seqan3::nucleotide_scoring_scheme< score_type > Class Template Reference

A data structure for managing and computing the score of two nucleotides. More...

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

Inheritance diagram for seqan3::nucleotide_scoring_scheme< score_type >:

Public Types
Member types
using	score_type = score_t
	Type of the score values.
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	nucleotide_scoring_scheme () noexcept
	The default constructor (delegates to set_hamming_distance()). More...
template<Arithmetic score_arg_t>
constexpr	nucleotide_scoring_scheme (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	nucleotide_scoring_scheme (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.
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
constexpr score_t &	score (alph1_t const alph1, alph2_t const alph2) noexcept
	Score two letters (either two nucleotids or two amino acids). More...
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== (nucleotide_scoring_scheme< score_type > const &rhs) const noexcept
	Checks whether *this is equal to rhs.
constexpr bool	operator!= (nucleotide_scoring_scheme< score_type > const &rhs) const noexcept
	Checks whether *this is not equal to rhs.

Static Public Attributes
static constexpr matrix_size_type	matrix_size
	Size of the matrix dimensions (i.e. size of the alphabet).

Related Functions
(Note that these are not member functions.)
Type deduction guides
	nucleotide_scoring_scheme () -> nucleotide_scoring_scheme< int8_t >
	Default constructed objects deduce to int8_t.
template<Arithmetic score_arg_type>
	nucleotide_scoring_scheme (match_score< score_arg_type >, mismatch_score< score_arg_type >) -> nucleotide_scoring_scheme< int8_t >
	Attention: This guide does not actually deduce from the underlying type, but always defaults to int8_t. To use a larger type, specify the template argument manually.
template<Arithmetic score_arg_type>
	nucleotide_scoring_scheme (std::array< std::array< score_arg_type, 15 >, 15 >) -> nucleotide_scoring_scheme< score_arg_type >
	Deduce the score type from the provided matrix.
Requirements for seqan3::ScoringScheme
You can expect these members on all types that implement seqan3::ScoringScheme.
typedef IMPLEMENTATION_DEFINED	score_type
	The type returned by seqan3::ScoringScheme::score(), usually a seqan3::Arithmetic. More...
score_type	score (alph1_t const alph1, alph2_t const alph2)
	Compute the score of two letters. More...

Detailed Description

template<Arithmetic score_type = int8_t>
class seqan3::nucleotide_scoring_scheme< score_type >

A data structure for managing and computing the score of two nucleotides.

Template Parameters

score_type

The underlying type.

You can use an instance of this class to score two nucleotides, the nucleotides need not be of the same type. Different scoring behaviour can be set via the member functions.

Example

Score two letters:

nucleotide_scoring_scheme scheme; // hamming is default
debug_stream << "Score between DNA5 A and G: " << (int) scheme.score('A'_dna5, 'G'_dna5) << "\n"; // == -1
debug_stream << "Score between DNA5 A and A: " << (int) scheme.score('A'_dna5, 'A'_dna5) << "\n"; // == 0

scheme.set_simple_scheme(match_score{3}, mismatch_score{-2});
debug_stream << "Score between DNA5 A and RNA15 G: " << (int) scheme.score('A'_dna5, 'G'_rna15) << "\n"; // == -2
debug_stream << "Score between DNA5 A and RNA15 A: " << (int) scheme.score('A'_dna5, 'A'_rna15) << "\n"; // == 3
// you can score differenct nucleotides  ^

You can "edit" a given matrix directly:

nucleotide_scoring_scheme scheme; // hamming distance is default
debug_stream << "Score between DNA A and G before edit: "
          << (int) scheme.score('A'_dna15, 'G'_dna15) << "\n"; // == -1
scheme.score('A'_dna15, 'G'_dna15) = 3;
debug_stream << "Score after editing: " << (int) scheme.score('A'_dna15, 'G'_dna15) << "\n"; // == 3

Score two sequences:

std::vector<dna15> one = "AGAATA"_dna15;
std::vector<dna15> two = "ATACTA"_dna15;
nucleotide_scoring_scheme scheme; // hamming distance is default

int score = 0;
for (auto pair : std::view::zip(one, two))
    score += scheme.score(std::get<0>(pair), std::get<1>(pair));
debug_stream << "Score: " << score << "\n"; // == 0 - 1 + 0 - 1 + 0 + 0 = -2

Constructor & Destructor Documentation

nucleotide_scoring_scheme() [1/3]

template<Arithmetic score_type = int8_t>

constexpr seqan3::nucleotide_scoring_scheme< score_type >::nucleotide_scoring_scheme ( )

inlinenoexcept

The default constructor (delegates to set_hamming_distance()).

nucleotide_scoring_scheme() [2/3]

template<Arithmetic score_type = int8_t>

template<Arithmetic score_arg_t>

constexpr seqan3::nucleotide_scoring_scheme< score_type >::nucleotide_scoring_scheme ( match_score< score_arg_t > const  ms, mismatch_score< score_arg_t > const  mms  )

inline

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.

nucleotide_scoring_scheme() [3/3]

template<Arithmetic score_type = int8_t>

constexpr seqan3::nucleotide_scoring_scheme< score_type >::nucleotide_scoring_scheme ( matrix_type const &  _matrix )

inlinenoexcept

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]

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

inlinenoexceptinherited

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]

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

inlinenoexceptinherited

Compute the score of two letters.

Parameters

alph1	First letter.
alph2	Second letter.

Attention

This is a concept requirement, not an actual function (however types satisfying this concept will provide an implementation).

set_custom_matrix()

constexpr void seqan3::scoring_scheme_base< nucleotide_scoring_scheme< score_type > , alphabet_t, score_t >::set_custom_matrix ( matrix_type const &  _matrix )

inlinenoexceptinherited

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()

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

inlineinherited

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.

Friends And Related Function Documentation

score()

score_type score ( alph1_t const  alph1, alph2_t const  alph2  )

related

Compute the score of two letters.

Parameters

alph1	First letter.
alph2	Second letter.

Attention

This is a concept requirement, not an actual function (however types satisfying this concept will provide an implementation).

score_type()

typedef IMPLEMENTATION_DEFINED score_type

related

The type returned by seqan3::ScoringScheme::score(), usually a seqan3::Arithmetic.

Attention

This is a concept requirement, not an actual typedef (however types satisfying this concept will provide an implementation).

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

• seqan3/alignment/scoring/nucleotide_scoring_scheme.hpp