seqan3::detail::policy_scoring_scheme< alignment_configuration_t, scoring_scheme_t > Class Template Reference

Stores the configured scoring scheme used for this algorithm. More...

#include <seqan3/alignment/pairwise/detail/policy_scoring_scheme.hpp>

Protected 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
	policy_scoring_scheme ()=default
	Defaulted.
	policy_scoring_scheme (policy_scoring_scheme const &)=default
	Defaulted.
	policy_scoring_scheme (policy_scoring_scheme &&)=default
	Defaulted.
policy_scoring_scheme &	operator= (policy_scoring_scheme const &)=default
	Defaulted.
policy_scoring_scheme &	operator= (policy_scoring_scheme &&)=default
	Defaulted.
	~policy_scoring_scheme ()=default
	Defaulted.
	policy_scoring_scheme (alignment_configuration_t const &config)
	Construction and initialisation using the alignment configuration.

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

Detailed Description

template<typename alignment_configuration_t, typename scoring_scheme_t>
class seqan3::detail::policy_scoring_scheme< alignment_configuration_t, scoring_scheme_t >

Stores the configured scoring scheme used for this algorithm.

Template Parameters

alignment_configuration_t	The type of the alignment configuration; must be a type specialisation of seqan3::configuration.
scoring_scheme_t	The type of the scoring scheme.

Stores and initialises the configured scoring scheme from the given alignment configuration.

Constructor & Destructor Documentation

policy_scoring_scheme()

template<typename alignment_configuration_t , typename scoring_scheme_t >

seqan3::detail::policy_scoring_scheme< alignment_configuration_t, scoring_scheme_t >::policy_scoring_scheme ( alignment_configuration_t const &  config )

inlineexplicitprotected

Construction and initialisation using the alignment configuration.

Parameters

[in]

config

The alignment configuration with the stored scoring scheme.

Member Function Documentation

scoring_scheme_profile_column()

template<typename alignment_configuration_t , typename scoring_scheme_t >

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

auto seqan3::detail::policy_scoring_scheme< alignment_configuration_t, scoring_scheme_t >::scoring_scheme_profile_column ( alphabet_t &&  alphabet ) const

inlineprotectednoexcept

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

Template Parameters

alphabet_t

The type of the actual alphabet; must model either seqan3::simd::simd_concept or seqan3::semialphabet.

Parameters

[in]

alphabet

The alphabet value to get a score profile for.

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:

• policy_scoring_scheme.hpp