AbstractClassifier
AbstractMixtureModel
AbstractMixtureModel.Algorithm
AbstractMixtureModel.Parameterization
AbstractMixtureScoringFunction
AbstractModel
AbstractNormalizableScoringFunction
AbstractScoreBasedClassifier
AbstractScoreBasedClassifier.DoubleTableResult
Alignment
Alignment.Costs
Alignment.Costs.Direction
Alignment.SimpleCosts
Alignment.StringAlignment
Alphabet
Alphabet.AlphabetParameterSet
AlphabetContainer
AlphabetContainerParameterSet
AlphabetContainerParameterSet.AlphabetArrayParameterSet
AlphabetContainerParameterSet.SectionDefinedAlphabetParameterSet
ArbitrarySequence
ArrayHandler
ArrayParameterSet
AsymmetricTensor
BayesianNetworkModel
BayesianNetworkModelParameterSet
BayesianNetworkScoringFunction
BioJavaAdapter
BTExplainingAwayResidual
BTMutualInformation
BurnInTest
ByteSequence
CategoricalResult
Chu_Liu_Edmonds
CisRegulatoryModuleAnnotation
ClassDimensionException
Classification
ClassificationVisualizer
ClassifierAssessment
ClassifierAssessmentAssessParameterSet
CLLClassifier
CLLClassifierParameterSet
CollectionParameter
CombinationIterator
ComparableElement
ComplementableDiscreteAlphabet
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
Edge
EmptySampleException
EnumParameter
EqualParts
ErlangMRG
ErlangMRGParams
EvaluationException
ExpandableParameterSet
FastDirichletMRGParams
FileManager
FileParameter
FileParameter.FileRepresentation
FSDAGModel
FSDAGModelForGibbsSampling
FSDAGMParameterSet
Function
GibbsSamplingComponent
GUIProgressUpdater
HMM0ScoringFunction
HMMScoringFunction
HomogeneousScoringFunction
IDGMParameterSet
ImageResult
IndependentProductScoringFunction
InhCondProb
InhConstraint
InhomogeneousDGM
InhomogeneousMarkov
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
ModelTester.SeqIterator
MotifAnnotation
MRFScoringFunction
MRGParams
MST
MultiSelectionCollectionParameter
MultivariateRandomGenerator
NegativeDifferentiableFunction
NegativeFunction
NegativeOneDimensionalFunction
NonParsableException
Normalisation
NormalizableScoringFunction
NormConditionalLogLikelihood
NotTrainedException
NullProgressUpdater
NumberValidator
NumericalDifferentiableFunction
NumericalResult
NumericalResultSet
OneDimensionalFunction
OneDimensionalSubFunction
OptimizableFunction
Optimizer
Optimizer.TerminationCondition
Parameter
Parameter
ParameterException
ParameterSet
ParameterSetContainer
ParameterSetParser
ParameterSetParser.NotInstantiableException
ParameterSetParser.WrongParameterTypeException
ParameterTree
ParameterValidator
PermutedSequence
PMMExplainingAwayResidual
PMMMutualInformation
ProgressUpdater
PValueComputation
QuadraticFunction
RandomNumberGenerator
Rangeable
RangeIterator
RangeParameter
RangeParameter.RangeType
RangeParameter.Scale
RealTime
RecursiveSequence
ReferenceConstraint
REnvironment
RepeatedHoldOutAssessParameterSet
RepeatedHoldOutExperiment
RepeatedSubSamplingAssessParameterSet
RepeatedSubSamplingExperiment
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
SharedStructureClassifier
SharedStructureMixture
ShortSequence
SimpleBurnInTest
SimpleGaussianSumLogPrior
SimpleParameter
SimpleParameter.DatatypeNotValidException
SimpleParameter.IllegalValueException
SimpleParameterSet
SimpleReferenceConstraint
SimpleResult
SimpleSequenceIterator
SimpleStaticConstraint
SinglePositionSequenceAnnotation
SinglePositionSequenceAnnotation.Type
SoftOneOfN
SparseSequence
StartDistanceForecaster
StationaryDistribution
StatisticalTest
Storable
StorableResult
StorableValidator
StrandedLocatedSequenceAnnotationWithLength
StrandedLocatedSequenceAnnotationWithLength.Strand
StrandModel
StringExtractor
StructureLearner
StructureLearner.LearningType
StructureLearner.ModelType
SubstringFilenameFilter
SubstringFilenameFilter.PartOfName
SymbolExtractor
SymmetricTensor
Tensor
TerminationException
Time
TimeLimitedProgressUpdater
TopSort
TwoPointEvaluater
UniformHomogeneousScoringFunction
UniformModel
UniformScoringFunction
UnionFind
UnivariateRandomGenerator
UserTime
VariableLengthScoringFunction
WrongAlphabetException
WrongLengthException
WrongSequenceTypeException
XMLParser
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