seqan3::scoring_scheme_base< derived_t, alphabet_t, score_t > Class Template Reference

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 Descriptionno-api

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] [no-api]

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  )

no-apiinlineconstexpr

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] [no-api]

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 )

no-apiinlineconstexprnoexcept

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] [no-api]

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

no-apiinlineconstexprnoexcept

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] [no-api]

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  )

no-apiinlineconstexprnoexcept

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() [no-api]

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 )

no-apiinlineconstexprnoexcept

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() [no-api]

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  )

no-apiinlineconstexpr

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.

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

• seqan3/alignment/scoring/scoring_scheme_base.hpp