All Classes
AAindex
AAindexStreamReader
ABIFChromatogram
ABIFParser
ABIFParser.DataAccess
ABIFParser.TaggedDataRecord
ABITools
ABITrace
AbiTraceRenderer
AbstractAlignmentStyler
AbstractAlphabet
AbstractAnnotation
AbstractBeadRenderer
AbstractBean
AbstractBioEntryDB
AbstractChangeable
AbstractChromatogram
AbstractCrossOverFunction
AbstractDistribution
AbstractFeatureHolder
AbstractGeneticAlgorithm
AbstractLocation
AbstractLocationDecorator
AbstractManyToOneTranslationTable
AbstractMatrixPairDPCursor
AbstractMutationFunction
AbstractOrderNDistribution
AbstractOrganism
AbstractOrthologueSet
AbstractOrthoPairCollection
AbstractOrthoPairSet
AbstractPeptideDigestRenderer
AbstractPopulation
AbstractRangeLocation
AbstractReversibleTranslationTable
AbstractRichSequenceDB
AbstractSequenceDB
AbstractSVMClassifierModel
AbstractSVMTarget
AbstractSymbol
AbstractSymbolList
AbstractTaxon
AbstractTerm
AbstractTrainer
AbstractULAlignment
AbstractWrapper
AcnumHitReader
AcnumTrgReader
ActivityListener
Agave2AgaveAnnotFilter
AGAVEAltIdsPropHandler
AGAVEAnnotationsHandler
AGAVEAnnotFilter
AGAVEAnnotFilterFactory
AGAVEAssemblyHandler
AGAVEBioSeqCallbackItf
AGAVEBioSeqHandler
AGAVEBioSequenceHandler
AGAVECallbackItf
AGAVECdsHandler
AGAVEChromosomeCallbackItf
AGAVEChromosomeHandler
AGAVEClassificationHandler
AGAVECompResultHandler
AGAVEComputationHandler
AGAVEContigCallbackItf
AGAVEContigHandler
AGAVEDbId
AGAVEDbIdCallbackItf
AGAVEDbIdPropCallbackItf
AGAVEDbIdPropHandler
AGAVEDescPropHandler
AGAVEElementIdPropHandler
AGAVEEvidenceCallbackItf
AGAVEEvidenceHandler
AGAVEExonsPropHandler
AGAVEFeatureCallbackItf
AGAVEFragmentOrderHandler
AGAVEFragmentOrientationHandler
AGAVEGeneHandler
AGAVEHandler
AGAVEIdAlias
AGAVEIdAliasCallbackItf
AGAVEIdAliasPropHandler
AGAVEKeywordPropHandler
AGAVEMapLocation
AGAVEMapLocationPropHandler
AGAVEMapPosition
AGAVEMapPositionPropHandler
AGAVEMatchAlignPropHandler
AGAVEMatchDescPropHandler
AGAVEMatchRegion
AGAVEMatchRegionPropHandler
AGAVEMrnaHandler
AGAVENotePropHandler
AGAVEPredictedProteinHandler
AGAVEProperty
AGAVEQualifierPropHandler
AGAVEQueryRegion
AGAVEQueryRegionPropHandler
AGAVERelatedAnnot
AGAVERelatedAnnotPropHandler
AGAVEResultGroupHandler
AGAVEResultPropertyPropHandler
AGAVESciPropertyPropHandler
AGAVESeqFeatureHandler
AGAVESeqLocationPropHandler
AGAVESeqMapHandler
AGAVESeqPropHandler
AGAVETranscriptHandler
AGAVEUnorderedFragmentsHandler
AGAVEViewPropHandler
AgaveWriter
AGAVEXref
AGAVEXrefCallbackItf
AGAVEXrefPropHandler
AGAVEXrefPropPropHandler
AGAVEXrefs
AGAVEXrefsPropHandler
Aggregator
AligMatEl
Alignable
AlignedPosition
AlignIOConstants
Alignment
Alignment
Alignment.SymbolListIterator
AlignmentCalc
AlignmentElement
AlignmentFormat
AlignmentGui
AlignmentMarker
AlignmentPositionListener
AlignmentRenderer
AlignmentStAXHandler
AligNPE
AlignTools
Alphabet
AlphabetIndex
AlphabetManager
AlphabetResolver
AlphaCTools
AlreadyExistsException
AltAligComparator
AlternateTokenization
AlternativeAlignment
AlternativeAlignmentFrame
AminoAcid
AminoAcidImpl
Annotatable
Annotatable.AnnotationForwarder
AnnotatedSequenceDB
Annotation
AnnotationBuilder
AnnotationChanger
AnnotationDB
AnnotationFactory
AnnotationRenamer
AnnotationTools
AnnotationType
AnnotationType.Abstract
AnnotationType.Impl
AppBeanRunner
AppEntry
AppException
ARAlignment
ArrayStateMachineToolkit
ArrowedFeatureRenderer
ArrowGlyph
AssembledSymbolList
AssertionFailure
Atom
AtomicSymbol
AtomImpl
AtomIterator
AtomSite
Author
AutomatonException
BackMatrixPairDPCursor
BackPointer
BarLogoPainter
BaseXMLWriter
BasicFeatureRenderer
BasicImapRenderer
BasicXFFHelper
BasisSymbol
BaumWelchSampler
BaumWelchTrainer
BeadFeatureRenderer
BeanAsAnnotation
BeanAsMap
BetweenLocation
BiblioArticle
BiblioBook
BiblioBookArticle
BiblioCriterion
BiblioDescription
BiblioEntryStatus
BiblioJournal
BiblioJournalArticle
BiblioOrganisation
BiblioPatent
BiblioPerson
BiblioProceeding
BiblioProvider
BiblioScope
BiblioService
BiblioSubject
BiblioTechReport
BiblioThesis
BiblioWebResource
BibRef
BibRefException
BibRefQuery
BibRefSupport
BinarySearch
BioEntry
BioEntryDB
BioEntryDBLite
BioEntryIterator
BioEntryRelationship
BioError
BioException
BioFetchSequenceDB
BioFetchSequenceDBProvider
BioIndex
BiojavaJmol
BioMatcher
BioPattern
BioRuntimeException
BioSQLAcceptAllFilter
BioSQLAcceptNoneFilter
BioSQLBioEntryDB
BioSQLCrossReferenceResolver
BioSQLFeatureFilter
BioSQLFeatureFilter.And
BioSQLFeatureFilter.ByName
BioSQLFeatureFilter.ByNote
BioSQLFeatureFilter.ByNoteTermOnly
BioSQLFeatureFilter.ByRank
BioSQLFeatureFilter.BySequenceName
BioSQLFeatureFilter.BySourceTerm
BioSQLFeatureFilter.BySourceTermName
BioSQLFeatureFilter.ByStrand
BioSQLFeatureFilter.ByTypeTerm
BioSQLFeatureFilter.ByTypeTermName
BioSQLFeatureFilter.ContainedByRichLocation
BioSQLFeatureFilter.HibernateFeatureFilter
BioSQLFeatureFilter.Not
BioSQLFeatureFilter.Or
BioSQLFeatureFilter.OverlapsRichLocation
BioSQLFeatureFilter.Tools
BioSQLRichObjectBuilder
BioSQLRichSequenceDB
BioSQLRichSequenceHandler
BioSQLSequenceDB
BioSQLSequenceDBProvider
BioStore
BioStoreFactory
Blast2HTMLHandler
BlastLikeHomologyBuilder
BlastLikeSAXParser
BlastLikeSearchBuilder
BlastLikeSearchFilter
BlastLikeSearchFilter.AbstractBlastLikeSearchFilter
BlastLikeSearchFilter.And
BlastLikeSearchFilter.ByHitProperty
BlastLikeSearchFilter.BySearchProperty
BlastLikeSearchFilter.BySubHitProperty
BlastLikeSearchFilter.Node
BlastLikeSearchFilter.Not
BlastLikeSearchFilter.Or
BlastLikeToXMLConverter
BlastXMLParser
BlastXMLParserFacade
BlockPainter
BooleanElementHandlerBase
BoundaryFinder
BumpedRenderer
ByLocationMinMaxComparator
ByLocationMinMaxFeatureComparator
ByteElementHandlerBase
Cache
CacheMap
CacheReference
CachingInputStream
CachingKernel
CachingSequenceDB
CAConverter
Calc
CandyEntry
CandyException
CandyFinder
CandyVocabulary
CardinalityConstraint
Cell
CellCalculator
CellCalculatorFactory
CellCalculatorFactoryMaker
Chain
ChainImpl
Changeable
ChangeableCache
ChangeAdapter
ChangeEvent
ChangeForwarder
ChangeForwarder.Retyper
ChangeHub
ChangeListener
ChangeListener.AlwaysVetoListener
ChangeListener.ChangeEventRecorder
ChangeListener.LoggingListener
ChangeSupport
ChangeTable
ChangeTable.ChainedChanger
ChangeTable.Changer
ChangeTable.Splitter
ChangeType
ChangeVetoException
CharactersBlock
CharactersBlockBuilder
CharactersBlockListener
CharactersBlockParser
CharacterTokenization
CharElementHandlerBase
ChemComp
ChemCompConsumer
ChemCompTools
ChemicalComponentDictionary
CholeskyDecomposition
Chromatogram
ChromatogramFactory
ChromatogramGraphic
ChromatogramGraphic.Option
ChromatogramNonlinearScaler
ChromatogramNonlinearScaler.Identity
ChromatogramTools
ChunkedSymbolList
ChunkedSymbolListFactory
CircularFeatureFilteringRenderer
CircularFeatureRenderer
CircularFeaturesRenderer
CircularLocation
CircularMLR
CircularPaddedRenderer
CircularReferenceException
CircularRenderer
CircularRendererContext
CircularRendererPanel
CircularView
ClassifierExample
ClassifierExample.PointClassifier
Classify
ClassTools
ClustalWAlignmentSAXParser
ClusterAltAligs
CodonPref
CodonPrefFilter
CodonPrefFilter.AcceptAll
CodonPrefFilter.ByName
CodonPrefFilter.EverythingToXML
CodonPrefTools
CollectionConstraint
CollectionConstraint.AllValuesIn
CollectionConstraint.And
CollectionConstraint.Contains
CollectionConstraint.Or
ColourCommand
Comment
Commitable
CommitFailure
CompactedDataStore
CompactedDataStoreFactory
ComparableOntology
ComparableTerm
ComparableTriple
ComponentFeature
ComponentFeature.Template
Composition
Compound
CompoundRichLocation
ComputeObject
Constants
CoordManager
Count
CountedBufferedReader
CRC64Checksum
CrosshairRenderer
CrossOverFunction
CrossOverFunction.NoCross
CrossProductTokenization
CrossRef
CrossReferenceResolutionException
CrossReferenceResolver
DAS
DASAlignmentCall
DASAlignmentClient
DASAlignmentXMLResponseParser
DASException
DASLink
DASSequence
DASSequenceDB
DASSequenceDBProvider
DASStructureCall
DASStructureClient
DASStructureXMLResponseParser
DatabasePDBremark
DatabasePDBrev
DatabaseURLGenerator
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
Entity
EntityPolySeq
EntryNamIdxReader
EntryNamRandomAccess
Enzyme
ExecRunner
Exptl
ExternalProcess
FastaAlignmentFormat
FastaDescriptionLineParser
FastaDescriptionLineParser.Factory
FastaFormat
FastaFormat
FastaHeader
FastaSearchSAXParser
FastaSequenceSAXParser
Fastq
FastqBuilder
FastqReader
FastqVariant
FastqWriter
FastXMLWriter
Feature
Feature.ByLocationComparator
Feature.Template
FeatureBlockSequenceRenderer
FeatureFilter
FeatureFilter.And
FeatureFilter.AnnotationContains
FeatureFilter.ByAncestor
FeatureFilter.ByAnnotation
FeatureFilter.ByAnnotationType
FeatureFilter.ByChild
FeatureFilter.ByClass
FeatureFilter.ByComponentName
FeatureFilter.ByDescendant
FeatureFilter.ByFeature
FeatureFilter.ByPairwiseScore
FeatureFilter.ByParent
FeatureFilter.BySequenceName
FeatureFilter.BySource
FeatureFilter.ByType
FeatureFilter.ContainedByLocation
FeatureFilter.FrameFilter
FeatureFilter.HasAnnotation
FeatureFilter.Not
FeatureFilter.OnlyChildren
FeatureFilter.OnlyDescendants
FeatureFilter.Or
FeatureFilter.OverlapsLocation
FeatureFilter.ShadowContainedByLocation
FeatureFilter.ShadowOverlapsLocation
FeatureFilter.StrandFilter
FeatureHandler
FeatureHolder
FeatureHolder.EmptyFeatureHolder
FeatureHolderUtils
FeatureImpl
FeatureLabelRenderer
FeatureLabelRenderer.AnnotationLabelMaker
FeatureLabelRenderer.LabelMaker
FeatureLabelRenderer.SourceLabelMaker
FeatureLabelRenderer.TypeLabelMaker
FeatureRealizer
FeatureRenderer
FeatureSource
FeatureTableParser
FeatureTree
FeatureTypes
FeatureTypes.Repository
FeatureTypes.RepositoryImpl
FeatureTypes.Type
FetchURL
FileAsList
FileConvert
FilteringContentHandler
FilteringRenderer
FilterTest
FilterTest.Equals
FilterTest.FindRegex
FilterTest.GreaterThan
FilterTest.LessThan
FilterTest.MatchRegex
FilterTransformer
FilterUtils
FilterUtils.FilterTransformer
FiniteAlphabet
FiniteAutomaton
FitnessFunction
FixedBaseWidthScaler
FixedSizeCache
FixedSizeMap
FlatFileInstallation
FlatFileUnigeneFactory
FlatSequenceDB
FlatSequenceDBProvider
FlexibleAlignment
FloatElementHandlerBase
Format
Formats
FormatTools
FragmentJoiner
FragmentPair
Frame
FramedFeature
FramedFeature.ReadingFrame
FramedFeature.Template
FullHmmerProfileHMM
FundamentalAtomicSymbol
FuzzyLocation
FuzzyLocation.RangeResolver
FuzzyPointLocation
FuzzyPointLocation.PointResolver
GACross
GACrossResult
GAMEAnnotationHandler
GAMEAnnotationHandler
GAMEAspectHandler
GAMEAspectPropHandler
GAMEDbxrefHandler
GAMEDbxrefPropHandler
GAMEDescriptionPropHandler
GAMEFeatureCallbackItf
GAMEFeatureSetHandler
GAMEFeatureSetHandler
GAMEFeatureSetPropHandler
GAMEFeatureSpanHandler
GAMEFeatureSpanHandler
GAMEFormat
GAMEGeneHandler
GAMEGenePropHandler
GAMEHandler
GAMEHandler
GAMEMapPosPropHandler
GAMENameCallbackItf
GAMENamePropHandler
GAMEPropertyHandler
GAMEResiduesPropHandler
GAMESeqHandler
GAMESeqPropHandler
GAMESeqRelHandler
GAMESeqRelPropHandler
GAMESpanHandler
GAMESpanPropHandler
GAMETranscriptCallbackItf
GAMETypePropHandler
GapArray
GapDistribution
GappedRenderer
GappedSequence
GappedSymbolList
GAStoppingCriteria
GAStoppingCriteria.MaximumGeneration
GATools
GenbankFileFormer
GenbankFormat
GenbankFormat
GenbankFormat.Terms
GenbankLocationParser
GenbankProcessor
GenbankProcessor.Factory
GenbankRichSequenceDB
GenbankSequenceDB
GenbankXmlFormat
GenEmblFeatureComparator
GenEmblPropertyComparator
GeneticAlgorithm
GeneticCodes
GenpeptFormat
GenpeptRichSequenceDB
GenpeptSequenceDB
GFF3DocumentHandler
GFF3Parser
GFF3Record
GFF3Record.Impl
GFFDataSource
GFFDocumentHandler
GFFEntrySet
GFFErrorHandler
GFFErrorHandler.AbortErrorHandler
GFFErrorHandler.SkipRecordErrorHandler
GFFFilterer
GFFParser
GFFRecord
GFFRecordFilter
GFFRecordFilter.AcceptAll
GFFRecordFilter.FeatureFilter
GFFRecordFilter.FrameFilter
GFFRecordFilter.NotFilter
GFFRecordFilter.SequenceFilter
GFFRecordFilter.SourceFilter
GFFRecordFilter.StrandFilter
GFFTools
GFFWriter
Glyph
GlyphFeatureRenderer
GlyphUtils
GOParser
Gotoh
Group
GroupIterator
GroupType
GUITools
HashBioEntryDB
HashedFastaIterator
HashRichSequenceDB
HashSequenceDB
HeaderStAXHandler
HeadlessRenderContext
HelixGlyph
HetatomImpl
HitMerger
HitStAXHandler
HmmerProfileHMM
HmmerProfileParser
HMMTrainer
HomologeneBuilder
HomologeneDB
HomologeneTools
Homology
HomologyDB
HomologyFeature
HomologyFeature.Template
HSPStAXHandler
HSPSummaryStAXHandler
HTMLRenderer
HypersonicDBHelper
Identifiable
IDMaker
IDMaker.ByName
IDMaker.ByURN
IgnoreCountsTrainer
IgnoreRecordException
IllegalAlignmentEditException
IllegalAlphabetException
IllegalIDException
IllegalOrganismException
IllegalSymbolException
IllegalTransitionException
IlluminaFastqReader
IlluminaFastqWriter
ImageMap
ImageMap.ClientSide
ImageMap.HotSpot
ImageMap.ServerSide
ImageMapRenderer
Index
Index2Model
IndexedAnnotationDB
IndexedAnnotationDB.ParserListenerFactory
IndexedAnnotationDB.StaticMethodRPFactory
IndexedChangeHub
IndexedCount
IndexedSequenceDB
Indexer
Indexer2
IndexPair
IndexStore
IndexStore
IndexTools
InfinitelyAmbiguousSymbolList
Initializable
InputHandler
InputStreamProvider
INSDseqFormat
INSDseqFormat.Terms
IntegerAlphabet
IntegerAlphabet.IntegerSymbol
IntegerAlphabet.SubIntegerAlphabet
IntegerOntology
IntegerTokenization
IntElementHandlerBase
InvalidTermException
IsoelectricPointCalc
ItemValue
JDBCConnectionPool
JDBCPooledDataSource
JMatrixPanel
JmolAlignedPositionListener
JointFragments
JournalArticle
KeyedWeakReference
KnuthMorrisPrattSearch
LabelledSequenceRenderer
LabelRenderer
LabelRenderer.RenderNothing
LargeBuffer
LayeredRenderer
LazyFeatureHolder
LazyFilteredAnnotationDB
LazyFilterFeatureHolder
LazySearchedAnnotationDB
LifeScienceIdentifier
LifeScienceIdentifierParseException
Ligand
Ligand.Compound
Ligand.Enzyme
Ligand.Reaction
LightPairDPCursor
LinearKernel
LineInfo
LineSplitParser
ListSumKernel
ListTools
ListTools.Doublet
ListTools.Mapper
ListTools.SeriesList
ListTools.Triplet
Location
LocationHandlerBase
LocationTools
LogoContext
LogoPainter
LongElementHandlerBase
LUDecomposition
MagicalState
ManyToOneTranslationTable
MappedDataStoreFactory
MarkovModel
MassCalc
Matcher
Maths
Matrix
MatrixPairDPCursor
MaxMismatchMatcher
MaxMismatchPattern
Meme
MenuCreator
MergeAnnotation
MergeFeatureHolder
MergeLocation
MergingAnnotationDB
MergingIterator
MergingSet
MMcifConsumer
MMCIFFileInstallation
MMCIFFileReader
MMcifParser
ModelInState
ModelTrainer
MotifTools
MSFAlignmentFormat
MultiLineRenderer
MultipleHitCorrection
MultiSourceCompoundRichLocation
MultiTagger
MutationFunction
MutationFunction.NoMutation
Mutator
MySQLDBHelper
Namespace
NameTokenization
NcbiDatabaseURLGenerator
NCBISequenceDB
NCBITaxon
NCBITaxonomyLoader
NeedlemanWunsch
NestedKernel
NewAssembledSymbolList
NewSimpleAssembly
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
OboFileEventListener
OboFileHandler
OboFileParser
OboFileParser.SOPair
OboParser
OffsetRulerRenderer
Ontology
Ontology.Impl
OntologyException
OntologyFactory
OntologyOps
OntologyTerm
OntologyTerm.Impl
OntoTools
OptimizableFilter
OracleDBHelper
OrderCrossover
OrderNDistribution
OrderNDistributionFactory
Organism
OrganismParser
OrganismParser.Factory
Orthologue
OrthologueFilter
OrthologueFilter.AcceptAll
OrthologueFilter.And
OrthologueFilter.ByAccession
OrthologueFilter.ByHomologeneID
OrthologueFilter.ByLocusID
OrthologueFilter.ByTaxon
OrthologueFilter.ByTaxonID
OrthologueFilter.ByTitle
OrthologueFilter.Not
OrthologueFilter.Or
OrthologueFilter.Xor
OrthologueSet
OrthologueSet.Iterator
OrthoPair
OrthoPairCollection
OrthoPairCollection.Iterator
OrthoPairFilter
OrthoPairFilter.AcceptAll
OrthoPairFilter.And
OrthoPairFilter.ByMaxIdentity
OrthoPairFilter.ByMinIdentity
OrthoPairFilter.ByRef
OrthoPairFilter.BySimilarityType
OrthoPairFilter.Not
OrthoPairFilter.Or
OrthoPairFilter.Xor
OrthoPairSet
OrthoPairSet.Iterator
OrthoPairSetFilter
OrthoPairSetFilter.AcceptAll
OrthoPairSetFilter.AllPairsInCollection
OrthoPairSetFilter.And
OrthoPairSetFilter.ByMinIdentity
OrthoPairSetFilter.ByTaxon
OrthoPairSetFilter.Not
OrthoPairSetFilter.Or
OrthoPairSetFilter.SomePairsInCollection
OrthoPairSetFilter.Xor
OutputHandler
OverlayAnnotation
OverlayMap
OverlayMarker
OverlayRendererWrapper
PackedSymbolList
PackedSymbolListFactory
Packing
PackingFactory
PaddingRenderer
PairDistribution
PairDPCursor
PairDPMatrix
PairwiseDiagonalRenderer
PairwiseDP
PairwiseFilteringRenderer
PairwiseOverlayRenderer
PairwiseRenderContext
PairwiseSequencePanel
PairwiseSequenceRenderer
PairwiseSequenceRenderer.PairwiseRendererForwarder
ParseErrorEvent
ParseErrorListener
ParseErrorSource
ParseException
Parser
ParserException
ParserListener
ParsimonyTreeMethod
Pattern
PatternBlitz
PatternFactory
PatternListener
PatternMaker
PDBDirPanel
PDBFileParser
PDBFileReader
PDBFilter
PDBHeader
PDBInstallation
PDBMSDReader
PDBParseException
PDBRecord
PdbSAXParser
PDBServerPanel
PDBSRSReader
PdbToXMLConverter
PDBUploadPanel
PdbxEntityNonPoly
PdbxNonPolyScheme
PdbxPolySeqScheme
PeptideDigestRenderer
PhredFormat
PhredSequence
PhredTools
PHYLIPFileBuilder
PHYLIPFileFormat
PHYLIPFileListener
PlainBlock
PlainStyle
PointLocation
PolymerType
PolynomialKernel
Population
Position
PositionResolver
PositionResolver.AverageResolver
PositionResolver.MaximalResolver
PositionResolver.MinimalResolver
PostgreSQLDBHelper
PrepareIndexFile
PrepareMMcifIndexFile
PrettyXMLWriter
ProcessTimeoutException
ProcessTools
ProfileEmissionState
ProfileHMM
ProjectedFeature
ProjectedFeatureHolder
Projection
ProjectionContext
ProjectionEngine
ProjectionEngine.Instantiator
ProjectionEngine.TemplateProjector
ProjectionUtils
PropDetailHandler
PropertyChanger
PropertyConstraint
PropertyConstraint.And
PropertyConstraint.ByAnnotationType
PropertyConstraint.ByClass
PropertyConstraint.Enumeration
PropertyConstraint.ExactValue
PropertyConstraint.Or
PropertyWriter
ProportionalSelection
Protease
ProteaseManager
ProteinRefSeqFileFormer
ProteinRefSeqProcessor
ProteinRefSeqProcessor.Factory
ProteinTools
ProviderNotFoundException
QRDecomposition
Qualitative
QualitativeAlignment
RadialBaseKernel
RAF
RandomAccessReader
RangeLocation
RankedCrossRef
RankedCrossRefable
RankedDocRef
RasmolCommandListener
ReaderInputHandler
ReaderWriterPipe
RealizingFeatureHolder
Record
Record.Impl
RectangleGlyph
RectangularBeadRenderer
RectangularImapRenderer
ReferenceAnnotation
ReferenceServer
Refine
RegexChanger
RegexException
RegexFieldFinder
RegexParser
RegexSplitter
Registry
RegistryConfiguration
RegistryConfiguration.Composite
RegistryConfiguration.Impl
RegistryException
RelabeledAlignment
RemoteFeature
RemoteFeature.Region
RemoteFeature.Resolver
RemoteFeature.Template
RemoteTerm
RemoteTerm.Impl
ReparentContext
RepeatedCharSequence
ResidueType
ResourceEntityResolver
RestrictionEnzyme
RestrictionEnzymeManager
RestrictionMapper
RestrictionSite
RestrictionSite.Template
RevCompSequence
ReversibleTranslationTable
RichAnnotatable
RichAnnotation
RichFeature
RichFeature.Template
RichFeature.Tools
RichFeatureRelationship
RichFeatureRelationshipHolder
RichLocation
RichLocation.Strand
RichLocation.Tools
RichObjectBuilder
RichObjectFactory
RichSeqIOAdapter
RichSeqIOListener
RichSequence
RichSequence.IOTools
RichSequence.IOTools.SingleRichSeqIterator
RichSequence.Terms
RichSequence.Tools
RichSequenceBuilder
RichSequenceBuilderFactory
RichSequenceDB
RichSequenceDBLite
RichSequenceFormat
RichSequenceFormat.BasicFormat
RichSequenceFormat.HeaderlessFormat
RichSequenceHandler
RichSequenceIterator
RichStreamReader
RichStreamWriter
RNATools
RoundRectangularBeadRenderer
RulerRenderer
SangerFastqReader
SangerFastqWriter
SAX2StAXAdaptor
SAX2StAXAdaptor
ScaleableMatrixPanel
SCF
ScoreType
ScoreType.NullModel
ScoreType.Odds
ScoreType.Probability
Search
Search.Listener
SearchBuilder
SearchContentAdapter
SearchContentFilter
SearchContentHandler
SearchContentHandlerDebugger
SearchException
SearchListener
SearchListener.Echo
SearchListener.FilterByLength
SearchListener.Tee
SearchListener.Wrapper
SecondaryStructureFeatureRenderer
Seekable
SelectionFunction
SelectionFunction.SelectAll
SelectionFunction.Threshold
SeqContentPattern
SeqFileFormer
SeqIOAdapter
SeqIOConstants
SeqIOEventEmitter
SeqIOFilter
SeqIOListener
SeqIOTools
SeqRes2AtomAligner
SeqSimilarityAdapter
SeqSimilaritySearcher
SeqSimilaritySearchHit
SeqSimilaritySearchHit.ByScoreComparator
SeqSimilaritySearchHit.BySubHitCountComparator
SeqSimilaritySearchResult
SeqSimilaritySearchSubHit
SeqSimilaritySearchSubHit.ByScoreComparator
SeqSimilaritySearchSubHit.BySubjectStartComparator
SeqSimilarityStAXAdapter
SeqSimilarityStAXHandler
Sequence
SequenceAlignment
SequenceAlignmentSAXParser
SequenceAnnotator
SequenceBuilder
SequenceBuilderBase
SequenceBuilderFactory
SequenceBuilderFilter
SequenceContentHandlerBase
SequenceDB
SequenceDBDataSource
SequenceDBInstallation
SequenceDBLite
SequenceDBProvider
SequenceDBSearchHit
SequenceDBSearchResult
SequenceDBSearchSubHit
SequenceDBSequenceBuilder
SequenceDBWrapper
SequenceDisplay
SequenceFactory
SequenceFormat
SequenceHandler
SequenceIterator
SequenceMouseListener
SequencePanel
SequencePanelWrapper
SequencePoster
SequenceRenderContext
SequenceRenderContext.Border
SequenceRenderer
SequenceRenderer.RendererForwarder
SequenceRendererWrapper
SequencesAsGFF
SequenceScalePanel
SequenceStreamer
SequenceStreamer.FileStreamer
SequenceStreamer.SequenceDBStreamer
SequenceTools
SequenceViewerEvent
SequenceViewerListener
SequenceViewerMotionListener
SequenceViewerMotionSupport
SequenceViewerSupport
Services
SigmoidKernel
SimilarityPairBuilder
SimilarityPairFeature
SimilarityPairFeature.EmptyPairwiseAlignment
SimilarityPairFeature.Template
SimilarityType
SimilarityType.PlaceHolder
SimpleAlignment
SimpleAlignmentElement
SimpleAlignmentStyler
SimpleAlphabet
SimpleAnnotation
SimpleAnnotationDB
SimpleAnnotFilter
SimpleAssembly
SimpleAssemblyBuilder
SimpleAtomicSymbol
SimpleBioEntry
SimpleBioEntryRelationship
SimpleChromatogram
SimpleCodonPref
SimpleComment
SimpleComparableOntology
SimpleComparableTerm
SimpleComparableTriple
SimpleCrossOverFunction
SimpleCrossRef
SimpleDistribution
SimpleDistributionTrainer
SimpleDistributionTrainerContext
SimpleDocRef
SimpleDocRefAuthor
SimpleDotState
SimpleEmissionState
SimpleFeature
SimpleFeatureHolder
SimpleFeatureRealizer
SimpleFramedFeature
SimpleGACrossResult
SimpleGappedSequence
SimpleGappedSymbolList
SimpleGappedSymbolList.Block
SimpleGeneticAlgorithm
SimpleGeneticCodeTable
SimpleGFFRecord
SimpleHMMTrainer
SimpleHomologeneBuilder
SimpleHomologeneDB
SimpleHomology
SimpleHomologyFeature
SimpleIndex
SimpleInputHandler
SimpleItemValue
SimpleLabelRenderer
SimpleManyToOneTranslationTable
SimpleMarkovModel
SimpleMMcifConsumer
SimpleMMcifParser
SimpleModelInState
SimpleModelTrainer
SimpleMutationFunction
SimpleNamespace
SimpleNCBITaxon
SimpleNCBITaxonName
SimpleNCBITaxonomyLoader
SimpleNote
SimpleOrganism
SimpleOrthologue
SimpleOrthologueSet
SimpleOrthoPair
SimpleOrthoPairCollection
SimpleOrthoPairSet
SimpleOutputHandler
SimplePopulation
SimplePosition
SimpleRankedCrossRef
SimpleRankedDocRef
SimpleRemoteFeature
SimpleRemoteFeature.DBResolver
SimpleRestrictionSite
SimpleReversibleTranslationTable
SimpleRichAnnotation
SimpleRichFeature
SimpleRichFeatureRelationship
SimpleRichLocation
SimpleRichObjectBuilder
SimpleRichSequence
SimpleRichSequenceBuilder
SimpleRichSequenceBuilderFactory
SimpleSeqSimilaritySearchHit
SimpleSeqSimilaritySearchResult
SimpleSeqSimilaritySearchSubHit
SimpleSequence
SimpleSequenceBuilder
SimpleSequenceDBInstallation
SimpleSequenceFactory
SimpleSimilarityPairFeature
SimpleStatePath
SimpleStrandedFeature
SimpleStructureServer
SimpleSVMClassifierModel
SimpleSVMTarget
SimpleSymbolList
SimpleSymbolListFactory
SimpleSymbolPropertyTable
SimpleSymbolPropertyTableDB
SimpleSymbolStyle
SimpleTagValueWrapper
SimpleTaxon
SimpleTaxonFactory
SimpleThreadPool
SimpleTrackLayout
SimpleTranslationTable
SimpleWeightMatrix
SimpleXMLEmitter
SingleDP
SingleDPMatrix
SingletonAlphabet
SingletonList
SingularValueDecomposition
SixFrameRenderer
SixFrameZiggyRenderer
SmallAnnotation
SmallCursor
SmallMap
SmallSet
SmartSequenceBuilder
SmithWaterman
SMORegressionTrainer
SMOTrainer
SoftMaskedAlphabet
SoftMaskedAlphabet.MaskingDetector
SoftMaskedAlphabet.MaskingDetector.DefaultMaskingDetector
SoftReferenceCache
SolexaFastqReader
SolexaFastqWriter
SparseVector
SparseVector.NormalizingKernel
SQLUnigeneFactory
SSBond
StackedFeatureRenderer
StackedLogoPainter
StandardAminoAcid
State
StateMachine
StateMachine.ExitNotification
StateMachine.State
StateMachineFactory
StateMachineInstance
StatePath
StaticMemberPlaceHolder
StAXContentHandler
StAXContentHandler
StAXContentHandlerBase
StAXContentHandlerBase
StAXFeatureHandler
StAXFeatureHandler
StAXFeatureHandler
StAXHandlerBinding
StAXHandlerFactory
StAXHandlerFactory
StAXHandlerFactory
StAXHandlerFactory
StAXPropertyHandler
StAXPropertyHandler
StoppingCriteria
StopRenderer
StrandedFeature
StrandedFeature.Strand
StrandedFeature.Template
StrandedFeatureHandler
StrandParser
StrCompAlignment
StreamParser
StreamPipe
StreamReader
StreamWriter
StringElementHandlerBase
StringTools
StrucAligParameters
Struct
StructAsym
StructKeywords
StructRef
StructRefSeq
Structure
StructureEvent
StructureEventImpl
StructureException
StructureFetcherRunnable
StructureImpl
StructureIO
StructureIOFile
StructureListener
StructurePairAligner
StructurePairSelector
StructureServer
StructureTools
StructureTools
SubCircularRendererContext
SubIntegerTokenization
SubPairwiseRenderContext
SubSequence
SubSequence.SubProjectedFeatureContext
SubSequenceDB
SubSequenceRenderContext
SubstitutionMatrix
SuffixTree
SuffixTree.SuffixNode
SuffixTreeKernel
SuffixTreeKernel.DepthScaler
SuffixTreeKernel.MultipleScalar
SuffixTreeKernel.NullModelScaler
SuffixTreeKernel.SelectionScalar
SuffixTreeKernel.UniformScaler
SVDSuperimposer
SVM_Light
SVM_Light.LabelledVector
SVMClassifierModel
SVMKernel
SVMRegressionModel
SVMTarget
SwapMutationFunction
Swissprot
SwissprotFileFormer
SwissprotProcessor
SwissprotProcessor.Factory
SwissprotSequenceDB
Symbol
SymbolList
SymbolListCharSequence
SymbolListFactory
SymbolListViews
SymbolPropertyTable
SymbolPropertyTableDB
SymbolPropertyTableIterator
SymbolReader
SymbolSequenceRenderer
SymbolStyle
SymbolTokenization
SymbolTokenization.TokenType
Synonym
SystemRegistry
TabDelimParser
TabIndexStore
TagDelegator
TagDropper
TagMapper
TagRenamer
TagValue
TagValueContext
TagValueListener
TagValueParser
TagValueWrapper
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