SeqAlphabets.hpp File Reference

#include <array>
#include <functional>

Go to the source code of this file.

Classes
struct	Sequence::ambiguousNucleotide
	Tests if a character is in the set A,G,C,T. More...
struct	Sequence::invalidPolyChar
	This functor can be used to determine if a range contains characters that the SNP analysis routines in this library cannot handle gracefully. More...

Namespaces
	Sequence
	The namespace in which this library resides.

Typedefs
using	Sequence::alphabet_t = std::array< const char, 16 >
	Container type for nucleotide alphabets.

Functions
bool	Sequence::isDNA (const char &ch)
	test if character is part of Sequence::dna_alphabet More...

Variables
const alphabet_t	Sequence::dna_alphabet
	Alphabet for DNA sequences Valid DNA characters. Upper-case only. Only - is accepted as gap characters. More...
const alphabet_t	Sequence::dna_poly_alphabet
	Alphabet for polymorphism (SNP) analysis. 16 characters are used so that we may encode 2 nucleotides in a 8-bit integer. More...
const alphabet_t::size_type	Sequence::NOTPOLYCHAR = dna_poly_alphabet.size()
	An index from dna_poly_alphabet >= this is not a valid character for variation analysis.
const alphabet_t::size_type	Sequence::POLYEOS
	The value of terminating an encoded string of SNP data. More...