seqan3::hamming_scoring_scheme Class Reference

A scoring scheme that assigns a score of 0 to matching letters and -1 to mismatching letters. More...

#include <seqan3/alignment/scoring/hamming_scoring_scheme.hpp>

Public Types
using	score_type = int32_t
	The underlying score type.

Public Member Functions
Constructors, destructor and assignment
	hamming_scoring_scheme () noexcept=default
	Defaulted.
	hamming_scoring_scheme (hamming_scoring_scheme const &)=default
	Defaulted.
	hamming_scoring_scheme (hamming_scoring_scheme &&) noexcept=default
	Defaulted.
hamming_scoring_scheme &	operator= (hamming_scoring_scheme const &)=default
	Defaulted.
hamming_scoring_scheme &	operator= (hamming_scoring_scheme &&) noexcept=default
	Defaulted.
	~hamming_scoring_scheme ()=default
Accessors
template<typename alph1_t , typename alph2_t > requires std::equality_comparable_with<alph1_t, alph2_t>
constexpr score_type	score (alph1_t const alph1, alph2_t const alph2) const noexcept
	Returns the score of two letters.
Comparison operators
constexpr bool	operator== (hamming_scoring_scheme const &) const noexcept
	Always true.
constexpr bool	operator!= (hamming_scoring_scheme const &) const noexcept
	Always false.

Detailed Description

A scoring scheme that assigns a score of 0 to matching letters and -1 to mismatching letters.

This stateless scoring scheme is equivalent to the Hamming distance and assigns a score of 0 to matching letters and -1 to mismatching letters. This scheme is independent of the alphabet type and can be used whenever the two compared alphabets model the std::equality_comparable_with concept. Use this scheme if you want to use the use the more efficient bitparallel alignment algorithm often used in the context of computing the edit distance. See the documentation for seqan3::align_cfg::edit_scheme for more details.

Constructor & Destructor Documentation

~hamming_scoring_scheme()

seqan3::hamming_scoring_scheme::~hamming_scoring_scheme ( )

default

Defaulted.

Member Function Documentation

score()

template<typename alph1_t , typename alph2_t >
requires std::equality_comparable_with<alph1_t, alph2_t>

constexpr score_type seqan3::hamming_scoring_scheme::score ( alph1_t const  alph1, alph2_t const  alph2  ) const

inlineconstexprnoexcept

Returns the score of two letters.

Template Parameters

alph1_t	The type of the first letter.
alph2_t	The type of the second letter.

Parameters

[in]	alph1	The first letter to compare.
[in]	alph2	The second letter to compare.

This function returns 0 if the two letters are equal and -1 otherwise. Note that both alphabet types of the compared letters must model the std::equality_comparable_with concept or no overload of this function is available.

Returns

The score of the two letters. 0 if the letters are equal, -1 otherwise.

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The documentation for this class was generated from the following file:

• hamming_scoring_scheme.hpp