21template <
typename alignment_configuration_t>
76 template <
typename affine_cell_t>
78 affine_cell_t previous_cell,
79 score_type const sequence_score)
const noexcept
81 diagonal_score += sequence_score;
83 diagonal_score = (diagonal_score < horizontal_score) ? horizontal_score : diagonal_score;
86 horizontal_score = (horizontal_score < from_optimal_score) ? from_optimal_score : horizontal_score;
87 return {diagonal_score, horizontal_score, from_optimal_score};
A proxy for an affine score matrix cell.
Definition affine_cell_proxy.hpp:114
decltype(auto) horizontal_score() &noexcept
Access the horizontal score of the wrapped score matrix cell.
Definition affine_cell_proxy.hpp:210
Implements the alignment recursion function for the banded alignment algorithm using affine gap costs...
Definition policy_affine_gap_recursion_banded.hpp:23
policy_affine_gap_recursion_banded & operator=(policy_affine_gap_recursion_banded &&)=default
Defaulted.
policy_affine_gap_recursion_banded()=default
Defaulted.
policy_affine_gap_recursion_banded(policy_affine_gap_recursion_banded &&)=default
Defaulted.
affine_cell_type initialise_band_first_cell(score_type diagonal_score, affine_cell_t previous_cell, score_type const sequence_score) const noexcept
Initialises the first cell of a banded column that does not start in the first row of the matrix.
Definition policy_affine_gap_recursion_banded.hpp:77
score_type gap_extension_score
The score for a gap extension.
Definition policy_affine_gap_recursion.hpp:56
~policy_affine_gap_recursion_banded()=default
Defaulted.
typename traits_type::score_type score_type
The configured score type.
Definition policy_affine_gap_recursion.hpp:49
score_type gap_open_score
The score for a gap opening including the gap extension.
Definition policy_affine_gap_recursion.hpp:58
policy_affine_gap_recursion_banded(alignment_configuration_t const &config)
Construction and initialisation using the alignment configuration.
Definition policy_affine_gap_recursion_banded.hpp:56
policy_affine_gap_recursion_banded(policy_affine_gap_recursion_banded const &)=default
Defaulted.
policy_affine_gap_recursion_banded & operator=(policy_affine_gap_recursion_banded const &)=default
Defaulted.
Implements the alignment recursion function for the alignment algorithm using affine gap costs.
Definition policy_affine_gap_recursion.hpp:42
affine_cell_proxy< affine_score_tuple_t > affine_cell_type
The affine cell type returned by the functions.
Definition policy_affine_gap_recursion.hpp:53
score_type gap_extension_score
The score for a gap extension.
Definition policy_affine_gap_recursion.hpp:56
typename traits_type::score_type score_type
The configured score type.
Definition policy_affine_gap_recursion.hpp:49
score_type gap_open_score
The score for a gap opening including the gap extension.
Definition policy_affine_gap_recursion.hpp:58
alignment_configuration_traits< alignment_configuration_t > traits_type
The configuration traits type.
Definition policy_affine_gap_recursion.hpp:45
The internal SeqAn3 namespace.
Definition aligned_sequence_concept.hpp:26
Provides seqan3::detail::policy_affine_gap_recursion.