleTranslationTable AbstractRichSequenceDB AbstractSequenceDB AbstractSVMClassifierModel AbstractSVMTarget AbstractSymbol AbstractSymbolList AbstractTaxon AbstractTerm AbstractTrainer AbstractULAlignment AbstractWrapper AcnumHitReader AcnumTrgReader ActivityListener Agave2AgaveAnnotFilter AGAVEAltIdsPropHandler AGAVEAnnotationsHandler AGAVEAnnotFilter AGAVEAnnotFilterFactory 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 AgaveWriter AGAVEXref AGAVEXrefCallbackItf AGAVEXrefPropHandler AGAVEXrefPropPropHandler AGAVEXrefs AGAVEXrefsPropHandler Aggregator AligMatEl Alignable AlignedPosition AlignIOConstants Alignment Alignment Alignment.SymbolListIterator AlignmentCalc AlignmentElement AlignmentFormat AlignmentGui AlignmentMarker AlignmentPositionListener AlignmentRenderer AlignmentStAXHandler AligNPE AlignTools Alphabet AlphabetIndex AlphabetManager AlphabetResolver AlphaCTools AlreadyExistsException AltAligComparator AlternateTokenization AlternativeAlignment AlternativeAlignmentFrame AminoAcid AminoAcidImpl Annotatable Annotatable.AnnotationForwarder AnnotatedSequenceDB Annotation AnnotationBuilder AnnotationChanger AnnotationDB AnnotationFactory AnnotationRenamer AnnotationTools AnnotationType AnnotationType.Abstract AnnotationType.Impl AppBeanRunner AppEntry AppException ARAlignment ArrayStateMachineToolkit ArrowedFeatureRenderer ArrowGlyph AssembledSymbolList AssertionFailure Atom AtomicSymbol AtomImpl AtomIterator AtomSite Author AutomatonException BackMatrixPairDPCursor BackPointer BarLogoPainter BaseXMLWriter BasicFeatureRenderer BasicImapRenderer BasicXFFHelper BasisSymbol BaumWelchSampler BaumWelchTrainer BeadFeatureRenderer BeanAsAnnotation BeanAsMap BetweenLocation BiblioArticle BiblioBook BiblioBookArticle BiblioCriterion BiblioDescription BiblioEntryStatus BiblioJournal BiblioJournalArticle BiblioOrganisation BiblioPatent BiblioPerson BiblioProceeding BiblioProvider BiblioScope BiblioService BiblioSubject BiblioTechReport BiblioThesis BiblioWebResource BibRef BibRefException BibRefQuery BibRefSupport BinarySearch BioEntry BioEntryDB BioEntryDBLite BioEntryIterator BioEntryRelationship BioError BioException BioFetchSequenceDB BioFetchSequenceDBProvider BioIndex BiojavaJmol BioMatcher BioPattern BioRuntimeException BioSQLAcceptAllFilter BioSQLAcceptNoneFilter BioSQLBioEntryDB BioSQLCrossReferenceResolver BioSQLFeatureFilter BioSQLFeatureFilter.And BioSQLFeatureFilter.ByName BioSQLFeatureFilter.ByNote BioSQLFeatureFilter.ByNoteTermOnly BioSQLFeatureFilter.ByRank BioSQLFeatureFilter.BySequenceName BioSQLFeatureFilter.BySourceTerm BioSQLFeatureFilter.BySourceTermName BioSQLFeatureFilter.ByStrand BioSQLFeatureFilter.ByTypeTerm BioSQLFeatureFilter.ByTypeTermName BioSQLFeatureFilter.ContainedByRichLocation BioSQLFeatureFilter.HibernateFeatureFilter BioSQLFeatureFilter.Not BioSQLFeatureFilter.Or BioSQLFeatureFilter.OverlapsRichLocation BioSQLFeatureFilter.Tools BioSQLRichObjectBuilder BioSQLRichSequenceDB BioSQLRichSequenceHandler BioSQLSequenceDB BioSQLSequenceDBProvider BioStore BioStoreFactory Blast2HTMLHandler BlastLikeHomologyBuilder BlastLikeSAXParser BlastLikeSearchBuilder BlastLikeSearchFilter BlastLikeSearchFilter.AbstractBlastLikeSearchFilter BlastLikeSearchFilter.And BlastLikeSearchFilter.ByHitProperty BlastLikeSearchFilter.BySearchProperty BlastLikeSearchFilter.BySubHitProperty BlastLikeSearchFilter.Node BlastLikeSearchFilter.Not BlastLikeSearchFilter.Or BlastLikeToXMLConverter BlastXMLParser BlastXMLParserFacade BlockPainter BooleanElementHandlerBase BoundaryFinder BumpedRenderer ByLocationMinMaxComparator ByLocationMinMaxFeatureComparator ByteElementHandlerBase Cache CacheMap CacheReference CachingInputStream CachingKernel CachingSequenceDB CAConverter Calc CandyEntry CandyException CandyFinder CandyVocabulary CardinalityConstraint Cell CellCalculator CellCalculatorFactory CellCalculatorFactoryMaker Chain ChainImpl Changeable ChangeableCache ChangeAdapter ChangeEvent ChangeForwarder ChangeForwarder.Retyper ChangeHub ChangeListener ChangeListener.AlwaysVetoListener ChangeListener.ChangeEventRecorder ChangeListener.LoggingListener ChangeSupport ChangeTable ChangeTable.ChainedChanger ChangeTable.Changer ChangeTable.Splitter ChangeType ChangeVetoException CharacterTokenization CharElementHandlerBase ChemComp ChemCompConsumer ChemCompTools ChemicalComponentDictionary CholeskyDecomposition Chromatogram ChromatogramFactory ChromatogramGraphic ChromatogramGraphic.Option ChromatogramNonlinearScaler ChromatogramNonlinearScaler.Identity ChromatogramTools ChunkedSymbolList ChunkedSymbolListFactory CircularFeatureFilteringRenderer CircularFeatureRenderer CircularFeaturesRenderer CircularLocation CircularMLR CircularPaddedRenderer CircularReferenceException CircularRenderer CircularRendererContext CircularRendererPanel CircularView ClassifierExample ClassifierExample.PointClassifier Classify ClassTools ClustalWAlignmentSAXParser ClusterAltAligs CodonPref CodonPrefFilter CodonPrefFilter.AcceptAll CodonPrefFilter.ByName CodonPrefFilter.EverythingToXML CodonPrefTools CollectionConstraint CollectionConstraint.AllValuesIn CollectionConstraint.And CollectionConstraint.Contains CollectionConstraint.Or ColourCommand Comment Commitable CommitFailure CompactedDataStore CompactedDataStoreFactory ComparableOntology ComparableTerm ComparableTriple ComponentFeature ComponentFeature.Template Composition Compound CompoundRichLocation ComputeObject Constants CoordManager Count CountedBufferedReader CRC64Checksum CrosshairRenderer CrossOverFunction CrossOverFunction.NoCross CrossProductTokenization CrossRef CrossReferenceResolutionException CrossReferenceResolver DAS DASAlignmentCall DASAlignmentClient DASAlignmentXMLResponseParser DASException DASLink DASSequence DASSequenceDB DASSequenceDBProvider DASStructureCall DASStructureClient DASStructureXMLResponseParser DatabasePDBremark DatabasePDBrev DatabaseURLGenerator DataSource DataStore DataStoreFactory DBHelper DBHelper.BioSequenceStyle DBHelper.DeleteStyle DBHelper.JoinStyle DBRef DebuggingRichSeqIOListener DefaultOps DefaultURLGeneratorFactory DelegationManager DelegationManager DemoStructureServer DfaBuilder DiagonalAddKernel DiagonalCachingKernel Digest DistDataSource DistributedSequenceDB Distribution Distribution.NullModelForwarder DistributionFactory DistributionFactory.DefaultDistributionFactory DistributionLogo DistributionTools DistributionTrainer DistributionTrainerContext DivisionLkpReader DNAAmbPack DNAComposition DNANoAmbPack DNAStyle DNATools DocRef DocRefAuthor DocRefAuthor.Tools DotState DoubleAlphabet DoubleAlphabet.DoubleRange DoubleAlphabet.DoubleSymbol DoubleAlphabet.SubDoubleAlphabet DoubleElementHandlerBase DoubleTokenization DP DP.ReverseIterator DPCompiler DPCursor DPFactory DPFactory.DefaultFactory DPInterpreter DPInterpreter.Maker DPMatrix DummyCrossReferenceResolver DummyRichSequenceHandler DummySequence DummySequenceDB DummySequenceDBInstallation DummySymbolList DuplicateTaxonException EbiDatabaseURLGenerator EbiFormat Echo EcNumber EcNumber.Impl Edit EditableAlignment EigenvalueDecomposition 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 EMBLFormat EMBLFormat.Terms EmblLikeFormat EmblLikeLocationParser EmblProcessor EmblProcessor.Factory EmblReferenceComparator EMBLxmlFormat EMBLxmlFormat.Terms EmissionCache EmissionState EmptyRichAnnotation EmptyRichLocation Entity EntityPolySeq EntryNamIdxReader EntryNamRandomAccess Enzyme ExecRunner Exptl ExternalProcess FastaAlignmentFormat FastaDescriptionLineParser FastaDescriptionLineParser.Factory FastaFormat FastaFormat FastaHeader FastaSearchSAXParser FastaSequenceSAXParser Fastq FastqBuilder FastqReader FastqVariant FastqWriter FastXMLWriter 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 FeatureHolderUtils FeatureImpl FeatureLabelRenderer FeatureLabelRenderer.AnnotationLabelMaker FeatureLabelRenderer.LabelMaker FeatureLabelRenderer.SourceLabelMaker FeatureLabelRenderer.TypeLabelMaker FeatureRealizer FeatureRenderer FeatureSource FeatureTableParser FeatureTree FeatureTypes FeatureTypes.Repository FeatureTypes.RepositoryImpl FeatureTypes.Type FetchURL FileAsList FileConvert FilteringContentHandler FilteringRenderer FilterTest FilterTest.Equals FilterTest.FindRegex FilterTest.GreaterThan FilterTest.LessThan FilterTest.MatchRegex FilterTransformer FilterUtils FilterUtils.FilterTransformer FiniteAlphabet FiniteAutomaton FitnessFunction FixedBaseWidthScaler FixedSizeCache FixedSizeMap FlatFileInstallation FlatFileUnigeneFactory FlatSequenceDB FlatSequenceDBProvider FlexibleAlignment FloatElementHandlerBase Format Formats FormatTools FragmentJoiner FragmentPair Frame FramedFeature FramedFeature.ReadingFrame FramedFeature.Template FullHmmerProfileHMM FundamentalAtomicSymbol FuzzyLocation FuzzyLocation.RangeResolver FuzzyPointLocation FuzzyPointLocation.PointResolver GACross GACrossResult 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 GapArray GapDistribution GappedRenderer GappedSequence GappedSymbolList GAStoppingCriteria GAStoppingCriteria.MaximumGeneration GATools GenbankFileFormer GenbankFormat GenbankFormat GenbankFormat.Terms GenbankLocationParser GenbankProcessor GenbankProcessor.Factory GenbankRichSequenceDB GenbankSequenceDB GenbankXmlFormat GenEmblFeatureComparator GenEmblPropertyComparator GeneticAlgorithm GeneticCodes GenpeptFormat GenpeptRichSequenceDB GenpeptSequenceDB 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 Glyph GlyphFeatureRenderer GlyphUtils GOParser Gotoh Group GroupIterator GroupType GUITools HashBioEntryDB HashedFastaIterator HashRichSequenceDB HashSequenceDB HeaderStAXHandler HeadlessRenderContext HelixGlyph HetatomImpl HitMerger HitStAXHandler HmmerProfileHMM HmmerProfileParser HMMTrainer HomologeneBuilder HomologeneDB HomologeneTools Homology HomologyDB HomologyFeature HomologyFeature.Template HSPStAXHandler HSPSummaryStAXHandler HTMLRenderer HypersonicDBHelper Identifiable IDMaker IDMaker.ByName IDMaker.ByURN IgnoreCountsTrainer IgnoreRecordException IllegalAlignmentEditException IllegalAlphabetException IllegalIDException IllegalOrganismException IllegalSymbolException IllegalTransitionException IlluminaFastqReader IlluminaFastqWriter ImageMap ImageMap.ClientSide ImageMap.HotSpot ImageMap.ServerSide ImageMapRenderer Index Index2Model IndexedAnnotationDB IndexedAnnotationDB.ParserListenerFactory IndexedAnnotationDB.StaticMethodRPFactory IndexedChangeHub IndexedCount IndexedSequenceDB Indexer Indexer2 IndexPair IndexStore IndexStore IndexTools InfinitelyAmbiguousSymbolList Initializable InputHandler InputStreamProvider INSDseqFormat INSDseqFormat.Terms IntegerAlphabet IntegerAlphabet.IntegerSymbol IntegerAlphabet.SubIntegerAlphabet IntegerOntology IntegerTokenization IntElementHandlerBase InvalidTermException IsoelectricPointCalc ItemValue JDBCConnectionPool JDBCPooledDataSource JMatrixPanel JmolAlignedPositionListener JointFragments JournalArticle KeyedWeakReference KnuthMorrisPrattSearch LabelledSequenceRenderer LabelRenderer LabelRenderer.RenderNothing LargeBuffer LayeredRenderer LazyFeatureHolder LazyFilteredAnnotationDB LazyFilterFeatureHolder LazySearchedAnnotationDB LifeScienceIdentifier LifeScienceIdentifierParseException Ligand Ligand.Compound Ligand.Enzyme Ligand.Reaction LightPairDPCursor LinearKernel LineInfo LineSplitParser ListSumKernel ListTools ListTools.Doublet ListTools.Mapper ListTools.SeriesList ListTools.Triplet Location LocationHandlerBase LocationTools LogoContext LogoPainter LongElementHandlerBase LUDecomposition MagicalState ManyToOneTranslationTable MappedDataStoreFactory MarkovModel MassCalc Matcher Maths Matrix MatrixPairDPCursor MaxMismatchMatcher MaxMismatchPattern Meme MenuCreator MergeAnnotation MergeFeatureHolder MergeLocation MergingAnnotationDB MergingIterator MergingSet MMcifConsumer MMCIFFileInstallation MMCIFFileReader MMcifParser ModelInState ModelTrainer MotifTools MSFAlignmentFormat MultiLineRenderer MultipleHitCorrection MultiSourceCompoundRichLocation MultiTagger MutationFunction MutationFunction.NoMutation Mutator MySQLDBHelper Namespace NameTokenization NcbiDatabaseURLGenerator NCBISequenceDB NCBITaxon NCBITaxonomyLoader NeedlemanWunsch NestedKernel NewAssembledSymbolList NewSimpleAssembly Nfa NfaBuilder NfaSubModel NIODataStoreFactory NormalizingKernel Note NucleotideImpl NucleotideTools ObdaContext ObdaInitialContextFactory OBDARegistryParser ObdaUriParser ObjectUtil OboFileEventListener OboFileHandler OboFileParser OboFileParser.SOPair OboParser OffsetRulerRenderer Ontology Ontology.Impl OntologyException OntologyFactory OntologyOps OntologyTerm OntologyTerm.Impl OntoTools OptimizableFilter OracleDBHelper OrderCrossover OrderNDistribution OrderNDistributionFactory Organism OrganismParser OrganismParser.Factory 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 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 OutputHandler OverlayAnnotation OverlayMap OverlayMarker OverlayRendererWrapper PackedSymbolList PackedSymbolListFactory Packing PackingFactory PaddingRenderer PairDistribution PairDPCursor PairDPMatrix PairwiseDiagonalRenderer PairwiseDP PairwiseFilteringRenderer PairwiseOverlayRenderer PairwiseRenderContext PairwiseSequencePanel PairwiseSequenceRenderer PairwiseSequenceRenderer.PairwiseRendererForwarder ParseErrorEvent ParseErrorListener ParseErrorSource ParseException Parser ParserException ParserListener Pattern PatternBlitz PatternFactory PatternListener PatternMaker PDBDirPanel PDBFileParser PDBFileReader PDBFilter PDBHeader PDBInstallation PDBMSDReader PDBParseException PDBRecord PdbSAXParser PDBServerPanel PDBSRSReader PdbToXMLConverter PDBUploadPanel PdbxEntityNonPoly PdbxNonPolyScheme PdbxPolySeqScheme PeptideDigestRenderer PhredFormat PhredSequence PhredTools PHYLIPFileBuilder PHYLIPFileFormat PHYLIPFileListener PlainBlock PlainStyle PointLocation PolymerType PolynomialKernel Population Position PositionResolver PositionResolver.AverageResolver PositionResolver.MaximalResolver PositionResolver.MinimalResolver PostgreSQLDBHelper PrepareIndexFile PrepareMMcifIndexFile 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 ProportionalSelection Protease ProteaseManager ProteinRefSeqFileFormer ProteinRefSeqProcessor ProteinRefSeqProcessor.Factory ProteinTools ProviderNotFoundException QRDecomposition Qualitative QualitativeAlignment RadialBaseKernel RAF RandomAccessReader RangeLocation RankedCrossRef RankedCrossRefable RankedDocRef RasmolCommandListener ReaderInputHandler ReaderWriterPipe RealizingFeatureHolder Record Record.Impl RectangleGlyph RectangularBeadRenderer RectangularImapRenderer ReferenceAnnotation ReferenceServer Refine 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 ResidueType ResourceEntityResolver RestrictionEnzyme RestrictionEnzymeManager RestrictionMapper RestrictionSite RestrictionSite.Template RevCompSequence ReversibleTranslationTable RichAnnotatable RichAnnotation RichFeature RichFeature.Template RichFeature.Tools RichFeatureRelationship RichFeatureRelationshipHolder RichLocation RichLocation.Strand RichLocation.Tools RichObjectBuilder RichObjectFactory RichSeqIOAdapter RichSeqIOListener RichSequence RichSequence.IOTools RichSequence.IOTools.SingleRichSeqIterator RichSequence.Terms RichSequence.Tools RichSequenceBuilder RichSequenceBuilderFactory RichSequenceDB RichSequenceDBLite RichSequenceFormat RichSequenceFormat.BasicFormat RichSequenceFormat.HeaderlessFormat RichSequenceHandler RichSequenceIterator RichStreamReader RichStreamWriter RNATools RoundRectangularBeadRenderer RulerRenderer SangerFastqReader SangerFastqWriter SAX2StAXAdaptor SAX2StAXAdaptor ScaleableMatrixPanel SCF ScoreType ScoreType.NullModel ScoreType.Odds ScoreType.Probability Search Search.Listener SearchBuilder SearchContentAdapter SearchContentFilter SearchContentHandler SearchContentHandlerDebugger SearchException SearchListener SearchListener.Echo SearchListener.FilterByLength SearchListener.Tee SearchListener.Wrapper SecondaryStructureFeatureRenderer Seekable SelectionFunction SelectionFunction.SelectAll SelectionFunction.Threshold SeqContentPattern SeqFileFormer SeqIOAdapter SeqIOConstants SeqIOEventEmitter SeqIOFilter SeqIOListener SeqIOTools SeqRes2AtomAligner SeqSimilarityAdapter SeqSimilaritySearcher SeqSimilaritySearchHit SeqSimilaritySearchHit.ByScoreComparator SeqSimilaritySearchHit.BySubHitCountComparator SeqSimilaritySearchResult SeqSimilaritySearchSubHit SeqSimilaritySearchSubHit.ByScoreComparator SeqSimilaritySearchSubHit.BySubjectStartComparator SeqSimilarityStAXAdapter SeqSimilarityStAXHandler Sequence SequenceAlignment SequenceAlignmentSAXParser SequenceAnnotator SequenceBuilder SequenceBuilderBase SequenceBuilderFactory SequenceBuilderFilter SequenceContentHandlerBase SequenceDB SequenceDBDataSource SequenceDBInstallation SequenceDBLite SequenceDBProvider SequenceDBSearchHit SequenceDBSearchResult SequenceDBSearchSubHit SequenceDBSequenceBuilder SequenceDBWrapper SequenceDisplay SequenceFactory SequenceFormat SequenceHandler SequenceIterator SequenceMouseListener SequencePanel SequencePanelWrapper SequencePoster SequenceRenderContext SequenceRenderContext.Border SequenceRenderer SequenceRenderer.RendererForwarder SequenceRendererWrapper SequencesAsGFF SequenceScalePanel SequenceStreamer SequenceStreamer.FileStreamer SequenceStreamer.SequenceDBStreamer SequenceTools SequenceViewerEvent SequenceViewerListener SequenceViewerMotionListener SequenceViewerMotionSupport SequenceViewerSupport Services SigmoidKernel SimilarityPairBuilder SimilarityPairFeature SimilarityPairFeature.EmptyPairwiseAlignment SimilarityPairFeature.Template SimilarityType SimilarityType.PlaceHolder SimpleAlignment SimpleAlignmentElement SimpleAlignmentStyler SimpleAlphabet SimpleAnnotation SimpleAnnotationDB SimpleAnnotFilter SimpleAssembly SimpleAssemblyBuilder SimpleAtomicSymbol SimpleBioEntry SimpleBioEntryRelationship SimpleChromatogram SimpleCodonPref SimpleComment SimpleComparableOntology SimpleComparableTerm SimpleComparableTriple SimpleCrossOverFunction SimpleCrossRef SimpleDistribution SimpleDistributionTrainer SimpleDistributionTrainerContext SimpleDocRef SimpleDocRefAuthor SimpleDotState SimpleEmissionState SimpleFeature SimpleFeatureHolder SimpleFeatureRealizer SimpleFramedFeature SimpleGACrossResult SimpleGappedSequence SimpleGappedSymbolList SimpleGappedSymbolList.Block SimpleGeneticAlgorithm SimpleGeneticCodeTable SimpleGFFRecord SimpleHMMTrainer SimpleHomologeneBuilder SimpleHomologeneDB SimpleHomology SimpleHomologyFeature SimpleIndex SimpleInputHandler SimpleItemValue SimpleLabelRenderer SimpleManyToOneTranslationTable SimpleMarkovModel SimpleMMcifConsumer SimpleMMcifParser SimpleModelInState SimpleModelTrainer SimpleMutationFunction SimpleNamespace SimpleNCBITaxon SimpleNCBITaxonName SimpleNCBITaxonomyLoader SimpleNote SimpleOrganism SimpleOrthologue SimpleOrthologueSet SimpleOrthoPair SimpleOrthoPairCollection SimpleOrthoPairSet SimpleOutputHandler SimplePopulation SimplePosition SimpleRankedCrossRef SimpleRankedDocRef SimpleRemoteFeature SimpleRemoteFeature.DBResolver SimpleRestrictionSite SimpleReversibleTranslationTable SimpleRichAnnotation SimpleRichFeature SimpleRichFeatureRelationship SimpleRichLocation SimpleRichObjectBuilder SimpleRichSequence SimpleRichSequenceBuilder SimpleRichSequenceBuilderFactory SimpleSeqSimilaritySearchHit SimpleSeqSimilaritySearchResult SimpleSeqSimilaritySearchSubHit SimpleSequence SimpleSequenceBuilder SimpleSequenceDBInstallation SimpleSequenceFactory SimpleSimilarityPairFeature SimpleStatePath SimpleStrandedFeature SimpleStructureServer SimpleSVMClassifierModel SimpleSVMTarget SimpleSymbolList SimpleSymbolListFactory SimpleSymbolPropertyTable SimpleSymbolPropertyTableDB SimpleSymbolStyle SimpleTagValueWrapper SimpleTaxon SimpleTaxonFactory SimpleThreadPool SimpleTrackLayout SimpleTranslationTable SimpleWeightMatrix SimpleXMLEmitter SingleDP SingleDPMatrix SingletonAlphabet SingletonList SingularValueDecomposition SixFrameRenderer SixFrameZiggyRenderer SmallAnnotation SmallCursor SmallMap SmallSet SmartSequenceBuilder SmithWaterman SMORegressionTrainer SMOTrainer SoftMaskedAlphabet SoftMaskedAlphabet.MaskingDetector SoftMaskedAlphabet.MaskingDetector.DefaultMaskingDetector SoftReferenceCache SolexaFastqReader SolexaFastqWriter SparseVector SparseVector.NormalizingKernel SQLUnigeneFactory SSBond StackedFeatureRenderer StackedLogoPainter StandardAminoAcid State StateMachine StateMachine.ExitNotification StateMachine.State StateMachineFactory StateMachineInstance StatePath StaticMemberPlaceHolder StAXContentHandler StAXContentHandler StAXContentHandlerBase StAXContentHandlerBase StAXFeatureHandler StAXFeatureHandler StAXFeatureHandler StAXHandlerBinding StAXHandlerFactory StAXHandlerFactory StAXHandlerFactory StAXHandlerFactory StAXPropertyHandler StAXPropertyHandler StoppingCriteria StopRenderer StrandedFeature StrandedFeature.Strand StrandedFeature.Template StrandedFeatureHandler StrandParser StrCompAlignment StreamParser StreamPipe StreamReader StreamWriter StringElementHandlerBase StringTools StrucAligParameters Struct StructAsym StructKeywords StructRef StructRefSeq Structure StructureEvent StructureEventImpl StructureException StructureFetcherRunnable StructureImpl StructureIO StructureIOFile StructureListener StructurePairAligner StructurePairSelector StructureServer StructureTools StructureTools SubCircularRendererContext SubIntegerTokenization SubPairwiseRenderContext SubSequence SubSequence.SubProjectedFeatureContext SubSequenceDB SubSequenceRenderContext SubstitutionMatrix SuffixTree SuffixTree.SuffixNode SuffixTreeKernel SuffixTreeKernel.DepthScaler SuffixTreeKernel.MultipleScalar SuffixTreeKernel.NullModelScaler SuffixTreeKernel.SelectionScalar SuffixTreeKernel.UniformScaler SVDSuperimposer SVM_Light SVM_Light.LabelledVector SVMClassifierModel SVMKernel SVMRegressionModel SVMTarget SwapMutationFunction Swissprot SwissprotFileFormer SwissprotProcessor SwissprotProcessor.Factory SwissprotSequenceDB Symbol SymbolList SymbolListCharSequence SymbolListFactory SymbolListViews SymbolPropertyTable SymbolPropertyTableDB SymbolPropertyTableIterator SymbolReader SymbolSequenceRenderer SymbolStyle SymbolTokenization SymbolTokenization.TokenType Synonym 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 ThinRichSequence ThreadPool TickFeatureRenderer TournamentSelection TrackLayout Train Trainable TrainerTransition TrainingAlgorithm TrainingContext TrainingEvent TrainingListener TrainRegression Transition TransitionTrainer TranslatedDistribution TranslatedSequencePanel TranslateFlipContext TranslationTable Triple Triple.Impl TriState TurnGlyph TwoHeadedArrowGlyph TypedProperties UkkonenSuffixTree UkkonenSuffixTree.SuffixNode Unchangeable UncompressInputStream UnequalLengthAlignment UniformDistribution UnigeneCluster UnigeneDB UnigeneFactory UnigeneTools UniProtCommentParser UniProtCommentParser.Event UniProtCommentParser.Interaction UniProtCommentParser.Isoform UniProtCommentParser.SeqCaution UniProtFormat UniProtFormat.Terms UniProtLocationParser UniProtXMLFormat UniProtXMLFormat.Terms UnknownDBHelper UnsupportedChromatogramFormatException UntrainableDistribution URLFactory URLGeneratorFactory UserDefinedTrackLayout UtilHelper ValueChanger Variable Variable.Impl ViewingSequenceDB ViewSequence ViewSequenceFactory Visitor Walker WalkerFactory WeakCacheMap WeakTaxon WeakTaxonFactory WeakValueHashMap WebSequenceDB WeightedSet WeightMatrix WeightMatrixAnnotator WMAsMM WobbleDistribution WordTokenization WriterOutputHandler 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 XmlMarkovModel XMLTools XMLWritable XMLWriter ZiggyFeatureRenderer ZiggyImapRenderer