Gap

Provides the gap alphabet and functionality to make an alphabet a gapped alphabet. More...

Collaboration diagram for Gap:

Classes
class	bio::alphabet::gap
	The alphabet of a gap character '-'. More...

Typedefs
template<typename alphabet_t >
using	bio::alphabet::gapped = variant< alphabet_t, gap >
	Extends a given alphabet with a gap character.

Detailed Description

Provides the gap alphabet and functionality to make an alphabet a gapped alphabet.

Introduction

The gap symbol (-) is used in alignments to represent an interruption in an alignment, usually the result of an insertion or deletion. The bio::alphabet::gap alphabet represents this (single) gap symbol and satisfies the bio::alphabet::alphabet.

The main purpose of bio::alphabet::gap is to be combined with other alphabets. This can easily be achieved by using the bio::alphabet::gapped<> template which transforms any other alphabet to be a composite of that alphabet + the gap character.

Typedef Documentation

gapped

template<typename alphabet_t >

using bio::alphabet::gapped = typedef variant<alphabet_t, gap>

Extends a given alphabet with a gap character.

Template Parameters

alphabet_t

Type of the letter, e.g. dna4; must satisfy bio::alphabet::writable_alphabet.

The gapped alphabet represents the variant of a given alphabet and the bio::alphabet::gap alphabet (e.g. the four letter DNA alphabet + a gap character).

The gapped alphabet may be brace initialized from the static letter members of the underlying alphabet and the bio::alphabet::gap alphabet. Note that you cannot assign the alphabet by using letters of type char, but you instead have to use the function assign_char() of the underlying alphabet or bio::alphabet::gap::assign_char().

#include <bio/alphabet/gap/gapped.hpp>
#include <bio/alphabet/nucleotide/dna4.hpp>
 
int main()
{
    using namespace bio::alphabet::literals;
 
    bio::alphabet::gapped<bio::alphabet::dna4> gapped_letter{};
    bio::alphabet::gapped<bio::alphabet::dna4> converted_letter{'C'_dna4};
    bio::alphabet::gapped<bio::alphabet::dna4> gap_letter{bio::alphabet::gap{}};
 
    bio::alphabet::gapped<bio::alphabet::dna4>{}.assign_char('C');
    bio::alphabet::gapped<bio::alphabet::dna4>{}.assign_char('-'); // gap character
    bio::alphabet::gapped<bio::alphabet::dna4>{}.assign_char('K'); // unknown characters map to the default/unknown
                                                     // character of the given alphabet type (i.e. A of dna4)
}

See also

For more details see variant, which is the base class and more general than the gapped alphabet.