- 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
- AlignIOConstants
- Alignment
- Alignment.SymbolListIterator
- AlignmentAlgorithm
- AlignmentElement
- AlignmentFormat
- AlignmentMarker
- AlignmentPair
- AlignmentRenderer
- AlignmentStAXHandler
- Alphabet
- AlphabetIndex
- AlphabetManager
- AlphabetResolver
- AlreadyExistsException
- AlternateTokenization
- Annotatable
- Annotatable.AnnotationForwarder
- AnnotatedSequenceDB
- Annotation
- AnnotationBuilder
- AnnotationChanger
- AnnotationDB
- AnnotationFactory
- AnnotationRenamer
- AnnotationTools
- AnnotationType
- AnnotationType.Abstract
- AnnotationType.Impl
- App
- AppBeanRunner
- AppEntry
- AppException
- ARAlignment
- ArrayStateMachineToolkit
- ArrowedFeatureRenderer
- ArrowGlyph
- AssembledSymbolList
- AssertionFailure
- AtomicSymbol
- 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
- 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
- ByteCode
- ByteElementHandlerBase
- Cache
- CacheMap
- CacheReference
- CachingInputStream
- CachingKernel
- CachingSequenceDB
- CandyEntry
- CandyException
- CandyFinder
- CandyVocabulary
- CardinalityConstraint
- Cell
- CellCalculator
- CellCalculatorFactory
- CellCalculatorFactoryMaker
- 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
- 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
- CodeClass
- CodeContext
- CodeException
- CodeField
- CodeGenerator
- CodeMethod
- CodeUtils
- 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
- CompoundRichLocation
- ComputeObject
- ConstantPool
- Constants
- Count
- CountedBufferedReader
- CRC64Checksum
- CrosshairRenderer
- CrossOverFunction
- CrossOverFunction.NoCross
- CrossProductTokenization
- CrossRef
- CrossReferenceResolutionException
- CrossReferenceResolver
- DatabaseURLGenerator
- DataBlock
- DataBlockBuilder
- DataBlockListener
- DataBlockParser
- DataStore
- DataStoreFactory
- DBHelper
- DBHelper.BioSequenceStyle
- DBHelper.DeleteStyle
- DBHelper.JoinStyle
- DebuggingRichSeqIOListener
- DefaultOps
- DefaultURLGeneratorFactory
- DelegationManager
- DelegationManager
- 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
- 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
- Fastq
- FastqBuilder
- FastqReader
- FastqTools
- 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
- FilteringContentHandler
- FilteringRenderer
- FilterTest
- FilterTest.Equals
- FilterTest.FindRegex
- FilterTest.GreaterThan
- FilterTest.LessThan
- FilterTest.MatchRegex
- FilterTransformer
- FilterUtils
- FilterUtils.FilterTransformer
- FiniteAlphabet
- FiniteAutomaton
- FitnessFunction
- FixedBaseWidthScaler
- FixedSizeCache
- FixedSizeMap
- FlatFileCache
- FlatFileUnigeneFactory
- FlatSequenceDB
- FlatSequenceDBProvider
- FlexibleAlignment
- FloatElementHandlerBase
- Format
- Formats
- FormatTools
- 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
- GapDistribution
- GappedRenderer
- GappedSequence
- GappedSymbolList
- GAStoppingCriteria
- GAStoppingCriteria.MaximumGeneration
- GATools
- GenbankFileFormer
- GenbankFormat
- GenbankFormat
- GenbankFormat.Terms
- GenbankLocationParser
- GenbankProcessor
- GenbankProcessor.Factory
- GenbankRichSequenceDB
- GenbankSequenceDB
- GenbankXmlFormat
- GenEmblFeatureComparator
- GenEmblPropertyComparator
- GeneratedClassLoader
- GeneratedCodeClass
- GeneratedCodeMethod
- 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
- GUITools
- HashBioEntryDB
- HashedFastaIterator
- HashRichSequenceDB
- HashSequenceDB
- HeaderStAXHandler
- HeadlessRenderContext
- HelixGlyph
- HitMerger
- HitStAXHandler
- HmmerProfileHMM
- HmmerProfileParser
- HMMTrainer
- HomologeneBuilder
- HomologeneDB
- HomologeneTools
- Homology
- HomologyDB
- HomologyFeature
- HomologyFeature.Template
- HSPStAXHandler
- HSPSummaryStAXHandler
- HTMLRenderer
- HypersonicDBHelper
- Identifiable
- IDMaker
- IDMaker.ByName
- IDMaker.ByURN
- IfExpression
- 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
- IndexStore
- IndexStore
- IndexTools
- InfinitelyAmbiguousSymbolList
- Initializable
- InputHandler
- InputStreamProvider
- INSDseqFormat
- INSDseqFormat.Terms
- Instruction
- InstructionVector
- IntegerAlphabet
- IntegerAlphabet.IntegerSymbol
- IntegerAlphabet.SubIntegerAlphabet
- IntegerOntology
- IntegerTokenization
- IntElementHandlerBase
- IntrospectedCodeClass
- InvalidTermException
- IsoelectricPointCalc
- ItemValue
- JDBCConnectionPool
- JDBCPooledDataSource
- KeyedWeakReference
- KnuthMorrisPrattSearch
- Label
- 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
- LocalVariable
- Location
- LocationHandlerBase
- LocationTools
- LogoContext
- LogoPainter
- LongElementHandlerBase
- MagicalState
- ManyToOneTranslationTable
- MappedDataStoreFactory
- MarkLabel
- MarkovModel
- MassCalc
- Matcher
- MatrixPairDPCursor
- MaxMismatchMatcher
- MaxMismatchPattern
- Meme
- MergeAnnotation
- MergeFeatureHolder
- MergeLocation
- MergingAnnotationDB
- MergingIterator
- MergingSet
- ModelInState
- ModelTrainer
- MotifTools
- MSFAlignmentFormat
- MultiLineRenderer
- MultipleHitCorrection
- MultiSourceCompoundRichLocation
- MultiTagger
- MutationFunction
- MutationFunction.NoMutation
- 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
- 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
- ParametricCodeGenerator
- ParametricType
- ParseErrorEvent
- ParseErrorListener
- ParseErrorSource
- ParseException
- ParseListener
- Parser
- ParserException
- ParserListener
- ParsimonyTreeMethod
- Pattern
- PatternBlitz
- PatternFactory
- PatternListener
- PatternMaker
- PdbSAXParser
- PdbToXMLConverter
- PeptideDigestRenderer
- PhredFormat
- PhredSequence
- PhredTools
- PHYLIPFileBuilder
- PHYLIPFileFormat
- PHYLIPFileListener
- PlainBlock
- PlainStyle
- PointLocation
- PolynomialKernel
- Population
- Position
- PositionResolver
- PositionResolver.AverageResolver
- PositionResolver.MaximalResolver
- PositionResolver.MinimalResolver
- PostgreSQLDBHelper
- PParametricCodeGenerator
- 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
- Qualitative
- QualitativeAlignment
- RadialBaseKernel
- RAF
- RandomAccessReader
- RangeLocation
- RankedCrossRef
- RankedCrossRefable
- RankedDocRef
- ReaderInputHandler
- ReaderWriterPipe
- RealizingFeatureHolder
- Record
- Record.Impl
- RectangleGlyph
- RectangularBeadRenderer
- RectangularImapRenderer
- ReferenceAnnotation
- RegexChanger
- RegexException
- RegexFieldFinder
- RegexParser
- RegexSplitter
- Registry
- RegistryConfiguration
- RegistryConfiguration.Composite
- RegistryConfiguration.Impl
- RegistryException
- RelabeledAlignment
- RemoteFeature
- RemoteFeature.Region
- RemoteFeature.Resolver
- RemoteFeature.Template
- RemotePairwiseAlignmentOutputProperties
- RemotePairwiseAlignmentProperties
- RemotePairwiseAlignmentService
- RemoteQBlastAlignmentProperties
- RemoteQBlastOutputFormat
- RemoteQBlastOutputProperties
- RemoteQBlastService
- RemoteTerm
- RemoteTerm.Impl
- ReparentContext
- RepeatedCharSequence
- 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
- 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
- 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
- SequencePanelWrapper
- 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
- 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
- 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
- SimpleSVMClassifierModel
- SimpleSVMTarget
- SimpleSymbolList
- SimpleSymbolListFactory
- SimpleSymbolPropertyTable
- SimpleSymbolPropertyTableDB
- SimpleSymbolStyle
- SimpleTagValueWrapper
- SimpleTaxon
- SimpleTaxonFactory
- SimpleThreadPool
- SimpleTrackLayout
- SimpleTranslationTable
- SimpleWeightMatrix
- SimpleXMLEmitter
- SingleDP
- SingleDPMatrix
- SingletonAlphabet
- SingletonList
- SixFrameRenderer
- SixFrameZiggyRenderer
- SmallAnnotation
- SmallCursor
- SmallMap
- SmallSet
- SmartSequenceBuilder
- SmithWaterman
- SMORegressionTrainer
- SMOTrainer
- SoftHashMap
- SoftMaskedAlphabet
- SoftMaskedAlphabet.MaskingDetector
- SoftMaskedAlphabet.MaskingDetector.DefaultMaskingDetector
- SoftReferenceCache
- SolexaFastqReader
- SolexaFastqWriter
- SparseVector
- SparseVector.NormalizingKernel
- SQLUnigeneFactory
- StackedFeatureRenderer
- StackedLogoPainter
- 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
- StreamListener
- StreamParser
- StreamPipe
- StreamReader
- StreamWriter
- StringElementHandlerBase
- StringTools
- StructureTools
- SubCircularRendererContext
- SubIntegerTokenization
- SubPairwiseRenderContext
- SubSequence
- SubSequence.SubProjectedFeatureContext
- SubSequenceDB
- SubSequenceRenderContext
- SubstitutionMatrix
- SuffixTree
- SuffixTree.SuffixNode
- SuffixTreeKernel
- SuffixTreeKernel.DepthScaler
- SuffixTreeKernel.MultipleScalar
- SuffixTreeKernel.NullModelScaler
- SuffixTreeKernel.SelectionScalar
- SuffixTreeKernel.UniformScaler
- 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
- TaxaBlock
- TaxaBlockBuilder
- TaxaBlockListener
- TaxaBlockParser
- 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
- TreesBlock
- TreesBlock.NewickTreeString
- TreesBlockBuilder
- TreesBlockListener
- TreesBlockParser
- 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