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## Hierarchy For All Packages

Package Hierarchies:
  de.jstacs, de.jstacs.algorithms, de.jstacs.algorithms.graphs, de.jstacs.algorithms.graphs.tensor, de.jstacs.algorithms.optimization, de.jstacs.classifier, de.jstacs.classifier.assessment, de.jstacs.classifier.modelBased, de.jstacs.classifier.scoringFunctionBased, de.jstacs.classifier.scoringFunctionBased.cll, de.jstacs.classifier.scoringFunctionBased.logPrior, de.jstacs.classifier.utils, de.jstacs.data, de.jstacs.data.alphabets, de.jstacs.data.bioJava, de.jstacs.data.sequences, de.jstacs.data.sequences.annotation, de.jstacs.io, de.jstacs.models, de.jstacs.models.discrete, de.jstacs.models.discrete.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.mixture, de.jstacs.models.mixture.gibbssampling, de.jstacs.models.mixture.motif, de.jstacs.models.mixture.motif.positionprior, de.jstacs.models.utils, de.jstacs.motifDiscovery, de.jstacs.motifDiscovery.history, de.jstacs.parameters, de.jstacs.parameters.validation, de.jstacs.results, de.jstacs.scoringFunctions, de.jstacs.scoringFunctions.directedGraphicalModels, de.jstacs.scoringFunctions.directedGraphicalModels.structureLearning.measures, de.jstacs.scoringFunctions.directedGraphicalModels.structureLearning.measures.btMeasures, de.jstacs.scoringFunctions.directedGraphicalModels.structureLearning.measures.pmmMeasures, de.jstacs.scoringFunctions.homogeneous, de.jstacs.scoringFunctions.mix, de.jstacs.scoringFunctions.mix.motifSearch, de.jstacs.utils, de.jstacs.utils.random

## Class Hierarchy

- java.lang.Object
  - de.jstacs.classifier.AbstractClassifier (implements java.lang.Cloneable, de.jstacs.Storable)
    - de.jstacs.classifier.AbstractScoreBasedClassifier
      - de.jstacs.classifier.MappingClassifier
      - de.jstacs.classifier.modelBased.ModelBasedClassifier
        - de.jstacs.models.discrete.inhomogeneous.shared.SharedStructureClassifier
      - de.jstacs.classifier.scoringFunctionBased.ScoreClassifier
        - de.jstacs.classifier.scoringFunctionBased.cll.CLLClassifier
  - java.util.AbstractCollection<E> (implements java.util.Collection<E>)
    - java.util.AbstractList<E> (implements java.util.List<E>)
      - java.util.ArrayList<E> (implements java.lang.Cloneable, java.util.List<E>, java.util.RandomAccess, java.io.Serializable)
        - de.jstacs.parameters.ParameterSet.ParameterList
  - de.jstacs.models.AbstractModel (implements java.lang.Cloneable, de.jstacs.models.Model, de.jstacs.Storable)
    - de.jstacs.models.mixture.AbstractMixtureModel
      - de.jstacs.models.mixture.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.mixture.gibbssampling.FSDAGModelForGibbsSampling (implements de.jstacs.models.mixture.gibbssampling.GibbsSamplingComponent)
    - de.jstacs.models.UniformModel
  - de.jstacs.scoringFunctions.AbstractNormalizableScoringFunction (implements de.jstacs.scoringFunctions.NormalizableScoringFunction)
    - de.jstacs.scoringFunctions.mix.AbstractMixtureScoringFunction
      - de.jstacs.scoringFunctions.mix.motifSearch.HiddenMotifsMixture (implements de.jstacs.motifDiscovery.MutableMotifDiscoverer)
      - de.jstacs.scoringFunctions.mix.MixtureScoringFunction
      - de.jstacs.scoringFunctions.mix.StrandScoringFunction (implements de.jstacs.motifDiscovery.Mutable)
    - de.jstacs.scoringFunctions.directedGraphicalModels.BayesianNetworkScoringFunction (implements de.jstacs.InstantiableFromParameterSet)
      - de.jstacs.scoringFunctions.directedGraphicalModels.MutableMarkovModelScoringFunction (implements de.jstacs.motifDiscovery.Mutable)
    - de.jstacs.scoringFunctions.IndependentProductScoringFunction (implements 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.scoringFunctions.VariableLengthScoringFunction
      - de.jstacs.scoringFunctions.homogeneous.HomogeneousScoringFunction
        - de.jstacs.scoringFunctions.homogeneous.HMM0ScoringFunction
        - de.jstacs.scoringFunctions.homogeneous.HMMScoringFunction
        - de.jstacs.scoringFunctions.homogeneous.UniformHomogeneousScoringFunction
  - de.jstacs.io.AbstractStringExtractor (implements java.util.Enumeration<E>)
    - de.jstacs.io.SimpleStringExtractor
    - de.jstacs.io.SparseStringExtractor
    - de.jstacs.io.StringExtractor
  - de.jstacs.algorithms.Alignment
  - de.jstacs.algorithms.Alignment.SimpleCosts (implements de.jstacs.algorithms.Alignment.Costs)
  - de.jstacs.algorithms.Alignment.StringAlignment
  - de.jstacs.data.Alphabet (implements java.lang.Comparable<T>, de.jstacs.InstantiableFromParameterSet, de.jstacs.Storable)
    - de.jstacs.data.alphabets.ContinuousAlphabet
    - de.jstacs.data.alphabets.DiscreteAlphabet
      - de.jstacs.data.alphabets.ComplementableDiscreteAlphabet
        - de.jstacs.data.alphabets.DNAAlphabet
  - de.jstacs.data.AlphabetContainer (implements java.lang.Comparable<T>, de.jstacs.InstantiableFromParameterSet, de.jstacs.Storable)
  - de.jstacs.io.ArrayHandler
  - de.jstacs.data.bioJava.BioJavaAdapter
  - de.jstacs.models.mixture.gibbssampling.BurnInTest (implements java.lang.Cloneable, de.jstacs.Storable)
    - de.jstacs.models.mixture.gibbssampling.AbstractBurnInTest
      - de.jstacs.models.mixture.gibbssampling.VarianceRatioBurnInTest
    - de.jstacs.models.mixture.gibbssampling.SimpleBurnInTest
  - 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.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.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.cll.NormConditionalLogLikelihood
  - de.jstacs.models.utils.DiscreteInhomogenousSampleEmitter
  - de.jstacs.data.DiscreteSequenceEnumerator (implements java.util.Enumeration<E>)
  - de.jstacs.utils.DoubleList (implements de.jstacs.Storable)
  - de.jstacs.algorithms.graphs.Edge (implements java.lang.Cloneable, java.lang.Comparable<T>)
  - javax.swing.filechooser.FileFilter
    - de.jstacs.io.SubstringFilenameFilter (implements java.io.FileFilter, java.io.FilenameFilter)
  - de.jstacs.io.FileManager
  - de.jstacs.parameters.FileParameter.FileRepresentation (implements java.lang.Cloneable, de.jstacs.Storable)
  - de.jstacs.utils.GUIProgressUpdater (implements java.awt.event.ActionListener, de.jstacs.utils.ProgressUpdater)
  - de.jstacs.utils.IntList
  - de.jstacs.algorithms.optimization.LimitedMedianStartDistance (implements de.jstacs.algorithms.optimization.StartDistanceForecaster)
  - de.jstacs.scoringFunctions.directedGraphicalModels.structureLearning.measures.Measure (implements java.lang.Cloneable, de.jstacs.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.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.utils.Normalisation
  - de.jstacs.utils.NullProgressUpdater (implements de.jstacs.utils.ProgressUpdater)
  - de.jstacs.parameters.validation.NumberValidator<E> (implements de.jstacs.parameters.validation.ParameterValidator)
  - de.jstacs.algorithms.optimization.OneDimensionalFunction (implements de.jstacs.algorithms.optimization.Function)
    - de.jstacs.algorithms.optimization.NegativeOneDimensionalFunction
    - de.jstacs.algorithms.optimization.OneDimensionalSubFunction
    - de.jstacs.algorithms.optimization.QuadraticFunction
  - de.jstacs.algorithms.optimization.Optimizer
  - java.io.OutputStream (implements java.io.Closeable, java.io.Flushable)
    - de.jstacs.utils.SafeOutputStream
  - de.jstacs.parameters.Parameter (implements java.lang.Cloneable, de.jstacs.Storable)
    - de.jstacs.parameters.CollectionParameter (implements de.jstacs.parameters.Rangeable)
      - de.jstacs.parameters.EnumParameter
      - de.jstacs.parameters.MultiSelectionCollectionParameter (implements de.jstacs.parameters.RangeIterator)
        - de.jstacs.classifier.MeasureParameters
    - de.jstacs.parameters.FileParameter
    - de.jstacs.parameters.ParameterSetContainer (implements de.jstacs.parameters.Rangeable, de.jstacs.parameters.RangeIterator)
    - de.jstacs.parameters.RangeParameter (implements de.jstacs.parameters.RangeIterator)
    - de.jstacs.parameters.SimpleParameter (implements de.jstacs.parameters.Rangeable)
  - de.jstacs.scoringFunctions.directedGraphicalModels.Parameter (implements java.lang.Cloneable, de.jstacs.Storable)
  - de.jstacs.parameters.ParameterSet (implements java.lang.Cloneable, de.jstacs.parameters.RangeIterator, de.jstacs.Storable)
    - de.jstacs.classifier.assessment.ClassifierAssessmentAssessParameterSet
      - de.jstacs.classifier.assessment.KFoldCVAssessParameterSet
      - de.jstacs.classifier.assessment.RepeatedHoldOutAssessParameterSet
      - de.jstacs.classifier.assessment.RepeatedSubSamplingAssessParameterSet
      - de.jstacs.classifier.assessment.Sampled_RepeatedHoldOutAssessParameterSet
    - de.jstacs.parameters.ExpandableParameterSet
      - de.jstacs.data.AlphabetContainerParameterSet.SectionDefinedAlphabetParameterSet
      - de.jstacs.parameters.ArrayParameterSet
        - de.jstacs.data.AlphabetContainerParameterSet.AlphabetArrayParameterSet
    - de.jstacs.parameters.InstanceParameterSet
      - de.jstacs.data.Alphabet.AlphabetParameterSet
        - de.jstacs.data.alphabets.ContinuousAlphabet.ContinuousAlphabetParameterSet
        - de.jstacs.data.alphabets.DiscreteAlphabet.DiscreteAlphabetParameterSet
        - de.jstacs.data.alphabets.DNAAlphabet.DNAAlphabetParameterSet
      - de.jstacs.data.AlphabetContainerParameterSet
      - de.jstacs.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.mixture.gibbssampling.FSDAGModelForGibbsSamplingParameterSet
        - de.jstacs.classifier.scoringFunctionBased.ScoreClassifierParameterSet
          - de.jstacs.classifier.scoringFunctionBased.cll.CLLClassifierParameterSet
    - de.jstacs.parameters.SimpleParameterSet
  - de.jstacs.io.ParameterSetParser
  - de.jstacs.scoringFunctions.directedGraphicalModels.ParameterTree (implements java.lang.Cloneable)
  - de.jstacs.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.results.ImageResult
    - de.jstacs.results.ListResult
    - de.jstacs.results.SampleResult
    - de.jstacs.results.SimpleResult (implements java.lang.Comparable<T>)
      - de.jstacs.results.CategoricalResult
      - de.jstacs.results.NumericalResult
    - de.jstacs.results.StorableResult
  - de.jstacs.results.ResultSet (implements de.jstacs.Storable)
    - de.jstacs.results.NumericalResultSet
      - de.jstacs.results.MeanResultSet
    - de.jstacs.data.sequences.annotation.SequenceAnnotation
      - de.jstacs.data.sequences.annotation.CisRegulatoryModuleAnnotation
      - de.jstacs.data.sequences.annotation.LocatedSequenceAnnotation
        - de.jstacs.data.sequences.annotation.LocatedSequenceAnnotationWithLength
          - de.jstacs.data.sequences.annotation.IntronAnnotation
          - de.jstacs.data.sequences.annotation.StrandedLocatedSequenceAnnotationWithLength
            - de.jstacs.data.sequences.annotation.MotifAnnotation
        - de.jstacs.data.sequences.annotation.SinglePositionSequenceAnnotation
  - de.jstacs.utils.RUtils
  - de.jstacs.data.Sample
  - de.jstacs.data.Sample.ElementEnumerator (implements java.util.Enumeration<E>)
  - de.jstacs.data.Sample.WeightedSampleFactory
  - de.jstacs.classifier.ScoreBasedPerformanceMeasureDefinitions
  - de.jstacs.classifier.ScoreBasedPerformanceMeasureDefinitions.ThresholdMeasurePair
  - de.jstacs.data.Sequence (implements java.lang.Comparable<T>)
    - de.jstacs.data.sequences.ArbitrarySequence
    - de.jstacs.data.sequences.DiscreteSequence
      - de.jstacs.data.sequences.ByteSequence
      - de.jstacs.data.sequences.IntSequence
      - de.jstacs.data.sequences.ShortSequence
      - de.jstacs.data.sequences.SparseSequence
    - de.jstacs.data.sequences.RecursiveSequence
      - de.jstacs.data.sequences.PermutedSequence
      - de.jstacs.data.Sequence.CompositeSequence
      - de.jstacs.data.Sequence.SubSequence
  - de.jstacs.models.discrete.inhomogeneous.SequenceIterator
  - de.jstacs.motifDiscovery.SignificantMotifOccurrencesFinder
  - de.jstacs.data.bioJava.SimpleSequenceIterator (implements org.biojava.bio.seq.SequenceIterator)
  - de.jstacs.parameters.validation.SimpleStaticConstraint (implements de.jstacs.parameters.validation.Constraint)
  - de.jstacs.models.utils.StationaryDistribution
  - de.jstacs.models.utils.StatisticalTest
  - de.jstacs.parameters.validation.StorableValidator (implements de.jstacs.parameters.validation.ParameterValidator)
  - de.jstacs.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.SymmetricTensor
  - java.lang.Throwable (implements java.io.Serializable)
    - java.lang.Exception
      - de.jstacs.classifier.ClassDimensionException
      - de.jstacs.algorithms.optimization.DimensionException
      - de.jstacs.data.alphabets.DoubleSymbolException
      - de.jstacs.data.EmptySampleException
      - de.jstacs.algorithms.optimization.EvaluationException
      - de.jstacs.results.MeanResultSet.AdditionImpossibleException
      - de.jstacs.results.MeanResultSet.InconsistentResultNumberException
      - de.jstacs.NonParsableException
      - de.jstacs.NotTrainedException
      - de.jstacs.parameters.ParameterException
        - de.jstacs.parameters.CollectionParameter.InconsistentCollectionException
        - de.jstacs.io.ParameterSetParser.NotInstantiableException
        - de.jstacs.io.ParameterSetParser.WrongParameterTypeException
        - de.jstacs.parameters.SimpleParameter.DatatypeNotValidException
        - de.jstacs.parameters.SimpleParameter.IllegalValueException
      - de.jstacs.algorithms.optimization.TerminationException
      - de.jstacs.WrongAlphabetException
      - de.jstacs.data.WrongLengthException
      - de.jstacs.data.sequences.WrongSequenceTypeException
  - de.jstacs.utils.Time
    - de.jstacs.utils.RealTime
    - de.jstacs.utils.UserTime
  - de.jstacs.algorithms.graphs.TopSort
  - de.jstacs.models.discrete.inhomogeneous.TwoPointEvaluater
  - de.jstacs.algorithms.graphs.UnionFind
  - de.jstacs.io.XMLParser

## Interface Hierarchy

- de.jstacs.algorithms.Alignment.Costs
- java.lang.Cloneable
  - de.jstacs.parameters.validation.Constraint (also extends de.jstacs.Storable)
  - de.jstacs.motifDiscovery.history.History
  - 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.parameters.validation.ParameterValidator (also extends de.jstacs.Storable)
  - de.jstacs.scoringFunctions.ScoringFunction (also extends de.jstacs.Storable)
    - de.jstacs.scoringFunctions.NormalizableScoringFunction
- de.jstacs.algorithms.optimization.Function
- de.jstacs.models.mixture.gibbssampling.GibbsSamplingComponent
- de.jstacs.InstantiableFromParameterSet
- de.jstacs.motifDiscovery.Mutable
- de.jstacs.utils.ProgressUpdater
- de.jstacs.parameters.Rangeable
- de.jstacs.parameters.RangeIterator
- de.jstacs.algorithms.optimization.StartDistanceForecaster
- de.jstacs.Storable
  - de.jstacs.parameters.validation.Constraint (also extends java.lang.Cloneable)
  - de.jstacs.models.Model (also extends java.lang.Cloneable)
  - de.jstacs.motifDiscovery.MotifDiscoverer (also extends java.lang.Cloneable)
    - de.jstacs.motifDiscovery.MutableMotifDiscoverer
  - de.jstacs.motifDiscovery.MutableMotifDiscoverer
  - de.jstacs.scoringFunctions.NormalizableScoringFunction
  - de.jstacs.parameters.validation.ParameterValidator (also extends java.lang.Cloneable)
  - de.jstacs.scoringFunctions.ScoringFunction (also extends java.lang.Cloneable)
    - de.jstacs.scoringFunctions.NormalizableScoringFunction

## Enum Hierarchy

- java.lang.Object
  - java.lang.Enum<E> (implements java.lang.Comparable<T>, java.io.Serializable)
    - de.jstacs.DataType
    - de.jstacs.algorithms.Alignment.Costs.Direction
    - de.jstacs.algorithms.optimization.Optimizer.TerminationCondition
    - de.jstacs.classifier.MeasureParameters.Measure
    - de.jstacs.classifier.scoringFunctionBased.OptimizableFunction.KindOfParameter
    - de.jstacs.data.Sample.PartitionMethod
    - de.jstacs.data.Sample.WeightedSampleFactory.SortOperation
    - de.jstacs.data.AlphabetContainer.AlphabetContainerType
    - de.jstacs.data.sequences.annotation.StrandedLocatedSequenceAnnotationWithLength.Strand
    - de.jstacs.data.sequences.annotation.SinglePositionSequenceAnnotation.Type
    - de.jstacs.io.SubstringFilenameFilter.PartOfName
    - de.jstacs.models.discrete.inhomogeneous.StructureLearner.LearningType
    - de.jstacs.models.discrete.inhomogeneous.StructureLearner.ModelType
    - de.jstacs.models.mixture.AbstractMixtureModel.Parameterization
    - de.jstacs.models.mixture.AbstractMixtureModel.Algorithm
    - de.jstacs.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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