Hierarchy For All Packages

Package Hierarchies:

• Alignments,
• Ancestors,
• Exceptions,
• Executable,
• Likelihood,
• Maths,
• Models,
• ModelTest,
• Optimizers,
• Parameters,
• Simulations,
• Trees,
• Utils

Class Hierarchy

• java.lang.Object
  • ModelTest.AIC
  • Alignments.Alignment (implements java.lang.Iterable<T>)
  • Alignments.Ambiguous (implements java.io.Serializable)
  • Ancestors.AncestralJoint
    • Ancestors.AncestralJointBB
    • Ancestors.AncestralJointDP
  • Ancestors.AncestralMarginal
  • Ancestors.AncestralMarginal.Result
  • Ancestors.AncestralMarginal.SiteResult
  • Utils.Array1D
  • Utils.Array2D
  • Ancestors.Assignment
  • ModelTest.BIC
  • Trees.Branch
  • Likelihood.Calculator<R> (implements Optimizers.Optimizable<R>)
    • Likelihood.StandardCalculator
  • Likelihood.Calculator.SiteCalculator (implements java.util.concurrent.Callable<V>)
  • Utils.CommentedFileReader
  • Maths.CompiledFunction.Add (implements Maths.CompiledFunction)
  • Maths.CompiledFunction.Constant (implements Maths.CompiledFunction)
  • Maths.CompiledFunction.Divide (implements Maths.CompiledFunction)
  • Maths.CompiledFunction.Function (implements Maths.CompiledFunction)
  • Maths.CompiledFunction.Multiply (implements Maths.CompiledFunction)
  • Maths.CompiledFunction.Power (implements Maths.CompiledFunction)
  • Maths.CompiledFunction.Subtract (implements Maths.CompiledFunction)
  • Maths.CompiledFunction.Variable (implements Maths.CompiledFunction)
  • Likelihood.ConfidenceInterval
  • Optimizers.ConjugateGradient (implements Optimizers.Optimizer)
  • Utils.DaemonThreadFactory (implements java.util.concurrent.ThreadFactory)
  • Models.Distributions
  • Models.DNAModelFactory
  • Alignments.DuplicationAlignment
  • Models.DuplicationModelFactory
  • Maths.EigenvalueDecomposition (implements java.io.Serializable)
  • ModelTest.EmpiricalAdapter (implements ModelTest.Adapter)
  • ModelTest.EqualAdapter (implements ModelTest.Adapter)
  • Alignments.FastaAlignment
  • Likelihood.FitzJohnRoot (implements Likelihood.Root)
  • Maths.Gamma
  • Executable.GeLL
  • Alignments.GenericAlignment
  • Optimizers.GoldenSection (implements Optimizers.Optimizer)
  • ModelTest.HypothesisTest
  • ModelTest.IdentityAdapter (implements ModelTest.Adapter)
  • Likelihood.Likelihood
    • Likelihood.StandardLikelihood (implements java.io.Serializable)
  • Maths.LUDecomposition (implements java.io.Serializable)
  • Maths.MathsParse
  • Models.Model (implements java.lang.Iterable<T>)
  • Optimizers.NelderMead (implements Optimizers.Optimizer)
  • Parameters.Parameter (implements java.io.Serializable)
  • Parameters.Parameters (implements java.lang.Iterable<T>, java.io.Serializable)
  • Alignments.PhylipAlignment
  • Utils.PossibleSettings
  • Likelihood.Probabilities
  • Likelihood.Probabilities.RateProbabilities
  • Utils.Range
  • Models.RateCategory (implements java.io.Serializable)
  • Maths.RealFactory
  • Models.RYModelFactory
  • Utils.SetSettings
  • Utils.Settings
  • Utils.SetUtils
  • Simulations.Simulate
  • Alignments.Site (implements java.io.Serializable)
    • Alignments.UniqueSite
  • Likelihood.SiteLikelihood (implements java.io.Serializable)
  • Likelihood.SiteLikelihood.NodeLikelihood (implements java.io.Serializable)
  • Likelihood.SiteLikelihood.RateLikelihood (implements java.io.Serializable)
  • Maths.SmallDouble (implements Maths.Real, java.io.Serializable)
  • Trees.Split
  • Maths.SquareMatrix (implements java.io.Serializable)
  • Maths.StandardDouble (implements Maths.Real, java.io.Serializable)
  • Likelihood.StandardRoot (implements Likelihood.Root)
  • ModelTest.TestInstance
  • java.lang.Throwable (implements java.io.Serializable)
    • java.lang.Error
      • Exceptions.UnexpectedError
    • java.lang.Exception
      • Models.Distributions.DistributionsException
      • Maths.EigenvalueDecomposition.ConvergenceException
      • Exceptions.GeneralException
        • Alignments.AlignmentException
        • Ancestors.AncestralException
        • Likelihood.Calculator.CalculatorException
        • Exceptions.InputException
        • Models.Model.ModelException
        • Optimizers.Optimizer.OptimizerException
        • Exceptions.OutputException
        • Parameters.Parameters.ParameterException
        • Models.RateCategory.RateException
        • Simulations.Simulate.SimulationException
        • Likelihood.SiteLikelihood.LikelihoodException
        • Trees.TreeException
      • Maths.NoSuchFunction
      • Maths.NoSuchVariable
      • Parameters.Parameter.FormatException
      • Utils.SettingException
      • Maths.SquareMatrix.SquareMatrixException
      • Maths.WrongNumberOfVariables
    • Utils.SetUtils.SetHasMultipleElementsException
  • Utils.TimePassed
  • Trees.Tree (implements java.lang.Iterable<T>)
  • Trees.TreeFigure

Interface Hierarchy

• ModelTest.Adapter
• Maths.CompiledFunction
• Maths.FunctionParser
• Optimizers.Optimizable<R>
• Optimizers.Optimizer
• Maths.Real
• Likelihood.Root

Enum Hierarchy

• java.lang.Object
  • java.lang.Enum<E> (implements java.lang.Comparable<T>, java.io.Serializable)
    • Exceptions.GeneralException.Debug
    • Maths.RealFactory.RealType
    • Maths.SquareMatrix.Calculation
    • Models.DNAModelFactory.DNAModel
    • Models.Distributions.Calculation
    • Models.RateCategory.FrequencyType
    • Optimizers.ConjugateGradient.Update
    • Optimizers.ConjugateGradient.ProgressLevel
    • Optimizers.GoldenSection.ProgressLevel
    • Optimizers.NelderMead.DebugLevel