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Package Alignments |
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Class Alignments.Alignment.UniqueSite extends Site implements Serializable |
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Serialized Fields |
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int c
Class Alignments.AlignmentException extends GeneralException implements Serializable |
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Class Alignments.Ambiguous extends java.lang.Object implements Serializable |
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serialVersionUID: 1L
Serialized Fields |
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java.util.Map<K,V> ambig
Class Alignments.Site extends java.lang.Object implements Serializable |
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serialVersionUID: 2L
Serialized Fields |
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java.util.LinkedHashMap<K,V> sites
Ambiguous ambig
java.lang.String siteClass
Package Ancestors |
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Class Ancestors.AncestralException extends GeneralException implements Serializable |
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Package Exceptions |
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Class Exceptions.GeneralException extends java.lang.Exception implements Serializable |
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Class Exceptions.InputException extends GeneralException implements Serializable |
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Class Exceptions.OutputException extends GeneralException implements Serializable |
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Class Exceptions.UnexpectedError extends java.lang.Error implements Serializable |
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Package Likelihood |
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Class Likelihood.Likelihood extends java.lang.Object implements Serializable |
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serialVersionUID: 1L
Serialized Fields |
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double l
ArrayMap<K,V> siteLikelihoods
ArrayMap<K,V> missingLikelihoods
Parameters p
Class Likelihood.Likelihood.LikelihoodException extends GeneralException implements Serializable |
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Class Likelihood.Likelihood.NodeLikelihood extends java.lang.Object implements Serializable |
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Serialized Fields |
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ArrayMap<K,V> states
double[] likelihoods
Class Likelihood.Likelihood.RateLikelihood extends java.lang.Object implements Serializable |
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serialVersionUID: 1L
Serialized Fields |
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double l
ArrayMap<K,V> nodeLikelihoods
Class Likelihood.Likelihood.SiteLikelihood extends java.lang.Object implements Serializable |
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serialVersionUID: 1L
Serialized Fields |
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ArrayMap<K,V> rateLikelihoods
double l
java.util.Map<K,V> rateProbability
RateCategory maxCat
Package Maths |
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Class Maths.EigenvalueDecomposition extends java.lang.Object implements Serializable |
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serialVersionUID: 1L
Serialized Fields |
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int n
boolean issymmetric
double[] d
double[] e
double[][] V
double[][] H
double[] ort
Class Maths.EigenvalueDecomposition.ConvergenceException extends java.lang.Exception implements Serializable |
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Class Maths.LUDecomposition extends java.lang.Object implements Serializable |
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serialVersionUID: 1L
Serialized Fields |
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double[][] LU
int m
int n
int pivsign
int[] piv
Class Maths.NoSuchFunction extends java.lang.Exception implements Serializable |
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Class Maths.NoSuchVariable extends java.lang.Exception implements Serializable |
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Class Maths.SquareMatrix extends java.lang.Object implements Serializable |
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serialVersionUID: 1L
Serialized Fields |
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double[][] m
int dim
SquareMatrix p
SquareMatrix pi
SquareMatrix d
EigenvalueDecomposition ed
LUDecomposition lu
double[][][] powers
int pdiv
Class Maths.SquareMatrix.SquareMatrixException extends java.lang.Exception implements Serializable |
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Class Maths.WrongNumberOfVariables extends java.lang.Exception implements Serializable |
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Package Models |
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Class Models.Distributions.DistributionsException extends java.lang.Exception implements Serializable |
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Class Models.Model.ModelException extends GeneralException implements Serializable |
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Class Models.RateCategory extends java.lang.Object implements Serializable |
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serialVersionUID: 1L
Serialized Fields |
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SquareMatrix sm
java.util.Map<K,V> cache
java.util.TreeSet<E> neededParams
SquareMatrix m
double[] f
CompiledFunction[] freq
CompiledFunction[][] rates
ArrayMap<K,V> map
RateCategory.FrequencyType freqType
java.lang.String name
Class Models.RateCategory.RateException extends GeneralException implements Serializable |
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Package Optimizers |
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Class Optimizers.Optimizer.OptimizerException extends GeneralException implements Serializable |
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Package Parameters |
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Class Parameters.Parameter extends java.lang.Object implements Serializable |
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serialVersionUID: 1L
Serialized Fields |
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java.lang.String name
double value
boolean estimate
double lbound
double ubound
boolean matrix
Class Parameters.Parameter.FormatException extends java.lang.Exception implements Serializable |
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Class Parameters.Parameters extends java.lang.Object implements Serializable |
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serialVersionUID: 1L
Serialized Fields |
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java.util.ArrayList<E> params
boolean recalc
Class Parameters.Parameters.ParameterException extends GeneralException implements Serializable |
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Package Simulations |
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Class Simulations.Simulate.SimulationException extends GeneralException implements Serializable |
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Package Trees |
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Class Trees.TreeException extends GeneralException implements Serializable |
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Package Utils |
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Class Utils.SettingException extends java.lang.Exception implements Serializable |
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Class Utils.SetUtils.SetHasMultipleElementsException extends java.lang.Throwable implements Serializable |
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Class Utils.ToDoubleHashMap extends java.util.HashMap<K,java.lang.Double> implements Serializable |
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