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