AbstractAlphabet
AbstractDistribution
AbstractFeatureHolder
AbstractSVMClassifierModel
AbstractSVMTarget
AbstractSymbolList
AbstractTrainer
Ace
AceAnnotation
AceElement
AceError
AceException
AceNode
AceObject
AcePerlParser
AceSequence
AceSequenceDB
AceSet
AceURL
AceURLException
AceUtils
AceValue
Alignment
AlignmentFormat
AllTokensAlphabet
Alphabet
Alphabet.EmptyAlphabet
AlphabetManager
AlphabetManager.ListWrapper
Annotatable
AnnotatedSequenceDB
Annotation
Annotation.EmptyAnnotation
AnonymousSeq
AnonymousSeqHelper
AnonymousSeqHolder
AnonymousSeqImpl
AssertionFailedException
AtomicSymbol
BarLogoPainter
BasicFeatureRenderer
BaumWelchSampler
BaumWelchTrainer
BioError
BioException
CachingKernel
CachingSequenceDB
ClassifierExample
ClassifierExample.PointClassifier
Classify
ComplementaryDistribution
CompoundLocation
Connection
Contract
CrossProductAlphabet
CrossProductSymbol
CrossProductSymbolNameParser
Database
DateValue
DefaultDescriptionReader
DiagonalAddKernel
DiagonalCachingKernel
Distribution
DistributionFactory
DistributionFactory.DefaultDistributionFactory
DistributionLogo
DistributionTrainer
DistributionTrainerContext
DNADistribution
DNAStyle
DNATools
DotState
DoubleAlphabet
DoubleAlphabet.DoubleSymbol
DP
DP.ReverseIterator
DPFactory
DPMatrix
Driver
EmblFormat
EmissionState
EndOfStream
EndOfStreamHelper
EndOfStreamHolder
FastaDescriptionReader
FastaFormat
Feature
Feature.Template
FeatureAdapter
FeatureBlockSequenceRenderer
FeatureBuilder
FeatureFilter
FeatureFilter.AcceptAllFilter
FeatureFilter.And
FeatureFilter.BySource
FeatureFilter.ByType
FeatureFilter.ContainedByLocation
FeatureFilter.Not
FeatureFilter.Or
FeatureFilter.OverlapsLocation
FeatureHolder
FeatureHolder.EmptyFeatureHolder
FeatureRealizer
FeatureRenderer
FiniteAlphabet
FixedWidthParser
FloatValue
GapDistribution
GappedSymbolList
GenbankFormat
GeneticCode
GFFDocumentHandler
GFFEntrySet
GFFErrorHandler
GFFErrorHandler.AbortErrorHandler
GFFErrorHandler.SkipRecordErrorHandler
GFFFilterer
GFFParser
GFFRecord
GFFRecordFilter
GFFRecordFilter.AcceptAll
GFFRecordFilter.FeatureFilter
GFFRecordFilter.SequenceFilter
GFFRecordFilter.SourceFilter
GFFWriter
Handler
HashSequenceDB
IDMaker
IDMaker.ByName
IDMaker.ByURN
IgnoreCountsTrainer
IgnoreRecordException
IllegalAlphabetException
IllegalSymbolException
IllegalTransitionException
IndexedSequenceDB
IntegerAlphabet
IntegerAlphabet.IntegerSymbol
IntValue
ItemValue
LinearKernel
ListSumKernel
Location
Location.EmptyLocation
Location.LocationComparator
LogoPainter
MagicalState
MarkovModel
Meme
MergeFeatureHolder
ModelChangeEvent
ModelInclude
ModelInState
ModelNode
ModelReference
ModelTrainer
ModelType
ModelVetoException
ModelView
NameParser
NameValueSet
NameValueSetHelper
NameValueSetHolder
NameValueSetListHelper
NameValueSetListHolder
NestedKernel
NormalizingKernel
ObjectUtil
OrderNSymbolList
OutOfRange
OutOfRangeHelper
OutOfRangeHolder
OverlayAnnotation
PairDistribution
PairDPMatrix
PairwiseDP
ParserException
PlainStyle
PointLocation
PolynomialKernel
PostconditionNotMetException
PreconditionNotMetException
primaryidListHelper
primaryidListHolder
PrimarySeq
PrimarySeqDB
PrimarySeqDBHelper
PrimarySeqDBHolder
PrimarySeqDBImpl
PrimarySeqHelper
PrimarySeqHolder
PrimarySeqImpl
PrimarySeqIterator
PrimarySeqIteratorHelper
PrimarySeqIteratorHolder
PrimarySeqIteratorImpl
ProfileHMM
ProteinTools
RadialBaseKernel
RangeLocation
RealizingFeatureHolder
Reference
RequestTooLarge
RequestTooLargeHelper
RequestTooLargeHolder
ReverseSymbolList
Seq
SeqDB
SeqDBHelper
SeqDBHolder
SeqDBImpl
SeqFeature
SeqFeatureHelper
SeqFeatureHolder
SeqFeatureImpl
SeqFeatureIterator
SeqFeatureIteratorHelper
SeqFeatureIteratorHolder
SeqFeatureIteratorImpl
SeqFeatureListHelper
SeqFeatureListHolder
SeqHelper
SeqHolder
SeqImpl
SeqSimilaritySearcher
SeqSimilaritySearchHit
SeqSimilaritySearchResult
SeqSimilaritySearchSubHit
SeqType
SeqTypeHelper
SeqTypeHolder
Sequence
SequenceAdapter
SequenceAnnotator
SequenceDB
SequenceDBAdapter
SequenceDBInstallation
SequenceFactory
SequenceFormat
SequenceIterator
SequenceIteratorAdapter
SequencePanel
SequenceRenderer
SequencesAsGFF
SigmoidKernel
SimpleAlignment
SimpleAlphabet
SimpleAnnotation
SimpleAtomicSymbol
SimpleDistribution
SimpleDistributionTrainer
SimpleDistributionTrainerContext
SimpleDotState
SimpleEmissionState
SimpleFeatureBuilder
SimpleFeatureHolder
SimpleFeatureRealizer
SimpleGFFRecord
SimpleItemValue
SimpleMarkovModel
SimpleModelInState
SimpleModelTrainer
SimpleSeqSimilaritySearchHit
SimpleSeqSimilaritySearchResult
SimpleSeqSimilaritySearchSubHit
SimpleSequence
SimpleSequenceDBInstallation
SimpleSequenceFactory
SimpleStatePath
SimpleSVMClassifierModel
SimpleSVMTarget
SimpleSymbol
SimpleSymbolList
SimpleSymbolStyle
SimpleTransitionTrainer
SimpleTranslationTable
SimpleWeightMatrix
SingletonAlphabet
SMORegressionTrainer
SMOTrainer
SocketDriver
SocketResultSet
SparseVector
SparseVector.NormalizingKernel
State
StatePath
StaticAceNode
StaticAceObject
StaticAceSet
StaticDateValue
StaticFloatValue
StaticIntValue
StaticMemberPlaceHolder
StaticModelInclude
StaticModelNode
StaticModelReference
StaticModelType
StaticReference
StaticStringValue
StoppingCriteria
StrandedFeature
StrandedFeature.Strand
StrandedFeature.Template
StreamReader
StreamReader.Context
StreamWriter
stringListHelper
stringListHolder
StringValue
SuffixTree
SuffixTree.SuffixNode
SuffixTreeKernel
SuffixTreeKernel.DepthScaler
SuffixTreeKernel.MultipleScalar
SuffixTreeKernel.NullModelScaler
SuffixTreeKernel.SelectionScalar
SuffixTreeKernel.UniformScaler
SVM_Light
SVM_Light.LabelledVector
SVMClassifierModel
SVMKernel
SVMRegressionModel
SVMTarget
Symbol
SymbolList
SymbolList.EmptySymbolList
SymbolListAdapter
SymbolParser
SymbolSequenceRenderer
SymbolStyle
TextLogoPainter
TokenParser
Train
Trainable
TrainerTransition
TrainingAlgorithm
TrainingContext
TrainingEvent
TrainingListener
TrainRegression
Transition
TransitionEvent
TransitionListener
TransitionTrainer
TranslatedSymbolList
TranslationTable
TypedProperties
UnableToProcess
UnableToProcessHelper
UnableToProcessHolder
UniformDistribution
Unknown
UnknownHelper
UnknownHolder
UnknownImpl
ViewSequence
WeightMatrix
WeightMatrixAnnotator
WindowedSymbolList
WMAsMM
XMLDispatcher
XmlMarkovModel
XMLPeerBuilder
XMLPeerFactory
_AnonymousSeq_Operations
_AnonymousSeq_Tie
_AnonymousSeqImplBase
_AnonymousSeqStub
_PrimarySeq_Operations
_PrimarySeq_Tie
_PrimarySeqDB_Operations
_PrimarySeqDB_Tie
_PrimarySeqDBImplBase
_PrimarySeqDBStub
_PrimarySeqImplBase
_PrimarySeqIterator_Operations
_PrimarySeqIterator_Tie
_PrimarySeqIteratorImplBase
_PrimarySeqIteratorStub
_PrimarySeqStub
_Seq_Operations
_Seq_Tie
_SeqDB_Operations
_SeqDB_Tie
_SeqDBImplBase
_SeqDBStub
_SeqFeature_Operations
_SeqFeature_Tie
_SeqFeatureImplBase
_SeqFeatureIterator_Operations
_SeqFeatureIterator_Tie
_SeqFeatureIteratorImplBase
_SeqFeatureIteratorStub
_SeqFeatureStub
_SeqImplBase
_SeqStub
_Unknown_Operations
_Unknown_Tie
_UnknownImplBase
_UnknownStub
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