The CRTP-policy that stores the scoring scheme used for this alignment algorithm. More...

#include <seqan3/alignment/pairwise/policy/scoring_scheme_policy.hpp>

Private Member Functions
template<typename alphabet_t > requires simd_concept<std::remove_cvref_t<alphabet_t>>
auto	scoring_scheme_profile_column (alphabet_t &&alphabet) const noexcept
	Maybe converts the given sequence value to a specific profile used by the underlying scoring scheme.

template<semialphabet alphabet_t>
alphabet_t	scoring_scheme_profile_column (alphabet_t &&alphabet) const noexcept
	This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.

Constructors, destructor and assignment
constexpr	scoring_scheme_policy ()=default
	Defaulted.

constexpr	scoring_scheme_policy (scoring_scheme_policy const &)=default
	Defaulted.

constexpr	scoring_scheme_policy (scoring_scheme_policy &&)=default
	Defaulted.

constexpr scoring_scheme_policy &	operator= (scoring_scheme_policy const &)=default
	Defaulted.

constexpr scoring_scheme_policy &	operator= (scoring_scheme_policy &&)=default
	Defaulted.

	~scoring_scheme_policy ()=default
	Defaulted.

template<typename configuration_t >
	scoring_scheme_policy (configuration_t const &)
	Initialise the policy.

Private Attributes
friend	alignment_algorithm_t
	Befriends the derived class to grant it access to the private members.

scoring_scheme_t	scoring_scheme {}
	The scoring scheme used for this alignment algorithm.

Detailed Description

template<typename alignment_algorithm_t, typename scoring_scheme_t>
class seqan3::detail::scoring_scheme_policy< alignment_algorithm_t, scoring_scheme_t >

The CRTP-policy that stores the scoring scheme used for this alignment algorithm.

Template Parameters

alignment_algorithm_t	The derived type (seqan3::detail::alignment_algorithm) to be augmented with this CRTP-policy.
scoring_scheme_t	The type of the scoring scheme.

Remarks: The template parameters of this CRTP-policy are selected in the seqan3::detail::alignment_configurator::configure_scoring_scheme when selecting the alignment for the given configuration.

Member Function Documentation

◆ scoring_scheme_profile_column()

template<typename alignment_algorithm_t , typename scoring_scheme_t >

template<typename alphabet_t >
requires simd_concept<std::remove_cvref_t<alphabet_t>>

auto seqan3::detail::scoring_scheme_policy< alignment_algorithm_t, scoring_scheme_t >::scoring_scheme_profile_column ( alphabet_t && alphabet ) const

inlineprivatenoexcept

Maybe converts the given sequence value to a specific profile used by the underlying scoring scheme.

In the vectorised alignment the scoring scheme might transform the sequence values of the first sequence into a profile for a more efficient comparison of the sequence characters in simd mode.

If the given sequence type models seqan3::semialphabet the function becomes a no-op function and returns the unmodified value.

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

scoring_scheme_policy.hpp

Private Member Functions

Private Attributes

Detailed Description

Member Function Documentation

◆ scoring_scheme_profile_column()