MutationDefinition-class - S4 class defining replacement and silent mutation definitions
MutationDefinition defines a common data structure for defining the whether
a mutation is annotated as a replacement or silent mutation.
- name of the MutationDefinition.
- description of the model and its source.
- named character vectors with single-letter amino acid codes as names
and amino acid classes as values, with
NAassigned to set of characters
c("X", "*", "-", "."). Replacement (R) is be defined as a change in amino acid class and silent (S) as no change in class.
- matrix of codons (columns) and substitutions (rows).
- publication source.
See MUTATION_SCHEMES for a set of predefined