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
  • 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