AbstractBurnInTest
AbstractClassifier
AbstractMixtureModel
AbstractMixtureModel.Algorithm
AbstractMixtureModel.Parameterization
AbstractMixtureScoringFunction
AbstractModel
AbstractNormalizableScoringFunction
AbstractOptimizableFunction
AbstractScoreBasedClassifier
AbstractScoreBasedClassifier.DoubleTableResult
AbstractStringExtractor
Alignment
Alignment.Costs
Alignment.Costs.Direction
Alignment.SimpleCosts
Alignment.StringAlignment
Alphabet
Alphabet.AlphabetParameterSet
AlphabetContainer
AlphabetContainer.AlphabetContainerType
AlphabetContainerParameterSet
AlphabetContainerParameterSet.AlphabetArrayParameterSet
AlphabetContainerParameterSet.SectionDefinedAlphabetParameterSet
ArbitrarySequence
ArrayHandler
ArrayParameterSet
AsymmetricTensor
BayesianNetworkModel
BayesianNetworkModelParameterSet
BayesianNetworkScoringFunction
BayesianNetworkScoringFunctionParameterSet
BioJavaAdapter
BTExplainingAwayResidual
BTExplainingAwayResidual.BTExplainingAwayResidualParameterSet
BTMutualInformation
BTMutualInformation.BTMutualInformationParameterSet
BTMutualInformation.DataSource
BurnInTest
ByteSequence
CategoricalResult
CDFOfNormal
Chu_Liu_Edmonds
CisRegulatoryModuleAnnotation
ClassDimensionException
ClassificationVisualizer
ClassifierAssessment
ClassifierAssessmentAssessParameterSet
CLLClassifier
CLLClassifierParameterSet
CollectionParameter
CombinationIterator
ComparableElement
ComplementableDiscreteAlphabet
CompositeLogPrior
CompositeModel
ConfusionMatrix
ConstantStartDistance
Constraint
Constraint
ConstraintManager
ConstraintValidator
ContinuousAlphabet
ContinuousAlphabet.ContinuousAlphabetParameterSet
DAG
DAGModel
DataType
DefaultProgressUpdater
DGMParameterSet
DifferentiableFunction
DimensionException
DiMRGParams
DirichletMRG
DirichletMRGParams
DiscreteAlphabet
DiscreteAlphabet.DiscreteAlphabetParameterSet
DiscreteGraphicalModel
DiscreteInhomogenousSampleEmitter
DiscreteSequence
DiscreteSequenceEnumerator
DNAAlphabet
DNAAlphabet.DNAAlphabetParameterSet
DoesNothingLogPrior
DoubleList
DoubleSymbolException
DurationScoringFunction
Edge
EmptySampleException
EnumParameter
EqualParts
ErlangMRG
ErlangMRGParams
EvaluationException
ExpandableParameterSet
FastDirichletMRGParams
FileManager
FileParameter
FileParameter.FileRepresentation
FSDAGModel
FSDAGModelForGibbsSampling
FSDAGModelForGibbsSamplingParameterSet
FSDAGMParameterSet
Function
GaussianLikePositionPrior
GibbsSamplingComponent
GUIProgressUpdater
HiddenMotifMixture
HiddenMotifsMixture
History
HMM0ScoringFunction
HMMScoringFunction
HomMMParameterSet
HomogeneousMM
HomogeneousModel
HomogeneousModelParameterSet
HomogeneousScoringFunction
IDGMParameterSet
ImageResult
IndependentProductScoringFunction
InhCondProb
InhConstraint
InhomogeneousDGM
InhomogeneousMarkov
InhomogeneousMarkov.InhomogeneousMarkovParameterSet
InstanceParameterSet
InstantiableFromParameterSet
IntList
IntronAnnotation
IntSequence
KFoldCrossValidation
KFoldCVAssessParameterSet
LimitedMedianStartDistance
ListResult
LocatedSequenceAnnotation
LocatedSequenceAnnotationWithLength
LogPrior
MappingClassifier
MeanResultSet
MeanResultSet.AdditionImpossibleException
MeanResultSet.InconsistentResultNumberException
Measure
MeasureParameters
MeasureParameters.Measure
MEMConstraint
MixtureModel
MixtureScoringFunction
Model
ModelBasedClassifier
ModelTester
MotifAnnotation
MotifDiscoverer
MotifDiscoverer.KindOfProfile
MotifDiscovererToolBox
MotifDiscoveryAssessment
MRFScoringFunction
MRGParams
MST
MultiSelectionCollectionParameter
MultivariateRandomGenerator
Mutable
MutableMarkovModelScoringFunction
MutableMotifDiscoverer
MutableMotifDiscovererToolbox
MutableMotifDiscovererToolbox.InitMethodForScoringFunction
NegativeDifferentiableFunction
NegativeFunction
NegativeOneDimensionalFunction
NonParsableException
Normalisation
NormalizableScoringFunction
NormalizedScoringFunction
NormConditionalLogLikelihood
NotTrainedException
NullProgressUpdater
NumberValidator
NumericalDifferentiableFunction
NumericalResult
NumericalResultSet
OneDimensionalFunction
OneDimensionalSubFunction
OptimizableFunction
OptimizableFunction.KindOfParameter
Optimizer
Optimizer.TerminationCondition
Parameter
Parameter
ParameterException
ParameterSet
ParameterSetContainer
ParameterSetParser
ParameterSetParser.NotInstantiableException
ParameterSetParser.WrongParameterTypeException
ParameterTree
ParameterValidator
PermutedSequence
PMMExplainingAwayResidual
PMMExplainingAwayResidual.PMMExplainingAwayResidualParameterSet
PMMMutualInformation
PMMMutualInformation.PMMMutualInformationParameterSet
PositionPrior
PositionScoringFunction
ProgressUpdater
PValueComputation
QuadraticFunction
RandomNumberGenerator
Rangeable
RangeIterator
RangeParameter
RangeParameter.RangeType
RangeParameter.Scale
RealTime
RecursiveSequence
ReferenceConstraint
REnvironment
RepeatedHoldOutAssessParameterSet
RepeatedHoldOutExperiment
RepeatedSubSamplingAssessParameterSet
RepeatedSubSamplingExperiment
RestrictedRepeatHistory
Result
ResultSet
RUtils
SafeOutputStream
Sample
Sample.ElementEnumerator
Sample.PartitionMethod
Sample.WeightedSampleFactory
Sample.WeightedSampleFactory.SortOperation
Sampled_RepeatedHoldOutAssessParameterSet
Sampled_RepeatedHoldOutExperiment
SampleResult
ScoreBasedPerformanceMeasureDefinitions
ScoreBasedPerformanceMeasureDefinitions.ThresholdMeasurePair
ScoreClassifier
ScoreClassifierParameterSet
ScoringFunction
SeparateGaussianLogPrior
SeparateLaplaceLogPrior
SeparateLogPrior
Sequence
Sequence.CompositeSequence
Sequence.SubSequence
SequenceAnnotation
SequenceIterator
SequenceScoringParameterSet
SharedStructureClassifier
SharedStructureMixture
ShortSequence
SignificantMotifOccurrencesFinder
SignificantMotifOccurrencesFinder.RandomSeqType
SimpleBurnInTest
SimpleGaussianSumLogPrior
SimpleParameter
SimpleParameter.DatatypeNotValidException
SimpleParameter.IllegalValueException
SimpleParameterSet
SimpleReferenceConstraint
SimpleResult
SimpleSequenceIterator
SimpleStaticConstraint
SimpleStringExtractor
SingleHiddenMotifMixture
SinglePositionSequenceAnnotation
SinglePositionSequenceAnnotation.Type
SkewNormalLikeScoringFunction
SoftOneOfN
SparseSequence
SparseStringExtractor
StartDistanceForecaster
StationaryDistribution
StatisticalTest
Storable
StorableResult
StorableValidator
StrandedLocatedSequenceAnnotationWithLength
StrandedLocatedSequenceAnnotationWithLength.Strand
StrandModel
StrandScoringFunction
StrandScoringFunction.InitMethod
StringExtractor
StructureLearner
StructureLearner.LearningType
StructureLearner.ModelType
SubclassFinder
SubstringFilenameFilter
SubstringFilenameFilter.PartOfName
SymbolExtractor
SymmetricTensor
Tensor
TerminationException
Time
TimeLimitedProgressUpdater
TopSort
TwoPointEvaluater
UniformDurationScoringFunction
UniformHomogeneousScoringFunction
UniformModel
UniformPositionPrior
UniformScoringFunction
UnionFind
UserTime
VariableLengthScoringFunction
VarianceRatioBurnInTest
WrongAlphabetException
WrongLengthException
WrongSequenceTypeException
XMLParser
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