Alphabets defined in libsequence

Various character sets for different types of analysis. More...

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...

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...

Detailed Description

Various character sets for different types of analysis.

Function Documentation

isDNA()

bool Sequence::isDNA

(

const char &

ch

)

test if character is part of Sequence::dna_alphabet

Parameters

ch	Character to test

Returns

true if ch is in Sequence::dna_alphabet, false otherwise

Note

case-insensitive via std::toupper

Definition at line 25 of file SeqAlphabets.cc.

Variable Documentation

dna_alphabet

const alphabet_t Sequence::dna_alphabet

Initial value:

{ {'A','C','G','T',
        'R','Y','S','W',
        'K','M','B','D',
        'H','V','N','-'} }

Alphabet for DNA sequences Valid DNA characters. Upper-case only. Only - is accepted as gap characters.

Note

http://www.bioinformatics.org/sms/iupac.html, excluding U, and ., which is redundant with -

Definition at line 8 of file SeqAlphabets.cc.

dna_poly_alphabet

const alphabet_t Sequence::dna_poly_alphabet

Initial value:

{ {'A','C','G','T', 
        '0','1','-','N', 
        '\0', 
        } }

Alphabet for polymorphism (SNP) analysis. 16 characters are used so that we may encode 2 nucleotides in a 8-bit integer.

Definition at line 13 of file SeqAlphabets.cc.

POLYEOS

const alphabet_t::size_type Sequence::POLYEOS

Initial value:

= alphabet_t::size_type( std::distance(dna_poly_alphabet.begin(),
                                                                             std::find(dna_poly_alphabet.begin(),
                                                                                       dna_poly_alphabet.end(),
                                                                                       '\0')
                                                                             ) )

The value of terminating an encoded string of SNP data.

Definition at line 20 of file SeqAlphabets.cc.