SeqAn3  3.0.3
The Modern C++ library for sequence analysis.
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()). More...
 
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()). More...
 
constexpr aminoacid_scoring_scheme (matrix_type const &matrix) noexcept
 Constructor for a custom scheme (delegates to set_custom_matrix()). More...
 
constexpr aminoacid_scoring_scheme (aminoacid_similarity_matrix const matrix_id)
 Construct for seqan3::aminoacid_similarity_matrix. More...
 
Scheme selection
constexpr void set_similarity_matrix (aminoacid_similarity_matrix const matrix_id)
 Set the similarity matrix scheme (e.g. BLOSUM62). More...
 
- Public Member Functions inherited from seqan3::scoring_scheme_base< aminoacid_scoring_scheme< int8_t >, aa27, int8_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 () noexcept
 The default constructor (delegates to set_hamming_distance()).
 
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...
 
constexpr scoring_scheme_baseoperator= (scoring_scheme_base const &) noexcept=default
 Defaulted.
 
constexpr scoring_scheme_baseoperator= (scoring_scheme_base &&) noexcept=default
 Defaulted.
 
 ~scoring_scheme_base () noexcept=default
 Defaulted.
 
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...
 
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...
 
constexpr bool operator== (aminoacid_scoring_scheme< int8_t > const &rhs) const noexcept
 Checks whether *this is equal to rhs.
 
constexpr bool operator!= (aminoacid_scoring_scheme< int8_t > const &rhs) const noexcept
 Checks whether *this is not equal to rhs.
 

Related Functions

(Note that these are not member functions.)

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< aminoacid_scoring_scheme< int8_t >, aa27, int8_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< aminoacid_scoring_scheme< int8_t >, aa27, int8_t >
static constexpr matrix_size_type matrix_size
 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

int main()
{
using namespace seqan3::literals;
// 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
// 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;
// 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
}
Provides seqan3::aa27, container aliases and string literals.
Meta-header for the aminoacid submodule; includes all headers from alphabet/aminoacid/.
Provides seqan3::aminoacid_scoring_scheme.
A data structure for managing and computing the score of two amino acids.
Definition: aminoacid_scoring_scheme.hpp:75
constexpr score_t & score(alph1_t const alph1, alph2_t const alph2) noexcept
Score two letters (either two nucleotids or two amino acids).
Definition: scoring_scheme_base.hpp:219
Provides seqan3::debug_stream and related types.
@ BLOSUM80
The BLOSUM80 matrix for closely related proteins.
@ BLOSUM62
The BLOSUM62 matrix recommended for most use-cases.
debug_stream_type debug_stream
A global instance of seqan3::debug_stream_type.
Definition: debug_stream.hpp:42
constexpr auto zip
A zip view.
Definition: zip.hpp:29
The SeqAn namespace for literals.
Provides seqan3::views::zip.

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_tThe underlying type of the arguments.
Parameters
[in]msMatches shall be given this value (of type seqan3::match_score).
[in]mmsMismatches shall be given this value (of type seqan3::mismatch_score).
Exceptions
std::invalid_argumentThrown 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]matrixA 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_idThe enum ID of the matrix, see seqan3::aminoacid_similarity_matrix.
Exceptions
std::invalid_argumentIf 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_idThe enum ID of the matrix, see seqan3::aminoacid_similarity_matrix.
Exceptions
std::invalid_argumentIf there is no matrix data for the given ID (usually a BUG).

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