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Hierarchy For All Packages
Package Hierarchies:
Alignments
,
Ancestors
,
Constraints
,
Exceptions
,
Executable
,
Likelihood
,
Maths
,
Models
,
Optimizers
,
Parameters
,
Simulations
,
Trees
,
Utils
Class Hierarchy
java.lang.Object
java.util.AbstractMap<K,V> (implements java.util.Map<K,V>)
java.util.HashMap<K,V> (implements java.lang.Cloneable, java.util.Map<K,V>, java.io.Serializable)
Utils.
ToDoubleHashMap
<K>
Alignments.
Alignment
(implements java.lang.Iterable<T>)
Alignments.
DuplicationAlignment
Alignments.
FastaAlignment
Alignments.
PhylipAlignment
Alignments.
SequenceAlignment
Alignments.
Ambiguous
(implements java.io.Serializable)
Ancestors.
AncestralJoint
Ancestors.
AncestralJointBB
Ancestors.
AncestralJointDP
Ancestors.
AncestralMarginal
Ancestors.
AncestralMarginal.Result
Ancestors.
AncestralMarginal.SiteResult
Utils.
Array1D
Utils.
Array2D
Utils.
ArrayMap
<K,V>
Trees.
Branch
Likelihood.
Calculator
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
Utils.
DaemonThreadFactory
(implements java.util.concurrent.ThreadFactory)
Models.
Distributions
Models.
DNAModelFactory
Models.
DuplicationModelFactory
Maths.
EigenvalueDecomposition
(implements java.io.Serializable)
Executable.
Example
Maths.
Gamma
Executable.
GeLL
Optimizers.
GoldenSection
(implements Optimizers.
Optimizer
)
Simulations.
HypothesisTest
Likelihood.
Likelihood
(implements java.io.Serializable)
Likelihood.
Likelihood.NodeLikelihood
(implements java.io.Serializable)
Likelihood.
Likelihood.RateLikelihood
(implements java.io.Serializable)
Likelihood.
Likelihood.SiteLikelihood
(implements java.io.Serializable)
Maths.
LUDecomposition
(implements java.io.Serializable)
Utils.
MapUtils
Maths.
MathsParse
Models.
Model
(implements java.lang.Iterable<T>)
Optimizers.
NelderMead
(implements Optimizers.
Optimizer
)
Constraints.
NoConstraints
(implements Constraints.
Constrainer
)
Parameters.
Parameter
(implements java.io.Serializable)
Parameters.
Parameters
(implements java.lang.Iterable<T>, java.io.Serializable)
Utils.
PossibleSettings
Likelihood.
Probabilities
Likelihood.
Probabilities.RateProbabilities
Utils.
Range
Models.
RateCategory
(implements java.io.Serializable)
Utils.
SetSettings
Utils.
Settings
Utils.
SetUtils
Simulations.
Simulate
Alignments.
Site
(implements java.io.Serializable)
Alignments.
Alignment.UniqueSite
Constraints.
SiteConstraints
Maths.
SquareMatrix
(implements java.io.Serializable)
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
Exceptions.
InputException
Likelihood.
Likelihood.LikelihoodException
Models.
Model.ModelException
Optimizers.
Optimizer.OptimizerException
Exceptions.
OutputException
Parameters.
Parameters.ParameterException
Models.
RateCategory.RateException
Simulations.
Simulate.SimulationException
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
Maths.
CompiledFunction
Constraints.
Constrainer
Maths.
FunctionParser
Optimizers.
Optimizer
Enum Hierarchy
java.lang.Object
java.lang.Enum<E> (implements java.lang.Comparable<T>, java.io.Serializable)
Exceptions.
GeneralException.Debug
Maths.
SquareMatrix.Calculation
Models.
Distributions.Calculation
Models.
RateCategory.FrequencyType
Optimizers.
GoldenSection.ProgressLevel
Optimizers.
NelderMead.DebugLevel
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