SeqAn3 3.4.0-rc.1
The Modern C++ library for sequence analysis.
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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. | |
Stores the configured scoring scheme used for this algorithm.
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.
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inlineexplicitprotected |
Construction and initialisation using the alignment configuration.
[in] | config | The alignment configuration with the stored scoring scheme. |
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inlineprotectednoexcept |
Maybe converts the given sequence value to a specific profile used by the underlying scoring scheme.
alphabet_t | The type of the actual alphabet; must model either seqan3::simd::simd_concept or seqan3::semialphabet. |
[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.