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Packages that use Exceptions | |
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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 | |
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GeneralException
Custom exception class that provides different levels of information in a call to toString() based on a debug level. |
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InputException
General excpetion for an exeption in or about an input file |
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OutputException
Exception for problems writing an output file |
Classes in Exceptions used by Ancestors | |
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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 | |
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GeneralException
Custom exception class that provides different levels of information in a call to toString() based on a debug level. |
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GeneralException.Debug
Enumeration of the different debug levels |
Classes in Exceptions used by Likelihood | |
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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 | |
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GeneralException
Custom exception class that provides different levels of information in a call to toString() based on a debug level. |
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InputException
General excpetion for an exeption in or about an input file |
Classes in Exceptions used by Optimizers | |
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GeneralException
Custom exception class that provides different levels of information in a call to toString() based on a debug level. |
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InputException
General excpetion for an exeption in or about an input file |
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OutputException
Exception for problems writing an output file |
Classes in Exceptions used by Parameters | |
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GeneralException
Custom exception class that provides different levels of information in a call to toString() based on a debug level. |
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InputException
General excpetion for an exeption in or about an input file |
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OutputException
Exception for problems writing an output file |
Classes in Exceptions used by Simulations | |
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GeneralException
Custom exception class that provides different levels of information in a call to toString() based on a debug level. |
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OutputException
Exception for problems writing an output file |
Classes in Exceptions used by Trees | |
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GeneralException
Custom exception class that provides different levels of information in a call to toString() based on a debug level. |
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InputException
General excpetion for an exeption in or about an input file |
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OutputException
Exception for problems writing an output file |
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