Serialized Form


Package Alignments

Class Alignments.Alignment.UniqueSite extends Site implements Serializable

Serialized Fields

c

int c

Class Alignments.AlignmentException extends GeneralException implements Serializable

Class Alignments.Ambiguous extends java.lang.Object implements Serializable

serialVersionUID: 1L

Serialized Fields

ambig

java.util.Map<K,V> ambig

Class Alignments.Site extends java.lang.Object implements Serializable

serialVersionUID: 2L

Serialized Fields

sites

java.util.LinkedHashMap<K,V> sites

ambig

Ambiguous ambig

siteClass

java.lang.String siteClass

Package Ancestors

Class Ancestors.AncestralException extends GeneralException implements Serializable


Package Exceptions

Class Exceptions.GeneralException extends java.lang.Exception implements Serializable

Class Exceptions.InputException extends GeneralException implements Serializable

Class Exceptions.OutputException extends GeneralException implements Serializable

Class Exceptions.UnexpectedError extends java.lang.Error implements Serializable


Package Likelihood

Class Likelihood.Likelihood extends java.lang.Object implements Serializable

serialVersionUID: 1L

Serialized Fields

l

double l

siteLikelihoods

ArrayMap<K,V> siteLikelihoods

missingLikelihoods

ArrayMap<K,V> missingLikelihoods

p

Parameters p

Class Likelihood.Likelihood.LikelihoodException extends GeneralException implements Serializable

Class Likelihood.Likelihood.NodeLikelihood extends java.lang.Object implements Serializable

Serialized Fields

states

ArrayMap<K,V> states

likelihoods

double[] likelihoods

Class Likelihood.Likelihood.RateLikelihood extends java.lang.Object implements Serializable

serialVersionUID: 1L

Serialized Fields

l

double l

nodeLikelihoods

ArrayMap<K,V> nodeLikelihoods

Class Likelihood.Likelihood.SiteLikelihood extends java.lang.Object implements Serializable

serialVersionUID: 1L

Serialized Fields

rateLikelihoods

ArrayMap<K,V> rateLikelihoods

l

double l

rateProbability

java.util.Map<K,V> rateProbability

maxCat

RateCategory maxCat

Package Maths

Class Maths.EigenvalueDecomposition extends java.lang.Object implements Serializable

serialVersionUID: 1L

Serialized Fields

n

int n
Row and column dimension (square matrix).

matrix dimension.

issymmetric

boolean issymmetric
Symmetry flag.

internal symmetry flag.

d

double[] d
Arrays for internal storage of eigenvalues.

internal storage of eigenvalues.

e

double[] e
Arrays for internal storage of eigenvalues.

internal storage of eigenvalues.

V

double[][] V
Array for internal storage of eigenvectors.

internal storage of eigenvectors.

H

double[][] H
Array for internal storage of nonsymmetric Hessenberg form.

internal storage of nonsymmetric Hessenberg form.

ort

double[] ort
Working storage for nonsymmetric algorithm.

working storage for nonsymmetric algorithm.

Class Maths.EigenvalueDecomposition.ConvergenceException extends java.lang.Exception implements Serializable

Class Maths.LUDecomposition extends java.lang.Object implements Serializable

serialVersionUID: 1L

Serialized Fields

LU

double[][] LU
Array for internal storage of decomposition.

internal array storage.

m

int m
Row and column dimensions, and pivot sign.

column dimension.

n

int n
Row and column dimensions, and pivot sign.

column dimension.

pivsign

int pivsign
Row and column dimensions, and pivot sign.

column dimension.

piv

int[] piv
Internal storage of pivot vector.

pivot vector.

Class Maths.NoSuchFunction extends java.lang.Exception implements Serializable

Class Maths.NoSuchVariable extends java.lang.Exception implements Serializable

Class Maths.SquareMatrix extends java.lang.Object implements Serializable

serialVersionUID: 1L

Serialized Fields

m

double[][] m

dim

int dim

p

SquareMatrix p

pi

SquareMatrix pi

d

SquareMatrix d

ed

EigenvalueDecomposition ed

lu

LUDecomposition lu

powers

double[][][] powers

pdiv

int pdiv

Class Maths.SquareMatrix.SquareMatrixException extends java.lang.Exception implements Serializable

Class Maths.WrongNumberOfVariables extends java.lang.Exception implements Serializable


Package Models

Class Models.Distributions.DistributionsException extends java.lang.Exception implements Serializable

Class Models.Model.ModelException extends GeneralException implements Serializable

Class Models.RateCategory extends java.lang.Object implements Serializable

serialVersionUID: 1L

Serialized Fields

sm

SquareMatrix sm

cache

java.util.Map<K,V> cache

neededParams

java.util.TreeSet<E> neededParams

m

SquareMatrix m

f

double[] f

freq

CompiledFunction[] freq

rates

CompiledFunction[][] rates

map

ArrayMap<K,V> map

freqType

RateCategory.FrequencyType freqType

name

java.lang.String name

Class Models.RateCategory.RateException extends GeneralException implements Serializable


Package Optimizers

Class Optimizers.Optimizer.OptimizerException extends GeneralException implements Serializable


Package Parameters

Class Parameters.Parameter extends java.lang.Object implements Serializable

serialVersionUID: 1L

Serialized Fields

name

java.lang.String name

value

double value

estimate

boolean estimate

lbound

double lbound

ubound

double ubound

matrix

boolean matrix

Class Parameters.Parameter.FormatException extends java.lang.Exception implements Serializable

Class Parameters.Parameters extends java.lang.Object implements Serializable

serialVersionUID: 1L

Serialized Fields

params

java.util.ArrayList<E> params

recalc

boolean recalc

Class Parameters.Parameters.ParameterException extends GeneralException implements Serializable


Package Simulations

Class Simulations.Simulate.SimulationException extends GeneralException implements Serializable


Package Trees

Class Trees.TreeException extends GeneralException implements Serializable


Package Utils

Class Utils.SettingException extends java.lang.Exception implements Serializable

Class Utils.SetUtils.SetHasMultipleElementsException extends java.lang.Throwable implements Serializable

Class Utils.ToDoubleHashMap extends java.util.HashMap<K,java.lang.Double> implements Serializable