Uses of Package
Exceptions

Packages that use Exceptions
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. 
 

Classes in Exceptions used by Alignments
GeneralException
          Custom exception class that provides different levels of information in a call to toString() based on a debug level.
InputException
          General excpetion for an exeption in or about an input file
OutputException
          Exception for problems writing an output file
 

Classes in Exceptions used by Ancestors
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
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
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
GeneralException
          Custom exception class that provides different levels of information in a call to toString() based on a debug level.
InputException
          General excpetion for an exeption in or about an input file
 

Classes in Exceptions used by Optimizers
GeneralException
          Custom exception class that provides different levels of information in a call to toString() based on a debug level.
InputException
          General excpetion for an exeption in or about an input file
OutputException
          Exception for problems writing an output file
 

Classes in Exceptions used by Parameters
GeneralException
          Custom exception class that provides different levels of information in a call to toString() based on a debug level.
InputException
          General excpetion for an exeption in or about an input file
OutputException
          Exception for problems writing an output file
 

Classes in Exceptions used by Simulations
GeneralException
          Custom exception class that provides different levels of information in a call to toString() based on a debug level.
OutputException
          Exception for problems writing an output file
 

Classes in Exceptions used by Trees
GeneralException
          Custom exception class that provides different levels of information in a call to toString() based on a debug level.
InputException
          General excpetion for an exeption in or about an input file
OutputException
          Exception for problems writing an output file