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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.classifiers, de.jstacs.classifiers.assessment, de.jstacs.classifiers.differentiableSequenceScoreBased, de.jstacs.classifiers.differentiableSequenceScoreBased.gendismix, de.jstacs.classifiers.differentiableSequenceScoreBased.logPrior, de.jstacs.classifiers.differentiableSequenceScoreBased.msp, de.jstacs.classifiers.differentiableSequenceScoreBased.sampling, de.jstacs.classifiers.performanceMeasures, de.jstacs.classifiers.trainSMBased, de.jstacs.classifiers.utils, de.jstacs.data, de.jstacs.data.alphabets, de.jstacs.data.bioJava, de.jstacs.data.sequences, de.jstacs.data.sequences.annotation, de.jstacs.io, de.jstacs.motifDiscovery, de.jstacs.motifDiscovery.history, de.jstacs.parameters, de.jstacs.parameters.validation, de.jstacs.results, de.jstacs.sampling, de.jstacs.sequenceScores, de.jstacs.sequenceScores.differentiable, de.jstacs.sequenceScores.differentiable.logistic, de.jstacs.sequenceScores.statisticalModels, de.jstacs.sequenceScores.statisticalModels.differentiable, de.jstacs.sequenceScores.statisticalModels.differentiable.directedGraphicalModels, de.jstacs.sequenceScores.statisticalModels.differentiable.directedGraphicalModels.structureLearning.measures, de.jstacs.sequenceScores.statisticalModels.differentiable.directedGraphicalModels.structureLearning.measures.btMeasures, de.jstacs.sequenceScores.statisticalModels.differentiable.directedGraphicalModels.structureLearning.measures.pmmMeasures, de.jstacs.sequenceScores.statisticalModels.differentiable.homogeneous, de.jstacs.sequenceScores.statisticalModels.differentiable.mixture, de.jstacs.sequenceScores.statisticalModels.differentiable.mixture.motif, de.jstacs.sequenceScores.statisticalModels.trainable, de.jstacs.sequenceScores.statisticalModels.trainable.discrete, de.jstacs.sequenceScores.statisticalModels.trainable.discrete.homogeneous, de.jstacs.sequenceScores.statisticalModels.trainable.discrete.homogeneous.parameters, de.jstacs.sequenceScores.statisticalModels.trainable.discrete.inhomogeneous, de.jstacs.sequenceScores.statisticalModels.trainable.discrete.inhomogeneous.parameters, de.jstacs.sequenceScores.statisticalModels.trainable.discrete.inhomogeneous.shared, de.jstacs.sequenceScores.statisticalModels.trainable.hmm, de.jstacs.sequenceScores.statisticalModels.trainable.hmm.models, de.jstacs.sequenceScores.statisticalModels.trainable.hmm.states, de.jstacs.sequenceScores.statisticalModels.trainable.hmm.states.emissions, de.jstacs.sequenceScores.statisticalModels.trainable.hmm.states.emissions.continuous, de.jstacs.sequenceScores.statisticalModels.trainable.hmm.states.emissions.discrete, de.jstacs.sequenceScores.statisticalModels.trainable.hmm.training, de.jstacs.sequenceScores.statisticalModels.trainable.hmm.transitions, de.jstacs.sequenceScores.statisticalModels.trainable.hmm.transitions.elements, de.jstacs.sequenceScores.statisticalModels.trainable.mixture, de.jstacs.sequenceScores.statisticalModels.trainable.mixture.motif, de.jstacs.sequenceScores.statisticalModels.trainable.mixture.motif.positionprior, de.jstacs.sequenceScores.statisticalModels.trainable.phylo, de.jstacs.sequenceScores.statisticalModels.trainable.phylo.parser, de.jstacs.utils, de.jstacs.utils.galaxy, de.jstacs.utils.random

## Class Hierarchy

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

## Interface Hierarchy

- java.lang.Cloneable
  - de.jstacs.sampling.BurnInTest (also extends de.jstacs.Storable)
  - de.jstacs.parameters.validation.Constraint (also extends de.jstacs.Storable)
  - de.jstacs.sequenceScores.statisticalModels.trainable.hmm.states.emissions.DifferentiableEmission
  - de.jstacs.sequenceScores.differentiable.DifferentiableSequenceScore
    - de.jstacs.sequenceScores.statisticalModels.differentiable.DifferentiableStatisticalModel (also extends de.jstacs.sequenceScores.statisticalModels.StatisticalModel)
      - de.jstacs.sequenceScores.statisticalModels.differentiable.SamplingDifferentiableStatisticalModel
      - de.jstacs.sequenceScores.statisticalModels.differentiable.VariableLengthDiffSM
    - de.jstacs.sequenceScores.statisticalModels.differentiable.SamplingDifferentiableStatisticalModel
    - de.jstacs.sequenceScores.statisticalModels.differentiable.VariableLengthDiffSM
  - de.jstacs.sequenceScores.statisticalModels.differentiable.DifferentiableStatisticalModel (also extends de.jstacs.sequenceScores.differentiable.DifferentiableSequenceScore, de.jstacs.sequenceScores.statisticalModels.StatisticalModel)
    - de.jstacs.sequenceScores.statisticalModels.differentiable.SamplingDifferentiableStatisticalModel
    - de.jstacs.sequenceScores.statisticalModels.differentiable.VariableLengthDiffSM
  - de.jstacs.sequenceScores.statisticalModels.trainable.hmm.transitions.DifferentiableTransition
    - de.jstacs.sequenceScores.statisticalModels.trainable.hmm.transitions.TrainableAndDifferentiableTransition (also extends de.jstacs.sequenceScores.statisticalModels.trainable.hmm.transitions.TrainableTransition)
  - de.jstacs.sequenceScores.statisticalModels.trainable.hmm.states.emissions.Emission (also extends de.jstacs.Storable)
    - de.jstacs.sequenceScores.statisticalModels.trainable.hmm.states.emissions.DifferentiableEmission
    - de.jstacs.sequenceScores.statisticalModels.trainable.hmm.states.emissions.SamplingEmission (also extends de.jstacs.sampling.SamplingFromStatistic)
  - de.jstacs.motifDiscovery.history.History (also extends de.jstacs.Storable)
  - de.jstacs.sequenceScores.differentiable.logistic.LogisticConstraint (also extends de.jstacs.Storable)
  - de.jstacs.motifDiscovery.MotifDiscoverer (also extends de.jstacs.Storable)
    - de.jstacs.motifDiscovery.MutableMotifDiscoverer
  - de.jstacs.motifDiscovery.MutableMotifDiscoverer
  - de.jstacs.parameters.validation.ParameterValidator (also extends de.jstacs.Storable)
  - de.jstacs.sequenceScores.statisticalModels.differentiable.SamplingDifferentiableStatisticalModel
  - de.jstacs.sequenceScores.statisticalModels.trainable.hmm.states.emissions.SamplingEmission (also extends de.jstacs.sequenceScores.statisticalModels.trainable.hmm.states.emissions.Emission, de.jstacs.sampling.SamplingFromStatistic)
  - de.jstacs.sequenceScores.statisticalModels.trainable.hmm.transitions.SamplingTransition (also extends de.jstacs.sampling.SamplingFromStatistic, de.jstacs.sequenceScores.statisticalModels.trainable.hmm.transitions.TransitionWithSufficientStatistic)
  - de.jstacs.sequenceScores.SequenceScore (also extends de.jstacs.Storable)
    - de.jstacs.sequenceScores.differentiable.DifferentiableSequenceScore
      - de.jstacs.sequenceScores.statisticalModels.differentiable.DifferentiableStatisticalModel (also extends de.jstacs.sequenceScores.statisticalModels.StatisticalModel)
        - de.jstacs.sequenceScores.statisticalModels.differentiable.SamplingDifferentiableStatisticalModel
        - de.jstacs.sequenceScores.statisticalModels.differentiable.VariableLengthDiffSM
      - de.jstacs.sequenceScores.statisticalModels.differentiable.SamplingDifferentiableStatisticalModel
      - de.jstacs.sequenceScores.statisticalModels.differentiable.VariableLengthDiffSM
    - de.jstacs.sequenceScores.statisticalModels.differentiable.DifferentiableStatisticalModel (also extends de.jstacs.sequenceScores.differentiable.DifferentiableSequenceScore, de.jstacs.sequenceScores.statisticalModels.StatisticalModel)
      - de.jstacs.sequenceScores.statisticalModels.differentiable.SamplingDifferentiableStatisticalModel
      - de.jstacs.sequenceScores.statisticalModels.differentiable.VariableLengthDiffSM
    - de.jstacs.sequenceScores.statisticalModels.differentiable.SamplingDifferentiableStatisticalModel
    - de.jstacs.sequenceScores.statisticalModels.StatisticalModel
      - de.jstacs.sequenceScores.statisticalModels.differentiable.DifferentiableStatisticalModel (also extends de.jstacs.sequenceScores.differentiable.DifferentiableSequenceScore)
        - de.jstacs.sequenceScores.statisticalModels.differentiable.SamplingDifferentiableStatisticalModel
        - de.jstacs.sequenceScores.statisticalModels.differentiable.VariableLengthDiffSM
      - de.jstacs.sequenceScores.statisticalModels.differentiable.SamplingDifferentiableStatisticalModel
      - de.jstacs.sequenceScores.statisticalModels.trainable.TrainableStatisticalModel
      - de.jstacs.sequenceScores.statisticalModels.differentiable.VariableLengthDiffSM
    - de.jstacs.sequenceScores.statisticalModels.trainable.TrainableStatisticalModel
    - de.jstacs.sequenceScores.statisticalModels.differentiable.VariableLengthDiffSM
  - de.jstacs.sequenceScores.statisticalModels.StatisticalModel
    - de.jstacs.sequenceScores.statisticalModels.differentiable.DifferentiableStatisticalModel (also extends de.jstacs.sequenceScores.differentiable.DifferentiableSequenceScore)
      - de.jstacs.sequenceScores.statisticalModels.differentiable.SamplingDifferentiableStatisticalModel
      - de.jstacs.sequenceScores.statisticalModels.differentiable.VariableLengthDiffSM
    - de.jstacs.sequenceScores.statisticalModels.differentiable.SamplingDifferentiableStatisticalModel
    - de.jstacs.sequenceScores.statisticalModels.trainable.TrainableStatisticalModel
    - de.jstacs.sequenceScores.statisticalModels.differentiable.VariableLengthDiffSM
  - de.jstacs.algorithms.optimization.termination.TerminationCondition (also extends de.jstacs.InstantiableFromParameterSet, de.jstacs.Storable)
  - de.jstacs.sequenceScores.statisticalModels.trainable.hmm.transitions.TrainableAndDifferentiableTransition (also extends de.jstacs.sequenceScores.statisticalModels.trainable.hmm.transitions.DifferentiableTransition, de.jstacs.sequenceScores.statisticalModels.trainable.hmm.transitions.TrainableTransition)
  - de.jstacs.sequenceScores.statisticalModels.trainable.TrainableStatisticalModel
  - de.jstacs.sequenceScores.statisticalModels.trainable.hmm.transitions.TrainableTransition
    - de.jstacs.sequenceScores.statisticalModels.trainable.hmm.transitions.TrainableAndDifferentiableTransition (also extends de.jstacs.sequenceScores.statisticalModels.trainable.hmm.transitions.DifferentiableTransition)
  - de.jstacs.sequenceScores.statisticalModels.trainable.hmm.transitions.Transition (also extends de.jstacs.Storable)
    - de.jstacs.sequenceScores.statisticalModels.trainable.hmm.transitions.DifferentiableTransition
      - de.jstacs.sequenceScores.statisticalModels.trainable.hmm.transitions.TrainableAndDifferentiableTransition (also extends de.jstacs.sequenceScores.statisticalModels.trainable.hmm.transitions.TrainableTransition)
    - de.jstacs.sequenceScores.statisticalModels.trainable.hmm.transitions.SamplingTransition (also extends de.jstacs.sampling.SamplingFromStatistic, de.jstacs.sequenceScores.statisticalModels.trainable.hmm.transitions.TransitionWithSufficientStatistic)
    - de.jstacs.sequenceScores.statisticalModels.trainable.hmm.transitions.TrainableAndDifferentiableTransition (also extends de.jstacs.sequenceScores.statisticalModels.trainable.hmm.transitions.DifferentiableTransition, de.jstacs.sequenceScores.statisticalModels.trainable.hmm.transitions.TrainableTransition)
    - de.jstacs.sequenceScores.statisticalModels.trainable.hmm.transitions.TrainableTransition
      - de.jstacs.sequenceScores.statisticalModels.trainable.hmm.transitions.TrainableAndDifferentiableTransition (also extends de.jstacs.sequenceScores.statisticalModels.trainable.hmm.transitions.DifferentiableTransition)
    - de.jstacs.sequenceScores.statisticalModels.trainable.hmm.transitions.TransitionWithSufficientStatistic
      - de.jstacs.sequenceScores.statisticalModels.trainable.hmm.transitions.SamplingTransition (also extends de.jstacs.sampling.SamplingFromStatistic)
      - de.jstacs.sequenceScores.statisticalModels.trainable.hmm.transitions.TrainableAndDifferentiableTransition (also extends de.jstacs.sequenceScores.statisticalModels.trainable.hmm.transitions.DifferentiableTransition, de.jstacs.sequenceScores.statisticalModels.trainable.hmm.transitions.TrainableTransition)
      - de.jstacs.sequenceScores.statisticalModels.trainable.hmm.transitions.TrainableTransition
        - de.jstacs.sequenceScores.statisticalModels.trainable.hmm.transitions.TrainableAndDifferentiableTransition (also extends de.jstacs.sequenceScores.statisticalModels.trainable.hmm.transitions.DifferentiableTransition)
  - de.jstacs.sequenceScores.statisticalModels.trainable.hmm.transitions.TransitionWithSufficientStatistic
    - de.jstacs.sequenceScores.statisticalModels.trainable.hmm.transitions.SamplingTransition (also extends de.jstacs.sampling.SamplingFromStatistic)
    - de.jstacs.sequenceScores.statisticalModels.trainable.hmm.transitions.TrainableAndDifferentiableTransition (also extends de.jstacs.sequenceScores.statisticalModels.trainable.hmm.transitions.DifferentiableTransition, de.jstacs.sequenceScores.statisticalModels.trainable.hmm.transitions.TrainableTransition)
    - de.jstacs.sequenceScores.statisticalModels.trainable.hmm.transitions.TrainableTransition
      - de.jstacs.sequenceScores.statisticalModels.trainable.hmm.transitions.TrainableAndDifferentiableTransition (also extends de.jstacs.sequenceScores.statisticalModels.trainable.hmm.transitions.DifferentiableTransition)
  - de.jstacs.sequenceScores.statisticalModels.differentiable.VariableLengthDiffSM
- de.jstacs.algorithms.alignment.cost.Costs
- java.util.Enumeration<E>
  - de.jstacs.data.RecyclableSequenceEnumerator
- de.jstacs.algorithms.optimization.Function
- de.jstacs.parameters.GalaxyConvertible
- de.jstacs.InstantiableFromParameterSet
  - de.jstacs.algorithms.optimization.termination.TerminationCondition (also extends java.lang.Cloneable, de.jstacs.Storable)
- de.jstacs.motifDiscovery.Mutable
- de.jstacs.classifiers.performanceMeasures.NumericalPerformanceMeasure
- de.jstacs.utils.ProgressUpdater
- de.jstacs.parameters.Rangeable
- de.jstacs.parameters.RangeIterator
- de.jstacs.sampling.SamplingComponent
  - de.jstacs.sampling.GibbsSamplingModel
  - de.jstacs.sequenceScores.statisticalModels.trainable.hmm.states.emissions.SamplingEmission (also extends de.jstacs.sequenceScores.statisticalModels.trainable.hmm.states.emissions.Emission, de.jstacs.sampling.SamplingFromStatistic)
  - de.jstacs.sampling.SamplingFromStatistic
    - de.jstacs.sequenceScores.statisticalModels.trainable.hmm.states.emissions.SamplingEmission (also extends de.jstacs.sequenceScores.statisticalModels.trainable.hmm.states.emissions.Emission)
    - de.jstacs.sequenceScores.statisticalModels.trainable.hmm.states.SamplingState (also extends de.jstacs.sequenceScores.statisticalModels.trainable.hmm.states.TrainableState)
    - de.jstacs.sequenceScores.statisticalModels.trainable.hmm.transitions.SamplingTransition (also extends de.jstacs.sequenceScores.statisticalModels.trainable.hmm.transitions.TransitionWithSufficientStatistic)
  - de.jstacs.sequenceScores.statisticalModels.trainable.hmm.states.SamplingState (also extends de.jstacs.sampling.SamplingFromStatistic, de.jstacs.sequenceScores.statisticalModels.trainable.hmm.states.TrainableState)
  - de.jstacs.sequenceScores.statisticalModels.trainable.hmm.transitions.SamplingTransition (also extends de.jstacs.sampling.SamplingFromStatistic, de.jstacs.sequenceScores.statisticalModels.trainable.hmm.transitions.TransitionWithSufficientStatistic)
- de.jstacs.data.sequences.annotation.SequenceAnnotationParser
- de.jstacs.motifDiscovery.SignificantMotifOccurrencesFinder.JoinMethod
- de.jstacs.Singleton
- de.jstacs.algorithms.optimization.StartDistanceForecaster
- de.jstacs.sequenceScores.statisticalModels.trainable.hmm.states.State
  - de.jstacs.sequenceScores.statisticalModels.trainable.hmm.states.DifferentiableState
  - de.jstacs.sequenceScores.statisticalModels.trainable.hmm.states.SamplingState (also extends de.jstacs.sampling.SamplingFromStatistic, de.jstacs.sequenceScores.statisticalModels.trainable.hmm.states.TrainableState)
  - de.jstacs.sequenceScores.statisticalModels.trainable.hmm.states.TrainableState
    - de.jstacs.sequenceScores.statisticalModels.trainable.hmm.states.SamplingState (also extends de.jstacs.sampling.SamplingFromStatistic)
- de.jstacs.Storable
  - de.jstacs.sampling.BurnInTest (also extends java.lang.Cloneable)
  - de.jstacs.parameters.validation.Constraint (also extends java.lang.Cloneable)
  - de.jstacs.sequenceScores.statisticalModels.trainable.hmm.states.emissions.DifferentiableEmission
  - de.jstacs.sequenceScores.differentiable.DifferentiableSequenceScore
    - de.jstacs.sequenceScores.statisticalModels.differentiable.DifferentiableStatisticalModel (also extends de.jstacs.sequenceScores.statisticalModels.StatisticalModel)
      - de.jstacs.sequenceScores.statisticalModels.differentiable.SamplingDifferentiableStatisticalModel
      - de.jstacs.sequenceScores.statisticalModels.differentiable.VariableLengthDiffSM
    - de.jstacs.sequenceScores.statisticalModels.differentiable.SamplingDifferentiableStatisticalModel
    - de.jstacs.sequenceScores.statisticalModels.differentiable.VariableLengthDiffSM
  - de.jstacs.sequenceScores.statisticalModels.differentiable.DifferentiableStatisticalModel (also extends de.jstacs.sequenceScores.differentiable.DifferentiableSequenceScore, de.jstacs.sequenceScores.statisticalModels.StatisticalModel)
    - de.jstacs.sequenceScores.statisticalModels.differentiable.SamplingDifferentiableStatisticalModel
    - de.jstacs.sequenceScores.statisticalModels.differentiable.VariableLengthDiffSM
  - de.jstacs.sequenceScores.statisticalModels.trainable.hmm.transitions.DifferentiableTransition
    - de.jstacs.sequenceScores.statisticalModels.trainable.hmm.transitions.TrainableAndDifferentiableTransition (also extends de.jstacs.sequenceScores.statisticalModels.trainable.hmm.transitions.TrainableTransition)
  - de.jstacs.sequenceScores.statisticalModels.trainable.hmm.states.emissions.Emission (also extends java.lang.Cloneable)
    - de.jstacs.sequenceScores.statisticalModels.trainable.hmm.states.emissions.DifferentiableEmission
    - de.jstacs.sequenceScores.statisticalModels.trainable.hmm.states.emissions.SamplingEmission (also extends de.jstacs.sampling.SamplingFromStatistic)
  - de.jstacs.motifDiscovery.history.History (also extends java.lang.Cloneable)
  - de.jstacs.sequenceScores.differentiable.logistic.LogisticConstraint (also extends java.lang.Cloneable)
  - de.jstacs.motifDiscovery.MotifDiscoverer (also extends java.lang.Cloneable)
    - de.jstacs.motifDiscovery.MutableMotifDiscoverer
  - de.jstacs.motifDiscovery.MutableMotifDiscoverer
  - de.jstacs.parameters.validation.ParameterValidator (also extends java.lang.Cloneable)
  - de.jstacs.sequenceScores.statisticalModels.differentiable.SamplingDifferentiableStatisticalModel
  - de.jstacs.sequenceScores.statisticalModels.trainable.hmm.states.emissions.SamplingEmission (also extends de.jstacs.sequenceScores.statisticalModels.trainable.hmm.states.emissions.Emission, de.jstacs.sampling.SamplingFromStatistic)
  - de.jstacs.sequenceScores.statisticalModels.trainable.hmm.transitions.SamplingTransition (also extends de.jstacs.sampling.SamplingFromStatistic, de.jstacs.sequenceScores.statisticalModels.trainable.hmm.transitions.TransitionWithSufficientStatistic)
  - de.jstacs.sequenceScores.SequenceScore (also extends java.lang.Cloneable)
    - de.jstacs.sequenceScores.differentiable.DifferentiableSequenceScore
      - de.jstacs.sequenceScores.statisticalModels.differentiable.DifferentiableStatisticalModel (also extends de.jstacs.sequenceScores.statisticalModels.StatisticalModel)
        - de.jstacs.sequenceScores.statisticalModels.differentiable.SamplingDifferentiableStatisticalModel
        - de.jstacs.sequenceScores.statisticalModels.differentiable.VariableLengthDiffSM
      - de.jstacs.sequenceScores.statisticalModels.differentiable.SamplingDifferentiableStatisticalModel
      - de.jstacs.sequenceScores.statisticalModels.differentiable.VariableLengthDiffSM
    - de.jstacs.sequenceScores.statisticalModels.differentiable.DifferentiableStatisticalModel (also extends de.jstacs.sequenceScores.differentiable.DifferentiableSequenceScore, de.jstacs.sequenceScores.statisticalModels.StatisticalModel)
      - de.jstacs.sequenceScores.statisticalModels.differentiable.SamplingDifferentiableStatisticalModel
      - de.jstacs.sequenceScores.statisticalModels.differentiable.VariableLengthDiffSM
    - de.jstacs.sequenceScores.statisticalModels.differentiable.SamplingDifferentiableStatisticalModel
    - de.jstacs.sequenceScores.statisticalModels.StatisticalModel
      - de.jstacs.sequenceScores.statisticalModels.differentiable.DifferentiableStatisticalModel (also extends de.jstacs.sequenceScores.differentiable.DifferentiableSequenceScore)
        - de.jstacs.sequenceScores.statisticalModels.differentiable.SamplingDifferentiableStatisticalModel
        - de.jstacs.sequenceScores.statisticalModels.differentiable.VariableLengthDiffSM
      - de.jstacs.sequenceScores.statisticalModels.differentiable.SamplingDifferentiableStatisticalModel
      - de.jstacs.sequenceScores.statisticalModels.trainable.TrainableStatisticalModel
      - de.jstacs.sequenceScores.statisticalModels.differentiable.VariableLengthDiffSM
    - de.jstacs.sequenceScores.statisticalModels.trainable.TrainableStatisticalModel
    - de.jstacs.sequenceScores.statisticalModels.differentiable.VariableLengthDiffSM
  - de.jstacs.sequenceScores.statisticalModels.StatisticalModel
    - de.jstacs.sequenceScores.statisticalModels.differentiable.DifferentiableStatisticalModel (also extends de.jstacs.sequenceScores.differentiable.DifferentiableSequenceScore)
      - de.jstacs.sequenceScores.statisticalModels.differentiable.SamplingDifferentiableStatisticalModel
      - de.jstacs.sequenceScores.statisticalModels.differentiable.VariableLengthDiffSM
    - de.jstacs.sequenceScores.statisticalModels.differentiable.SamplingDifferentiableStatisticalModel
    - de.jstacs.sequenceScores.statisticalModels.trainable.TrainableStatisticalModel
    - de.jstacs.sequenceScores.statisticalModels.differentiable.VariableLengthDiffSM
  - de.jstacs.algorithms.optimization.termination.TerminationCondition (also extends java.lang.Cloneable, de.jstacs.InstantiableFromParameterSet)
  - de.jstacs.sequenceScores.statisticalModels.trainable.hmm.transitions.TrainableAndDifferentiableTransition (also extends de.jstacs.sequenceScores.statisticalModels.trainable.hmm.transitions.DifferentiableTransition, de.jstacs.sequenceScores.statisticalModels.trainable.hmm.transitions.TrainableTransition)
  - de.jstacs.sequenceScores.statisticalModels.trainable.TrainableStatisticalModel
  - de.jstacs.sequenceScores.statisticalModels.trainable.hmm.transitions.TrainableTransition
    - de.jstacs.sequenceScores.statisticalModels.trainable.hmm.transitions.TrainableAndDifferentiableTransition (also extends de.jstacs.sequenceScores.statisticalModels.trainable.hmm.transitions.DifferentiableTransition)
  - de.jstacs.sequenceScores.statisticalModels.trainable.hmm.transitions.Transition (also extends java.lang.Cloneable)
    - de.jstacs.sequenceScores.statisticalModels.trainable.hmm.transitions.DifferentiableTransition
      - de.jstacs.sequenceScores.statisticalModels.trainable.hmm.transitions.TrainableAndDifferentiableTransition (also extends de.jstacs.sequenceScores.statisticalModels.trainable.hmm.transitions.TrainableTransition)
    - de.jstacs.sequenceScores.statisticalModels.trainable.hmm.transitions.SamplingTransition (also extends de.jstacs.sampling.SamplingFromStatistic, de.jstacs.sequenceScores.statisticalModels.trainable.hmm.transitions.TransitionWithSufficientStatistic)
    - de.jstacs.sequenceScores.statisticalModels.trainable.hmm.transitions.TrainableAndDifferentiableTransition (also extends de.jstacs.sequenceScores.statisticalModels.trainable.hmm.transitions.DifferentiableTransition, de.jstacs.sequenceScores.statisticalModels.trainable.hmm.transitions.TrainableTransition)
    - de.jstacs.sequenceScores.statisticalModels.trainable.hmm.transitions.TrainableTransition
      - de.jstacs.sequenceScores.statisticalModels.trainable.hmm.transitions.TrainableAndDifferentiableTransition (also extends de.jstacs.sequenceScores.statisticalModels.trainable.hmm.transitions.DifferentiableTransition)
    - de.jstacs.sequenceScores.statisticalModels.trainable.hmm.transitions.TransitionWithSufficientStatistic
      - de.jstacs.sequenceScores.statisticalModels.trainable.hmm.transitions.SamplingTransition (also extends de.jstacs.sampling.SamplingFromStatistic)
      - de.jstacs.sequenceScores.statisticalModels.trainable.hmm.transitions.TrainableAndDifferentiableTransition (also extends de.jstacs.sequenceScores.statisticalModels.trainable.hmm.transitions.DifferentiableTransition, de.jstacs.sequenceScores.statisticalModels.trainable.hmm.transitions.TrainableTransition)
      - de.jstacs.sequenceScores.statisticalModels.trainable.hmm.transitions.TrainableTransition
        - de.jstacs.sequenceScores.statisticalModels.trainable.hmm.transitions.TrainableAndDifferentiableTransition (also extends de.jstacs.sequenceScores.statisticalModels.trainable.hmm.transitions.DifferentiableTransition)
  - de.jstacs.sequenceScores.statisticalModels.trainable.hmm.transitions.TransitionWithSufficientStatistic
    - de.jstacs.sequenceScores.statisticalModels.trainable.hmm.transitions.SamplingTransition (also extends de.jstacs.sampling.SamplingFromStatistic)
    - de.jstacs.sequenceScores.statisticalModels.trainable.hmm.transitions.TrainableAndDifferentiableTransition (also extends de.jstacs.sequenceScores.statisticalModels.trainable.hmm.transitions.DifferentiableTransition, de.jstacs.sequenceScores.statisticalModels.trainable.hmm.transitions.TrainableTransition)
    - de.jstacs.sequenceScores.statisticalModels.trainable.hmm.transitions.TrainableTransition
      - de.jstacs.sequenceScores.statisticalModels.trainable.hmm.transitions.TrainableAndDifferentiableTransition (also extends de.jstacs.sequenceScores.statisticalModels.trainable.hmm.transitions.DifferentiableTransition)
  - de.jstacs.sequenceScores.statisticalModels.differentiable.VariableLengthDiffSM

## Enum Hierarchy

- java.lang.Object
  - java.lang.Enum<E> (implements java.lang.Comparable<T>, java.io.Serializable)
    - de.jstacs.DataType
    - de.jstacs.algorithms.alignment.Alignment.AlignmentType
    - de.jstacs.classifiers.differentiableSequenceScoreBased.OptimizableFunction.KindOfParameter
    - de.jstacs.classifiers.differentiableSequenceScoreBased.gendismix.LearningPrinciple
    - de.jstacs.classifiers.differentiableSequenceScoreBased.sampling.SamplingScoreBasedClassifier.SamplingScheme
    - de.jstacs.data.DinucleotideProperty
    - de.jstacs.data.DinucleotideProperty.Type
    - de.jstacs.data.DinucleotideProperty.HowCreated
    - de.jstacs.data.DataSet.PartitionMethod
    - de.jstacs.data.DataSet.WeightedDataSetFactory.SortOperation
    - de.jstacs.data.AlphabetContainer.AlphabetContainerType
    - de.jstacs.data.sequences.annotation.StrandedLocatedSequenceAnnotationWithLength.Strand
    - de.jstacs.data.sequences.annotation.SinglePositionSequenceAnnotation.Type
    - de.jstacs.motifDiscovery.SignificantMotifOccurrencesFinder.RandomSeqType
    - de.jstacs.motifDiscovery.MutableMotifDiscovererToolbox.InitMethodForDiffSM
    - de.jstacs.motifDiscovery.MotifDiscoverer.KindOfProfile
    - de.jstacs.parameters.RangeParameter.Scale
    - de.jstacs.parameters.RangeParameter.RangeType
    - de.jstacs.sequenceScores.statisticalModels.differentiable.directedGraphicalModels.structureLearning.measures.btMeasures.BTMutualInformation.DataSource
    - de.jstacs.sequenceScores.statisticalModels.differentiable.mixture.StrandDiffSM.InitMethod
    - de.jstacs.sequenceScores.statisticalModels.trainable.discrete.inhomogeneous.StructureLearner.LearningType
    - de.jstacs.sequenceScores.statisticalModels.trainable.discrete.inhomogeneous.StructureLearner.ModelType
    - de.jstacs.sequenceScores.statisticalModels.trainable.hmm.HMMFactory.HMMType
    - de.jstacs.sequenceScores.statisticalModels.trainable.hmm.models.SamplingHigherOrderHMM.ViterbiComputation
    - de.jstacs.sequenceScores.statisticalModels.trainable.hmm.models.HigherOrderHMM.Type
    - de.jstacs.sequenceScores.statisticalModels.trainable.mixture.AbstractMixtureTrainSM.Parameterization
    - de.jstacs.sequenceScores.statisticalModels.trainable.mixture.AbstractMixtureTrainSM.Algorithm

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