seqan3::aminoacid_scoring_scheme< score_type > Class Template Reference

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

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

Inheritance diagram for seqan3::aminoacid_scoring_scheme< score_type >:

Public Member Functions
Constructors, destructor and assignment
constexpr	aminoacid_scoring_scheme () noexcept=default
	The default constructor (delegates to set_hamming_distance()).
template<arithmetic score_arg_t>
constexpr	aminoacid_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()).
constexpr	aminoacid_scoring_scheme (matrix_type const &matrix) noexcept
	Constructor for a custom scheme (delegates to set_custom_matrix()).
constexpr	aminoacid_scoring_scheme (aminoacid_similarity_matrix const matrix_id)
	Construct for seqan3::aminoacid_similarity_matrix.
Scheme selection
constexpr void	set_similarity_matrix (aminoacid_similarity_matrix const matrix_id)
	Set the similarity matrix scheme (e.g. blosum62).
Public Member Functions inherited from seqan3::scoring_scheme_base< derived_t, alphabet_t, score_t >
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()).
constexpr	scoring_scheme_base (matrix_type const &matrix) noexcept
	Constructor for a custom scheme (delegates to set_custom_matrix()).
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).
constexpr void	set_custom_matrix (matrix_type const &matrix) noexcept
	Set a custom scheme by passing a full matrix with arbitrary content.
template<typename alph1_t , typename alph2_t > requires explicitly_convertible_to<alph1_t, alphabet_t> && explicitly_convertible_to<alph2_t, alphabet_t>
constexpr score_t &	score (alph1_t const alph1, alph2_t const alph2) noexcept
	Score two letters (either two nucleotids or two amino acids).
template<typename alph1_t , typename alph2_t > requires explicitly_convertible_to<alph1_t, alphabet_t> && explicitly_convertible_to<alph2_t, alphabet_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).
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.

Related Symbols
(Note that these are not member symbols.)
Type deduction guides
	aminoacid_scoring_scheme () -> aminoacid_scoring_scheme< int8_t >
	Default constructed objects deduce to int8_t.
template<arithmetic score_arg_type>
	aminoacid_scoring_scheme (match_score< score_arg_type >, mismatch_score< score_arg_type >) -> aminoacid_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>
	aminoacid_scoring_scheme (std::array< std::array< score_arg_type, 27 >, 27 >) -> aminoacid_scoring_scheme< score_arg_type >
	Deduce the score type from the provided matrix.
	aminoacid_scoring_scheme (aminoacid_similarity_matrix) -> aminoacid_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.

Additional Inherited Members
Public Types inherited from seqan3::scoring_scheme_base< derived_t, alphabet_t, score_t >
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).
Static Public Attributes inherited from seqan3::scoring_scheme_base< derived_t, alphabet_t, score_t >
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<arithmetic score_type = int8_t>
class seqan3::aminoacid_scoring_scheme< score_type >

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

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

Example

// SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin
// SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik
// SPDX-License-Identifier: CC0-1.0
 
#include <seqan3/alignment/scoring/aminoacid_scoring_scheme.hpp>
#include <seqan3/alphabet/aminoacid/aa27.hpp>
#include <seqan3/alphabet/aminoacid/all.hpp>
#include <seqan3/core/debug_stream.hpp>
#include <seqan3/utility/views/zip.hpp>
 
int main()
{
    using namespace seqan3::literals;
 
    seqan3::aminoacid_scoring_scheme scheme{seqan3::aminoacid_similarity_matrix::blosum62};
    // How to score two letters:
    seqan3::debug_stream << "blosum62 score for T and S: " << (int)scheme.score('T'_aa27, 'S'_aa27) << "\n"; // == 1
 
    scheme.set_similarity_matrix(seqan3::aminoacid_similarity_matrix::blosum80);
    // You can also score aa20 against aa27:
    seqan3::debug_stream << "blosum80 score for 'T'_aa27 and 'S'_aa20: " << (int)scheme.score('T'_aa27, 'S'_aa20)
                         << "\n"; // == 2
    scheme.set_hamming_distance();
    seqan3::debug_stream << "Hamming distance between T and S: " << (int)scheme.score('T'_aa27, 'S'_aa20)
                         << "\n"; // == -1
    seqan3::debug_stream << "Hamming distance between T and T: " << (int)scheme.score('T'_aa27, 'T'_aa20)
                         << "\n"; // == 0
 
    seqan3::aminoacid_scoring_scheme scheme2{seqan3::aminoacid_similarity_matrix::blosum80};
    // You can "edit" a given matrix directly:
    seqan3::debug_stream << "blosum80 score between T and S: " << (int)scheme2.score('T'_aa27, 'S'_aa27)
                         << "\n"; // == 2
    auto & cell = scheme2.score('T'_aa27, 'S'_aa27);
    cell = 3;
    seqan3::debug_stream << "New score after editing entry: " << (int)scheme2.score('T'_aa27, 'S'_aa27) << "\n"; // == 3
 
    std::vector<seqan3::aa27> one = "ALIGATOR"_aa27;
    std::vector<seqan3::aa27> two = "ANIMATOR"_aa27;
 
    seqan3::aminoacid_scoring_scheme scheme3{seqan3::aminoacid_similarity_matrix::blosum62};
    // You can also score two sequences:
    int score = 0;
    for (auto pair : seqan3::views::zip(one, two))
        score += scheme3.score(std::get<0>(pair), std::get<1>(pair));
    seqan3::debug_stream << "Score: " << score << "\n"; // 4 + -3 + 4 + -3 + 4 + 5 + -1 + 5 = 15
}

Constructor & Destructor Documentation

aminoacid_scoring_scheme() [1/4]

template<arithmetic score_type = int8_t>

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

constexprdefaultnoexcept

The default constructor (delegates to set_hamming_distance()).

aminoacid_scoring_scheme() [2/4]

template<arithmetic score_type = int8_t>

template<arithmetic score_arg_t>

constexpr seqan3::aminoacid_scoring_scheme< score_type >::aminoacid_scoring_scheme ( 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.

aminoacid_scoring_scheme() [3/4]

template<arithmetic score_type = int8_t>

constexpr seqan3::aminoacid_scoring_scheme< score_type >::aminoacid_scoring_scheme ( 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.

aminoacid_scoring_scheme() [4/4]

template<arithmetic score_type = int8_t>

constexpr seqan3::aminoacid_scoring_scheme< score_type >::aminoacid_scoring_scheme ( aminoacid_similarity_matrix const  matrix_id )

inlineconstexpr

Construct for seqan3::aminoacid_similarity_matrix.

Parameters

[in]

matrix_id

The enum ID of the matrix, see seqan3::aminoacid_similarity_matrix.

Exceptions

std::invalid_argument

If there is no matrix data for the given ID (usually a BUG).

Member Function Documentation

set_similarity_matrix()

template<arithmetic score_type = int8_t>

constexpr void seqan3::aminoacid_scoring_scheme< score_type >::set_similarity_matrix ( aminoacid_similarity_matrix const  matrix_id )

inlineconstexpr

Set the similarity matrix scheme (e.g. blosum62).

Parameters

[in]

matrix_id

The enum ID of the matrix, see seqan3::aminoacid_similarity_matrix.

Exceptions

std::invalid_argument

If there is no matrix data for the given ID (usually a BUG).

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

• aminoacid_scoring_scheme.hpp