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## Hierarchy For All Packages

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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