31template <
typename alignment_algorithm_t>
56 template <
typename configuration_t>
59 if constexpr (configuration_t::template exists<align_cfg::method_local>())
80 template <
typename cell_t,
typename score_t>
89 template <
typename other_alignment_algorithm_t,
typename score_t,
typename is_local_t>
92 template <
typename other_alignment_algorithm_t, simd_concept score_t,
typename is_local_t>
96 template <
typename other_alignment_algorithm_t>
111 template <
typename cell_t,
typename score_t>
133 template <
typename alignment_column_t,
typename score_t>
140 for (
auto && cell : last_column)
156 template <
typename cell_t,
typename score_t>
173 template <
typename cell_t,
typename score_t>
176 auto const & [score_cell, trace_cell] = cell;
177 state.optimum.update_if_new_optimal_score(score_cell.current,
Provides global and local alignment configurations.
Provides seqan3::detail::alignment_algorithm_state.
Provides seqan3::detail::alignment_optimum.
Sets the global alignment method.
Definition align_config_method.hpp:119
The CRTP-policy that implements the initialisation of the dynamic programming matrix with affine gaps...
Definition affine_gap_init_policy.hpp:34
The CRTP-policy that computes a single cell in the alignment matrix.
Definition affine_gap_policy.hpp:44
The CRTP-policy to determine the optimum of the dynamic programming matrix.
Definition find_optimum_policy.hpp:33
~find_optimum_policy()=default
Defaulted.
constexpr void check_score_of_cells_in_last_column(alignment_column_t &&last_column, alignment_algorithm_state< score_t > &state) const noexcept
Checks all cells of the last alignment column for a new alignment optimum.
Definition find_optimum_policy.hpp:135
constexpr find_optimum_policy & operator=(find_optimum_policy &&)=default
Defaulted.
constexpr void check_score_of_last_cell(cell_t const &last_cell, alignment_algorithm_state< score_t > &state) const noexcept
Checks if the last cell of the alignment matrix is a new optimum in the alignment.
Definition find_optimum_policy.hpp:157
friend alignment_algorithm_t
Befriends the derived class to grant it access to the private members.
Definition find_optimum_policy.hpp:36
constexpr void check_and_update(cell_t const &cell, alignment_algorithm_state< score_t > &state) const noexcept
Tests if the score in the current cell is greater than the current alignment optimum.
Definition find_optimum_policy.hpp:174
constexpr void check_score_of_last_row_cell(cell_t const &last_row_cell, alignment_algorithm_state< score_t > &state) const noexcept
Checks if a cell in the last row of the alignment matrix is a new optimum in the alignment.
Definition find_optimum_policy.hpp:113
constexpr void check_score_of_cell(cell_t const ¤t_cell, alignment_algorithm_state< score_t > &state) const noexcept
Checks if a given cell is a new optimum in the alignment.
Definition find_optimum_policy.hpp:81
bool test_last_column_cell
Whether cells of the last column shall be tracked.
Definition find_optimum_policy.hpp:43
constexpr find_optimum_policy()=default
Defaulted.
bool test_every_cell
Whether every cell of the alignment matrix shall be tracked.
Definition find_optimum_policy.hpp:39
bool test_last_row_cell
Whether cells of the last row shall be tracked.
Definition find_optimum_policy.hpp:41
constexpr find_optimum_policy & operator=(find_optimum_policy const &)=default
Defaulted.
constexpr find_optimum_policy(find_optimum_policy &&)=default
Defaulted.
find_optimum_policy(configuration_t const &config)
Initialises the policy with the configuration.
Definition find_optimum_policy.hpp:57
constexpr find_optimum_policy(find_optimum_policy const &)=default
Defaulted.
The CRTP-policy that computes a batch of cells in the alignment matrix using simd instructions.
Definition simd_affine_gap_policy.hpp:51
The internal SeqAn3 namespace.
Definition aligned_sequence_concept.hpp:26
Local state for the standard alignment algorithm.
Definition alignment_algorithm_state.hpp:32
A strong type for designated initialisation of the column index of a matrix.
Definition matrix_coordinate.hpp:29
A strong type for designated initialisation of the row index of a matrix.
Definition matrix_coordinate.hpp:58