Uses of Package
Exceptions

Packages that use Exceptions

Package	Description
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.
ModelTest
Models	Provides classes for defining 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 simulated data.
Trees	Provides classes to define a tree.

Classes in Exceptions used by Alignments

Class and Description
GeneralException Custom exception class that provides different levels of information in a call to toString() based on a debug level.
InputException General exception for an exception in or about an input file
OutputException Exception for problems writing an output file

Classes in Exceptions used by Ancestors

Class and Description
GeneralException Custom exception class that provides different levels of information in a call to toString() based on a debug level.

Classes in Exceptions used by Exceptions

Class and Description
GeneralException Custom exception class that provides different levels of information in a call to toString() based on a debug level.
GeneralException.Debug Enumeration of the different debug levels

Classes in Exceptions used by Likelihood

Class and Description
GeneralException Custom exception class that provides different levels of information in a call to toString() based on a debug level.

Classes in Exceptions used by ModelTest

Class and Description
GeneralException Custom exception class that provides different levels of information in a call to toString() based on a debug level.

Classes in Exceptions used by Models

Class and Description
GeneralException Custom exception class that provides different levels of information in a call to toString() based on a debug level.
InputException General exception for an exception in or about an input file

Classes in Exceptions used by Optimizers

Class and Description
GeneralException Custom exception class that provides different levels of information in a call to toString() based on a debug level.

Classes in Exceptions used by Parameters

Class and Description
GeneralException Custom exception class that provides different levels of information in a call to toString() based on a debug level.
InputException General exception for an exception in or about an input file
OutputException Exception for problems writing an output file

Classes in Exceptions used by Simulations

Class and Description
GeneralException Custom exception class that provides different levels of information in a call to toString() based on a debug level.

Classes in Exceptions used by Trees

Class and Description
GeneralException Custom exception class that provides different levels of information in a call to toString() based on a debug level.
InputException General exception for an exception in or about an input file
OutputException Exception for problems writing an output file