Serialized Form (GeLL)

Package Alignments
- 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
```
    - id
```
java.lang.String id
```
- Class Alignments.UniqueSite extends Site implements Serializable
  - Serialized Fields
    - c
```
int c
```
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.Calculator.CalculatorException extends GeneralException implements Serializable
- Class Likelihood.SiteLikelihood extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - rateLikelihoods
```
java.util.Map<K,V> rateLikelihoods
```
    - l
```
Real l
```
    - rateProbability
```
java.util.Map<K,V> rateProbability
```
    - maxCat
```
RateCategory maxCat
```
- Class Likelihood.SiteLikelihood.LikelihoodException extends GeneralException implements Serializable
- Class Likelihood.SiteLikelihood.NodeLikelihood extends java.lang.Object implements Serializable
  - Serialized Fields
    - states
```
java.util.Map<K,V> states
```
    - likelihoods
```
Real[] likelihoods
```
- Class Likelihood.SiteLikelihood.RateLikelihood extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - l
```
Real l
```
    - nodeLikelihoods
```
java.util.Map<K,V> nodeLikelihoods
```
- Class Likelihood.StandardLikelihood extends Likelihood implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - siteLikelihoods
```
java.util.Map<K,V> siteLikelihoods
```
    - missingLikelihoods
```
java.util.Map<K,V> missingLikelihoods
```
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.SmallDouble extends java.lang.Object implements Serializable
  - Serialized Fields
    - m
```
double m
```
    - e
```
int e
```
- 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.StandardDouble extends java.lang.Object implements Serializable
  - Serialized Fields
    - d
```
double d
```
- 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
```
    - paramValues
```
java.util.TreeMap<K,V> paramValues
```
    - m
```
SquareMatrix m
```
    - f
```
double[] f
```
    - freq
```
CompiledFunction[] freq
```
    - rates
```
CompiledFunction[][] rates
```
    - map
```
java.util.Map<K,V> map
```
    - freqType
```
RateCategory.FrequencyType freqType
```
    - scale
```
double scale
```
    - 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
```
- 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
```
- 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

Serialized Form

Package Alignments

Class Alignments.AlignmentException extends GeneralException implements Serializable

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

Serialized Fields

ambig

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

Serialized Fields

sites

ambig

siteClass

id

Class Alignments.UniqueSite extends Site implements Serializable

Serialized Fields

c

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.Calculator.CalculatorException extends GeneralException implements Serializable

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

Serialized Fields

rateLikelihoods

l

rateProbability

maxCat

Class Likelihood.SiteLikelihood.LikelihoodException extends GeneralException implements Serializable

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

Serialized Fields

states

likelihoods

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

Serialized Fields

l

nodeLikelihoods

Class Likelihood.StandardLikelihood extends Likelihood implements Serializable

Serialized Fields

siteLikelihoods

missingLikelihoods

Package Maths

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

Serialized Fields

n

issymmetric

d

e

V

H

ort

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

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

Serialized Fields

LU

m

n

pivsign

piv

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

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

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

Serialized Fields

m

e

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

Serialized Fields

m

dim

p

pi

d

ed

lu

powers

pdiv

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

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