SeqAn3  3.0.3
The Modern C++ library for sequence analysis.
seqan3::align_cfg::scoring_scheme< scoring_scheme_t > Struct Template Reference

Sets the scoring scheme for the alignment algorithm. More...

#include <seqan3/alignment/configuration/align_config_scoring_scheme.hpp>

+ Inheritance diagram for seqan3::align_cfg::scoring_scheme< scoring_scheme_t >:

Public Member Functions

Constructors, destructor and assignment
constexpr scoring_scheme ()=default
 Defaulted.
 
constexpr scoring_scheme (scoring_scheme const &)=default
 Defaulted.
 
constexpr scoring_scheme (scoring_scheme &&)=default
 Defaulted.
 
constexpr scoring_schemeoperator= (scoring_scheme const &)=default
 Defaulted.
 
constexpr scoring_schemeoperator= (scoring_scheme &&)=default
 Defaulted.
 
 ~scoring_scheme ()=default
 Defaulted.
 
constexpr scoring_scheme (scoring_scheme_t scheme)
 Initialises the scoring scheme config with the given scheme. More...
 

Public Attributes

scoring_scheme_t scheme {}
 The scoring scheme to be used in the alignment algorithm.
 

Related Functions

(Note that these are not member functions.)

Type deduction guides
template<typename scheme_t >
 scoring_scheme (scheme_t) -> scoring_scheme< std::remove_cvref_t< scheme_t >>
 Deduces the scoring scheme type from the constructor argument.
 

Detailed Description

template<std::semiregular scoring_scheme_t>
struct seqan3::align_cfg::scoring_scheme< scoring_scheme_t >

Sets the scoring scheme for the alignment algorithm.

Template Parameters
scoring_scheme_tThe type of the scoring scheme; must model std::semiregular.

The scoring scheme allows to specify how two symbols of an alphabet are scored inside of the alignment algorithm. The scheme depends on the alphabet type of the passed sequences and must be chosen accordingly. During the configuration of the pairwise alignment algorithm a static assert is triggered if the scoring scheme is not compatible with the given alphabet types (see seqan3::scoring_scheme_for). Accordingly, this configuration cannot be defaulted since it depends on the sequences and must be given as a minimal configuration.

Example

Constructor & Destructor Documentation

◆ scoring_scheme()

template<std::semiregular scoring_scheme_t>
constexpr seqan3::align_cfg::scoring_scheme< scoring_scheme_t >::scoring_scheme ( scoring_scheme_t  scheme)
inlineexplicitconstexpr

Initialises the scoring scheme config with the given scheme.

Parameters
[in]schemeThe scoring scheme to be used in the alignment algorithm.

This config stores a copy of the provided scheme.


The documentation for this struct was generated from the following file:
debug_stream.hpp
Provides seqan3::debug_stream and related types.
dna4.hpp
Provides seqan3::dna4, container aliases and string literals.
align_pairwise.hpp
Provides pairwise alignment function.
align_config_method.hpp
Provides global and local alignment configurations.
align_config_scoring_scheme.hpp
Provides seqan3::align_cfg::scoring_scheme.
seqan3::nucleotide_scoring_scheme
A data structure for managing and computing the score of two nucleotides.
Definition: nucleotide_scoring_scheme.hpp:38
nucleotide_scoring_scheme.hpp
Provides seqan3::nucleotide_scoring_scheme.
seqan3::align_pairwise
constexpr auto align_pairwise(sequence_t &&seq, alignment_config_t const &config)
Computes the pairwise alignment for a pair of sequences or a range over sequence pairs.
Definition: align_pairwise.hpp:138
std::tie
T tie(T... args)
seqan3::mismatch_score
A strong type of underlying type score_type that represents the score two different characters.
Definition: scoring_scheme_base.hpp:66
seqan3::align_cfg::scoring_scheme
Sets the scoring scheme for the alignment algorithm.
Definition: align_config_scoring_scheme.hpp:45
seqan3::align_cfg::method_global
Sets the global alignment method.
Definition: align_config_method.hpp:106
seqan3::debug_stream
debug_stream_type debug_stream
A global instance of seqan3::debug_stream_type.
Definition: debug_stream.hpp:42
seqan3::match_score
A strong type of underlying type score_type that represents the score of two matching characters.
Definition: scoring_scheme_base.hpp:41