AbsoluteValueCondition
AbsoluteValueCondition.AbsoluteValueConditionParameterSet
AbstractBurnInTest
AbstractBurnInTestParameterSet
AbstractClassifier
AbstractConditionalDiscreteEmission
AbstractDifferentiableSequenceScore
AbstractDifferentiableStatisticalModel
AbstractHMM
AbstractMixtureDiffSM
AbstractMixtureTrainSM
AbstractMixtureTrainSM.Algorithm
AbstractMixtureTrainSM.Parameterization
AbstractMultiThreadedOptimizableFunction
AbstractOptimizableFunction
AbstractPerformanceMeasure
AbstractScoreBasedClassifier
AbstractScoreBasedClassifier.DoubleTableResult
AbstractSelectionParameter
AbstractStringExtractor
AbstractTerminationCondition
AbstractTerminationCondition.AbstractTerminationConditionParameterSet
AbstractTrainableStatisticalModel
AbstractVariableLengthDiffSM
AffineCosts
Alignment
Alignment.AlignmentType
Alphabet
Alphabet.AlphabetParameterSet
AlphabetContainer
AlphabetContainer.AbstractAlphabetContainerParameterSet
AlphabetContainer.AlphabetContainerType
AlphabetContainerParameterSet
AlphabetContainerParameterSet.AlphabetArrayParameterSet
AlphabetContainerParameterSet.SectionDefinedAlphabetParameterSet
AnnotatedEntity
AnnotatedEntityList
ArbitraryFloatSequence
ArbitrarySequence
ArrayHandler
ArrayParameterSet
AsymmetricTensor
AucPR
AucROC
BasicHigherOrderTransition
BasicHigherOrderTransition.AbstractTransitionElement
BasicPluginTransitionElement
BasicTransitionElement
BaumWelchParameterSet
BayesianNetworkDiffSM
BayesianNetworkDiffSMParameterSet
BayesianNetworkTrainSM
BayesianNetworkTrainSMParameterSet
BioJavaAdapter
BNDiffSMParameter
BNDiffSMParameterTree
BTExplainingAwayResidual
BTExplainingAwayResidual.BTExplainingAwayResidualParameterSet
BTMutualInformation
BTMutualInformation.BTMutualInformationParameterSet
BTMutualInformation.DataSource
BurnInTest
ByteSequence
CappedHistory
CategoricalResult
CDFOfNormal
Chu_Liu_Edmonds
CisRegulatoryModuleAnnotation
ClassDimensionException
ClassificationRate
ClassificationVisualizer
ClassifierAssessment
ClassifierAssessmentAssessParameterSet
CombinationIterator
CombinedCondition
CombinedCondition.CombinedConditionParameterSet
CombinedFileFilter
ComparableElement
ComplementableDiscreteAlphabet
CompositeLogPrior
CompositeTrainSM
ConfusionMatrix
ConstantStartDistance
Constraint
Constraint
ConstraintManager
ConstraintValidator
ContinuousAlphabet
ContinuousAlphabet.ContinuousAlphabetParameterSet
Costs
CyclicMarkovModelDiffSM
DAG
DAGTrainSM
DataSet
DataSet.ElementEnumerator
DataSet.PartitionMethod
DataSet.WeightedDataSetFactory
DataSet.WeightedDataSetFactory.SortOperation
DataSetKMerEnumerator
DataSetResult
DataType
DateFileFilter
DefaultProgressUpdater
DGTrainSMParameterSet
DifferentiableEmission
DifferentiableFunction
DifferentiableHigherOrderHMM
DifferentiableSequenceScore
DifferentiableState
DifferentiableStatisticalModel
DifferentiableStatisticalModelFactory
DifferentiableStatisticalModelWrapperTrainSM
DifferentiableTransition
DiffSSBasedOptimizableFunction
DimensionException
DiMRGParams
DinucleotideProperty
DinucleotideProperty.HowCreated
DinucleotideProperty.MeanSmoothing
DinucleotideProperty.MedianSmoothing
DinucleotideProperty.NoSmoothing
DinucleotideProperty.Smoothing
DinucleotideProperty.Type
DirichletMRG
DirichletMRGParams
DiscreteAlphabet
DiscreteAlphabet.DiscreteAlphabetParameterSet
DiscreteAlphabetMapping
DiscreteEmission
DiscreteGraphicalTrainSM
DiscreteInhomogenousDataSetEmitter
DiscreteSequenceEnumerator
DistanceBasedScaledTransitionElement
DNAAlphabet
DNAAlphabet.DNAAlphabetParameterSet
DNAAlphabetContainer
DNAAlphabetContainer.DNAAlphabetContainerParameterSet
DNADataSet
DoesNothingLogPrior
DoubleList
DoubleSymbolException
DurationDiffSM
Edge
Emission
EmptyDataSetException
EnumParameter
EqualParts
ErlangMRG
ErlangMRGParams
EvaluationException
ExpandableParameterSet
ExtendedZOOPSDiffSM
FalsePositiveRateForFixedSensitivity
FastDirichletMRGParams
FileManager
FileParameter
FileParameter.FileRepresentation
FSDAGModelForGibbsSampling
FSDAGModelForGibbsSamplingParameterSet
FSDAGTrainSM
FSDAGTrainSMParameterSet
Function
GalaxyAdaptor
GalaxyAdaptor.FileResult
GalaxyAdaptor.LinkedImageResult
GalaxyAdaptor.Protocol
GalaxyConvertible
GaussianEmission
GaussianLikePositionPrior
GenDisMixClassifier
GenDisMixClassifierParameterSet
GenericComplementableDiscreteAlphabet
GenericComplementableDiscreteAlphabet.GenericComplementableDiscreteAlphabetParameterSet
GibbsSamplingModel
GUIProgressUpdater
HiddenMotifMixture
HigherOrderHMM
HigherOrderHMM.Type
HigherOrderTransition
History
HMMFactory
HMMFactory.HMMType
HMMFactory.PseudoTransitionElement
HMMTrainingParameterSet
HomMMParameterSet
HomogeneousDiffSM
HomogeneousMM
HomogeneousMM0DiffSM
HomogeneousMMDiffSM
HomogeneousTrainSM
HomogeneousTrainSMParameterSet
IDGTrainSMParameterSet
ImageResult
IndependentProductDiffSM
IndependentProductDiffSS
InfixStringExtractor
InhCondProb
InhConstraint
InhomogeneousDGTrainSM
InhomogeneousMarkov
InhomogeneousMarkov.InhomogeneousMarkovParameterSet
InstanceParameterSet
InstantiableFromParameterSet
IntList
IntronAnnotation
IntSequence
IterationCondition
IterationCondition.IterationConditionParameterSet
KFoldCrossValidation
KFoldCrossValidationAssessParameterSet
KMereStatistic
LearningPrinciple
LimitedMedianStartDistance
LimitedStringExtractor
ListResult
LocatedSequenceAnnotation
LocatedSequenceAnnotationWithLength
LogGenDisMixFunction
LogisticConstraint
LogisticDiffSS
LogPrior
MappedDiscreteSequence
MappingClassifier
MappingDiffSM
MarkovModelDiffSM
MarkovRandomFieldDiffSM
MatrixCosts
MaxHMMTrainingParameterSet
MaximumCorrelationCoefficient
MaximumFMeasure
MaximumNumericalTwoClassMeasure
MeanResultSet
MeanResultSet.AdditionImpossibleException
MeanResultSet.InconsistentResultNumberException
Measure
Measure.MeasureParameterSet
MEMConstraint
MixtureDiffSM
MixtureDurationDiffSM
MixtureEmission
MixtureTrainSM
MotifAnnotation
MotifAnnotationParser
MotifDiscoverer
MotifDiscoverer.KindOfProfile
MotifDiscovererToolBox
MotifDiscoveryAssessment
MRGParams
MSPClassifier
MST
MultiDimensionalArbitrarySequence
MultiDimensionalDiscreteSequence
MultiDimensionalSequence
MultiDimensionalSequenceWrapperDiffSM
MultiSelectionParameter
MultiThreadedTrainingParameterSet
MultivariateRandomGenerator
Mutable
MutableMotifDiscoverer
MutableMotifDiscovererToolbox
MutableMotifDiscovererToolbox.InitMethodForDiffSM
NegativeDifferentiableFunction
NegativeFunction
NegativeOneDimensionalFunction
NewickParser
NonParsableException
NoRevertHistory
Normalisation
NormalizedDiffSM
NotTrainedException
NullProgressUpdater
NullSequenceAnnotationParser
NumberValidator
NumericalDifferentiableFunction
NumericalHMMTrainingParameterSet
NumericalPerformanceMeasure
NumericalPerformanceMeasureParameterSet
NumericalResult
NumericalResultSet
OneDataSetLogGenDisMixFunction
OneDimensionalFunction
OneDimensionalSubFunction
OptimizableFunction
OptimizableFunction.KindOfParameter
Optimizer
Pair
PairwiseStringAlignment
Parameter
ParameterException
ParameterSet
ParameterSetContainer
ParameterSetParser
ParameterSetParser.NotInstantiableException
ParameterSetParser.WrongParameterTypeException
ParameterSetTagger
ParameterSetTagger.KeyEntryComparator
ParameterValidator
PerformanceMeasureParameterSet
PermutedSequence
PhyloDiscreteEmission
PhyloNode
PhyloTree
PluginGaussianEmission
PMMExplainingAwayResidual
PMMExplainingAwayResidual.PMMExplainingAwayResidualParameterSet
PMMMutualInformation
PMMMutualInformation.PMMMutualInformationParameterSet
PositionDiffSM
PositionPrior
PositivePredictiveValueForFixedSensitivity
PRCurve
ProductConstraint
ProgressUpdater
ProteinAlphabet
ProteinAlphabet.ProteinAlphabetParameterSet
PValueComputation
QuadraticFunction
RandomNumberGenerator
Rangeable
RangeIterator
RangeParameter
RangeParameter.RangeType
RangeParameter.Scale
RealTime
RecyclableSequenceEnumerator
ReferenceBasedTransitionElement
ReferenceSequenceAnnotation
ReferenceSequenceAnnotationParser
ReferenceSequenceDiscreteEmission
RegExFilenameFilter
RegExFilterOutputStream
REnvironment
RepeatedHoldOutAssessParameterSet
RepeatedHoldOutExperiment
RepeatedSubSamplingAssessParameterSet
RepeatedSubSamplingExperiment
RestrictedRepeatHistory
Result
ResultSet
ROCCurve
RUtils
SafeOutputStream
Sampled_RepeatedHoldOutAssessParameterSet
Sampled_RepeatedHoldOutExperiment
SamplingComponent
SamplingDifferentiableStatisticalModel
SamplingEmission
SamplingFromStatistic
SamplingGenDisMixClassifier
SamplingGenDisMixClassifierParameterSet
SamplingHigherOrderHMM
SamplingHigherOrderHMM.ViterbiComputation
SamplingHMMTrainingParameterSet
SamplingPhyloHMM
SamplingScoreBasedClassifier
SamplingScoreBasedClassifier.SamplingScheme
SamplingScoreBasedClassifierParameterSet
SamplingState
SamplingTransition
ScaledTransitionElement
ScoreClassifier
ScoreClassifierParameterSet
SelectionParameter
SensitivityForFixedSpecificity
SeparateGaussianLogPrior
SeparateLaplaceLogPrior
SeparateLogPrior
Sequence
Sequence.CompositeSequence
Sequence.RecursiveSequence
Sequence.SubSequence
SequenceAnnotation
SequenceAnnotationParser
SequenceEnumeration
SequenceIterator
SequenceScore
SequenceScoringParameterSet
SharedStructureClassifier
SharedStructureMixture
ShortSequence
SignificantMotifOccurrencesFinder
SignificantMotifOccurrencesFinder.JoinMethod
SignificantMotifOccurrencesFinder.RandomSeqType
SignificantMotifOccurrencesFinder.SumOfProbabilities
SilentEmission
SimpleBurnInTest
SimpleCosts
SimpleDifferentiableState
SimpleDiscreteSequence
SimpleGaussianSumLogPrior
SimpleHistory
SimpleParameter
SimpleParameter.DatatypeNotValidException
SimpleParameter.IllegalValueException
SimpleParameterSet
SimpleResult
SimpleSamplingState
SimpleSequenceAnnotationParser
SimpleSequenceIterator
SimpleState
SimpleStaticConstraint
SimpleStringExtractor
SinglePositionSequenceAnnotation
SinglePositionSequenceAnnotation.Type
Singleton
Singleton.SingletonHandler
SkewNormalLikeDurationDiffSM
SmallDifferenceOfFunctionEvaluationsCondition
SmallDifferenceOfFunctionEvaluationsCondition.SmallDifferenceOfFunctionEvaluationsConditionParameterSet
SmallGradientConditon
SmallGradientConditon.SmallGradientConditonParameterSet
SmallStepCondition
SmallStepCondition.SmallStepConditionParameterSet
SoftOneOfN
SparseSequence
SparseStringExtractor
SplitSequenceAnnotationParser
StartDistanceForecaster
State
StationaryDistribution
StatisticalModel
StatisticalModelTester
StatisticalTest
Storable
StorableResult
StorableValidator
StrandDiffSM
StrandDiffSM.InitMethod
StrandedLocatedSequenceAnnotationWithLength
StrandedLocatedSequenceAnnotationWithLength.Strand
StrandTrainSM
StringAlignment
StringExtractor
StructureLearner
StructureLearner.LearningType
StructureLearner.ModelType
SubclassFinder
SubTensor
SymbolExtractor
SymmetricTensor
Tensor
TerminationCondition
TerminationException
Time
TimeCondition
TimeCondition.TimeConditionParameterSet
TimeLimitedProgressUpdater
ToolBox
TopSort
TrainableAndDifferentiableTransition
TrainableState
TrainableStatisticalModel
TrainableStatisticalModelFactory
TrainableTransition
TrainSMBasedClassifier
Transition
TransitionElement
TransitionWithSufficientStatistic
TwoClassAbstractPerformanceMeasure
TwoPointEvaluater
UniformDiffSM
UniformDiffSS
UniformDurationDiffSM
UniformEmission
UniformHomogeneousDiffSM
UniformPositionPrior
UniformTrainSM
UnionFind
UserTime
VariableLengthDiffSM
VariableLengthMixtureDiffSM
VariableLengthWrapperTrainSM
VarianceRatioBurnInTest
VarianceRatioBurnInTestParameterSet
ViterbiParameterSet
WrongAlphabetException
WrongLengthException
WrongSequenceTypeException
XMLParser
ZOOPSTrainSM
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