SeqAn3  3.0.2
The Modern C++ library for sequence analysis.
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_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 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_tThe derived type.
alphabet_tType of the largest target alphabet.
score_typeType 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 
)
inline

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.

◆ 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)
inlinenoexcept

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

Parameters
[in]matrixA 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 
)
inlinenoexcept

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

Template Parameters
alph1_tType of the first letter.
alph2_tType of the second letter (needn't be the same as alph1_t).
Parameters
[in]alph1The first letter to score.
[in]alph2The 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 
) const
inlinenoexcept

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

Template Parameters
alph1_tType of the first letter.
alph2_tType of the second letter (needn't be the same as alph1_t).
Parameters
[in]alph1The first letter to score.
[in]alph2The 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)
inlinenoexcept

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

Parameters
[in]matrixA 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 
)
inline

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

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.

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