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Package Hierarchies:
de.jstacs
,
de.jstacs.algorithms.alignment
,
de.jstacs.algorithms.alignment.cost
,
de.jstacs.algorithms.graphs
,
de.jstacs.algorithms.graphs.tensor
,
de.jstacs.algorithms.optimization
,
de.jstacs.algorithms.optimization.termination
,
de.jstacs.classifiers
,
de.jstacs.classifiers.assessment
,
de.jstacs.classifiers.differentiableSequenceScoreBased
,
de.jstacs.classifiers.differentiableSequenceScoreBased.gendismix
,
de.jstacs.classifiers.differentiableSequenceScoreBased.logPrior
,
de.jstacs.classifiers.differentiableSequenceScoreBased.msp
,
de.jstacs.classifiers.differentiableSequenceScoreBased.sampling
,
de.jstacs.classifiers.performanceMeasures
,
de.jstacs.classifiers.trainSMBased
,
de.jstacs.classifiers.utils
,
de.jstacs.data
,
de.jstacs.data.alphabets
,
de.jstacs.data.bioJava
,
de.jstacs.data.sequences
,
de.jstacs.data.sequences.annotation
,
de.jstacs.io
,
de.jstacs.motifDiscovery
,
de.jstacs.motifDiscovery.history
,
de.jstacs.parameters
,
de.jstacs.parameters.validation
,
de.jstacs.results
,
de.jstacs.sampling
,
de.jstacs.sequenceScores
,
de.jstacs.sequenceScores.differentiable
,
de.jstacs.sequenceScores.differentiable.logistic
,
de.jstacs.sequenceScores.statisticalModels
,
de.jstacs.sequenceScores.statisticalModels.differentiable
,
de.jstacs.sequenceScores.statisticalModels.differentiable.directedGraphicalModels
,
de.jstacs.sequenceScores.statisticalModels.differentiable.directedGraphicalModels.structureLearning.measures
,
de.jstacs.sequenceScores.statisticalModels.differentiable.directedGraphicalModels.structureLearning.measures.btMeasures
,
de.jstacs.sequenceScores.statisticalModels.differentiable.directedGraphicalModels.structureLearning.measures.pmmMeasures
,
de.jstacs.sequenceScores.statisticalModels.differentiable.homogeneous
,
de.jstacs.sequenceScores.statisticalModels.differentiable.mixture
,
de.jstacs.sequenceScores.statisticalModels.differentiable.mixture.motif
,
de.jstacs.sequenceScores.statisticalModels.trainable
,
de.jstacs.sequenceScores.statisticalModels.trainable.discrete
,
de.jstacs.sequenceScores.statisticalModels.trainable.discrete.homogeneous
,
de.jstacs.sequenceScores.statisticalModels.trainable.discrete.homogeneous.parameters
,
de.jstacs.sequenceScores.statisticalModels.trainable.discrete.inhomogeneous
,
de.jstacs.sequenceScores.statisticalModels.trainable.discrete.inhomogeneous.parameters
,
de.jstacs.sequenceScores.statisticalModels.trainable.discrete.inhomogeneous.shared
,
de.jstacs.sequenceScores.statisticalModels.trainable.hmm
,
de.jstacs.sequenceScores.statisticalModels.trainable.hmm.models
,
de.jstacs.sequenceScores.statisticalModels.trainable.hmm.states
,
de.jstacs.sequenceScores.statisticalModels.trainable.hmm.states.emissions
,
de.jstacs.sequenceScores.statisticalModels.trainable.hmm.states.emissions.continuous
,
de.jstacs.sequenceScores.statisticalModels.trainable.hmm.states.emissions.discrete
,
de.jstacs.sequenceScores.statisticalModels.trainable.hmm.training
,
de.jstacs.sequenceScores.statisticalModels.trainable.hmm.transitions
,
de.jstacs.sequenceScores.statisticalModels.trainable.hmm.transitions.elements
,
de.jstacs.sequenceScores.statisticalModels.trainable.mixture
,
de.jstacs.sequenceScores.statisticalModels.trainable.mixture.motif
,
de.jstacs.sequenceScores.statisticalModels.trainable.mixture.motif.positionprior
,
de.jstacs.sequenceScores.statisticalModels.trainable.phylo
,
de.jstacs.sequenceScores.statisticalModels.trainable.phylo.parser
,
de.jstacs.utils
,
de.jstacs.utils.galaxy
,
de.jstacs.utils.random
Class Hierarchy
java.lang.
Object
de.jstacs.sampling.
AbstractBurnInTest
(implements de.jstacs.sampling.
BurnInTest
, de.jstacs.
InstantiableFromParameterSet
)
de.jstacs.sampling.
VarianceRatioBurnInTest
de.jstacs.classifiers.
AbstractClassifier
(implements java.lang.
Cloneable
, de.jstacs.
Storable
)
de.jstacs.classifiers.
AbstractScoreBasedClassifier
de.jstacs.classifiers.
MappingClassifier
de.jstacs.classifiers.differentiableSequenceScoreBased.sampling.
SamplingScoreBasedClassifier
de.jstacs.classifiers.differentiableSequenceScoreBased.sampling.
SamplingGenDisMixClassifier
de.jstacs.classifiers.differentiableSequenceScoreBased.
ScoreClassifier
de.jstacs.classifiers.differentiableSequenceScoreBased.gendismix.
GenDisMixClassifier
de.jstacs.classifiers.differentiableSequenceScoreBased.msp.
MSPClassifier
de.jstacs.classifiers.trainSMBased.
TrainSMBasedClassifier
de.jstacs.sequenceScores.statisticalModels.trainable.discrete.inhomogeneous.shared.
SharedStructureClassifier
de.jstacs.sequenceScores.statisticalModels.trainable.hmm.states.emissions.discrete.
AbstractConditionalDiscreteEmission
(implements de.jstacs.sequenceScores.statisticalModels.trainable.hmm.states.emissions.
DifferentiableEmission
, de.jstacs.sequenceScores.statisticalModels.trainable.hmm.states.emissions.
SamplingEmission
)
de.jstacs.sequenceScores.statisticalModels.trainable.hmm.states.emissions.discrete.
DiscreteEmission
de.jstacs.sequenceScores.statisticalModels.trainable.hmm.states.emissions.discrete.
PhyloDiscreteEmission
(implements de.jstacs.sequenceScores.statisticalModels.trainable.hmm.states.emissions.
SamplingEmission
)
de.jstacs.sequenceScores.statisticalModels.trainable.hmm.states.emissions.discrete.
ReferenceSequenceDiscreteEmission
de.jstacs.sequenceScores.differentiable.
AbstractDifferentiableSequenceScore
(implements de.jstacs.sequenceScores.differentiable.
DifferentiableSequenceScore
)
de.jstacs.sequenceScores.statisticalModels.differentiable.
AbstractDifferentiableStatisticalModel
(implements de.jstacs.sequenceScores.statisticalModels.differentiable.
DifferentiableStatisticalModel
)
de.jstacs.sequenceScores.statisticalModels.differentiable.mixture.
AbstractMixtureDiffSM
(implements de.jstacs.sequenceScores.statisticalModels.differentiable.
SamplingDifferentiableStatisticalModel
)
de.jstacs.sequenceScores.statisticalModels.differentiable.mixture.motif.
ExtendedZOOPSDiffSM
(implements de.jstacs.motifDiscovery.
MutableMotifDiscoverer
)
de.jstacs.sequenceScores.statisticalModels.differentiable.mixture.
MixtureDiffSM
(implements de.jstacs.motifDiscovery.
MutableMotifDiscoverer
)
de.jstacs.sequenceScores.statisticalModels.differentiable.mixture.
VariableLengthMixtureDiffSM
(implements de.jstacs.sequenceScores.statisticalModels.differentiable.
VariableLengthDiffSM
)
de.jstacs.sequenceScores.statisticalModels.differentiable.mixture.
StrandDiffSM
(implements de.jstacs.motifDiscovery.
Mutable
)
de.jstacs.sequenceScores.statisticalModels.differentiable.
AbstractVariableLengthDiffSM
(implements de.jstacs.sequenceScores.statisticalModels.differentiable.
VariableLengthDiffSM
)
de.jstacs.sequenceScores.statisticalModels.differentiable.
CyclicMarkovModelDiffSM
(implements de.jstacs.sequenceScores.statisticalModels.differentiable.
SamplingDifferentiableStatisticalModel
)
de.jstacs.sequenceScores.statisticalModels.differentiable.homogeneous.
HomogeneousDiffSM
(implements de.jstacs.sequenceScores.statisticalModels.differentiable.
SamplingDifferentiableStatisticalModel
)
de.jstacs.sequenceScores.statisticalModels.differentiable.homogeneous.
HomogeneousMM0DiffSM
de.jstacs.sequenceScores.statisticalModels.differentiable.homogeneous.
HomogeneousMMDiffSM
de.jstacs.sequenceScores.statisticalModels.differentiable.homogeneous.
UniformHomogeneousDiffSM
de.jstacs.sequenceScores.statisticalModels.differentiable.directedGraphicalModels.
BayesianNetworkDiffSM
(implements de.jstacs.
InstantiableFromParameterSet
)
de.jstacs.sequenceScores.statisticalModels.differentiable.directedGraphicalModels.
MarkovModelDiffSM
(implements de.jstacs.motifDiscovery.
Mutable
, de.jstacs.sequenceScores.statisticalModels.differentiable.
SamplingDifferentiableStatisticalModel
)
de.jstacs.sequenceScores.statisticalModels.differentiable.
MappingDiffSM
(implements de.jstacs.motifDiscovery.
Mutable
, de.jstacs.motifDiscovery.
MutableMotifDiscoverer
)
de.jstacs.sequenceScores.statisticalModels.differentiable.
MarkovRandomFieldDiffSM
de.jstacs.sequenceScores.statisticalModels.differentiable.
NormalizedDiffSM
(implements de.jstacs.motifDiscovery.
Mutable
)
de.jstacs.sequenceScores.statisticalModels.differentiable.mixture.motif.
PositionDiffSM
de.jstacs.sequenceScores.statisticalModels.differentiable.mixture.motif.
DurationDiffSM
de.jstacs.sequenceScores.statisticalModels.differentiable.mixture.motif.
MixtureDurationDiffSM
de.jstacs.sequenceScores.statisticalModels.differentiable.mixture.motif.
SkewNormalLikeDurationDiffSM
de.jstacs.sequenceScores.statisticalModels.differentiable.mixture.motif.
UniformDurationDiffSM
de.jstacs.sequenceScores.differentiable.
IndependentProductDiffSS
de.jstacs.sequenceScores.statisticalModels.differentiable.
IndependentProductDiffSM
(implements de.jstacs.sequenceScores.statisticalModels.differentiable.
DifferentiableStatisticalModel
, de.jstacs.motifDiscovery.
MutableMotifDiscoverer
)
de.jstacs.sequenceScores.differentiable.logistic.
LogisticDiffSS
de.jstacs.sequenceScores.statisticalModels.differentiable.
MultiDimensionalSequenceWrapperDiffSM
de.jstacs.sequenceScores.differentiable.
UniformDiffSS
de.jstacs.sequenceScores.statisticalModels.differentiable.
UniformDiffSM
(implements de.jstacs.sequenceScores.statisticalModels.differentiable.
SamplingDifferentiableStatisticalModel
)
de.jstacs.io.
AbstractStringExtractor
(implements java.util.
Enumeration
<E>)
de.jstacs.io.
InfixStringExtractor
de.jstacs.io.
LimitedStringExtractor
de.jstacs.io.
SimpleStringExtractor
de.jstacs.io.
SparseStringExtractor
de.jstacs.io.
StringExtractor
de.jstacs.algorithms.optimization.termination.
AbstractTerminationCondition
(implements de.jstacs.algorithms.optimization.termination.
TerminationCondition
)
de.jstacs.algorithms.optimization.termination.
AbsoluteValueCondition
de.jstacs.algorithms.optimization.termination.
CombinedCondition
de.jstacs.algorithms.optimization.termination.
IterationCondition
de.jstacs.algorithms.optimization.termination.
SmallDifferenceOfFunctionEvaluationsCondition
de.jstacs.algorithms.optimization.termination.
SmallGradientConditon
de.jstacs.algorithms.optimization.termination.
SmallStepCondition
de.jstacs.algorithms.optimization.termination.
TimeCondition
de.jstacs.sequenceScores.statisticalModels.trainable.
AbstractTrainableStatisticalModel
(implements java.lang.
Cloneable
, de.jstacs.
Storable
, de.jstacs.sequenceScores.statisticalModels.trainable.
TrainableStatisticalModel
)
de.jstacs.sequenceScores.statisticalModels.trainable.hmm.
AbstractHMM
(implements java.lang.
Cloneable
, de.jstacs.
Storable
)
de.jstacs.sequenceScores.statisticalModels.trainable.hmm.models.
HigherOrderHMM
de.jstacs.sequenceScores.statisticalModels.trainable.hmm.models.
DifferentiableHigherOrderHMM
(implements de.jstacs.sequenceScores.statisticalModels.differentiable.
SamplingDifferentiableStatisticalModel
)
de.jstacs.sequenceScores.statisticalModels.trainable.hmm.models.
SamplingHigherOrderHMM
de.jstacs.sequenceScores.statisticalModels.trainable.hmm.models.
SamplingPhyloHMM
de.jstacs.sequenceScores.statisticalModels.trainable.mixture.
AbstractMixtureTrainSM
de.jstacs.sequenceScores.statisticalModels.trainable.mixture.motif.
HiddenMotifMixture
(implements de.jstacs.motifDiscovery.
MotifDiscoverer
)
de.jstacs.sequenceScores.statisticalModels.trainable.mixture.motif.
ZOOPSTrainSM
de.jstacs.sequenceScores.statisticalModels.trainable.mixture.
MixtureTrainSM
de.jstacs.sequenceScores.statisticalModels.trainable.discrete.inhomogeneous.shared.
SharedStructureMixture
de.jstacs.sequenceScores.statisticalModels.trainable.mixture.
StrandTrainSM
de.jstacs.sequenceScores.statisticalModels.trainable.
CompositeTrainSM
de.jstacs.sequenceScores.statisticalModels.trainable.
DifferentiableStatisticalModelWrapperTrainSM
de.jstacs.sequenceScores.statisticalModels.trainable.discrete.
DiscreteGraphicalTrainSM
(implements de.jstacs.
InstantiableFromParameterSet
)
de.jstacs.sequenceScores.statisticalModels.trainable.discrete.homogeneous.
HomogeneousTrainSM
de.jstacs.sequenceScores.statisticalModels.trainable.discrete.homogeneous.
HomogeneousMM
de.jstacs.sequenceScores.statisticalModels.trainable.discrete.inhomogeneous.
InhomogeneousDGTrainSM
de.jstacs.sequenceScores.statisticalModels.trainable.discrete.inhomogeneous.
DAGTrainSM
de.jstacs.sequenceScores.statisticalModels.trainable.discrete.inhomogeneous.
BayesianNetworkTrainSM
de.jstacs.sequenceScores.statisticalModels.trainable.discrete.inhomogeneous.
FSDAGTrainSM
de.jstacs.sequenceScores.statisticalModels.trainable.discrete.inhomogeneous.
FSDAGModelForGibbsSampling
(implements de.jstacs.sampling.
GibbsSamplingModel
)
de.jstacs.sequenceScores.statisticalModels.trainable.
UniformTrainSM
de.jstacs.sequenceScores.statisticalModels.trainable.
VariableLengthWrapperTrainSM
de.jstacs.algorithms.alignment.cost.
AffineCosts
(implements de.jstacs.algorithms.alignment.cost.
Costs
)
de.jstacs.algorithms.alignment.
Alignment
de.jstacs.data.alphabets.
Alphabet
(implements java.lang.
Comparable
<T>, de.jstacs.
InstantiableFromParameterSet
, de.jstacs.
Storable
)
de.jstacs.data.alphabets.
ContinuousAlphabet
de.jstacs.data.alphabets.
DiscreteAlphabet
de.jstacs.data.alphabets.
ComplementableDiscreteAlphabet
de.jstacs.data.alphabets.
DNAAlphabet
(implements de.jstacs.
Singleton
)
de.jstacs.data.alphabets.
GenericComplementableDiscreteAlphabet
de.jstacs.data.alphabets.
ProteinAlphabet
(implements de.jstacs.
Singleton
)
de.jstacs.data.
AlphabetContainer
(implements java.lang.
Comparable
<T>, de.jstacs.
InstantiableFromParameterSet
, de.jstacs.
Storable
)
de.jstacs.data.alphabets.
DNAAlphabetContainer
(implements de.jstacs.
Singleton
)
de.jstacs.
AnnotatedEntity
(implements de.jstacs.
Storable
)
de.jstacs.parameters.
Parameter
(implements java.lang.
Cloneable
)
de.jstacs.parameters.
AbstractSelectionParameter
(implements de.jstacs.parameters.
GalaxyConvertible
, de.jstacs.parameters.
Rangeable
)
de.jstacs.parameters.
MultiSelectionParameter
(implements de.jstacs.parameters.
RangeIterator
)
de.jstacs.parameters.
SelectionParameter
(implements de.jstacs.parameters.
GalaxyConvertible
, de.jstacs.parameters.
Rangeable
)
de.jstacs.parameters.
EnumParameter
de.jstacs.parameters.
FileParameter
(implements de.jstacs.parameters.
GalaxyConvertible
)
de.jstacs.parameters.
ParameterSetContainer
(implements de.jstacs.parameters.
GalaxyConvertible
)
de.jstacs.parameters.
RangeParameter
(implements de.jstacs.parameters.
GalaxyConvertible
, de.jstacs.parameters.
RangeIterator
)
de.jstacs.parameters.
SimpleParameter
(implements de.jstacs.parameters.
GalaxyConvertible
, de.jstacs.parameters.
Rangeable
)
de.jstacs.results.
Result
de.jstacs.classifiers.
AbstractScoreBasedClassifier.DoubleTableResult
de.jstacs.results.
DataSetResult
de.jstacs.utils.galaxy.
GalaxyAdaptor.FileResult
de.jstacs.results.
ImageResult
de.jstacs.utils.galaxy.
GalaxyAdaptor.LinkedImageResult
de.jstacs.results.
ListResult
de.jstacs.results.
SimpleResult
(implements java.lang.
Comparable
<T>)
de.jstacs.results.
CategoricalResult
de.jstacs.results.
NumericalResult
de.jstacs.results.
StorableResult
de.jstacs.
AnnotatedEntityList
<T>
de.jstacs.parameters.
ParameterSet.ParameterList
de.jstacs.io.
ArrayHandler
de.jstacs.sequenceScores.statisticalModels.trainable.hmm.transitions.
BasicHigherOrderTransition
(implements de.jstacs.sequenceScores.statisticalModels.trainable.hmm.transitions.
TrainableTransition
)
de.jstacs.sequenceScores.statisticalModels.trainable.hmm.transitions.
HigherOrderTransition
(implements de.jstacs.sequenceScores.statisticalModels.trainable.hmm.transitions.
DifferentiableTransition
, de.jstacs.sequenceScores.statisticalModels.trainable.hmm.transitions.
SamplingTransition
)
de.jstacs.sequenceScores.statisticalModels.trainable.hmm.transitions.
BasicHigherOrderTransition.AbstractTransitionElement
(implements java.lang.
Cloneable
, de.jstacs.
Storable
)
de.jstacs.sequenceScores.statisticalModels.trainable.hmm.transitions.elements.
BasicTransitionElement
de.jstacs.sequenceScores.statisticalModels.trainable.hmm.transitions.elements.
BasicPluginTransitionElement
de.jstacs.sequenceScores.statisticalModels.trainable.hmm.transitions.elements.
ReferenceBasedTransitionElement
de.jstacs.sequenceScores.statisticalModels.trainable.hmm.transitions.elements.
DistanceBasedScaledTransitionElement
de.jstacs.sequenceScores.statisticalModels.trainable.hmm.transitions.elements.
ScaledTransitionElement
de.jstacs.sequenceScores.statisticalModels.trainable.hmm.transitions.elements.
TransitionElement
de.jstacs.data.bioJava.
BioJavaAdapter
de.jstacs.sequenceScores.statisticalModels.differentiable.directedGraphicalModels.
BNDiffSMParameter
(implements java.lang.
Cloneable
, de.jstacs.
Storable
)
de.jstacs.sequenceScores.statisticalModels.differentiable.directedGraphicalModels.
BNDiffSMParameterTree
(implements java.lang.
Cloneable
, de.jstacs.
Storable
)
de.jstacs.sequenceScores.statisticalModels.differentiable.directedGraphicalModels.
BNDiffSMParameterTree.TreeElement
(implements java.lang.
Cloneable
, de.jstacs.
Storable
)
de.jstacs.motifDiscovery.history.
CappedHistory
(implements de.jstacs.motifDiscovery.history.
History
)
de.jstacs.sequenceScores.statisticalModels.differentiable.mixture.motif.
CDFOfNormal
de.jstacs.algorithms.graphs.
Chu_Liu_Edmonds
de.jstacs.classifiers.utils.
ClassificationVisualizer
de.jstacs.classifiers.assessment.
ClassifierAssessment
de.jstacs.classifiers.assessment.
KFoldCrossValidation
de.jstacs.classifiers.assessment.
RepeatedHoldOutExperiment
de.jstacs.classifiers.assessment.
RepeatedSubSamplingExperiment
de.jstacs.classifiers.assessment.
Sampled_RepeatedHoldOutExperiment
de.jstacs.sequenceScores.statisticalModels.trainable.discrete.inhomogeneous.
CombinationIterator
de.jstacs.io.
CombinedFileFilter
(implements java.io.
FileFilter
)
de.jstacs.utils.
ComparableElement
<E,C> (implements java.lang.
Comparable
<T>)
de.jstacs.algorithms.optimization.
ConstantStartDistance
(implements de.jstacs.algorithms.optimization.
StartDistanceForecaster
)
de.jstacs.sequenceScores.statisticalModels.trainable.discrete.
Constraint
(implements de.jstacs.
Storable
)
de.jstacs.sequenceScores.statisticalModels.trainable.discrete.homogeneous.
HomogeneousTrainSM.HomCondProb
de.jstacs.sequenceScores.statisticalModels.trainable.discrete.inhomogeneous.
InhConstraint
(implements java.lang.
Cloneable
)
de.jstacs.sequenceScores.statisticalModels.trainable.discrete.inhomogeneous.
InhCondProb
de.jstacs.sequenceScores.statisticalModels.trainable.discrete.inhomogeneous.
MEMConstraint
de.jstacs.sequenceScores.statisticalModels.trainable.discrete.
ConstraintManager
de.jstacs.parameters.validation.
ConstraintValidator
(implements de.jstacs.parameters.validation.
ParameterValidator
)
de.jstacs.algorithms.graphs.
DAG
de.jstacs.data.
DataSet
(implements java.lang.
Iterable
<T>)
de.jstacs.data.
DNADataSet
de.jstacs.data.
DataSet.ElementEnumerator
(implements java.util.
Iterator
<E>, de.jstacs.data.
RecyclableSequenceEnumerator
)
de.jstacs.data.
DataSet.WeightedDataSetFactory
de.jstacs.data.
DataSetKMerEnumerator
(implements de.jstacs.data.
RecyclableSequenceEnumerator
)
de.jstacs.io.
DateFileFilter
(implements java.io.
FileFilter
)
de.jstacs.utils.
DefaultProgressUpdater
(implements de.jstacs.utils.
ProgressUpdater
)
de.jstacs.utils.
TimeLimitedProgressUpdater
de.jstacs.algorithms.optimization.
DifferentiableFunction
(implements de.jstacs.algorithms.optimization.
Function
)
de.jstacs.classifiers.differentiableSequenceScoreBased.logPrior.
LogPrior
(implements de.jstacs.
Storable
)
de.jstacs.classifiers.differentiableSequenceScoreBased.logPrior.
CompositeLogPrior
de.jstacs.classifiers.differentiableSequenceScoreBased.logPrior.
DoesNothingLogPrior
de.jstacs.classifiers.differentiableSequenceScoreBased.logPrior.
SeparateLogPrior
(implements java.lang.
Cloneable
)
de.jstacs.classifiers.differentiableSequenceScoreBased.logPrior.
SeparateGaussianLogPrior
de.jstacs.classifiers.differentiableSequenceScoreBased.logPrior.
SeparateLaplaceLogPrior
de.jstacs.classifiers.differentiableSequenceScoreBased.logPrior.
SimpleGaussianSumLogPrior
de.jstacs.algorithms.optimization.
NegativeDifferentiableFunction
de.jstacs.algorithms.optimization.
NumericalDifferentiableFunction
de.jstacs.classifiers.differentiableSequenceScoreBased.
OptimizableFunction
de.jstacs.classifiers.differentiableSequenceScoreBased.
AbstractOptimizableFunction
de.jstacs.classifiers.differentiableSequenceScoreBased.
AbstractMultiThreadedOptimizableFunction
de.jstacs.classifiers.differentiableSequenceScoreBased.
DiffSSBasedOptimizableFunction
de.jstacs.classifiers.differentiableSequenceScoreBased.gendismix.
LogGenDisMixFunction
de.jstacs.classifiers.differentiableSequenceScoreBased.gendismix.
OneDataSetLogGenDisMixFunction
de.jstacs.sequenceScores.statisticalModels.differentiable.
DifferentiableStatisticalModelFactory
de.jstacs.data.
DinucleotideProperty.Smoothing
de.jstacs.data.
DinucleotideProperty.MeanSmoothing
de.jstacs.data.
DinucleotideProperty.MedianSmoothing
de.jstacs.data.
DinucleotideProperty.NoSmoothing
de.jstacs.data.alphabets.
DiscreteAlphabetMapping
(implements de.jstacs.
Storable
)
de.jstacs.utils.
DiscreteInhomogenousDataSetEmitter
de.jstacs.data.
DiscreteSequenceEnumerator
(implements de.jstacs.data.
RecyclableSequenceEnumerator
)
de.jstacs.utils.
DoubleList
(implements java.lang.
Cloneable
, de.jstacs.
Storable
)
de.jstacs.algorithms.graphs.
Edge
(implements java.lang.
Cloneable
, java.lang.
Comparable
<T>)
javax.swing.filechooser.
FileFilter
de.jstacs.io.
RegExFilenameFilter
(implements java.io.
FileFilter
, java.io.
FilenameFilter
)
de.jstacs.io.
FileManager
de.jstacs.parameters.
FileParameter.FileRepresentation
(implements java.lang.
Cloneable
, de.jstacs.
Storable
)
de.jstacs.utils.galaxy.
GalaxyAdaptor
de.jstacs.utils.galaxy.
GalaxyAdaptor.Protocol
de.jstacs.sequenceScores.statisticalModels.trainable.hmm.states.emissions.continuous.
GaussianEmission
(implements de.jstacs.sequenceScores.statisticalModels.trainable.hmm.states.emissions.
DifferentiableEmission
)
de.jstacs.sequenceScores.statisticalModels.trainable.hmm.states.emissions.continuous.
PluginGaussianEmission
de.jstacs.utils.
GUIProgressUpdater
(implements java.awt.event.
ActionListener
, de.jstacs.utils.
ProgressUpdater
)
de.jstacs.sequenceScores.statisticalModels.trainable.hmm.
HMMFactory
de.jstacs.sequenceScores.statisticalModels.trainable.hmm.
HMMFactory.PseudoTransitionElement
de.jstacs.utils.
IntList
(implements java.lang.
Cloneable
)
de.jstacs.motifDiscovery.
KMereStatistic
de.jstacs.algorithms.optimization.
LimitedMedianStartDistance
(implements de.jstacs.algorithms.optimization.
StartDistanceForecaster
)
de.jstacs.algorithms.alignment.cost.
MatrixCosts
(implements de.jstacs.algorithms.alignment.cost.
Costs
)
de.jstacs.sequenceScores.statisticalModels.differentiable.directedGraphicalModels.structureLearning.measures.
Measure
(implements java.lang.
Cloneable
, de.jstacs.
InstantiableFromParameterSet
, de.jstacs.
Storable
)
de.jstacs.sequenceScores.statisticalModels.differentiable.directedGraphicalModels.structureLearning.measures.btMeasures.
BTExplainingAwayResidual
de.jstacs.sequenceScores.statisticalModels.differentiable.directedGraphicalModels.structureLearning.measures.btMeasures.
BTMutualInformation
de.jstacs.sequenceScores.statisticalModels.differentiable.directedGraphicalModels.structureLearning.measures.
InhomogeneousMarkov
de.jstacs.sequenceScores.statisticalModels.differentiable.directedGraphicalModels.structureLearning.measures.pmmMeasures.
PMMExplainingAwayResidual
de.jstacs.sequenceScores.statisticalModels.differentiable.directedGraphicalModels.structureLearning.measures.pmmMeasures.
PMMMutualInformation
de.jstacs.sequenceScores.statisticalModels.trainable.hmm.states.emissions.
MixtureEmission
(implements de.jstacs.sequenceScores.statisticalModels.trainable.hmm.states.emissions.
Emission
)
de.jstacs.motifDiscovery.
MotifDiscovererToolBox
de.jstacs.motifDiscovery.
MutableMotifDiscovererToolbox
de.jstacs.motifDiscovery.
MotifDiscoveryAssessment
de.jstacs.utils.random.
MRGParams
de.jstacs.utils.random.
DiMRGParams
de.jstacs.utils.random.
DirichletMRGParams
de.jstacs.utils.random.
FastDirichletMRGParams
de.jstacs.utils.random.
ErlangMRGParams
de.jstacs.algorithms.graphs.
MST
de.jstacs.utils.random.
MultivariateRandomGenerator
de.jstacs.utils.random.
DirichletMRG
de.jstacs.utils.random.
EqualParts
de.jstacs.utils.random.
ErlangMRG
de.jstacs.utils.random.
SoftOneOfN
de.jstacs.algorithms.optimization.
NegativeFunction
(implements de.jstacs.algorithms.optimization.
Function
)
de.jstacs.sequenceScores.statisticalModels.trainable.phylo.parser.
NewickParser
de.jstacs.motifDiscovery.history.
NoRevertHistory
(implements de.jstacs.motifDiscovery.history.
History
)
de.jstacs.utils.
Normalisation
de.jstacs.utils.
NullProgressUpdater
(implements de.jstacs.utils.
ProgressUpdater
)
de.jstacs.data.sequences.annotation.
NullSequenceAnnotationParser
(implements de.jstacs.data.sequences.annotation.
SequenceAnnotationParser
)
de.jstacs.parameters.validation.
NumberValidator
<E> (implements de.jstacs.parameters.
GalaxyConvertible
, de.jstacs.parameters.validation.
ParameterValidator
)
de.jstacs.algorithms.optimization.
OneDimensionalFunction
(implements de.jstacs.algorithms.optimization.
Function
)
de.jstacs.algorithms.optimization.
NegativeOneDimensionalFunction
de.jstacs.algorithms.optimization.
OneDimensionalSubFunction
de.jstacs.algorithms.optimization.
QuadraticFunction
de.jstacs.algorithms.optimization.
Optimizer
java.io.
OutputStream
(implements java.io.
Closeable
, java.io.
Flushable
)
de.jstacs.utils.
RegExFilterOutputStream
de.jstacs.utils.
SafeOutputStream
de.jstacs.utils.
Pair
<E1,E2>
de.jstacs.parameters.
ParameterSet
(implements java.lang.
Cloneable
, de.jstacs.parameters.
GalaxyConvertible
, de.jstacs.
Storable
)
de.jstacs.classifiers.performanceMeasures.
AbstractPerformanceMeasure
de.jstacs.classifiers.performanceMeasures.
ClassificationRate
(implements de.jstacs.classifiers.performanceMeasures.
NumericalPerformanceMeasure
)
de.jstacs.classifiers.performanceMeasures.
ConfusionMatrix
de.jstacs.classifiers.performanceMeasures.
TwoClassAbstractPerformanceMeasure
de.jstacs.classifiers.performanceMeasures.
FalsePositiveRateForFixedSensitivity
(implements de.jstacs.classifiers.performanceMeasures.
NumericalPerformanceMeasure
)
de.jstacs.classifiers.performanceMeasures.
MaximumNumericalTwoClassMeasure
(implements de.jstacs.classifiers.performanceMeasures.
NumericalPerformanceMeasure
)
de.jstacs.classifiers.performanceMeasures.
MaximumCorrelationCoefficient
(implements de.jstacs.classifiers.performanceMeasures.
NumericalPerformanceMeasure
)
de.jstacs.classifiers.performanceMeasures.
MaximumFMeasure
de.jstacs.classifiers.performanceMeasures.
PositivePredictiveValueForFixedSensitivity
(implements de.jstacs.classifiers.performanceMeasures.
NumericalPerformanceMeasure
)
de.jstacs.classifiers.performanceMeasures.
PRCurve
de.jstacs.classifiers.performanceMeasures.
AucPR
(implements de.jstacs.classifiers.performanceMeasures.
NumericalPerformanceMeasure
)
de.jstacs.classifiers.performanceMeasures.
ROCCurve
de.jstacs.classifiers.performanceMeasures.
AucROC
(implements de.jstacs.classifiers.performanceMeasures.
NumericalPerformanceMeasure
)
de.jstacs.classifiers.performanceMeasures.
SensitivityForFixedSpecificity
(implements de.jstacs.classifiers.performanceMeasures.
NumericalPerformanceMeasure
)
de.jstacs.classifiers.assessment.
ClassifierAssessmentAssessParameterSet
de.jstacs.classifiers.assessment.
KFoldCrossValidationAssessParameterSet
de.jstacs.classifiers.assessment.
RepeatedHoldOutAssessParameterSet
de.jstacs.classifiers.assessment.
RepeatedSubSamplingAssessParameterSet
de.jstacs.classifiers.assessment.
Sampled_RepeatedHoldOutAssessParameterSet
de.jstacs.parameters.
ExpandableParameterSet
de.jstacs.data.
AlphabetContainerParameterSet.SectionDefinedAlphabetParameterSet
de.jstacs.parameters.
ArrayParameterSet
de.jstacs.data.
AlphabetContainerParameterSet.AlphabetArrayParameterSet
de.jstacs.classifiers.performanceMeasures.
PerformanceMeasureParameterSet
de.jstacs.classifiers.performanceMeasures.
NumericalPerformanceMeasureParameterSet
de.jstacs.sequenceScores.statisticalModels.trainable.hmm.training.
HMMTrainingParameterSet
de.jstacs.sequenceScores.statisticalModels.trainable.hmm.training.
MaxHMMTrainingParameterSet
de.jstacs.sequenceScores.statisticalModels.trainable.hmm.training.
MultiThreadedTrainingParameterSet
de.jstacs.sequenceScores.statisticalModels.trainable.hmm.training.
BaumWelchParameterSet
de.jstacs.sequenceScores.statisticalModels.trainable.hmm.training.
NumericalHMMTrainingParameterSet
de.jstacs.sequenceScores.statisticalModels.trainable.hmm.training.
ViterbiParameterSet
de.jstacs.sequenceScores.statisticalModels.trainable.hmm.training.
SamplingHMMTrainingParameterSet
de.jstacs.parameters.
InstanceParameterSet
<T>
de.jstacs.sampling.
AbstractBurnInTestParameterSet
de.jstacs.sampling.
VarianceRatioBurnInTestParameterSet
de.jstacs.algorithms.optimization.termination.
AbstractTerminationCondition.AbstractTerminationConditionParameterSet
de.jstacs.algorithms.optimization.termination.
AbsoluteValueCondition.AbsoluteValueConditionParameterSet
de.jstacs.algorithms.optimization.termination.
CombinedCondition.CombinedConditionParameterSet
de.jstacs.algorithms.optimization.termination.
IterationCondition.IterationConditionParameterSet
de.jstacs.algorithms.optimization.termination.
SmallDifferenceOfFunctionEvaluationsCondition.SmallDifferenceOfFunctionEvaluationsConditionParameterSet
de.jstacs.algorithms.optimization.termination.
SmallGradientConditon.SmallGradientConditonParameterSet
de.jstacs.algorithms.optimization.termination.
SmallStepCondition.SmallStepConditionParameterSet
de.jstacs.algorithms.optimization.termination.
TimeCondition.TimeConditionParameterSet
de.jstacs.data.alphabets.
Alphabet.AlphabetParameterSet
<T>
de.jstacs.data.alphabets.
ContinuousAlphabet.ContinuousAlphabetParameterSet
de.jstacs.data.alphabets.
DiscreteAlphabet.DiscreteAlphabetParameterSet
de.jstacs.data.alphabets.
GenericComplementableDiscreteAlphabet.GenericComplementableDiscreteAlphabetParameterSet
de.jstacs.data.alphabets.
DNAAlphabet.DNAAlphabetParameterSet
(implements de.jstacs.
Singleton
)
de.jstacs.data.alphabets.
ProteinAlphabet.ProteinAlphabetParameterSet
(implements de.jstacs.
Singleton
)
de.jstacs.data.
AlphabetContainer.AbstractAlphabetContainerParameterSet
<T>
de.jstacs.data.
AlphabetContainerParameterSet
de.jstacs.data.alphabets.
DNAAlphabetContainer.DNAAlphabetContainerParameterSet
(implements de.jstacs.
Singleton
)
de.jstacs.sequenceScores.statisticalModels.differentiable.directedGraphicalModels.structureLearning.measures.
Measure.MeasureParameterSet
de.jstacs.sequenceScores.statisticalModels.differentiable.directedGraphicalModels.structureLearning.measures.btMeasures.
BTExplainingAwayResidual.BTExplainingAwayResidualParameterSet
de.jstacs.sequenceScores.statisticalModels.differentiable.directedGraphicalModels.structureLearning.measures.btMeasures.
BTMutualInformation.BTMutualInformationParameterSet
de.jstacs.sequenceScores.statisticalModels.differentiable.directedGraphicalModels.structureLearning.measures.
InhomogeneousMarkov.InhomogeneousMarkovParameterSet
de.jstacs.sequenceScores.statisticalModels.differentiable.directedGraphicalModels.structureLearning.measures.pmmMeasures.
PMMExplainingAwayResidual.PMMExplainingAwayResidualParameterSet
de.jstacs.sequenceScores.statisticalModels.differentiable.directedGraphicalModels.structureLearning.measures.pmmMeasures.
PMMMutualInformation.PMMMutualInformationParameterSet
de.jstacs.parameters.
SequenceScoringParameterSet
<T>
de.jstacs.sequenceScores.statisticalModels.differentiable.directedGraphicalModels.
BayesianNetworkDiffSMParameterSet
de.jstacs.sequenceScores.statisticalModels.trainable.discrete.
DGTrainSMParameterSet
<T>
de.jstacs.sequenceScores.statisticalModels.trainable.discrete.homogeneous.parameters.
HomogeneousTrainSMParameterSet
de.jstacs.sequenceScores.statisticalModels.trainable.discrete.homogeneous.parameters.
HomMMParameterSet
de.jstacs.sequenceScores.statisticalModels.trainable.discrete.inhomogeneous.parameters.
IDGTrainSMParameterSet
de.jstacs.sequenceScores.statisticalModels.trainable.discrete.inhomogeneous.parameters.
BayesianNetworkTrainSMParameterSet
de.jstacs.sequenceScores.statisticalModels.trainable.discrete.inhomogeneous.parameters.
FSDAGTrainSMParameterSet
de.jstacs.sequenceScores.statisticalModels.trainable.discrete.inhomogeneous.parameters.
FSDAGModelForGibbsSamplingParameterSet
de.jstacs.classifiers.differentiableSequenceScoreBased.sampling.
SamplingScoreBasedClassifierParameterSet
de.jstacs.classifiers.differentiableSequenceScoreBased.sampling.
SamplingGenDisMixClassifierParameterSet
de.jstacs.classifiers.differentiableSequenceScoreBased.
ScoreClassifierParameterSet
de.jstacs.classifiers.differentiableSequenceScoreBased.gendismix.
GenDisMixClassifierParameterSet
de.jstacs.parameters.
SimpleParameterSet
de.jstacs.io.
ParameterSetParser
de.jstacs.parameters.
ParameterSetTagger
de.jstacs.parameters.
ParameterSetTagger.KeyEntryComparator
<K,V> (implements java.util.
Comparator
<T>)
de.jstacs.parameters.
ParameterSetTagger.RankEntryComparator
<K,V> (implements java.util.
Comparator
<T>)
de.jstacs.sequenceScores.statisticalModels.trainable.phylo.
PhyloNode
(implements java.lang.
Cloneable
, de.jstacs.
Storable
)
de.jstacs.sequenceScores.statisticalModels.trainable.phylo.
PhyloTree
(implements java.lang.
Cloneable
, de.jstacs.
Storable
)
de.jstacs.sequenceScores.statisticalModels.trainable.mixture.motif.positionprior.
PositionPrior
(implements java.lang.
Cloneable
, de.jstacs.
Storable
)
de.jstacs.sequenceScores.statisticalModels.trainable.mixture.motif.positionprior.
GaussianLikePositionPrior
de.jstacs.sequenceScores.statisticalModels.trainable.mixture.motif.positionprior.
UniformPositionPrior
de.jstacs.sequenceScores.differentiable.logistic.
ProductConstraint
(implements de.jstacs.sequenceScores.differentiable.logistic.
LogisticConstraint
)
de.jstacs.classifiers.utils.
PValueComputation
de.jstacs.utils.random.
RandomNumberGenerator
(implements java.io.
Serializable
)
de.jstacs.utils.
REnvironment
de.jstacs.motifDiscovery.history.
RestrictedRepeatHistory
(implements de.jstacs.motifDiscovery.history.
History
)
de.jstacs.results.
ResultSet
(implements de.jstacs.
Storable
)
de.jstacs.results.
NumericalResultSet
de.jstacs.results.
MeanResultSet
de.jstacs.data.sequences.annotation.
SequenceAnnotation
de.jstacs.data.sequences.annotation.
CisRegulatoryModuleAnnotation
de.jstacs.data.sequences.annotation.
LocatedSequenceAnnotation
de.jstacs.data.sequences.annotation.
LocatedSequenceAnnotationWithLength
de.jstacs.data.sequences.annotation.
IntronAnnotation
de.jstacs.data.sequences.annotation.
StrandedLocatedSequenceAnnotationWithLength
de.jstacs.data.sequences.annotation.
MotifAnnotation
de.jstacs.data.sequences.annotation.
SinglePositionSequenceAnnotation
de.jstacs.data.sequences.annotation.
ReferenceSequenceAnnotation
de.jstacs.utils.
RUtils
de.jstacs.classifiers.differentiableSequenceScoreBased.sampling.
SamplingScoreBasedClassifier.DiffSMSamplingComponent
(implements de.jstacs.sampling.
SamplingComponent
)
de.jstacs.data.sequences.
Sequence
<T> (implements java.lang.
Comparable
<T>)
de.jstacs.data.sequences.
ArbitraryFloatSequence
de.jstacs.data.sequences.
ArbitrarySequence
de.jstacs.data.sequences.
MultiDimensionalSequence
<T>
de.jstacs.data.sequences.
MultiDimensionalArbitrarySequence
de.jstacs.data.sequences.
MultiDimensionalDiscreteSequence
de.jstacs.data.sequences.
Sequence.RecursiveSequence
<T>
de.jstacs.data.sequences.
PermutedSequence
<T>
de.jstacs.data.sequences.
Sequence.CompositeSequence
<T>
de.jstacs.data.sequences.
Sequence.SubSequence
<T>
de.jstacs.data.sequences.
SimpleDiscreteSequence
de.jstacs.data.sequences.
ByteSequence
de.jstacs.data.sequences.
IntSequence
de.jstacs.data.sequences.
MappedDiscreteSequence
de.jstacs.data.sequences.
ShortSequence
de.jstacs.data.sequences.
SparseSequence
de.jstacs.data.
SequenceEnumeration
(implements de.jstacs.data.
RecyclableSequenceEnumerator
)
de.jstacs.sequenceScores.statisticalModels.trainable.discrete.inhomogeneous.
SequenceIterator
(implements java.lang.
Cloneable
)
de.jstacs.motifDiscovery.
SignificantMotifOccurrencesFinder
de.jstacs.motifDiscovery.
SignificantMotifOccurrencesFinder.SumOfProbabilities
(implements de.jstacs.motifDiscovery.
SignificantMotifOccurrencesFinder.JoinMethod
)
de.jstacs.sequenceScores.statisticalModels.trainable.hmm.states.emissions.
SilentEmission
(implements de.jstacs.sequenceScores.statisticalModels.trainable.hmm.states.emissions.
DifferentiableEmission
, de.jstacs.sequenceScores.statisticalModels.trainable.hmm.states.emissions.
SamplingEmission
)
de.jstacs.sampling.
SimpleBurnInTest
(implements de.jstacs.sampling.
BurnInTest
)
de.jstacs.algorithms.alignment.cost.
SimpleCosts
(implements de.jstacs.algorithms.alignment.cost.
Costs
)
de.jstacs.motifDiscovery.history.
SimpleHistory
(implements de.jstacs.motifDiscovery.history.
History
)
de.jstacs.data.sequences.annotation.
SimpleSequenceAnnotationParser
(implements de.jstacs.data.sequences.annotation.
SequenceAnnotationParser
)
de.jstacs.data.bioJava.
SimpleSequenceIterator
(implements org.biojava.bio.seq.
SequenceIterator
)
de.jstacs.sequenceScores.statisticalModels.trainable.hmm.states.
SimpleState
(implements de.jstacs.sequenceScores.statisticalModels.trainable.hmm.states.
TrainableState
)
de.jstacs.sequenceScores.statisticalModels.trainable.hmm.states.
SimpleDifferentiableState
(implements de.jstacs.sequenceScores.statisticalModels.trainable.hmm.states.
DifferentiableState
)
de.jstacs.sequenceScores.statisticalModels.trainable.hmm.states.
SimpleSamplingState
(implements de.jstacs.sequenceScores.statisticalModels.trainable.hmm.states.
SamplingState
)
de.jstacs.parameters.validation.
SimpleStaticConstraint
(implements de.jstacs.parameters.validation.
Constraint
)
de.jstacs.
Singleton.SingletonHandler
de.jstacs.data.sequences.annotation.
SplitSequenceAnnotationParser
(implements de.jstacs.data.sequences.annotation.
SequenceAnnotationParser
)
de.jstacs.data.sequences.annotation.
MotifAnnotationParser
de.jstacs.data.sequences.annotation.
ReferenceSequenceAnnotationParser
de.jstacs.utils.
StationaryDistribution
de.jstacs.utils.
StatisticalModelTester
de.jstacs.utils.
StatisticalTest
de.jstacs.parameters.validation.
StorableValidator
(implements de.jstacs.parameters.validation.
ParameterValidator
)
de.jstacs.algorithms.alignment.
StringAlignment
de.jstacs.algorithms.alignment.
PairwiseStringAlignment
de.jstacs.sequenceScores.statisticalModels.trainable.discrete.inhomogeneous.
StructureLearner
de.jstacs.utils.
SubclassFinder
de.jstacs.io.
SymbolExtractor
(implements java.util.
Enumeration
<E>)
de.jstacs.algorithms.graphs.tensor.
Tensor
de.jstacs.algorithms.graphs.tensor.
AsymmetricTensor
de.jstacs.algorithms.graphs.tensor.
SubTensor
de.jstacs.algorithms.graphs.tensor.
SymmetricTensor
java.lang.
Throwable
(implements java.io.
Serializable
)
java.lang.
Exception
de.jstacs.classifiers.
ClassDimensionException
de.jstacs.algorithms.optimization.
DimensionException
de.jstacs.data.alphabets.
DoubleSymbolException
de.jstacs.data.
EmptyDataSetException
de.jstacs.algorithms.optimization.
EvaluationException
de.jstacs.results.
MeanResultSet.AdditionImpossibleException
de.jstacs.results.
MeanResultSet.InconsistentResultNumberException
de.jstacs.io.
NonParsableException
de.jstacs.
NotTrainedException
de.jstacs.parameters.
ParameterException
de.jstacs.parameters.
AbstractSelectionParameter.InconsistentCollectionException
de.jstacs.io.
ParameterSetParser.NotInstantiableException
de.jstacs.io.
ParameterSetParser.WrongParameterTypeException
de.jstacs.parameters.
SimpleParameter.DatatypeNotValidException
de.jstacs.parameters.
SimpleParameter.IllegalValueException
de.jstacs.algorithms.optimization.
TerminationException
de.jstacs.data.
WrongAlphabetException
de.jstacs.data.
WrongLengthException
de.jstacs.data.sequences.
WrongSequenceTypeException
de.jstacs.utils.
Time
de.jstacs.utils.
RealTime
de.jstacs.utils.
UserTime
de.jstacs.utils.
ToolBox
de.jstacs.algorithms.graphs.
TopSort
de.jstacs.sequenceScores.statisticalModels.trainable.
TrainableStatisticalModelFactory
de.jstacs.sequenceScores.statisticalModels.trainable.discrete.inhomogeneous.
TwoPointEvaluater
de.jstacs.sequenceScores.statisticalModels.trainable.hmm.states.emissions.
UniformEmission
(implements de.jstacs.sequenceScores.statisticalModels.trainable.hmm.states.emissions.
DifferentiableEmission
)
de.jstacs.algorithms.graphs.
UnionFind
de.jstacs.io.
XMLParser
Interface Hierarchy
java.lang.
Cloneable
de.jstacs.sampling.
BurnInTest
(also extends de.jstacs.
Storable
)
de.jstacs.parameters.validation.
Constraint
(also extends de.jstacs.
Storable
)
de.jstacs.sequenceScores.statisticalModels.trainable.hmm.states.emissions.
DifferentiableEmission
de.jstacs.sequenceScores.differentiable.
DifferentiableSequenceScore
de.jstacs.sequenceScores.statisticalModels.differentiable.
DifferentiableStatisticalModel
(also extends de.jstacs.sequenceScores.statisticalModels.
StatisticalModel
)
de.jstacs.sequenceScores.statisticalModels.differentiable.
SamplingDifferentiableStatisticalModel
de.jstacs.sequenceScores.statisticalModels.differentiable.
VariableLengthDiffSM
de.jstacs.sequenceScores.statisticalModels.differentiable.
SamplingDifferentiableStatisticalModel
de.jstacs.sequenceScores.statisticalModels.differentiable.
VariableLengthDiffSM
de.jstacs.sequenceScores.statisticalModels.differentiable.
DifferentiableStatisticalModel
(also extends de.jstacs.sequenceScores.differentiable.
DifferentiableSequenceScore
, de.jstacs.sequenceScores.statisticalModels.
StatisticalModel
)
de.jstacs.sequenceScores.statisticalModels.differentiable.
SamplingDifferentiableStatisticalModel
de.jstacs.sequenceScores.statisticalModels.differentiable.
VariableLengthDiffSM
de.jstacs.sequenceScores.statisticalModels.trainable.hmm.transitions.
DifferentiableTransition
de.jstacs.sequenceScores.statisticalModels.trainable.hmm.transitions.
TrainableAndDifferentiableTransition
(also extends de.jstacs.sequenceScores.statisticalModels.trainable.hmm.transitions.
TrainableTransition
)
de.jstacs.sequenceScores.statisticalModels.trainable.hmm.states.emissions.
Emission
(also extends de.jstacs.
Storable
)
de.jstacs.sequenceScores.statisticalModels.trainable.hmm.states.emissions.
DifferentiableEmission
de.jstacs.sequenceScores.statisticalModels.trainable.hmm.states.emissions.
SamplingEmission
(also extends de.jstacs.sampling.
SamplingFromStatistic
)
de.jstacs.motifDiscovery.history.
History
(also extends de.jstacs.
Storable
)
de.jstacs.sequenceScores.differentiable.logistic.
LogisticConstraint
(also extends de.jstacs.
Storable
)
de.jstacs.motifDiscovery.
MotifDiscoverer
(also extends de.jstacs.
Storable
)
de.jstacs.motifDiscovery.
MutableMotifDiscoverer
de.jstacs.motifDiscovery.
MutableMotifDiscoverer
de.jstacs.parameters.validation.
ParameterValidator
(also extends de.jstacs.
Storable
)
de.jstacs.sequenceScores.statisticalModels.differentiable.
SamplingDifferentiableStatisticalModel
de.jstacs.sequenceScores.statisticalModels.trainable.hmm.states.emissions.
SamplingEmission
(also extends de.jstacs.sequenceScores.statisticalModels.trainable.hmm.states.emissions.
Emission
, de.jstacs.sampling.
SamplingFromStatistic
)
de.jstacs.sequenceScores.statisticalModels.trainable.hmm.transitions.
SamplingTransition
(also extends de.jstacs.sampling.
SamplingFromStatistic
, de.jstacs.sequenceScores.statisticalModels.trainable.hmm.transitions.
TransitionWithSufficientStatistic
)
de.jstacs.sequenceScores.
SequenceScore
(also extends de.jstacs.
Storable
)
de.jstacs.sequenceScores.differentiable.
DifferentiableSequenceScore
de.jstacs.sequenceScores.statisticalModels.differentiable.
DifferentiableStatisticalModel
(also extends de.jstacs.sequenceScores.statisticalModels.
StatisticalModel
)
de.jstacs.sequenceScores.statisticalModels.differentiable.
SamplingDifferentiableStatisticalModel
de.jstacs.sequenceScores.statisticalModels.differentiable.
VariableLengthDiffSM
de.jstacs.sequenceScores.statisticalModels.differentiable.
SamplingDifferentiableStatisticalModel
de.jstacs.sequenceScores.statisticalModels.differentiable.
VariableLengthDiffSM
de.jstacs.sequenceScores.statisticalModels.differentiable.
DifferentiableStatisticalModel
(also extends de.jstacs.sequenceScores.differentiable.
DifferentiableSequenceScore
, de.jstacs.sequenceScores.statisticalModels.
StatisticalModel
)
de.jstacs.sequenceScores.statisticalModels.differentiable.
SamplingDifferentiableStatisticalModel
de.jstacs.sequenceScores.statisticalModels.differentiable.
VariableLengthDiffSM
de.jstacs.sequenceScores.statisticalModels.differentiable.
SamplingDifferentiableStatisticalModel
de.jstacs.sequenceScores.statisticalModels.
StatisticalModel
de.jstacs.sequenceScores.statisticalModels.differentiable.
DifferentiableStatisticalModel
(also extends de.jstacs.sequenceScores.differentiable.
DifferentiableSequenceScore
)
de.jstacs.sequenceScores.statisticalModels.differentiable.
SamplingDifferentiableStatisticalModel
de.jstacs.sequenceScores.statisticalModels.differentiable.
VariableLengthDiffSM
de.jstacs.sequenceScores.statisticalModels.differentiable.
SamplingDifferentiableStatisticalModel
de.jstacs.sequenceScores.statisticalModels.trainable.
TrainableStatisticalModel
de.jstacs.sequenceScores.statisticalModels.differentiable.
VariableLengthDiffSM
de.jstacs.sequenceScores.statisticalModels.trainable.
TrainableStatisticalModel
de.jstacs.sequenceScores.statisticalModels.differentiable.
VariableLengthDiffSM
de.jstacs.sequenceScores.statisticalModels.
StatisticalModel
de.jstacs.sequenceScores.statisticalModels.differentiable.
DifferentiableStatisticalModel
(also extends de.jstacs.sequenceScores.differentiable.
DifferentiableSequenceScore
)
de.jstacs.sequenceScores.statisticalModels.differentiable.
SamplingDifferentiableStatisticalModel
de.jstacs.sequenceScores.statisticalModels.differentiable.
VariableLengthDiffSM
de.jstacs.sequenceScores.statisticalModels.differentiable.
SamplingDifferentiableStatisticalModel
de.jstacs.sequenceScores.statisticalModels.trainable.
TrainableStatisticalModel
de.jstacs.sequenceScores.statisticalModels.differentiable.
VariableLengthDiffSM
de.jstacs.algorithms.optimization.termination.
TerminationCondition
(also extends de.jstacs.
InstantiableFromParameterSet
, de.jstacs.
Storable
)
de.jstacs.sequenceScores.statisticalModels.trainable.hmm.transitions.
TrainableAndDifferentiableTransition
(also extends de.jstacs.sequenceScores.statisticalModels.trainable.hmm.transitions.
DifferentiableTransition
, de.jstacs.sequenceScores.statisticalModels.trainable.hmm.transitions.
TrainableTransition
)
de.jstacs.sequenceScores.statisticalModels.trainable.
TrainableStatisticalModel
de.jstacs.sequenceScores.statisticalModels.trainable.hmm.transitions.
TrainableTransition
de.jstacs.sequenceScores.statisticalModels.trainable.hmm.transitions.
TrainableAndDifferentiableTransition
(also extends de.jstacs.sequenceScores.statisticalModels.trainable.hmm.transitions.
DifferentiableTransition
)
de.jstacs.sequenceScores.statisticalModels.trainable.hmm.transitions.
Transition
(also extends de.jstacs.
Storable
)
de.jstacs.sequenceScores.statisticalModels.trainable.hmm.transitions.
DifferentiableTransition
de.jstacs.sequenceScores.statisticalModels.trainable.hmm.transitions.
TrainableAndDifferentiableTransition
(also extends de.jstacs.sequenceScores.statisticalModels.trainable.hmm.transitions.
TrainableTransition
)
de.jstacs.sequenceScores.statisticalModels.trainable.hmm.transitions.
SamplingTransition
(also extends de.jstacs.sampling.
SamplingFromStatistic
, de.jstacs.sequenceScores.statisticalModels.trainable.hmm.transitions.
TransitionWithSufficientStatistic
)
de.jstacs.sequenceScores.statisticalModels.trainable.hmm.transitions.
TrainableAndDifferentiableTransition
(also extends de.jstacs.sequenceScores.statisticalModels.trainable.hmm.transitions.
DifferentiableTransition
, de.jstacs.sequenceScores.statisticalModels.trainable.hmm.transitions.
TrainableTransition
)
de.jstacs.sequenceScores.statisticalModels.trainable.hmm.transitions.
TrainableTransition
de.jstacs.sequenceScores.statisticalModels.trainable.hmm.transitions.
TrainableAndDifferentiableTransition
(also extends de.jstacs.sequenceScores.statisticalModels.trainable.hmm.transitions.
DifferentiableTransition
)
de.jstacs.sequenceScores.statisticalModels.trainable.hmm.transitions.
TransitionWithSufficientStatistic
de.jstacs.sequenceScores.statisticalModels.trainable.hmm.transitions.
SamplingTransition
(also extends de.jstacs.sampling.
SamplingFromStatistic
)
de.jstacs.sequenceScores.statisticalModels.trainable.hmm.transitions.
TrainableAndDifferentiableTransition
(also extends de.jstacs.sequenceScores.statisticalModels.trainable.hmm.transitions.
DifferentiableTransition
, de.jstacs.sequenceScores.statisticalModels.trainable.hmm.transitions.
TrainableTransition
)
de.jstacs.sequenceScores.statisticalModels.trainable.hmm.transitions.
TrainableTransition
de.jstacs.sequenceScores.statisticalModels.trainable.hmm.transitions.
TrainableAndDifferentiableTransition
(also extends de.jstacs.sequenceScores.statisticalModels.trainable.hmm.transitions.
DifferentiableTransition
)
de.jstacs.sequenceScores.statisticalModels.trainable.hmm.transitions.
TransitionWithSufficientStatistic
de.jstacs.sequenceScores.statisticalModels.trainable.hmm.transitions.
SamplingTransition
(also extends de.jstacs.sampling.
SamplingFromStatistic
)
de.jstacs.sequenceScores.statisticalModels.trainable.hmm.transitions.
TrainableAndDifferentiableTransition
(also extends de.jstacs.sequenceScores.statisticalModels.trainable.hmm.transitions.
DifferentiableTransition
, de.jstacs.sequenceScores.statisticalModels.trainable.hmm.transitions.
TrainableTransition
)
de.jstacs.sequenceScores.statisticalModels.trainable.hmm.transitions.
TrainableTransition
de.jstacs.sequenceScores.statisticalModels.trainable.hmm.transitions.
TrainableAndDifferentiableTransition
(also extends de.jstacs.sequenceScores.statisticalModels.trainable.hmm.transitions.
DifferentiableTransition
)
de.jstacs.sequenceScores.statisticalModels.differentiable.
VariableLengthDiffSM
de.jstacs.algorithms.alignment.cost.
Costs
java.util.
Enumeration
<E>
de.jstacs.data.
RecyclableSequenceEnumerator
de.jstacs.algorithms.optimization.
Function
de.jstacs.parameters.
GalaxyConvertible
de.jstacs.
InstantiableFromParameterSet
de.jstacs.algorithms.optimization.termination.
TerminationCondition
(also extends java.lang.
Cloneable
, de.jstacs.
Storable
)
de.jstacs.motifDiscovery.
Mutable
de.jstacs.classifiers.performanceMeasures.
NumericalPerformanceMeasure
de.jstacs.utils.
ProgressUpdater
de.jstacs.parameters.
Rangeable
de.jstacs.parameters.
RangeIterator
de.jstacs.sampling.
SamplingComponent
de.jstacs.sampling.
GibbsSamplingModel
de.jstacs.sequenceScores.statisticalModels.trainable.hmm.states.emissions.
SamplingEmission
(also extends de.jstacs.sequenceScores.statisticalModels.trainable.hmm.states.emissions.
Emission
, de.jstacs.sampling.
SamplingFromStatistic
)
de.jstacs.sampling.
SamplingFromStatistic
de.jstacs.sequenceScores.statisticalModels.trainable.hmm.states.emissions.
SamplingEmission
(also extends de.jstacs.sequenceScores.statisticalModels.trainable.hmm.states.emissions.
Emission
)
de.jstacs.sequenceScores.statisticalModels.trainable.hmm.states.
SamplingState
(also extends de.jstacs.sequenceScores.statisticalModels.trainable.hmm.states.
TrainableState
)
de.jstacs.sequenceScores.statisticalModels.trainable.hmm.transitions.
SamplingTransition
(also extends de.jstacs.sequenceScores.statisticalModels.trainable.hmm.transitions.
TransitionWithSufficientStatistic
)
de.jstacs.sequenceScores.statisticalModels.trainable.hmm.states.
SamplingState
(also extends de.jstacs.sampling.
SamplingFromStatistic
, de.jstacs.sequenceScores.statisticalModels.trainable.hmm.states.
TrainableState
)
de.jstacs.sequenceScores.statisticalModels.trainable.hmm.transitions.
SamplingTransition
(also extends de.jstacs.sampling.
SamplingFromStatistic
, de.jstacs.sequenceScores.statisticalModels.trainable.hmm.transitions.
TransitionWithSufficientStatistic
)
de.jstacs.data.sequences.annotation.
SequenceAnnotationParser
de.jstacs.motifDiscovery.
SignificantMotifOccurrencesFinder.JoinMethod
de.jstacs.
Singleton
de.jstacs.algorithms.optimization.
StartDistanceForecaster
de.jstacs.sequenceScores.statisticalModels.trainable.hmm.states.
State
de.jstacs.sequenceScores.statisticalModels.trainable.hmm.states.
DifferentiableState
de.jstacs.sequenceScores.statisticalModels.trainable.hmm.states.
SamplingState
(also extends de.jstacs.sampling.
SamplingFromStatistic
, de.jstacs.sequenceScores.statisticalModels.trainable.hmm.states.
TrainableState
)
de.jstacs.sequenceScores.statisticalModels.trainable.hmm.states.
TrainableState
de.jstacs.sequenceScores.statisticalModels.trainable.hmm.states.
SamplingState
(also extends de.jstacs.sampling.
SamplingFromStatistic
)
de.jstacs.
Storable
de.jstacs.sampling.
BurnInTest
(also extends java.lang.
Cloneable
)
de.jstacs.parameters.validation.
Constraint
(also extends java.lang.
Cloneable
)
de.jstacs.sequenceScores.statisticalModels.trainable.hmm.states.emissions.
DifferentiableEmission
de.jstacs.sequenceScores.differentiable.
DifferentiableSequenceScore
de.jstacs.sequenceScores.statisticalModels.differentiable.
DifferentiableStatisticalModel
(also extends de.jstacs.sequenceScores.statisticalModels.
StatisticalModel
)
de.jstacs.sequenceScores.statisticalModels.differentiable.
SamplingDifferentiableStatisticalModel
de.jstacs.sequenceScores.statisticalModels.differentiable.
VariableLengthDiffSM
de.jstacs.sequenceScores.statisticalModels.differentiable.
SamplingDifferentiableStatisticalModel
de.jstacs.sequenceScores.statisticalModels.differentiable.
VariableLengthDiffSM
de.jstacs.sequenceScores.statisticalModels.differentiable.
DifferentiableStatisticalModel
(also extends de.jstacs.sequenceScores.differentiable.
DifferentiableSequenceScore
, de.jstacs.sequenceScores.statisticalModels.
StatisticalModel
)
de.jstacs.sequenceScores.statisticalModels.differentiable.
SamplingDifferentiableStatisticalModel
de.jstacs.sequenceScores.statisticalModels.differentiable.
VariableLengthDiffSM
de.jstacs.sequenceScores.statisticalModels.trainable.hmm.transitions.
DifferentiableTransition
de.jstacs.sequenceScores.statisticalModels.trainable.hmm.transitions.
TrainableAndDifferentiableTransition
(also extends de.jstacs.sequenceScores.statisticalModels.trainable.hmm.transitions.
TrainableTransition
)
de.jstacs.sequenceScores.statisticalModels.trainable.hmm.states.emissions.
Emission
(also extends java.lang.
Cloneable
)
de.jstacs.sequenceScores.statisticalModels.trainable.hmm.states.emissions.
DifferentiableEmission
de.jstacs.sequenceScores.statisticalModels.trainable.hmm.states.emissions.
SamplingEmission
(also extends de.jstacs.sampling.
SamplingFromStatistic
)
de.jstacs.motifDiscovery.history.
History
(also extends java.lang.
Cloneable
)
de.jstacs.sequenceScores.differentiable.logistic.
LogisticConstraint
(also extends java.lang.
Cloneable
)
de.jstacs.motifDiscovery.
MotifDiscoverer
(also extends java.lang.
Cloneable
)
de.jstacs.motifDiscovery.
MutableMotifDiscoverer
de.jstacs.motifDiscovery.
MutableMotifDiscoverer
de.jstacs.parameters.validation.
ParameterValidator
(also extends java.lang.
Cloneable
)
de.jstacs.sequenceScores.statisticalModels.differentiable.
SamplingDifferentiableStatisticalModel
de.jstacs.sequenceScores.statisticalModels.trainable.hmm.states.emissions.
SamplingEmission
(also extends de.jstacs.sequenceScores.statisticalModels.trainable.hmm.states.emissions.
Emission
, de.jstacs.sampling.
SamplingFromStatistic
)
de.jstacs.sequenceScores.statisticalModels.trainable.hmm.transitions.
SamplingTransition
(also extends de.jstacs.sampling.
SamplingFromStatistic
, de.jstacs.sequenceScores.statisticalModels.trainable.hmm.transitions.
TransitionWithSufficientStatistic
)
de.jstacs.sequenceScores.
SequenceScore
(also extends java.lang.
Cloneable
)
de.jstacs.sequenceScores.differentiable.
DifferentiableSequenceScore
de.jstacs.sequenceScores.statisticalModels.differentiable.
DifferentiableStatisticalModel
(also extends de.jstacs.sequenceScores.statisticalModels.
StatisticalModel
)
de.jstacs.sequenceScores.statisticalModels.differentiable.
SamplingDifferentiableStatisticalModel
de.jstacs.sequenceScores.statisticalModels.differentiable.
VariableLengthDiffSM
de.jstacs.sequenceScores.statisticalModels.differentiable.
SamplingDifferentiableStatisticalModel
de.jstacs.sequenceScores.statisticalModels.differentiable.
VariableLengthDiffSM
de.jstacs.sequenceScores.statisticalModels.differentiable.
DifferentiableStatisticalModel
(also extends de.jstacs.sequenceScores.differentiable.
DifferentiableSequenceScore
, de.jstacs.sequenceScores.statisticalModels.
StatisticalModel
)
de.jstacs.sequenceScores.statisticalModels.differentiable.
SamplingDifferentiableStatisticalModel
de.jstacs.sequenceScores.statisticalModels.differentiable.
VariableLengthDiffSM
de.jstacs.sequenceScores.statisticalModels.differentiable.
SamplingDifferentiableStatisticalModel
de.jstacs.sequenceScores.statisticalModels.
StatisticalModel
de.jstacs.sequenceScores.statisticalModels.differentiable.
DifferentiableStatisticalModel
(also extends de.jstacs.sequenceScores.differentiable.
DifferentiableSequenceScore
)
de.jstacs.sequenceScores.statisticalModels.differentiable.
SamplingDifferentiableStatisticalModel
de.jstacs.sequenceScores.statisticalModels.differentiable.
VariableLengthDiffSM
de.jstacs.sequenceScores.statisticalModels.differentiable.
SamplingDifferentiableStatisticalModel
de.jstacs.sequenceScores.statisticalModels.trainable.
TrainableStatisticalModel
de.jstacs.sequenceScores.statisticalModels.differentiable.
VariableLengthDiffSM
de.jstacs.sequenceScores.statisticalModels.trainable.
TrainableStatisticalModel
de.jstacs.sequenceScores.statisticalModels.differentiable.
VariableLengthDiffSM
de.jstacs.sequenceScores.statisticalModels.
StatisticalModel
de.jstacs.sequenceScores.statisticalModels.differentiable.
DifferentiableStatisticalModel
(also extends de.jstacs.sequenceScores.differentiable.
DifferentiableSequenceScore
)
de.jstacs.sequenceScores.statisticalModels.differentiable.
SamplingDifferentiableStatisticalModel
de.jstacs.sequenceScores.statisticalModels.differentiable.
VariableLengthDiffSM
de.jstacs.sequenceScores.statisticalModels.differentiable.
SamplingDifferentiableStatisticalModel
de.jstacs.sequenceScores.statisticalModels.trainable.
TrainableStatisticalModel
de.jstacs.sequenceScores.statisticalModels.differentiable.
VariableLengthDiffSM
de.jstacs.algorithms.optimization.termination.
TerminationCondition
(also extends java.lang.
Cloneable
, de.jstacs.
InstantiableFromParameterSet
)
de.jstacs.sequenceScores.statisticalModels.trainable.hmm.transitions.
TrainableAndDifferentiableTransition
(also extends de.jstacs.sequenceScores.statisticalModels.trainable.hmm.transitions.
DifferentiableTransition
, de.jstacs.sequenceScores.statisticalModels.trainable.hmm.transitions.
TrainableTransition
)
de.jstacs.sequenceScores.statisticalModels.trainable.
TrainableStatisticalModel
de.jstacs.sequenceScores.statisticalModels.trainable.hmm.transitions.
TrainableTransition
de.jstacs.sequenceScores.statisticalModels.trainable.hmm.transitions.
TrainableAndDifferentiableTransition
(also extends de.jstacs.sequenceScores.statisticalModels.trainable.hmm.transitions.
DifferentiableTransition
)
de.jstacs.sequenceScores.statisticalModels.trainable.hmm.transitions.
Transition
(also extends java.lang.
Cloneable
)
de.jstacs.sequenceScores.statisticalModels.trainable.hmm.transitions.
DifferentiableTransition
de.jstacs.sequenceScores.statisticalModels.trainable.hmm.transitions.
TrainableAndDifferentiableTransition
(also extends de.jstacs.sequenceScores.statisticalModels.trainable.hmm.transitions.
TrainableTransition
)
de.jstacs.sequenceScores.statisticalModels.trainable.hmm.transitions.
SamplingTransition
(also extends de.jstacs.sampling.
SamplingFromStatistic
, de.jstacs.sequenceScores.statisticalModels.trainable.hmm.transitions.
TransitionWithSufficientStatistic
)
de.jstacs.sequenceScores.statisticalModels.trainable.hmm.transitions.
TrainableAndDifferentiableTransition
(also extends de.jstacs.sequenceScores.statisticalModels.trainable.hmm.transitions.
DifferentiableTransition
, de.jstacs.sequenceScores.statisticalModels.trainable.hmm.transitions.
TrainableTransition
)
de.jstacs.sequenceScores.statisticalModels.trainable.hmm.transitions.
TrainableTransition
de.jstacs.sequenceScores.statisticalModels.trainable.hmm.transitions.
TrainableAndDifferentiableTransition
(also extends de.jstacs.sequenceScores.statisticalModels.trainable.hmm.transitions.
DifferentiableTransition
)
de.jstacs.sequenceScores.statisticalModels.trainable.hmm.transitions.
TransitionWithSufficientStatistic
de.jstacs.sequenceScores.statisticalModels.trainable.hmm.transitions.
SamplingTransition
(also extends de.jstacs.sampling.
SamplingFromStatistic
)
de.jstacs.sequenceScores.statisticalModels.trainable.hmm.transitions.
TrainableAndDifferentiableTransition
(also extends de.jstacs.sequenceScores.statisticalModels.trainable.hmm.transitions.
DifferentiableTransition
, de.jstacs.sequenceScores.statisticalModels.trainable.hmm.transitions.
TrainableTransition
)
de.jstacs.sequenceScores.statisticalModels.trainable.hmm.transitions.
TrainableTransition
de.jstacs.sequenceScores.statisticalModels.trainable.hmm.transitions.
TrainableAndDifferentiableTransition
(also extends de.jstacs.sequenceScores.statisticalModels.trainable.hmm.transitions.
DifferentiableTransition
)
de.jstacs.sequenceScores.statisticalModels.trainable.hmm.transitions.
TransitionWithSufficientStatistic
de.jstacs.sequenceScores.statisticalModels.trainable.hmm.transitions.
SamplingTransition
(also extends de.jstacs.sampling.
SamplingFromStatistic
)
de.jstacs.sequenceScores.statisticalModels.trainable.hmm.transitions.
TrainableAndDifferentiableTransition
(also extends de.jstacs.sequenceScores.statisticalModels.trainable.hmm.transitions.
DifferentiableTransition
, de.jstacs.sequenceScores.statisticalModels.trainable.hmm.transitions.
TrainableTransition
)
de.jstacs.sequenceScores.statisticalModels.trainable.hmm.transitions.
TrainableTransition
de.jstacs.sequenceScores.statisticalModels.trainable.hmm.transitions.
TrainableAndDifferentiableTransition
(also extends de.jstacs.sequenceScores.statisticalModels.trainable.hmm.transitions.
DifferentiableTransition
)
de.jstacs.sequenceScores.statisticalModels.differentiable.
VariableLengthDiffSM
Enum Hierarchy
java.lang.
Object
java.lang.
Enum
<E> (implements java.lang.
Comparable
<T>, java.io.
Serializable
)
de.jstacs.
DataType
de.jstacs.algorithms.alignment.
Alignment.AlignmentType
de.jstacs.classifiers.differentiableSequenceScoreBased.
OptimizableFunction.KindOfParameter
de.jstacs.classifiers.differentiableSequenceScoreBased.gendismix.
LearningPrinciple
de.jstacs.classifiers.differentiableSequenceScoreBased.sampling.
SamplingScoreBasedClassifier.SamplingScheme
de.jstacs.data.
DinucleotideProperty
de.jstacs.data.
DinucleotideProperty.Type
de.jstacs.data.
DinucleotideProperty.HowCreated
de.jstacs.data.
DataSet.PartitionMethod
de.jstacs.data.
DataSet.WeightedDataSetFactory.SortOperation
de.jstacs.data.
AlphabetContainer.AlphabetContainerType
de.jstacs.data.sequences.annotation.
StrandedLocatedSequenceAnnotationWithLength.Strand
de.jstacs.data.sequences.annotation.
SinglePositionSequenceAnnotation.Type
de.jstacs.motifDiscovery.
SignificantMotifOccurrencesFinder.RandomSeqType
de.jstacs.motifDiscovery.
MutableMotifDiscovererToolbox.InitMethodForDiffSM
de.jstacs.motifDiscovery.
MotifDiscoverer.KindOfProfile
de.jstacs.parameters.
RangeParameter.Scale
de.jstacs.parameters.
RangeParameter.RangeType
de.jstacs.sequenceScores.statisticalModels.differentiable.directedGraphicalModels.structureLearning.measures.btMeasures.
BTMutualInformation.DataSource
de.jstacs.sequenceScores.statisticalModels.differentiable.mixture.
StrandDiffSM.InitMethod
de.jstacs.sequenceScores.statisticalModels.trainable.discrete.inhomogeneous.
StructureLearner.LearningType
de.jstacs.sequenceScores.statisticalModels.trainable.discrete.inhomogeneous.
StructureLearner.ModelType
de.jstacs.sequenceScores.statisticalModels.trainable.hmm.
HMMFactory.HMMType
de.jstacs.sequenceScores.statisticalModels.trainable.hmm.models.
SamplingHigherOrderHMM.ViterbiComputation
de.jstacs.sequenceScores.statisticalModels.trainable.hmm.models.
HigherOrderHMM.Type
de.jstacs.sequenceScores.statisticalModels.trainable.mixture.
AbstractMixtureTrainSM.Parameterization
de.jstacs.sequenceScores.statisticalModels.trainable.mixture.
AbstractMixtureTrainSM.Algorithm
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