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Hierarchy For All Packages
Package Hierarchies:
de.jstacs
,
de.jstacs.algorithms
,
de.jstacs.algorithms.graphs
,
de.jstacs.algorithms.graphs.tensor
,
de.jstacs.algorithms.optimization
,
de.jstacs.classifier
,
de.jstacs.classifier.assessment
,
de.jstacs.classifier.modelBased
,
de.jstacs.classifier.scoringFunctionBased
,
de.jstacs.classifier.scoringFunctionBased.cll
,
de.jstacs.classifier.scoringFunctionBased.logPrior
,
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.inhomogeneous
,
de.jstacs.models.discrete.inhomogeneous.parameters
,
de.jstacs.models.discrete.inhomogeneous.shared
,
de.jstacs.models.mixture
,
de.jstacs.models.mixture.gibbssampling
,
de.jstacs.models.utils
,
de.jstacs.parameters
,
de.jstacs.parameters.validation
,
de.jstacs.results
,
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.utils
,
de.jstacs.utils.random
Class Hierarchy
java.lang.
Object
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.
ScoreClassifier
de.jstacs.classifier.scoringFunctionBased.cll.
CLLClassifier
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.
AbstractModel
(implements java.lang.
Cloneable
, de.jstacs.models.
Model
, de.jstacs.
Storable
)
de.jstacs.models.mixture.
AbstractMixtureModel
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.inhomogeneous.
InhomogeneousDGM
de.jstacs.models.discrete.inhomogeneous.
DAGModel
de.jstacs.models.discrete.inhomogeneous.
BayesianNetworkModel
de.jstacs.models.discrete.inhomogeneous.
FSDAGModel
de.jstacs.models.mixture.gibbssampling.
FSDAGModelForGibbsSampling
(implements de.jstacs.models.mixture.gibbssampling.
GibbsSamplingComponent
)
de.jstacs.models.
UniformModel
de.jstacs.scoringFunctions.
AbstractNormalizableScoringFunction
(implements de.jstacs.scoringFunctions.
NormalizableScoringFunction
)
de.jstacs.scoringFunctions.mix.
AbstractMixtureScoringFunction
de.jstacs.scoringFunctions.mix.
MixtureScoringFunction
de.jstacs.scoringFunctions.directedGraphicalModels.
BayesianNetworkScoringFunction
de.jstacs.scoringFunctions.
IndependentProductScoringFunction
de.jstacs.scoringFunctions.
MRFScoringFunction
de.jstacs.scoringFunctions.
UniformScoringFunction
de.jstacs.scoringFunctions.
VariableLengthScoringFunction
de.jstacs.scoringFunctions.homogeneous.
HomogeneousScoringFunction
de.jstacs.scoringFunctions.homogeneous.
HMM0ScoringFunction
de.jstacs.scoringFunctions.homogeneous.
HMMScoringFunction
de.jstacs.scoringFunctions.homogeneous.
UniformHomogeneousScoringFunction
de.jstacs.algorithms.
Alignment
de.jstacs.algorithms.
Alignment.SimpleCosts
(implements de.jstacs.algorithms.
Alignment.Costs
)
de.jstacs.algorithms.
Alignment.StringAlignment
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.
AlphabetContainer
(implements java.lang.
Comparable
<T>, de.jstacs.
InstantiableFromParameterSet
, de.jstacs.
Storable
)
de.jstacs.io.
ArrayHandler
de.jstacs.data.bioJava.
BioJavaAdapter
de.jstacs.models.mixture.gibbssampling.
BurnInTest
(implements java.lang.
Cloneable
, de.jstacs.
Storable
)
de.jstacs.models.mixture.gibbssampling.
SimpleBurnInTest
de.jstacs.algorithms.graphs.
Chu_Liu_Edmonds
de.jstacs.classifier.
Classification
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.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.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.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.
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.cll.
NormConditionalLogLikelihood
de.jstacs.models.utils.
DiscreteInhomogenousSampleEmitter
de.jstacs.data.
DiscreteSequenceEnumerator
(implements java.util.
Enumeration
<E>)
de.jstacs.utils.
DoubleList
de.jstacs.algorithms.graphs.
Edge
(implements java.lang.
Cloneable
, java.lang.
Comparable
<T>)
javax.swing.filechooser.
FileFilter
de.jstacs.io.
SubstringFilenameFilter
(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.
GUIProgressUpdater
(implements java.awt.event.
ActionListener
, de.jstacs.utils.
ProgressUpdater
)
de.jstacs.utils.
IntList
de.jstacs.algorithms.optimization.
LimitedMedianStartDistance
(implements de.jstacs.algorithms.optimization.
StartDistanceForecaster
)
de.jstacs.scoringFunctions.directedGraphicalModels.structureLearning.measures.
Measure
(implements java.lang.
Cloneable
, 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.utils.
ModelTester
de.jstacs.models.utils.
ModelTester.SeqIterator
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.utils.
Normalisation
de.jstacs.utils.
NullProgressUpdater
(implements de.jstacs.utils.
ProgressUpdater
)
de.jstacs.parameters.validation.
NumberValidator
<E> (implements 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.parameters.
Parameter
(implements java.lang.
Cloneable
, de.jstacs.
Storable
)
de.jstacs.parameters.
CollectionParameter
(implements 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
de.jstacs.parameters.
ParameterSetContainer
(implements de.jstacs.parameters.
Rangeable
, de.jstacs.parameters.
RangeIterator
)
de.jstacs.parameters.
RangeParameter
(implements de.jstacs.parameters.
RangeIterator
)
de.jstacs.parameters.
SimpleParameter
(implements 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.
RangeIterator
, de.jstacs.
Storable
)
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.
AlphabetContainerParameterSet
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.parameters.
InstanceParameterSet
de.jstacs.models.discrete.
DGMParameterSet
de.jstacs.models.discrete.inhomogeneous.parameters.
IDGMParameterSet
de.jstacs.models.discrete.inhomogeneous.parameters.
BayesianNetworkModelParameterSet
de.jstacs.models.discrete.inhomogeneous.parameters.
FSDAGMParameterSet
de.jstacs.classifier.scoringFunctionBased.
ScoreClassifierParameterSet
de.jstacs.classifier.scoringFunctionBased.cll.
CLLClassifierParameterSet
de.jstacs.parameters.
SimpleParameterSet
de.jstacs.io.
ParameterSetParser
de.jstacs.scoringFunctions.directedGraphicalModels.
ParameterTree
(implements java.lang.
Cloneable
)
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.results.
Result
(implements de.jstacs.
Storable
)
de.jstacs.classifier.
AbstractScoreBasedClassifier.DoubleTableResult
de.jstacs.results.
ImageResult
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.utils.
RUtils
de.jstacs.data.
Sample
de.jstacs.data.
Sample.ElementEnumerator
(implements java.util.
Enumeration
<E>)
de.jstacs.data.
Sample.WeightedSampleFactory
de.jstacs.classifier.
ScoreBasedPerformanceMeasureDefinitions
de.jstacs.classifier.
ScoreBasedPerformanceMeasureDefinitions.ThresholdMeasurePair
de.jstacs.data.
Sequence
(implements java.lang.
Comparable
<T>)
de.jstacs.data.sequences.
ArbitrarySequence
de.jstacs.data.sequences.
DiscreteSequence
de.jstacs.data.sequences.
ByteSequence
de.jstacs.data.sequences.
IntSequence
de.jstacs.data.sequences.
ShortSequence
de.jstacs.data.sequences.
SparseSequence
de.jstacs.data.sequences.
RecursiveSequence
de.jstacs.data.sequences.
PermutedSequence
de.jstacs.data.
Sequence.CompositeSequence
de.jstacs.data.
Sequence.SubSequence
de.jstacs.models.discrete.inhomogeneous.
SequenceIterator
de.jstacs.data.bioJava.
SimpleSequenceIterator
(implements org.biojava.bio.seq.
SequenceIterator
)
de.jstacs.parameters.validation.
SimpleStaticConstraint
(implements de.jstacs.parameters.validation.
Constraint
)
de.jstacs.models.utils.
StationaryDistribution
de.jstacs.models.utils.
StatisticalTest
de.jstacs.parameters.validation.
StorableValidator
(implements de.jstacs.parameters.validation.
ParameterValidator
)
de.jstacs.io.
StringExtractor
de.jstacs.models.discrete.inhomogeneous.
StructureLearner
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.
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.algorithms.graphs.
TopSort
de.jstacs.models.discrete.inhomogeneous.
TwoPointEvaluater
de.jstacs.algorithms.graphs.
UnionFind
de.jstacs.utils.random.
UnivariateRandomGenerator
de.jstacs.io.
XMLParser
Interface Hierarchy
de.jstacs.algorithms.
Alignment.Costs
java.lang.
Cloneable
de.jstacs.parameters.validation.
Constraint
(also extends de.jstacs.
Storable
)
de.jstacs.models.
Model
(also extends de.jstacs.
Storable
)
de.jstacs.scoringFunctions.
NormalizableScoringFunction
de.jstacs.parameters.validation.
ParameterValidator
(also extends de.jstacs.
Storable
)
de.jstacs.scoringFunctions.
ScoringFunction
(also extends de.jstacs.
Storable
)
de.jstacs.scoringFunctions.
NormalizableScoringFunction
de.jstacs.algorithms.optimization.
Function
de.jstacs.models.mixture.gibbssampling.
GibbsSamplingComponent
de.jstacs.
InstantiableFromParameterSet
de.jstacs.utils.
ProgressUpdater
de.jstacs.parameters.
Rangeable
de.jstacs.parameters.
RangeIterator
de.jstacs.algorithms.optimization.
StartDistanceForecaster
de.jstacs.
Storable
de.jstacs.parameters.validation.
Constraint
(also extends java.lang.
Cloneable
)
de.jstacs.models.
Model
(also extends java.lang.
Cloneable
)
de.jstacs.scoringFunctions.
NormalizableScoringFunction
de.jstacs.parameters.validation.
ParameterValidator
(also extends java.lang.
Cloneable
)
de.jstacs.scoringFunctions.
ScoringFunction
(also extends java.lang.
Cloneable
)
de.jstacs.scoringFunctions.
NormalizableScoringFunction
Enum Hierarchy
java.lang.
Object
java.lang.
Enum
<E> (implements java.lang.
Comparable
<T>, java.io.
Serializable
)
de.jstacs.
DataType
de.jstacs.algorithms.
Alignment.Costs.Direction
de.jstacs.algorithms.optimization.
Optimizer.TerminationCondition
de.jstacs.classifier.
MeasureParameters.Measure
de.jstacs.data.
Sample.PartitionMethod
de.jstacs.data.
Sample.WeightedSampleFactory.SortOperation
de.jstacs.data.sequences.annotation.
StrandedLocatedSequenceAnnotationWithLength.Strand
de.jstacs.data.sequences.annotation.
SinglePositionSequenceAnnotation.Type
de.jstacs.io.
SubstringFilenameFilter.PartOfName
de.jstacs.models.discrete.inhomogeneous.
StructureLearner.LearningType
de.jstacs.models.discrete.inhomogeneous.
StructureLearner.ModelType
de.jstacs.models.mixture.
AbstractMixtureModel.Parameterization
de.jstacs.models.mixture.
AbstractMixtureModel.Algorithm
de.jstacs.parameters.
RangeParameter.Scale
de.jstacs.parameters.
RangeParameter.RangeType
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