A CRTP base class for scoring schemes. More...

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

Inheritance diagram for seqan3::scoring_scheme_base< derived_t, alphabet_t, score_t >:

Public Types
Member types
using	score_type = score_t
	Type of the score values.

using	alphabet_type = alphabet_t
	Type of the underlying alphabet.

using	matrix_size_type = std::remove_const_t< decltype(alphabet_size< alphabet_t >)>
	Size type that can hold the dimension of the matrix (i.e. size of the alphabet).

using	matrix_type = std::array< std::array< score_type, matrix_size >, matrix_size >
	Type of the internal matrix (a two-dimensional array).

Public Member Functions
Constructors, destructor and assignment
constexpr	scoring_scheme_base (scoring_scheme_base const &) noexcept=default
	Defaulted.

constexpr	scoring_scheme_base (scoring_scheme_base &&) noexcept=default
	Defaulted.

constexpr scoring_scheme_base &	operator= (scoring_scheme_base const &) noexcept=default
	Defaulted.

constexpr scoring_scheme_base &	operator= (scoring_scheme_base &&) noexcept=default
	Defaulted.

	~scoring_scheme_base () noexcept=default
	Defaulted.

constexpr	scoring_scheme_base () noexcept
	The default constructor (delegates to set_hamming_distance()).

template<arithmetic score_arg_t>
constexpr	scoring_scheme_base (match_score< score_arg_t > const ms, mismatch_score< score_arg_t > const mms)
	Constructor for the simple scheme (delegates to set_simple_scheme()). More...

constexpr	scoring_scheme_base (matrix_type const &matrix) noexcept
	Constructor for a custom scheme (delegates to set_custom_matrix()). More...

Scheme selection
constexpr void	set_hamming_distance () noexcept
	Set the hamming scheme, a variant of the simple scheme where match is scored `0` and mismatch `-1`.

template<arithmetic score_arg_t>
constexpr void	set_simple_scheme (match_score< score_arg_t > const ms, mismatch_score< score_arg_t > const mms)
	Set the simple scheme (everything is either match or mismatch). More...

constexpr void	set_custom_matrix (matrix_type const &matrix) noexcept
	Set a custom scheme by passing a full matrix with arbitrary content. More...

Accessors
template<typename alph1_t , typename alph2_t >
constexpr score_t &	score (alph1_t const alph1, alph2_t const alph2) noexcept
	Score two letters (either two nucleotids or two amino acids). More...

template<typename alph1_t , typename alph2_t >
constexpr score_t	score (alph1_t const alph1, alph2_t const alph2) const noexcept
	Score two letters (either two nucleotids or two amino acids). More...

Comparison operators
constexpr bool	operator== (derived_t const &rhs) const noexcept
	Checks whether `*this` is equal to `rhs`.

constexpr bool	operator!= (derived_t const &rhs) const noexcept
	Checks whether `*this` is not equal to `rhs`.

Static Public Attributes
static constexpr matrix_size_type	matrix_size = alphabet_size<alphabet_t>
	Size of the matrix dimensions (i.e. size of the alphabet).

Detailed Description

template<typename derived_t, alphabet alphabet_t, arithmetic score_t>
class seqan3::scoring_scheme_base< derived_t, alphabet_t, score_t >

A CRTP base class for scoring schemes.

Template Parameters

derived_t	The derived type.
alphabet_t	Type of the largest target alphabet.
score_type	Type of the score values in the internal matrix.

This type is never used directly, instead use seqan3::nucleotide_scoring_scheme or seqan3::aminoacid_scoring_scheme.

This class is only implementation detail and not required for most users. Types that model seqan3::scoring_scheme can (but don't need to!) inherit from it.

Constructor & Destructor Documentation

◆ scoring_scheme_base() [1/2]

template<typename derived_t , alphabet alphabet_t, arithmetic score_t>

template<arithmetic score_arg_t>

constexpr seqan3::scoring_scheme_base< derived_t, alphabet_t, score_t >::scoring_scheme_base	(	match_score< score_arg_t > const	ms,
		mismatch_score< score_arg_t > const	mms
	)

inlineconstexpr

Constructor for the simple scheme (delegates to set_simple_scheme()).

Template Parameters

score_arg_t The underlying type of the arguments.

Parameters

[in]	ms	Matches shall be given this value (of type seqan3::match_score).
[in]	mms	Mismatches shall be given this value (of type seqan3::mismatch_score).

Exceptions

std::invalid_argument Thrown if you pass a value that is to large/low to be represented by score_t.

◆ scoring_scheme_base() [2/2]

template<typename derived_t , alphabet alphabet_t, arithmetic score_t>

constexpr seqan3::scoring_scheme_base< derived_t, alphabet_t, score_t >::scoring_scheme_base ( matrix_type const & matrix )

inlineconstexprnoexcept

Constructor for a custom scheme (delegates to set_custom_matrix()).

Parameters

[in] matrix A full matrix that is copied into the scheme.

Member Function Documentation

◆ score() [1/2]

template<typename derived_t , alphabet alphabet_t, arithmetic score_t>

template<typename alph1_t , typename alph2_t >

constexpr score_t seqan3::scoring_scheme_base< derived_t, alphabet_t, score_t >::score	(	alph1_t const	alph1,
		alph2_t const	alph2
	)		const

inlineconstexprnoexcept

Score two letters (either two nucleotids or two amino acids).

Template Parameters

alph1_t	Type of the first letter.
alph2_t	Type of the second letter (needn't be the same as alph1_t).

Parameters

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

Returns: The score of the two letters in the current scheme.

◆ score() [2/2]

template<typename derived_t , alphabet alphabet_t, arithmetic score_t>

template<typename alph1_t , typename alph2_t >

constexpr score_t& seqan3::scoring_scheme_base< derived_t, alphabet_t, score_t >::score	(	alph1_t const	alph1,
		alph2_t const	alph2
	)

inlineconstexprnoexcept

Score two letters (either two nucleotids or two amino acids).

Template Parameters

alph1_t	Type of the first letter.
alph2_t	Type of the second letter (needn't be the same as alph1_t).

Parameters

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

Returns: The score of the two letters in the current scheme.

◆ set_custom_matrix()

template<typename derived_t , alphabet alphabet_t, arithmetic score_t>

constexpr void seqan3::scoring_scheme_base< derived_t, alphabet_t, score_t >::set_custom_matrix ( matrix_type const & matrix )

inlineconstexprnoexcept

Set a custom scheme by passing a full matrix with arbitrary content.

Parameters

[in] matrix A full matrix that is copied into the scheme.

◆ set_simple_scheme()

template<typename derived_t , alphabet alphabet_t, arithmetic score_t>

template<arithmetic score_arg_t>

constexpr void seqan3::scoring_scheme_base< derived_t, alphabet_t, score_t >::set_simple_scheme	(	match_score< score_arg_t > const	ms,
		mismatch_score< score_arg_t > const	mms
	)

inlineconstexpr

Set the simple scheme (everything is either match or mismatch).

Template Parameters

score_arg_t The underlying type of the arguments.

Parameters

[in]	ms	Matches shall be given this value (of type seqan3::match_score).
[in]	mms	Mismatches shall be given this value (of type seqan3::mismatch_score).

Exceptions

std::invalid_argument Thrown if you pass a value that is to large/low to be represented by score_t.

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

seqan3/alignment/scoring/scoring_scheme_base.hpp

Public Types

Public Member Functions

Static Public Attributes

Detailed Description

template<typename derived_t, alphabet alphabet_t, arithmetic score_t> class seqan3::scoring_scheme_base< derived_t, alphabet_t, score_t >

Constructor & Destructor Documentation

◆ scoring_scheme_base() [1/2]

◆ scoring_scheme_base() [2/2]

Member Function Documentation

◆ score() [1/2]

◆ score() [2/2]

◆ set_custom_matrix()

◆ set_simple_scheme()

template<typename derived_t, alphabet alphabet_t, arithmetic score_t>
class seqan3::scoring_scheme_base< derived_t, alphabet_t, score_t >