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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.classifier
,
de.jstacs.classifier.assessment
,
de.jstacs.classifier.modelBased
,
de.jstacs.classifier.scoringFunctionBased
,
de.jstacs.classifier.scoringFunctionBased.gendismix
,
de.jstacs.classifier.scoringFunctionBased.logPrior
,
de.jstacs.classifier.scoringFunctionBased.msp
,
de.jstacs.classifier.scoringFunctionBased.sampling
,
de.jstacs.classifier.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.models
,
de.jstacs.models.discrete
,
de.jstacs.models.discrete.homogeneous
,
de.jstacs.models.discrete.homogeneous.parameters
,
de.jstacs.models.discrete.inhomogeneous
,
de.jstacs.models.discrete.inhomogeneous.parameters
,
de.jstacs.models.discrete.inhomogeneous.shared
,
de.jstacs.models.hmm
,
de.jstacs.models.hmm.models
,
de.jstacs.models.hmm.states
,
de.jstacs.models.hmm.states.emissions
,
de.jstacs.models.hmm.states.emissions.continuous
,
de.jstacs.models.hmm.states.emissions.discrete
,
de.jstacs.models.hmm.training
,
de.jstacs.models.hmm.transitions
,
de.jstacs.models.hmm.transitions.elements
,
de.jstacs.models.mixture
,
de.jstacs.models.mixture.motif
,
de.jstacs.models.mixture.motif.positionprior
,
de.jstacs.models.phylo
,
de.jstacs.models.phylo.parser
,
de.jstacs.models.utils
,
de.jstacs.motifDiscovery
,
de.jstacs.motifDiscovery.history
,
de.jstacs.parameters
,
de.jstacs.parameters.validation
,
de.jstacs.results
,
de.jstacs.sampling
,
de.jstacs.scoringFunctions
,
de.jstacs.scoringFunctions.directedGraphicalModels
,
de.jstacs.scoringFunctions.directedGraphicalModels.structureLearning.measures
,
de.jstacs.scoringFunctions.directedGraphicalModels.structureLearning.measures.btMeasures
,
de.jstacs.scoringFunctions.directedGraphicalModels.structureLearning.measures.pmmMeasures
,
de.jstacs.scoringFunctions.homogeneous
,
de.jstacs.scoringFunctions.mix
,
de.jstacs.scoringFunctions.mix.motifSearch
,
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.classifier.
AbstractClassifier
(implements java.lang.
Cloneable
, de.jstacs.
Storable
)
de.jstacs.classifier.
AbstractScoreBasedClassifier
de.jstacs.classifier.
MappingClassifier
de.jstacs.classifier.modelBased.
ModelBasedClassifier
de.jstacs.models.discrete.inhomogeneous.shared.
SharedStructureClassifier
de.jstacs.classifier.scoringFunctionBased.sampling.
SamplingScoreBasedClassifier
de.jstacs.classifier.scoringFunctionBased.sampling.
SamplingGenDisMixClassifier
de.jstacs.classifier.scoringFunctionBased.
ScoreClassifier
de.jstacs.classifier.scoringFunctionBased.gendismix.
GenDisMixClassifier
de.jstacs.classifier.scoringFunctionBased.msp.
MSPClassifier
java.util.
AbstractCollection
<E> (implements java.util.
Collection
<E>)
java.util.
AbstractList
<E> (implements java.util.
List
<E>)
java.util.
ArrayList
<E> (implements java.lang.
Cloneable
, java.util.
List
<E>, java.util.
RandomAccess
, java.io.
Serializable
)
de.jstacs.parameters.
ParameterSet.ParameterList
de.jstacs.models.hmm.states.emissions.discrete.
AbstractConditionalDiscreteEmission
(implements de.jstacs.models.hmm.states.emissions.
DifferentiableEmission
, de.jstacs.models.hmm.states.emissions.
SamplingEmission
)
de.jstacs.models.hmm.states.emissions.discrete.
DiscreteEmission
de.jstacs.models.hmm.states.emissions.discrete.
PhyloDiscreteEmission
(implements de.jstacs.models.hmm.states.emissions.
SamplingEmission
)
de.jstacs.models.hmm.states.emissions.discrete.
ReferenceSequenceDiscreteEmission
de.jstacs.models.hmm.
AbstractHMM
(implements java.lang.
Cloneable
, de.jstacs.models.
Model
, de.jstacs.
Storable
)
de.jstacs.models.hmm.models.
HigherOrderHMM
de.jstacs.models.hmm.models.
DifferentiableHigherOrderHMM
(implements de.jstacs.scoringFunctions.
SamplingScoringFunction
)
de.jstacs.models.hmm.models.
SamplingHigherOrderHMM
de.jstacs.models.hmm.models.
SamplingPhyloHMM
de.jstacs.models.
AbstractModel
(implements java.lang.
Cloneable
, de.jstacs.models.
Model
, de.jstacs.
Storable
)
de.jstacs.models.mixture.
AbstractMixtureModel
de.jstacs.models.mixture.motif.
HiddenMotifMixture
(implements de.jstacs.motifDiscovery.
MotifDiscoverer
)
de.jstacs.models.mixture.motif.
SingleHiddenMotifMixture
de.jstacs.models.mixture.
MixtureModel
de.jstacs.models.discrete.inhomogeneous.shared.
SharedStructureMixture
de.jstacs.models.mixture.
StrandModel
de.jstacs.models.
CompositeModel
de.jstacs.models.discrete.
DiscreteGraphicalModel
(implements de.jstacs.
InstantiableFromParameterSet
)
de.jstacs.models.discrete.homogeneous.
HomogeneousModel
de.jstacs.models.discrete.homogeneous.
HomogeneousMM
de.jstacs.models.discrete.inhomogeneous.
InhomogeneousDGM
de.jstacs.models.discrete.inhomogeneous.
DAGModel
de.jstacs.models.discrete.inhomogeneous.
BayesianNetworkModel
de.jstacs.models.discrete.inhomogeneous.
FSDAGModel
de.jstacs.models.discrete.inhomogeneous.
FSDAGModelForGibbsSampling
(implements de.jstacs.sampling.
GibbsSamplingModel
)
de.jstacs.models.
NormalizableScoringFunctionModel
de.jstacs.models.
UniformModel
de.jstacs.models.
VariableLengthWrapperModel
de.jstacs.scoringFunctions.
AbstractNormalizableScoringFunction
(implements de.jstacs.scoringFunctions.
NormalizableScoringFunction
)
de.jstacs.scoringFunctions.mix.
AbstractMixtureScoringFunction
de.jstacs.scoringFunctions.mix.motifSearch.
HiddenMotifsMixture
(implements de.jstacs.motifDiscovery.
MutableMotifDiscoverer
)
de.jstacs.scoringFunctions.mix.
MixtureScoringFunction
(implements de.jstacs.motifDiscovery.
MutableMotifDiscoverer
)
de.jstacs.scoringFunctions.mix.
VariableLengthMixtureScoringFunction
(implements de.jstacs.scoringFunctions.
VariableLengthScoringFunction
)
de.jstacs.scoringFunctions.mix.
StrandScoringFunction
(implements de.jstacs.motifDiscovery.
Mutable
)
de.jstacs.scoringFunctions.
AbstractVariableLengthScoringFunction
(implements de.jstacs.scoringFunctions.
VariableLengthScoringFunction
)
de.jstacs.scoringFunctions.
CMMScoringFunction
de.jstacs.scoringFunctions.homogeneous.
HomogeneousScoringFunction
de.jstacs.scoringFunctions.homogeneous.
HMM0ScoringFunction
de.jstacs.scoringFunctions.homogeneous.
HMMScoringFunction
de.jstacs.scoringFunctions.homogeneous.
UniformHomogeneousScoringFunction
de.jstacs.scoringFunctions.directedGraphicalModels.
BayesianNetworkScoringFunction
(implements de.jstacs.
InstantiableFromParameterSet
)
de.jstacs.scoringFunctions.directedGraphicalModels.
MutableMarkovModelScoringFunction
(implements de.jstacs.motifDiscovery.
Mutable
, de.jstacs.scoringFunctions.
SamplingScoringFunction
)
de.jstacs.scoringFunctions.
IndependentProductScoringFunction
(implements de.jstacs.motifDiscovery.
MutableMotifDiscoverer
)
de.jstacs.scoringFunctions.
MappingScoringFunction
(implements de.jstacs.motifDiscovery.
Mutable
, de.jstacs.motifDiscovery.
MutableMotifDiscoverer
)
de.jstacs.scoringFunctions.
MRFScoringFunction
de.jstacs.scoringFunctions.
NormalizedScoringFunction
(implements de.jstacs.motifDiscovery.
Mutable
)
de.jstacs.scoringFunctions.mix.motifSearch.
PositionScoringFunction
de.jstacs.scoringFunctions.mix.motifSearch.
DurationScoringFunction
de.jstacs.scoringFunctions.mix.motifSearch.
MixtureDuration
de.jstacs.scoringFunctions.mix.motifSearch.
SkewNormalLikeScoringFunction
de.jstacs.scoringFunctions.mix.motifSearch.
UniformDurationScoringFunction
de.jstacs.scoringFunctions.
UniformScoringFunction
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.algorithms.alignment.cost.
AffineCosts
(implements de.jstacs.algorithms.alignment.cost.
Costs
)
de.jstacs.algorithms.alignment.cost.
MatrixCosts
de.jstacs.algorithms.alignment.cost.
SimpleCosts
de.jstacs.algorithms.alignment.
Alignment
de.jstacs.data.
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
de.jstacs.data.alphabets.
GenericComplementableDiscreteAlphabet
de.jstacs.data.
AlphabetContainer
(implements java.lang.
Comparable
<T>, de.jstacs.
InstantiableFromParameterSet
, de.jstacs.
Storable
)
de.jstacs.io.
ArrayHandler
de.jstacs.models.hmm.transitions.
BasicHigherOrderTransition
(implements de.jstacs.models.hmm.transitions.
TrainableTransition
)
de.jstacs.models.hmm.transitions.
HigherOrderTransition
(implements de.jstacs.models.hmm.transitions.
DifferentiableTransition
, de.jstacs.models.hmm.transitions.
SamplingTransition
)
de.jstacs.models.hmm.transitions.
BasicHigherOrderTransition.AbstractTransitionElement
(implements java.lang.
Cloneable
, de.jstacs.
Storable
)
de.jstacs.models.hmm.transitions.elements.
BasicTransitionElement
de.jstacs.models.hmm.transitions.elements.
BasicPluginTransitionElement
de.jstacs.models.hmm.transitions.elements.
ReferenceBasedTransitionElement
de.jstacs.models.hmm.transitions.elements.
DistanceBasedScaledTransitionElement
de.jstacs.models.hmm.transitions.elements.
ScaledTransitionElement
de.jstacs.models.hmm.transitions.elements.
TransitionElement
de.jstacs.data.bioJava.
BioJavaAdapter
de.jstacs.motifDiscovery.history.
CappedHistory
(implements de.jstacs.motifDiscovery.history.
History
)
de.jstacs.scoringFunctions.mix.motifSearch.
CDFOfNormal
de.jstacs.algorithms.graphs.
Chu_Liu_Edmonds
de.jstacs.classifier.utils.
ClassificationVisualizer
de.jstacs.classifier.assessment.
ClassifierAssessment
de.jstacs.classifier.assessment.
KFoldCrossValidation
de.jstacs.classifier.assessment.
RepeatedHoldOutExperiment
de.jstacs.classifier.assessment.
RepeatedSubSamplingExperiment
de.jstacs.classifier.assessment.
Sampled_RepeatedHoldOutExperiment
de.jstacs.models.discrete.inhomogeneous.
CombinationIterator
de.jstacs.io.
CombinedFileFilter
(implements java.io.
FileFilter
)
de.jstacs.utils.
ComparableElement
<E,C> (implements java.lang.
Comparable
<T>)
de.jstacs.classifier.
ConfusionMatrix
(implements de.jstacs.
Storable
)
de.jstacs.algorithms.optimization.
ConstantStartDistance
(implements de.jstacs.algorithms.optimization.
StartDistanceForecaster
)
de.jstacs.models.discrete.
Constraint
(implements de.jstacs.
Storable
)
de.jstacs.models.discrete.homogeneous.
HomogeneousModel.HomCondProb
de.jstacs.models.discrete.inhomogeneous.
InhConstraint
(implements java.lang.
Cloneable
)
de.jstacs.models.discrete.inhomogeneous.
InhCondProb
de.jstacs.models.discrete.inhomogeneous.
MEMConstraint
de.jstacs.models.discrete.
ConstraintManager
de.jstacs.parameters.validation.
ConstraintValidator
(implements de.jstacs.parameters.validation.
ParameterValidator
)
de.jstacs.algorithms.graphs.
DAG
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.classifier.scoringFunctionBased.logPrior.
LogPrior
(implements de.jstacs.
Storable
)
de.jstacs.classifier.scoringFunctionBased.logPrior.
CompositeLogPrior
de.jstacs.classifier.scoringFunctionBased.logPrior.
DoesNothingLogPrior
de.jstacs.classifier.scoringFunctionBased.logPrior.
SeparateLogPrior
(implements java.lang.
Cloneable
)
de.jstacs.classifier.scoringFunctionBased.logPrior.
SeparateGaussianLogPrior
de.jstacs.classifier.scoringFunctionBased.logPrior.
SeparateLaplaceLogPrior
de.jstacs.classifier.scoringFunctionBased.logPrior.
SimpleGaussianSumLogPrior
de.jstacs.algorithms.optimization.
NegativeDifferentiableFunction
de.jstacs.algorithms.optimization.
NumericalDifferentiableFunction
de.jstacs.classifier.scoringFunctionBased.
OptimizableFunction
de.jstacs.classifier.scoringFunctionBased.
AbstractOptimizableFunction
de.jstacs.classifier.scoringFunctionBased.
AbstractMultiThreadedOptimizableFunction
de.jstacs.classifier.scoringFunctionBased.
SFBasedOptimizableFunction
de.jstacs.classifier.scoringFunctionBased.gendismix.
LogGenDisMixFunction
de.jstacs.classifier.scoringFunctionBased.gendismix.
OneSampleLogGenDisMixFunction
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.models.utils.
DiscreteInhomogenousSampleEmitter
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.models.hmm.states.emissions.continuous.
GaussianEmission
(implements de.jstacs.models.hmm.states.emissions.
DifferentiableEmission
)
de.jstacs.models.hmm.states.emissions.continuous.
PluginGaussianEmission
de.jstacs.utils.
GUIProgressUpdater
(implements java.awt.event.
ActionListener
, de.jstacs.utils.
ProgressUpdater
)
de.jstacs.models.hmm.
HMMFactory
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.scoringFunctions.directedGraphicalModels.structureLearning.measures.
Measure
(implements java.lang.
Cloneable
, de.jstacs.
InstantiableFromParameterSet
, de.jstacs.
Storable
)
de.jstacs.scoringFunctions.directedGraphicalModels.structureLearning.measures.btMeasures.
BTExplainingAwayResidual
de.jstacs.scoringFunctions.directedGraphicalModels.structureLearning.measures.btMeasures.
BTMutualInformation
de.jstacs.scoringFunctions.directedGraphicalModels.structureLearning.measures.
InhomogeneousMarkov
de.jstacs.scoringFunctions.directedGraphicalModels.structureLearning.measures.pmmMeasures.
PMMExplainingAwayResidual
de.jstacs.scoringFunctions.directedGraphicalModels.structureLearning.measures.pmmMeasures.
PMMMutualInformation
de.jstacs.models.hmm.states.emissions.
MixtureEmission
(implements de.jstacs.models.hmm.states.emissions.
Emission
)
de.jstacs.models.
ModelFactory
de.jstacs.models.utils.
ModelTester
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.models.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.
SafeOutputStream
de.jstacs.utils.
Pair
<E1,E2>
de.jstacs.parameters.
Parameter
(implements java.lang.
Cloneable
, de.jstacs.
Storable
)
de.jstacs.parameters.
CollectionParameter
(implements de.jstacs.parameters.
GalaxyConvertible
, de.jstacs.parameters.
Rangeable
)
de.jstacs.parameters.
EnumParameter
de.jstacs.parameters.
MultiSelectionCollectionParameter
(implements de.jstacs.parameters.
RangeIterator
)
de.jstacs.classifier.
MeasureParameters
de.jstacs.parameters.
FileParameter
(implements de.jstacs.parameters.
GalaxyConvertible
)
de.jstacs.parameters.
ParameterSetContainer
(implements de.jstacs.parameters.
GalaxyConvertible
, de.jstacs.parameters.
Rangeable
, de.jstacs.parameters.
RangeIterator
)
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.scoringFunctions.directedGraphicalModels.
Parameter
(implements java.lang.
Cloneable
, de.jstacs.
Storable
)
de.jstacs.parameters.
ParameterSet
(implements java.lang.
Cloneable
, de.jstacs.parameters.
GalaxyConvertible
, de.jstacs.parameters.
RangeIterator
, de.jstacs.
Storable
)
de.jstacs.classifier.assessment.
ClassifierAssessmentAssessParameterSet
de.jstacs.classifier.assessment.
KFoldCVAssessParameterSet
de.jstacs.classifier.assessment.
RepeatedHoldOutAssessParameterSet
de.jstacs.classifier.assessment.
RepeatedSubSamplingAssessParameterSet
de.jstacs.classifier.assessment.
Sampled_RepeatedHoldOutAssessParameterSet
de.jstacs.parameters.
ExpandableParameterSet
de.jstacs.data.
AlphabetContainerParameterSet.SectionDefinedAlphabetParameterSet
de.jstacs.parameters.
ArrayParameterSet
de.jstacs.data.
AlphabetContainerParameterSet.AlphabetArrayParameterSet
de.jstacs.models.hmm.
HMMTrainingParameterSet
de.jstacs.models.hmm.training.
MaxHMMTrainingParameterSet
de.jstacs.models.hmm.training.
BaumWelchParameterSet
de.jstacs.models.hmm.training.
NumericalHMMTrainingParameterSet
de.jstacs.models.hmm.training.
ViterbiParameterSet
de.jstacs.models.hmm.training.
SamplingHMMTrainingParameterSet
de.jstacs.parameters.
InstanceParameterSet
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.
Alphabet.AlphabetParameterSet
de.jstacs.data.alphabets.
ContinuousAlphabet.ContinuousAlphabetParameterSet
de.jstacs.data.alphabets.
DiscreteAlphabet.DiscreteAlphabetParameterSet
de.jstacs.data.alphabets.
DNAAlphabet.DNAAlphabetParameterSet
de.jstacs.data.alphabets.
GenericComplementableDiscreteAlphabet.GenericComplementableDiscreteAlphabetParameterSet
de.jstacs.data.
AlphabetContainerParameterSet
de.jstacs.scoringFunctions.directedGraphicalModels.structureLearning.measures.btMeasures.
BTExplainingAwayResidual.BTExplainingAwayResidualParameterSet
de.jstacs.scoringFunctions.directedGraphicalModels.structureLearning.measures.btMeasures.
BTMutualInformation.BTMutualInformationParameterSet
de.jstacs.scoringFunctions.directedGraphicalModels.structureLearning.measures.
InhomogeneousMarkov.InhomogeneousMarkovParameterSet
de.jstacs.scoringFunctions.directedGraphicalModels.structureLearning.measures.pmmMeasures.
PMMExplainingAwayResidual.PMMExplainingAwayResidualParameterSet
de.jstacs.scoringFunctions.directedGraphicalModels.structureLearning.measures.pmmMeasures.
PMMMutualInformation.PMMMutualInformationParameterSet
de.jstacs.parameters.
SequenceScoringParameterSet
de.jstacs.scoringFunctions.directedGraphicalModels.
BayesianNetworkScoringFunctionParameterSet
de.jstacs.models.discrete.
DGMParameterSet
de.jstacs.models.discrete.homogeneous.parameters.
HomogeneousModelParameterSet
de.jstacs.models.discrete.homogeneous.parameters.
HomMMParameterSet
de.jstacs.models.discrete.inhomogeneous.parameters.
IDGMParameterSet
de.jstacs.models.discrete.inhomogeneous.parameters.
BayesianNetworkModelParameterSet
de.jstacs.models.discrete.inhomogeneous.parameters.
FSDAGMParameterSet
de.jstacs.models.discrete.inhomogeneous.parameters.
FSDAGModelForGibbsSamplingParameterSet
de.jstacs.classifier.scoringFunctionBased.sampling.
SamplingScoreBasedClassifierParameterSet
de.jstacs.classifier.scoringFunctionBased.sampling.
SamplingGenDisMixClassifierParameterSet
de.jstacs.classifier.scoringFunctionBased.
ScoreClassifierParameterSet
de.jstacs.classifier.scoringFunctionBased.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.scoringFunctions.directedGraphicalModels.
ParameterTree
(implements java.lang.
Cloneable
, de.jstacs.
Storable
)
de.jstacs.scoringFunctions.directedGraphicalModels.
ParameterTree.TreeElement
(implements java.lang.
Cloneable
, de.jstacs.
Storable
)
de.jstacs.models.phylo.
PhyloNode
(implements java.lang.
Cloneable
, de.jstacs.
Storable
)
de.jstacs.models.phylo.
PhyloTree
(implements java.lang.
Cloneable
, de.jstacs.
Storable
)
de.jstacs.models.mixture.motif.positionprior.
PositionPrior
(implements java.lang.
Cloneable
, de.jstacs.
Storable
)
de.jstacs.models.mixture.motif.positionprior.
GaussianLikePositionPrior
de.jstacs.models.mixture.motif.positionprior.
UniformPositionPrior
de.jstacs.classifier.utils.
PValueComputation
de.jstacs.utils.random.
RandomNumberGenerator
(implements java.io.
Serializable
)
de.jstacs.parameters.validation.
ReferenceConstraint
(implements de.jstacs.parameters.validation.
Constraint
)
de.jstacs.parameters.validation.
SimpleReferenceConstraint
de.jstacs.utils.
REnvironment
de.jstacs.motifDiscovery.history.
RestrictedRepeatHistory
(implements de.jstacs.motifDiscovery.history.
History
)
de.jstacs.results.
Result
(implements de.jstacs.
Storable
)
de.jstacs.classifier.
AbstractScoreBasedClassifier.DoubleTableResult
de.jstacs.utils.galaxy.
GalaxyAdaptor.FileResult
de.jstacs.results.
ImageResult
de.jstacs.utils.galaxy.
GalaxyAdaptor.LinkedImageResult
de.jstacs.results.
ListResult
de.jstacs.results.
SampleResult
de.jstacs.results.
SimpleResult
(implements java.lang.
Comparable
<T>)
de.jstacs.results.
CategoricalResult
de.jstacs.results.
NumericalResult
de.jstacs.results.
StorableResult
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.data.
Sample
(implements java.lang.
Iterable
<T>)
de.jstacs.data.
DNASample
de.jstacs.data.
Sample.ElementEnumerator
(implements java.util.
Iterator
<E>, de.jstacs.data.
RecyclableSequenceEnumerator
)
de.jstacs.data.
Sample.WeightedSampleFactory
de.jstacs.data.
SampleKMerEnumerator
(implements de.jstacs.data.
RecyclableSequenceEnumerator
)
de.jstacs.classifier.scoringFunctionBased.sampling.
SamplingScoreBasedClassifier.ScoringFunctionSamplingComponent
(implements de.jstacs.sampling.
SamplingComponent
)
de.jstacs.classifier.
ScoreBasedPerformanceMeasureDefinitions
de.jstacs.classifier.
ScoreBasedPerformanceMeasureDefinitions.ThresholdMeasurePair
de.jstacs.data.
Sequence
<T> (implements java.lang.
Comparable
<T>)
de.jstacs.data.sequences.
ArbitrarySequence
de.jstacs.data.sequences.
DiscreteSequence
de.jstacs.data.sequences.
MultiDimensionalDiscreteSequence
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.
Sequence.RecursiveSequence
<T>
de.jstacs.data.sequences.
PermutedSequence
<T>
de.jstacs.data.
Sequence.CompositeSequence
<T>
de.jstacs.data.
Sequence.SubSequence
<T>
de.jstacs.data.
SequenceEnumeration
(implements de.jstacs.data.
RecyclableSequenceEnumerator
)
de.jstacs.models.discrete.inhomogeneous.
SequenceIterator
(implements java.lang.
Cloneable
)
de.jstacs.motifDiscovery.
SignificantMotifOccurrencesFinder
de.jstacs.motifDiscovery.
SignificantMotifOccurrencesFinder.SumOfProbabilities
(implements de.jstacs.motifDiscovery.
SignificantMotifOccurrencesFinder.JoinMethod
)
de.jstacs.models.hmm.states.emissions.
SilentEmission
(implements de.jstacs.models.hmm.states.emissions.
DifferentiableEmission
, de.jstacs.models.hmm.states.emissions.
SamplingEmission
)
de.jstacs.sampling.
SimpleBurnInTest
(implements de.jstacs.sampling.
BurnInTest
)
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.models.hmm.states.
SimpleState
(implements de.jstacs.models.hmm.states.
TrainableState
)
de.jstacs.models.hmm.states.
SimpleDifferentiableState
(implements de.jstacs.models.hmm.states.
DifferentiableState
)
de.jstacs.models.hmm.states.
SimpleSamplingState
(implements de.jstacs.models.hmm.states.
SamplingState
)
de.jstacs.parameters.validation.
SimpleStaticConstraint
(implements de.jstacs.parameters.validation.
Constraint
)
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.models.utils.
StationaryDistribution
de.jstacs.models.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.models.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.classifier.
ClassDimensionException
de.jstacs.algorithms.optimization.
DimensionException
de.jstacs.data.alphabets.
DoubleSymbolException
de.jstacs.data.
EmptySampleException
de.jstacs.algorithms.optimization.
EvaluationException
de.jstacs.results.
MeanResultSet.AdditionImpossibleException
de.jstacs.results.
MeanResultSet.InconsistentResultNumberException
de.jstacs.
NonParsableException
de.jstacs.
NotTrainedException
de.jstacs.parameters.
ParameterException
de.jstacs.parameters.
CollectionParameter.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.
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.models.discrete.inhomogeneous.
TwoPointEvaluater
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.models.hmm.states.emissions.
DifferentiableEmission
de.jstacs.models.hmm.transitions.
DifferentiableTransition
de.jstacs.models.hmm.transitions.
TrainableAndDifferentiableTransition
(also extends de.jstacs.models.hmm.transitions.
TrainableTransition
)
de.jstacs.models.hmm.states.emissions.
Emission
(also extends de.jstacs.
Storable
)
de.jstacs.models.hmm.states.emissions.
DifferentiableEmission
de.jstacs.models.hmm.states.emissions.
SamplingEmission
(also extends de.jstacs.sampling.
SamplingFromStatistic
)
de.jstacs.motifDiscovery.history.
History
(also extends de.jstacs.
Storable
)
de.jstacs.models.
Model
(also extends de.jstacs.
Storable
)
de.jstacs.motifDiscovery.
MotifDiscoverer
(also extends de.jstacs.
Storable
)
de.jstacs.motifDiscovery.
MutableMotifDiscoverer
de.jstacs.motifDiscovery.
MutableMotifDiscoverer
de.jstacs.scoringFunctions.
NormalizableScoringFunction
de.jstacs.scoringFunctions.
SamplingScoringFunction
de.jstacs.scoringFunctions.
VariableLengthScoringFunction
de.jstacs.parameters.validation.
ParameterValidator
(also extends de.jstacs.
Storable
)
de.jstacs.models.hmm.states.emissions.
SamplingEmission
(also extends de.jstacs.models.hmm.states.emissions.
Emission
, de.jstacs.sampling.
SamplingFromStatistic
)
de.jstacs.scoringFunctions.
SamplingScoringFunction
de.jstacs.models.hmm.transitions.
SamplingTransition
(also extends de.jstacs.sampling.
SamplingFromStatistic
, de.jstacs.models.hmm.transitions.
TransitionWithSufficientStatistic
)
de.jstacs.scoringFunctions.
ScoringFunction
(also extends de.jstacs.
Storable
)
de.jstacs.scoringFunctions.
NormalizableScoringFunction
de.jstacs.scoringFunctions.
SamplingScoringFunction
de.jstacs.scoringFunctions.
VariableLengthScoringFunction
de.jstacs.scoringFunctions.
SamplingScoringFunction
de.jstacs.scoringFunctions.
VariableLengthScoringFunction
de.jstacs.algorithms.optimization.termination.
TerminationCondition
(also extends de.jstacs.
InstantiableFromParameterSet
, de.jstacs.
Storable
)
de.jstacs.models.hmm.transitions.
TrainableAndDifferentiableTransition
(also extends de.jstacs.models.hmm.transitions.
DifferentiableTransition
, de.jstacs.models.hmm.transitions.
TrainableTransition
)
de.jstacs.models.hmm.transitions.
TrainableTransition
de.jstacs.models.hmm.transitions.
TrainableAndDifferentiableTransition
(also extends de.jstacs.models.hmm.transitions.
DifferentiableTransition
)
de.jstacs.models.hmm.
Transition
(also extends de.jstacs.
Storable
)
de.jstacs.models.hmm.transitions.
DifferentiableTransition
de.jstacs.models.hmm.transitions.
TrainableAndDifferentiableTransition
(also extends de.jstacs.models.hmm.transitions.
TrainableTransition
)
de.jstacs.models.hmm.transitions.
SamplingTransition
(also extends de.jstacs.sampling.
SamplingFromStatistic
, de.jstacs.models.hmm.transitions.
TransitionWithSufficientStatistic
)
de.jstacs.models.hmm.transitions.
TrainableAndDifferentiableTransition
(also extends de.jstacs.models.hmm.transitions.
DifferentiableTransition
, de.jstacs.models.hmm.transitions.
TrainableTransition
)
de.jstacs.models.hmm.transitions.
TrainableTransition
de.jstacs.models.hmm.transitions.
TrainableAndDifferentiableTransition
(also extends de.jstacs.models.hmm.transitions.
DifferentiableTransition
)
de.jstacs.models.hmm.transitions.
TransitionWithSufficientStatistic
de.jstacs.models.hmm.transitions.
SamplingTransition
(also extends de.jstacs.sampling.
SamplingFromStatistic
)
de.jstacs.models.hmm.transitions.
TrainableAndDifferentiableTransition
(also extends de.jstacs.models.hmm.transitions.
DifferentiableTransition
, de.jstacs.models.hmm.transitions.
TrainableTransition
)
de.jstacs.models.hmm.transitions.
TrainableTransition
de.jstacs.models.hmm.transitions.
TrainableAndDifferentiableTransition
(also extends de.jstacs.models.hmm.transitions.
DifferentiableTransition
)
de.jstacs.models.hmm.transitions.
TransitionWithSufficientStatistic
de.jstacs.models.hmm.transitions.
SamplingTransition
(also extends de.jstacs.sampling.
SamplingFromStatistic
)
de.jstacs.models.hmm.transitions.
TrainableAndDifferentiableTransition
(also extends de.jstacs.models.hmm.transitions.
DifferentiableTransition
, de.jstacs.models.hmm.transitions.
TrainableTransition
)
de.jstacs.models.hmm.transitions.
TrainableTransition
de.jstacs.models.hmm.transitions.
TrainableAndDifferentiableTransition
(also extends de.jstacs.models.hmm.transitions.
DifferentiableTransition
)
de.jstacs.scoringFunctions.
VariableLengthScoringFunction
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.utils.
ProgressUpdater
de.jstacs.parameters.
Rangeable
de.jstacs.parameters.
RangeIterator
de.jstacs.sampling.
SamplingComponent
de.jstacs.sampling.
GibbsSamplingModel
de.jstacs.models.hmm.states.emissions.
SamplingEmission
(also extends de.jstacs.models.hmm.states.emissions.
Emission
, de.jstacs.sampling.
SamplingFromStatistic
)
de.jstacs.sampling.
SamplingFromStatistic
de.jstacs.models.hmm.states.emissions.
SamplingEmission
(also extends de.jstacs.models.hmm.states.emissions.
Emission
)
de.jstacs.models.hmm.states.
SamplingState
(also extends de.jstacs.models.hmm.states.
TrainableState
)
de.jstacs.models.hmm.transitions.
SamplingTransition
(also extends de.jstacs.models.hmm.transitions.
TransitionWithSufficientStatistic
)
de.jstacs.models.hmm.states.
SamplingState
(also extends de.jstacs.sampling.
SamplingFromStatistic
, de.jstacs.models.hmm.states.
TrainableState
)
de.jstacs.models.hmm.transitions.
SamplingTransition
(also extends de.jstacs.sampling.
SamplingFromStatistic
, de.jstacs.models.hmm.transitions.
TransitionWithSufficientStatistic
)
de.jstacs.data.sequences.annotation.
SequenceAnnotationParser
de.jstacs.motifDiscovery.
SignificantMotifOccurrencesFinder.JoinMethod
de.jstacs.algorithms.optimization.
StartDistanceForecaster
de.jstacs.models.hmm.
State
de.jstacs.models.hmm.states.
DifferentiableState
de.jstacs.models.hmm.states.
SamplingState
(also extends de.jstacs.sampling.
SamplingFromStatistic
, de.jstacs.models.hmm.states.
TrainableState
)
de.jstacs.models.hmm.states.
TrainableState
de.jstacs.models.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.models.hmm.states.emissions.
DifferentiableEmission
de.jstacs.models.hmm.transitions.
DifferentiableTransition
de.jstacs.models.hmm.transitions.
TrainableAndDifferentiableTransition
(also extends de.jstacs.models.hmm.transitions.
TrainableTransition
)
de.jstacs.models.hmm.states.emissions.
Emission
(also extends java.lang.
Cloneable
)
de.jstacs.models.hmm.states.emissions.
DifferentiableEmission
de.jstacs.models.hmm.states.emissions.
SamplingEmission
(also extends de.jstacs.sampling.
SamplingFromStatistic
)
de.jstacs.motifDiscovery.history.
History
(also extends java.lang.
Cloneable
)
de.jstacs.models.
Model
(also extends java.lang.
Cloneable
)
de.jstacs.motifDiscovery.
MotifDiscoverer
(also extends java.lang.
Cloneable
)
de.jstacs.motifDiscovery.
MutableMotifDiscoverer
de.jstacs.motifDiscovery.
MutableMotifDiscoverer
de.jstacs.scoringFunctions.
NormalizableScoringFunction
de.jstacs.scoringFunctions.
SamplingScoringFunction
de.jstacs.scoringFunctions.
VariableLengthScoringFunction
de.jstacs.parameters.validation.
ParameterValidator
(also extends java.lang.
Cloneable
)
de.jstacs.models.hmm.states.emissions.
SamplingEmission
(also extends de.jstacs.models.hmm.states.emissions.
Emission
, de.jstacs.sampling.
SamplingFromStatistic
)
de.jstacs.scoringFunctions.
SamplingScoringFunction
de.jstacs.models.hmm.transitions.
SamplingTransition
(also extends de.jstacs.sampling.
SamplingFromStatistic
, de.jstacs.models.hmm.transitions.
TransitionWithSufficientStatistic
)
de.jstacs.scoringFunctions.
ScoringFunction
(also extends java.lang.
Cloneable
)
de.jstacs.scoringFunctions.
NormalizableScoringFunction
de.jstacs.scoringFunctions.
SamplingScoringFunction
de.jstacs.scoringFunctions.
VariableLengthScoringFunction
de.jstacs.scoringFunctions.
SamplingScoringFunction
de.jstacs.scoringFunctions.
VariableLengthScoringFunction
de.jstacs.algorithms.optimization.termination.
TerminationCondition
(also extends java.lang.
Cloneable
, de.jstacs.
InstantiableFromParameterSet
)
de.jstacs.models.hmm.transitions.
TrainableAndDifferentiableTransition
(also extends de.jstacs.models.hmm.transitions.
DifferentiableTransition
, de.jstacs.models.hmm.transitions.
TrainableTransition
)
de.jstacs.models.hmm.transitions.
TrainableTransition
de.jstacs.models.hmm.transitions.
TrainableAndDifferentiableTransition
(also extends de.jstacs.models.hmm.transitions.
DifferentiableTransition
)
de.jstacs.models.hmm.
Transition
(also extends java.lang.
Cloneable
)
de.jstacs.models.hmm.transitions.
DifferentiableTransition
de.jstacs.models.hmm.transitions.
TrainableAndDifferentiableTransition
(also extends de.jstacs.models.hmm.transitions.
TrainableTransition
)
de.jstacs.models.hmm.transitions.
SamplingTransition
(also extends de.jstacs.sampling.
SamplingFromStatistic
, de.jstacs.models.hmm.transitions.
TransitionWithSufficientStatistic
)
de.jstacs.models.hmm.transitions.
TrainableAndDifferentiableTransition
(also extends de.jstacs.models.hmm.transitions.
DifferentiableTransition
, de.jstacs.models.hmm.transitions.
TrainableTransition
)
de.jstacs.models.hmm.transitions.
TrainableTransition
de.jstacs.models.hmm.transitions.
TrainableAndDifferentiableTransition
(also extends de.jstacs.models.hmm.transitions.
DifferentiableTransition
)
de.jstacs.models.hmm.transitions.
TransitionWithSufficientStatistic
de.jstacs.models.hmm.transitions.
SamplingTransition
(also extends de.jstacs.sampling.
SamplingFromStatistic
)
de.jstacs.models.hmm.transitions.
TrainableAndDifferentiableTransition
(also extends de.jstacs.models.hmm.transitions.
DifferentiableTransition
, de.jstacs.models.hmm.transitions.
TrainableTransition
)
de.jstacs.models.hmm.transitions.
TrainableTransition
de.jstacs.models.hmm.transitions.
TrainableAndDifferentiableTransition
(also extends de.jstacs.models.hmm.transitions.
DifferentiableTransition
)
de.jstacs.models.hmm.transitions.
TransitionWithSufficientStatistic
de.jstacs.models.hmm.transitions.
SamplingTransition
(also extends de.jstacs.sampling.
SamplingFromStatistic
)
de.jstacs.models.hmm.transitions.
TrainableAndDifferentiableTransition
(also extends de.jstacs.models.hmm.transitions.
DifferentiableTransition
, de.jstacs.models.hmm.transitions.
TrainableTransition
)
de.jstacs.models.hmm.transitions.
TrainableTransition
de.jstacs.models.hmm.transitions.
TrainableAndDifferentiableTransition
(also extends de.jstacs.models.hmm.transitions.
DifferentiableTransition
)
de.jstacs.scoringFunctions.
VariableLengthScoringFunction
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.algorithms.alignment.cost.
Costs.Direction
de.jstacs.classifier.
MeasureParameters.Measure
de.jstacs.classifier.scoringFunctionBased.
OptimizableFunction.KindOfParameter
de.jstacs.classifier.scoringFunctionBased.gendismix.
LearningPrinciple
de.jstacs.classifier.scoringFunctionBased.sampling.
SamplingScoreBasedClassifier.SamplingScheme
de.jstacs.data.
Sample.PartitionMethod
de.jstacs.data.
Sample.WeightedSampleFactory.SortOperation
de.jstacs.data.
DinucleotideProperty
de.jstacs.data.
DinucleotideProperty.Type
de.jstacs.data.
DinucleotideProperty.HowCreated
de.jstacs.data.
AlphabetContainer.AlphabetContainerType
de.jstacs.data.sequences.annotation.
StrandedLocatedSequenceAnnotationWithLength.Strand
de.jstacs.data.sequences.annotation.
SinglePositionSequenceAnnotation.Type
de.jstacs.models.discrete.inhomogeneous.
StructureLearner.LearningType
de.jstacs.models.discrete.inhomogeneous.
StructureLearner.ModelType
de.jstacs.models.hmm.
HMMFactory.HMMType
de.jstacs.models.hmm.models.
SamplingHigherOrderHMM.ViterbiComputation
de.jstacs.models.hmm.models.
HigherOrderHMM.Type
de.jstacs.models.mixture.
AbstractMixtureModel.Parameterization
de.jstacs.models.mixture.
AbstractMixtureModel.Algorithm
de.jstacs.motifDiscovery.
SignificantMotifOccurrencesFinder.RandomSeqType
de.jstacs.motifDiscovery.
MutableMotifDiscovererToolbox.InitMethodForScoringFunction
de.jstacs.motifDiscovery.
MotifDiscoverer.KindOfProfile
de.jstacs.parameters.
RangeParameter.Scale
de.jstacs.parameters.
RangeParameter.RangeType
de.jstacs.scoringFunctions.directedGraphicalModels.structureLearning.measures.btMeasures.
BTMutualInformation.DataSource
de.jstacs.scoringFunctions.mix.
StrandScoringFunction.InitMethod
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