All Classes

ABIFChromatogram ABIFParser ABIFParser.DataAccess ABIFParser.TaggedDataRecord ABITools ABITrace AbiTraceRenderer AbstractAlignmentStyler AbstractAlphabet AbstractAnnotation AbstractBeadRenderer AbstractChangeable AbstractChromatogram AbstractDistribution AbstractFeatureHolder AbstractLocation AbstractLocationDecorator AbstractMatrixPairDPCursor AbstractOrderNDistribution AbstractRangeLocation AbstractSequenceDB AbstractSVMClassifierModel AbstractSVMTarget AbstractSymbol AbstractSymbolList AbstractTaxon AbstractTrainer AbstractULAlignment 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 AlignIOConstants Alignment Alignment.SymbolListIterator AlignmentElement AlignmentFormat AlignmentMarker AlignmentRenderer AlignmentStAXHandler Alphabet AlphabetIndex AlphabetManager AlphabetResolver Annotatable Annotatable.AnnotationForwarder AnnotatedSequenceDB Annotation AnnotationBuilder AnnotationChanger AnnotationFactory AnnotationRenamer AnnotationTools AnnotationType AnnotationType.Abstract AnnotationType.Impl AppBeanRunner AppEntry AppException ARAlignment AssembledSymbolList AtomicSymbol BackMatrixPairDPCursor BackPointer BarLogoPainter BaseXMLWriter BasicFeatureRenderer 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 BibRefQuery BibRefSupport BinarySearch BioError BioException BioFetchSequenceDB BioFetchSequenceDBProvider BioIndex BioRuntimeException BioSQLSequenceDB BioSQLSequenceDBProvider BioStore BioStoreFactory Blast2HTMLHandler BlastLikeHomologyBuilder BlastLikeSAXParser BlastLikeSearchBuilder BlastLikeToXMLConverter BlastXMLParser BlockPainter BooleanElementHandlerBase BumpedRenderer ByteElementHandlerBase Cache CacheMap CacheReference CachingInputStream CachingKernel CachingSequenceDB CandyEntry CandyFinder CandyVocabulary CardinalityConstraint Cell CellCalculator CellCalculatorFactory CellCalculatorFactoryMaker Changeable ChangeableCache ChangeAdapter ChangeEvent ChangeForwarder ChangeHub ChangeListener ChangeListener.AlwaysVetoListener ChangeListener.LoggingListener ChangeSupport ChangeTable ChangeTable.ChainedChanger ChangeTable.Changer ChangeTable.Splitter ChangeType ChangeVetoException CharacterTokenization CharElementHandlerBase Chromatogram ChromatogramFactory ChromatogramGraphic ChromatogramGraphic.Option ChromatogramTools ChunkedSymbolListBuilder ChunkedSymbolListFactory CircularLocation CircularReferenceException CircularView ClassifierExample ClassifierExample.PointClassifier Classify ClustalWAlignmentSAXParser CollectionConstraint CollectionConstraint.AllValuesIn CollectionConstraint.And CollectionConstraint.Contains CollectionConstraint.Or ColourCommand Commitable CompactedDataStore CompactedDataStoreFactory ComponentFeature ComponentFeature.Template ComputeObject Constants Count CountedBufferedReader CrosshairRenderer CrossProductTokenization DAS DASLink DASSequence DASSequenceDB DASSequenceDBProvider DatabaseURLGenerator DataSource DataStore DataStoreFactory DBHelper DBHelper.DeleteStyle DefaultURLGeneratorFactory DelegationManager DelegationManager DiagonalAddKernel DiagonalCachingKernel Digest DistDataSource DistributedSequenceDB Distribution Distribution.NullModelForwarder DistributionFactory DistributionFactory.DefaultDistributionFactory DistributionLogo DistributionTools DistributionTrainer DistributionTrainerContext DivisionLkpReader DNAAmbPack DNANoAmbPack DNAStyle DNATools DotState DoubleAlphabet DoubleAlphabet.DoubleRange DoubleAlphabet.DoubleSymbol DoubleAlphabet.SubDoubleAlphabet DoubleElementHandlerBase DoubleTokenization DP DP.ReverseIterator DPCompiler DPFactory DPFactory.DefaultFactory DPInterpreter DPInterpreter.Maker DPMatrix DummySequence DummySequenceDB DummySequenceDBInstallation DummySymbolList EbiDatabaseURLGenerator EbiFormat 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 Embl2AgaveAnnotFilter EmblCDROMIndexReader EmblCDROMIndexStore EmblCDROMRandomAccess EmblFileFormer EmblLikeFormat EmblLikeLocationParser EmblProcessor EmblProcessor.Factory EmissionCache EmissionState EntryNamIdxReader EntryNamRandomAccess FastaAlignmentFormat FastaDescriptionLineParser FastaDescriptionLineParser.Factory FastaFormat FastaSearchSAXParser FastaSequenceSAXParser 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 FeatureImpl FeatureLabelRenderer FeatureLabelRenderer.AnnotationLabelMaker FeatureLabelRenderer.LabelMaker FeatureLabelRenderer.SourceLabelMaker FeatureLabelRenderer.TypeLabelMaker FeatureRealizer FeatureRenderer FeatureTableParser FeatureTree FeatureTypes FeatureTypes.Repository FeatureTypes.RepositoryImpl FeatureTypes.Type FetchURL FileAsList FilteringRenderer FilterUtils FilterUtils.FilterTransformer FiniteAlphabet FixedSizeCache FixedSizeMap FlatFileUnigeneFactory FlatSequenceDB FlatSequenceDBProvider FlexibleAlignment FloatElementHandlerBase 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 GapDistribution GappedSequence GappedSymbolList GenbankFileFormer GenbankFormat GenbankProcessor GenbankProcessor.Factory GenbankSequenceDB GeneticCodes GenpeptSequenceDB 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 HashSequenceDB HeaderStAXHandler HeadlessRenderContext HitMerger HitStAXHandler HmmerProfileHMM HmmerProfileParser Homology HomologyDB HomologyFeature HomologyFeature.Template HSPStAXHandler HSPSummaryStAXHandler HTMLRenderer Identifiable IDMaker IDMaker.ByName IDMaker.ByURN IgnoreCountsTrainer IgnoreRecordException IllegalAlignmentEditException IllegalAlphabetException IllegalIDException IllegalSymbolException IllegalTransitionException ImageMap ImageMap.ClientSide ImageMap.HotSpot ImageMap.ServerSide ImageMapRenderer Index Index2Model IndexedChangeHub IndexedCount IndexedSequenceDB Indexer Indexer2 IndexStore IndexStore IndexTools Initializable IntegerAlphabet IntegerAlphabet.IntegerSymbol IntegerAlphabet.SubIntegerAlphabet IntegerTokenization IntElementHandlerBase IsoelectricPointCalc ItemValue JDBCConnectionPool KeyedWeakReference KnuthMorrisPrattSearch LabelledSequenceRenderer LabelRenderer LabelRenderer.RenderNothing LargeBuffer LayeredRenderer LazyFeatureHolder LazyFilterFeatureHolder LifeScienceIdentifier LifeScienceIdentifierParseException LightPairDPCursor LinearKernel LineInfo LineSplitParser ListSumKernel ListTools ListTools.Doublet ListTools.Triplet Location LocationHandlerBase LocationTools LocusLinkParser LogoContext LogoPainter LongElementHandlerBase MagicalState MappedDataStoreFactory MarkovModel MarkovModel.DistributionForwarder MassCalc MatrixPairDPCursor Meme MergeAnnotation MergeFeatureHolder MergeLocation ModelInState ModelTrainer MotifTools MSFAlignmentFormat MultiLineRenderer MySQLDBHelper NameTokenization NcbiDatabaseURLGenerator NCBISequenceDB NestedError NestedException NestedKernel NestedRuntimeException NIODataStoreFactory NormalizingKernel NucleotideTools OBDARegistryParser ObjectUtil OptimizableFilter OrderNDistribution OrderNDistributionFactory OrganismParser OrganismParser.Factory OverlayAnnotation OverlayMap OverlayMarker OverlayRendererWrapper PackedDnaSymbolList PackedSymbolList PackedSymbolListFactory Packing PackingFactory PaddingRenderer PairDistribution PairDPCursor PairDPMatrix PairwiseDiagonalRenderer PairwiseDP PairwiseFilteringRenderer PairwiseOverlayRenderer PairwiseRenderContext PairwiseSequencePanel PairwiseSequenceRenderer PairwiseSequenceRenderer.PairwiseRendererForwarder ParseErrorEvent ParseErrorListener ParseErrorSource ParseException Parser ParserException ParserListener PdbSAXParser PdbToXMLConverter PhredFormat PhredSequence PhredTools PlainBlock PlainStyle PointLocation PolynomialKernel PostgreSQLDBHelper PrettyXMLWriter ProfileEmissionState ProfileHMM ProjectedFeature ProjectedFeatureHolder ProjectedStrandedFeature Projection ProjectionContext ProjectionEngine ProjectionEngine.Instantiator ProjectionEngine.InstantiatorImpl ProjectionUtils PropDetailHandler PropertyConstraint PropertyConstraint.And PropertyConstraint.ByAnnotationType PropertyConstraint.ByClass PropertyConstraint.Enumeration PropertyConstraint.ExactValue PropertyConstraint.Or PropertyWriter Protease ProteaseManager ProteinRefSeqFileFormer ProteinRefSeqProcessor ProteinRefSeqProcessor.Factory ProteinTools ProviderNotFoundException Qualitative QualitativeAlignment RadialBaseKernel RAF RagbagAssembly RagbagComponentDirectory RagbagComponentDirectory.EmptyComponentDirectory RagbagFeatureTypeCatcher RagbagFileParserFactory RagbagFilteredCachedSeqFactory RagbagFilterFactory RagbagFixedCacheSeqFactory RagbagHashedComponentDirectory RagbagIdleSequenceBuilder RagbagMap RagbagSequenceFactory RagbagSoftRefSeqFactory RagbagUncachedSeqFactory RandomAccessReader RangeLocation RealizingFeatureHolder Record Record.Impl RectangularBeadRenderer RectangularImapRenderer ReferenceServer RegexChanger RegexFieldFinder RegexParser RegexSplitter Registry RegistryConfiguration RegistryConfiguration.Composite RegistryConfiguration.Impl RegistryException RelabeledAlignment RemoteFeature RemoteFeature.Region RemoteFeature.Resolver RemoteFeature.Template ResourceEntityResolver RestrictionEnzyme RestrictionEnzymeManager RestrictionMapper RestrictionSite RestrictionSite.Template RevCompSequence ReversibleTranslationTable RNATools RoundRectangularBeadRenderer RulerRenderer SAX2StAXAdaptor SAX2StAXAdaptor SCF ScoreType ScoreType.NullModel ScoreType.Odds ScoreType.Probability SearchBuilder SearchContentAdapter SearchContentFilter SearchContentHandler SearchListener Seekable SeqAlignReadWrite SeqFileFormer SeqIOAdapter SeqIOConstants SeqIOFilter SeqIOListener SeqIOTools SeqSimilarityAdapter SeqSimilaritySearcher SeqSimilaritySearchHit SeqSimilaritySearchHit.ByScoreComparator SeqSimilaritySearchHit.BySubHitCountComparator SeqSimilaritySearchResult SeqSimilaritySearchSubHit SeqSimilaritySearchSubHit.ByScoreComparator SeqSimilaritySearchSubHit.BySubjectStartComparator 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 SequencesAsGFF SequenceStreamer SequenceStreamer.FileStreamer SequenceStreamer.SequenceDBStreamer SequenceTools SequenceViewerEvent SequenceViewerListener SequenceViewerMotionListener SequenceViewerMotionSupport SequenceViewerSupport Services SigmoidKernel SimilarityPairBuilder SimilarityPairFeature SimilarityPairFeature.EmptyPairwiseAlignment SimilarityPairFeature.Template SimpleAlignment SimpleAlignmentElement SimpleAlignmentStyler SimpleAlphabet SimpleAnnotation SimpleAnnotFilter SimpleAssembly SimpleAssemblyBuilder SimpleAtomicSymbol SimpleChromatogram SimpleDistribution SimpleDistributionTrainer SimpleDistributionTrainerContext SimpleDotState SimpleEmissionState SimpleFeature SimpleFeatureHolder SimpleFeatureRealizer SimpleFramedFeature SimpleGappedSequence SimpleGappedSymbolList SimpleGFFRecord SimpleHomology SimpleHomologyFeature SimpleIndex SimpleItemValue SimpleLabelRenderer SimpleMarkovModel SimpleModelInState SimpleModelTrainer SimpleRemoteFeature SimpleRemoteFeature.DBResolver SimpleRestrictionSite SimpleReversibleTranslationTable SimpleSeqSimilaritySearchHit SimpleSeqSimilaritySearchResult SimpleSeqSimilaritySearchSubHit SimpleSequence SimpleSequenceBuilder SimpleSequenceDBInstallation SimpleSequenceFactory SimpleSimilarityPairFeature SimpleStatePath SimpleStrandedFeature SimpleSVMClassifierModel SimpleSVMTarget SimpleSymbolList SimpleSymbolListFactory SimpleSymbolPropertyTable SimpleSymbolStyle SimpleTaxon SimpleTaxonFactory SimpleThreadPool SimpleTranslationTable SimpleWeightMatrix SimpleXMLEmitter SingleDP SingleDPMatrix SingletonAlphabet SingletonList SixFrameRenderer SixFrameZiggyRenderer SmallAnnotation SmallMap SmallSet SmartSequenceBuilder SMORegressionTrainer SMOTrainer SoftReferenceCache SparseVector SparseVector.NormalizingKernel SQLUnigeneFactory StackedFeatureRenderer StackedLogoPainter State 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 StreamParser StreamReader StreamWriter StringElementHandlerBase StructureTools SubPairwiseRenderContext SubSequence SubSequenceDB SubSequenceRenderContext SuffixTree SuffixTree.SuffixNode SuffixTreeKernel SuffixTreeKernel.DepthScaler SuffixTreeKernel.MultipleScalar SuffixTreeKernel.NullModelScaler SuffixTreeKernel.SelectionScalar SuffixTreeKernel.UniformScaler SVM_Light SVM_Light.LabelledVector SVMClassifierModel SVMKernel SVMRegressionModel SVMTarget SwissprotFileFormer SwissprotProcessor SwissprotProcessor.Factory SwissprotSequenceDB Symbol SymbolList SymbolList.EmptySymbolList SymbolListCharSequence SymbolListFactory SymbolListViews SymbolPropertyTable SymbolReader SymbolSequenceRenderer SymbolStyle SymbolTokenization SymbolTokenization.TokenType SystemRegistry TabIndexStore TagDelegator TagDropper TagMapper TagRenamer TagValue TagValueContext TagValueListener TagValueParser TagValueWrapper Taxon TaxonFactory TaxonParser TextBlock TextLogoPainter ThreadPool TickFeatureRenderer Train Trainable TrainerTransition TrainingAlgorithm TrainingContext TrainingEvent TrainingListener TrainRegression Transition TransitionTrainer TranslatedDistribution TranslatedSequencePanel TranslationTable TypedProperties UkkonenSuffixTree Unchangeable UnequalLengthAlignment UniformDistribution UnigeneCluster UnigeneDB UnigeneFactory UnigeneTools UnknownDBHelper UnsupportedChromatogramFormatException UntrainableDistribution URLFactory URLGeneratorFactory UtilHelper ValueChanger ViewingSequenceDB ViewSequence ViewSequenceFactory WeakCacheMap WeakTaxon WeakTaxonFactory WeakValueHashMap WebSequenceDB WeightMatrix WeightMatrixAnnotator WMAsMM WordTokenization XFFFeatureSetHandler XFFHelper XFFPartHandlerFactory XFFTools XFFWriter XMLAnnotationTypeHandler XMLAnnotationTypeHandler.CollectionConstraintHandler XMLAnnotationTypeHandler.CollectionConstraintHandlerFactory XMLAnnotationTypeHandler.PropertyConstraintHandler XMLAnnotationTypeHandler.PropertyConstraintHandlerFactory XMLAnnotationTypeWriter XMLAnnotationTypeWriter.XMLCollectionConstraintWriter XMLAnnotationTypeWriter.XMLPropertyConstraintWriter XMLBeans XMLDispatcher XMLDistributionReader XMLDistributionWriter XMLFilterHandler XMLFilterHandler.FilterHandler XMLFilterHandler.FilterHandlerFactory XMLFilterWriter XMLFilterWriter.FilterWriter XmlMarkovModel XMLPeerBuilder XMLPeerFactory XMLWritable XMLWriter ZiggyFeatureRenderer ZiggyImapRenderer