This module defines concrete subclasses for the
abstract character matrix components
that all character matrices must implement. The subclasses
defined here apply to amino acid character data. In a verbose notation,
this data is represented as the "state" attribute which references an
explicitly defined state (either fundamental or ambiguous).
In a compact notation, the same data is represented as a sequence of
tokens (whitespace is allowed but has no meaning).
The AAToken simple type is a restriction of AbstractSymbol
that defines an IUPAC single character amino acid symbol.
A concrete implementation of the AbstractChar element.
The AAFormat class is the container of amino acid column definitions.
A container for a set of states.
The AAPolymorphicStateSet defines a polymorphic ambiguity mapping.
The AAUncertainStateSet defines an uncertain ambiguity mapping.
An IUPAC ambiguity mapping.
This is a concrete implementation of the state element, which requires
a symbol element, in this case restricted to AAToken, i.e. a single IUPAC amino acid
symbol, and optional mapping elements to refer to other states.
This is a single cell in a matrix containing
an amino acid observation.
This is a simple type that specifies a sequence of amino acid characters,
following IUPAC single character symbols for aa (and ambiguities).
This is a row in a matrix of amino acid data containing raw sequence data.
This is a row in a matrix of amino acid data containing granular observations.
A matrix of rows with amino acid data as sequence strings.
A matrix of rows with single character observations.
An amino acid characters block consisting of sequences preceded by metadata.
An amino acid characters block consisting of granular cells preceded by metadata.