AbsoluteValueCondition
AbsoluteValueCondition.AbsoluteValueConditionParameterSet
AbstractBurnInTest
AbstractBurnInTestParameterSet
AbstractClassifier
AbstractConditionalDiscreteEmission
AbstractHMM
AbstractMixtureModel
AbstractMixtureModel.Algorithm
AbstractMixtureModel.Parameterization
AbstractMixtureScoringFunction
AbstractModel
AbstractMultiThreadedOptimizableFunction
AbstractNormalizableScoringFunction
AbstractOptimizableFunction
AbstractScoreBasedClassifier
AbstractScoreBasedClassifier.DoubleTableResult
AbstractStringExtractor
AbstractTerminationCondition
AbstractTerminationCondition.AbstractTerminationConditionParameterSet
AbstractVariableLengthScoringFunction
AffineCosts
Alignment
Alignment.AlignmentType
Alphabet
Alphabet.AlphabetParameterSet
AlphabetContainer
AlphabetContainer.AlphabetContainerType
AlphabetContainerParameterSet
AlphabetContainerParameterSet.AlphabetArrayParameterSet
AlphabetContainerParameterSet.SectionDefinedAlphabetParameterSet
ArbitrarySequence
ArrayHandler
ArrayParameterSet
AsymmetricTensor
BasicHigherOrderTransition
BasicHigherOrderTransition.AbstractTransitionElement
BasicPluginTransitionElement
BasicTransitionElement
BaumWelchParameterSet
BayesianNetworkModel
BayesianNetworkModelParameterSet
BayesianNetworkScoringFunction
BayesianNetworkScoringFunctionParameterSet
BioJavaAdapter
BTExplainingAwayResidual
BTExplainingAwayResidual.BTExplainingAwayResidualParameterSet
BTMutualInformation
BTMutualInformation.BTMutualInformationParameterSet
BTMutualInformation.DataSource
BurnInTest
ByteSequence
CappedHistory
CategoricalResult
CDFOfNormal
Chu_Liu_Edmonds
CisRegulatoryModuleAnnotation
ClassDimensionException
ClassificationVisualizer
ClassifierAssessment
ClassifierAssessmentAssessParameterSet
CMMScoringFunction
CollectionParameter
CombinationIterator
CombinedCondition
CombinedCondition.CombinedConditionParameterSet
CombinedFileFilter
ComparableElement
ComplementableDiscreteAlphabet
CompositeLogPrior
CompositeModel
ConfusionMatrix
ConstantStartDistance
Constraint
Constraint
ConstraintManager
ConstraintValidator
ContinuousAlphabet
ContinuousAlphabet.ContinuousAlphabetParameterSet
Costs
Costs.Direction
DAG
DAGModel
DataType
DateFileFilter
DefaultProgressUpdater
DGMParameterSet
DifferentiableEmission
DifferentiableFunction
DifferentiableHigherOrderHMM
DifferentiableState
DifferentiableTransition
DimensionException
DiMRGParams
DinucleotideProperty
DinucleotideProperty.HowCreated
DinucleotideProperty.MeanSmoothing
DinucleotideProperty.MedianSmoothing
DinucleotideProperty.NoSmoothing
DinucleotideProperty.Smoothing
DinucleotideProperty.Type
DirichletMRG
DirichletMRGParams
DiscreteAlphabet
DiscreteAlphabet.DiscreteAlphabetParameterSet
DiscreteAlphabetMapping
DiscreteEmission
DiscreteGraphicalModel
DiscreteInhomogenousSampleEmitter
DiscreteSequence
DiscreteSequenceEnumerator
DistanceBasedScaledTransitionElement
DNAAlphabet
DNAAlphabet.DNAAlphabetParameterSet
DNASample
DoesNothingLogPrior
DoubleList
DoubleSymbolException
DurationScoringFunction
Edge
Emission
EmptySampleException
EnumParameter
EqualParts
ErlangMRG
ErlangMRGParams
EvaluationException
ExpandableParameterSet
FastDirichletMRGParams
FileManager
FileParameter
FileParameter.FileRepresentation
FSDAGModel
FSDAGModelForGibbsSampling
FSDAGModelForGibbsSamplingParameterSet
FSDAGMParameterSet
Function
GalaxyAdaptor
GalaxyAdaptor.FileResult
GalaxyAdaptor.LinkedImageResult
GalaxyAdaptor.Protocol
GalaxyConvertible
GaussianEmission
GaussianLikePositionPrior
GenDisMixClassifier
GenDisMixClassifierParameterSet
GenericComplementableDiscreteAlphabet
GenericComplementableDiscreteAlphabet.GenericComplementableDiscreteAlphabetParameterSet
GibbsSamplingModel
GUIProgressUpdater
HiddenMotifMixture
HiddenMotifsMixture
HigherOrderHMM
HigherOrderHMM.Type
HigherOrderTransition
History
HMM0ScoringFunction
HMMFactory
HMMFactory.HMMType
HMMScoringFunction
HMMTrainingParameterSet
HomMMParameterSet
HomogeneousMM
HomogeneousModel
HomogeneousModelParameterSet
HomogeneousScoringFunction
IDGMParameterSet
ImageResult
IndependentProductScoringFunction
InfixStringExtractor
InhCondProb
InhConstraint
InhomogeneousDGM
InhomogeneousMarkov
InhomogeneousMarkov.InhomogeneousMarkovParameterSet
InstanceParameterSet
InstantiableFromParameterSet
IntList
IntronAnnotation
IntSequence
IterationCondition
IterationCondition.IterationConditionParameterSet
KFoldCrossValidation
KFoldCVAssessParameterSet
KMereStatistic
LearningPrinciple
LimitedMedianStartDistance
LimitedStringExtractor
ListResult
LocatedSequenceAnnotation
LocatedSequenceAnnotationWithLength
LogGenDisMixFunction
LogPrior
MappedDiscreteSequence
MappingClassifier
MappingScoringFunction
MatrixCosts
MaxHMMTrainingParameterSet
MeanResultSet
MeanResultSet.AdditionImpossibleException
MeanResultSet.InconsistentResultNumberException
Measure
MeasureParameters
MeasureParameters.Measure
MEMConstraint
MixtureDuration
MixtureEmission
MixtureModel
MixtureScoringFunction
Model
ModelBasedClassifier
ModelFactory
ModelTester
MotifAnnotation
MotifAnnotationParser
MotifDiscoverer
MotifDiscoverer.KindOfProfile
MotifDiscovererToolBox
MotifDiscoveryAssessment
MRFScoringFunction
MRGParams
MSPClassifier
MST
MultiDimensionalDiscreteSequence
MultiSelectionCollectionParameter
MultivariateRandomGenerator
Mutable
MutableMarkovModelScoringFunction
MutableMotifDiscoverer
MutableMotifDiscovererToolbox
MutableMotifDiscovererToolbox.InitMethodForScoringFunction
NegativeDifferentiableFunction
NegativeFunction
NegativeOneDimensionalFunction
NewickParser
NonParsableException
NoRevertHistory
Normalisation
NormalizableScoringFunction
NormalizableScoringFunctionModel
NormalizedScoringFunction
NotTrainedException
NullProgressUpdater
NullSequenceAnnotationParser
NumberValidator
NumericalDifferentiableFunction
NumericalHMMTrainingParameterSet
NumericalResult
NumericalResultSet
OneDimensionalFunction
OneDimensionalSubFunction
OneSampleLogGenDisMixFunction
OptimizableFunction
OptimizableFunction.KindOfParameter
Optimizer
Pair
PairwiseStringAlignment
Parameter
Parameter
ParameterException
ParameterSet
ParameterSetContainer
ParameterSetParser
ParameterSetParser.NotInstantiableException
ParameterSetParser.WrongParameterTypeException
ParameterSetTagger
ParameterSetTagger.KeyEntryComparator
ParameterTree
ParameterValidator
PermutedSequence
PhyloDiscreteEmission
PhyloNode
PhyloTree
PluginGaussianEmission
PMMExplainingAwayResidual
PMMExplainingAwayResidual.PMMExplainingAwayResidualParameterSet
PMMMutualInformation
PMMMutualInformation.PMMMutualInformationParameterSet
PositionPrior
PositionScoringFunction
ProgressUpdater
PValueComputation
QuadraticFunction
RandomNumberGenerator
Rangeable
RangeIterator
RangeParameter
RangeParameter.RangeType
RangeParameter.Scale
RealTime
RecyclableSequenceEnumerator
ReferenceBasedTransitionElement
ReferenceConstraint
ReferenceSequenceAnnotation
ReferenceSequenceAnnotationParser
ReferenceSequenceDiscreteEmission
RegExFilenameFilter
REnvironment
RepeatedHoldOutAssessParameterSet
RepeatedHoldOutExperiment
RepeatedSubSamplingAssessParameterSet
RepeatedSubSamplingExperiment
RestrictedRepeatHistory
Result
ResultSet
RUtils
SafeOutputStream
Sample
Sample.ElementEnumerator
Sample.PartitionMethod
Sample.WeightedSampleFactory
Sample.WeightedSampleFactory.SortOperation
Sampled_RepeatedHoldOutAssessParameterSet
Sampled_RepeatedHoldOutExperiment
SampleKMerEnumerator
SampleResult
SamplingComponent
SamplingEmission
SamplingFromStatistic
SamplingGenDisMixClassifier
SamplingGenDisMixClassifierParameterSet
SamplingHigherOrderHMM
SamplingHigherOrderHMM.ViterbiComputation
SamplingHMMTrainingParameterSet
SamplingPhyloHMM
SamplingScoreBasedClassifier
SamplingScoreBasedClassifier.SamplingScheme
SamplingScoreBasedClassifierParameterSet
SamplingScoringFunction
SamplingState
SamplingTransition
ScaledTransitionElement
ScoreBasedPerformanceMeasureDefinitions
ScoreBasedPerformanceMeasureDefinitions.ThresholdMeasurePair
ScoreClassifier
ScoreClassifierParameterSet
ScoringFunction
SeparateGaussianLogPrior
SeparateLaplaceLogPrior
SeparateLogPrior
Sequence
Sequence.CompositeSequence
Sequence.RecursiveSequence
Sequence.SubSequence
SequenceAnnotation
SequenceAnnotationParser
SequenceEnumeration
SequenceIterator
SequenceScoringParameterSet
SFBasedOptimizableFunction
SharedStructureClassifier
SharedStructureMixture
ShortSequence
SignificantMotifOccurrencesFinder
SignificantMotifOccurrencesFinder.JoinMethod
SignificantMotifOccurrencesFinder.RandomSeqType
SignificantMotifOccurrencesFinder.SumOfProbabilities
SilentEmission
SimpleBurnInTest
SimpleCosts
SimpleDifferentiableState
SimpleDiscreteSequence
SimpleGaussianSumLogPrior
SimpleHistory
SimpleParameter
SimpleParameter.DatatypeNotValidException
SimpleParameter.IllegalValueException
SimpleParameterSet
SimpleReferenceConstraint
SimpleResult
SimpleSamplingState
SimpleSequenceAnnotationParser
SimpleSequenceIterator
SimpleState
SimpleStaticConstraint
SimpleStringExtractor
SingleHiddenMotifMixture
SinglePositionSequenceAnnotation
SinglePositionSequenceAnnotation.Type
SkewNormalLikeScoringFunction
SmallDifferenceOfFunctionEvaluationsCondition
SmallDifferenceOfFunctionEvaluationsCondition.SmallDifferenceOfFunctionEvaluationsConditionParameterSet
SmallGradientConditon
SmallGradientConditon.SmallGradientConditonParameterSet
SmallStepCondition
SmallStepCondition.SmallStepConditionParameterSet
SoftOneOfN
SparseSequence
SparseStringExtractor
SplitSequenceAnnotationParser
StartDistanceForecaster
State
StationaryDistribution
StatisticalTest
Storable
StorableResult
StorableValidator
StrandedLocatedSequenceAnnotationWithLength
StrandedLocatedSequenceAnnotationWithLength.Strand
StrandModel
StrandScoringFunction
StrandScoringFunction.InitMethod
StringAlignment
StringExtractor
StructureLearner
StructureLearner.LearningType
StructureLearner.ModelType
SubclassFinder
SubTensor
SymbolExtractor
SymmetricTensor
Tensor
TerminationCondition
TerminationException
Time
TimeCondition
TimeCondition.TimeConditionParameterSet
TimeLimitedProgressUpdater
ToolBox
TopSort
TrainableAndDifferentiableTransition
TrainableState
TrainableTransition
Transition
TransitionElement
TransitionWithSufficientStatistic
TwoPointEvaluater
UniformDurationScoringFunction
UniformHomogeneousScoringFunction
UniformModel
UniformPositionPrior
UniformScoringFunction
UnionFind
UserTime
VariableLengthMixtureScoringFunction
VariableLengthScoringFunction
VariableLengthWrapperModel
VarianceRatioBurnInTest
VarianceRatioBurnInTestParameterSet
ViterbiParameterSet
WrongAlphabetException
WrongLengthException
WrongSequenceTypeException
XMLParser
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