Uses of Class
Exceptions.GeneralException

Packages that use GeneralException
Alignments Provides class for dealing with "alignments" and the sites in an alignment. 
Ancestors Provides classed to calculate ancestral reconstruction. 
Exceptions Provides exceptions that are common across the package. 
Likelihood Provides classes for calculating the likelihood of a tree given a model and an alignment. 
Models Provides classes for defing a phylogenetic model. 
Optimizers Provides classes for optimising a likelihood. 
Parameters Provides classes for defining parameters used in the various calculations. 
Simulations Provides a class to create simulate data. 
Trees Provides classes to define a tree and any constraints on that tree. 
 

Uses of GeneralException in Alignments
 

Subclasses of GeneralException in Alignments
 class AlignmentException
          Exception related to an alignment (currently only input errors)
 

Uses of GeneralException in Ancestors
 

Subclasses of GeneralException in Ancestors
 class AncestralException
          Exception related to ancestral reconstruction
 

Uses of GeneralException in Exceptions
 

Subclasses of GeneralException in Exceptions
 class InputException
          General excpetion for an exeption in or about an input file
 class OutputException
          Exception for problems writing an output file
 

Uses of GeneralException in Likelihood
 

Subclasses of GeneralException in Likelihood
static class Likelihood.LikelihoodException
          Exception related to a likelihood calculation
 

Uses of GeneralException in Models
 

Subclasses of GeneralException in Models
 class Model.ModelException
          Exception thrown when there is a problem with the model
 class RateCategory.RateException
          Exception thrown if there is a problem within a RateClass
 

Uses of GeneralException in Optimizers
 

Subclasses of GeneralException in Optimizers
static class Optimizer.OptimizerException
          Exception for when there is a problem with an optimiser.
 

Uses of GeneralException in Parameters
 

Subclasses of GeneralException in Parameters
 class Parameters.ParameterException
          Exception related to the parameters
 

Uses of GeneralException in Simulations
 

Subclasses of GeneralException in Simulations
 class Simulate.SimulationException
          Exception for when there is a problem with the simulation
 

Uses of GeneralException in Trees
 

Subclasses of GeneralException in Trees
 class TreeException
          Exception thrown when there is a problem with a tree