All Classes

AAindex AAindexStreamReader ABIFChromatogram ABIFParser ABIFParser.DataAccess ABIFParser.TaggedDataRecord ABITools ABITrace AbiTraceRenderer AbstractAlignmentStyler AbstractAlphabet AbstractAnnotation AbstractBeadRenderer 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 AlignIOConstants Alignment Alignment Alignment.SymbolListIterator AlignmentElement AlignmentFormat AlignmentMarker AlignmentRenderer AlignmentStAXHandler AligNPE AlignTools Alphabet AlphabetIndex AlphabetManager AlphabetResolver AlphaCTools AlreadyExistsException AltAligComparator AlternateTokenization AlternativeAlignment 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 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 CharactersBlock CharactersBlockBuilder CharactersBlockListener CharactersBlockParser CharacterTokenization CharElementHandlerBase 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 Count CountedBufferedReader CRC64Checksum CrosshairRenderer CrossOverFunction CrossOverFunction.NoCross CrossProductTokenization CrossRef CrossReferenceResolutionException CrossReferenceResolver DAS DASAlignmentCall DASAlignmentClient DASAlignmentXMLResponseParser DASException DASLink DASSequence DASSequenceDB DASSequenceDBProvider DASStructureCall DASStructureClient DASStructureXMLResponseParser DatabaseURLGenerator DataBlock DataBlockBuilder DataBlockListener DataBlockParser DataSource DataStore DataStoreFactory DBHelper DBHelper.BioSequenceStyle DBHelper.DeleteStyle DBHelper.JoinStyle DBRef DebuggingRichSeqIOListener DefaultOps DefaultURLGeneratorFactory DelegationManager DelegationManager DemoStructureServer DfaBuilder DiagonalAddKernel DiagonalCachingKernel Digest DistanceBasedTreeMethod DistancesBlock DistancesBlockBuilder DistancesBlockListener DistancesBlockParser 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 EntryNamIdxReader EntryNamRandomAccess Enzyme ExecRunner ExternalProcess FastaAlignmentFormat FastaDescriptionLineParser FastaDescriptionLineParser.Factory FastaFormat FastaFormat FastaHeader 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 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 GUITools HashBioEntryDB 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 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 JointFragments 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 MergeAnnotation MergeFeatureHolder MergeLocation MergingAnnotationDB MergingIterator MergingSet ModelInState ModelTrainer MotifTools MSFAlignmentFormat MultiLineRenderer MultipleHitCorrection MultiSourceCompoundRichLocation MultiTagger MutationFunction MutationFunction.NoMutation Mutator MySQLDBHelper Namespace NameTokenization NcbiDatabaseURLGenerator NCBISequenceDB NCBITaxon NCBITaxonomyLoader NeedlemanWunsch NestedKernel NewAssembledSymbolList NewSimpleAssembly NexusBlock NexusBlock.Abstract NexusBlockBuilder NexusBlockBuilder.Abstract NexusBlockListener NexusBlockParser NexusBlockParser.Abstract NexusComment NexusFile NexusFileBuilder NexusFileFormat NexusFileListener NexusFileListener.Abstract NexusObject Nfa NfaBuilder NfaSubModel NIODataStoreFactory NormalizingKernel Note NucleotideImpl NucleotideTools ObdaContext ObdaInitialContextFactory OBDARegistryParser ObdaUriParser ObjectUtil 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 ParsimonyTreeMethod Pattern PatternBlitz PatternFactory PatternListener PatternMaker PDBFileParser PDBFileReader PDBFilter PDBHeader PDBInstallation PDBMSDReader PDBParseException PdbSAXParser PDBSRSReader PdbToXMLConverter