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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
(implements de.jstacs.motifDiscovery.
Mutable
, de.jstacs.sequenceScores.statisticalModels.differentiable.
SamplingDifferentiableStatisticalModel
)
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.differentiable.
MultiDimensionalSequenceWrapperDiffSS
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.
MultipleIterationsCondition
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.discrete.inhomogeneous.
MEManager
de.jstacs.sequenceScores.statisticalModels.trainable.discrete.inhomogeneous.
FSMEManager
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.utils.galaxy.
MultilineSimpleParameter
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
<T>
de.jstacs.classifiers.assessment.
KFoldCrossValidation
de.jstacs.classifiers.assessment.
RepeatedHoldOutExperiment
de.jstacs.classifiers.assessment.
RepeatedSubSamplingExperiment
de.jstacs.classifiers.assessment.
Sampled_RepeatedHoldOutExperiment
de.jstacs.classifiers.
ClassifierFactory
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.sequenceScores.statisticalModels.trainable.discrete.inhomogeneous.
MEMTools.DualFunction
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.
DoubleArrayComparator
(implements java.util.
Comparator
<T>)
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.discrete.inhomogeneous.
MEM
(implements java.lang.
Cloneable
, de.jstacs.
Storable
)
de.jstacs.sequenceScores.statisticalModels.trainable.discrete.inhomogeneous.
MEMTools
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.sequenceScores.statisticalModels.trainable.hmm.states.emissions.continuous.
MultivariateGaussianEmission
(implements de.jstacs.sequenceScores.statisticalModels.trainable.hmm.states.emissions.
Emission
)
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
(implements de.jstacs.classifiers.performanceMeasures.
PerformanceMeasure
)
de.jstacs.classifiers.performanceMeasures.
AbstractTwoClassPerformanceMeasure
de.jstacs.classifiers.performanceMeasures.
AbstractNumericalTwoClassPerformanceMeasure
(implements de.jstacs.classifiers.performanceMeasures.
NumericalPerformanceMeasure
)
de.jstacs.classifiers.performanceMeasures.
FalsePositiveRateForFixedSensitivity
(implements de.jstacs.classifiers.performanceMeasures.
NumericalPerformanceMeasure
)
de.jstacs.classifiers.performanceMeasures.
MaximumNumericalTwoClassMeasure
de.jstacs.classifiers.performanceMeasures.
MaximumCorrelationCoefficient
(implements de.jstacs.classifiers.performanceMeasures.
NumericalPerformanceMeasure
)
de.jstacs.classifiers.performanceMeasures.
MaximumFMeasure
de.jstacs.classifiers.performanceMeasures.
PositivePredictiveValueForFixedSensitivity
de.jstacs.classifiers.performanceMeasures.
SensitivityForFixedSpecificity
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.
ClassificationRate
(implements de.jstacs.classifiers.performanceMeasures.
NumericalPerformanceMeasure
)
de.jstacs.classifiers.performanceMeasures.
ConfusionMatrix
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.sequenceScores.statisticalModels.trainable.discrete.inhomogeneous.parameters.
ConstraintParameterSet
de.jstacs.parameters.
ExpandableParameterSet
de.jstacs.classifiers.performanceMeasures.
AbstractPerformanceMeasureParameterSet
<T>
de.jstacs.classifiers.performanceMeasures.
NumericalPerformanceMeasureParameterSet
de.jstacs.classifiers.performanceMeasures.
PerformanceMeasureParameterSet
de.jstacs.data.
AlphabetContainerParameterSet.SectionDefinedAlphabetParameterSet
de.jstacs.parameters.
ArrayParameterSet
de.jstacs.data.
AlphabetContainerParameterSet.AlphabetArrayParameterSet
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.
MultipleIterationsCondition.MultipleIterationsConditionParameterSet
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.sequenceScores.statisticalModels.trainable.discrete.inhomogeneous.parameters.
MEManagerParameterSet
de.jstacs.sequenceScores.statisticalModels.trainable.discrete.inhomogeneous.parameters.
FSMEMParameterSet
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.utils.
PFMComparator
de.jstacs.utils.
PFMComparator.PFMDistance
de.jstacs.utils.
PFMComparator.NormalizedEuclideanDistance
de.jstacs.utils.
PFMComparator.OneMinusPearsonCorrelationCoefficient
de.jstacs.utils.
PFMComparator.SymmetricKullbackLeiblerDivergence
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.utils.
SeqLogoPlotter
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
(implements java.lang.
Comparable
<T>)
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.
PerformanceMeasure
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.io.
RegExFilenameFilter.Directory
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.
ConstraintManager.Decomposition
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
de.jstacs.utils.
ToolBox.TiedRanks
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