38template <
typename score_t>
45 "The score type must be either an arithmetic type or a simd vector type.");
56 using typename range_base_t::alignment_column_type;
107 template <std::ranges::forward_range first_sequence_t, std::ranges::forward_range second_sequence_t>
122 return alignment_column_type{
128 template <std::random_access_iterator iter_t>
131 return {std::get<0>(*host_iter),
133 std::get<1>(*host_iter),
134 std::get<1>(*host_iter),
139 template <std::random_access_iterator iter_t>
147 template <std::random_access_iterator iter_t>
155 template <std::random_access_iterator iter_t>
Provides seqan3::detail::alignment_matrix_column_major_range_base.
Provides seqan3::detail::alignment_score_matrix_one_column_base.
Provides seqan3::detail::alignment_score_matrix_proxy.
Allocates uninitialized storage whose memory-alignment is specified by alignment.
Definition aligned_allocator.hpp:74
Provides a range interface for alignment matrices.
Definition alignment_matrix_column_major_range_base.hpp:60
std::default_sentinel_t sentinel
The type of sentinel.
Definition alignment_matrix_column_major_range_base.hpp:477
iterator_type iterator
The type of the iterator.
Definition alignment_matrix_column_major_range_base.hpp:475
An alignment score matrix storing only a single column for the computation.
Definition alignment_score_matrix_one_column.hpp:42
alignment_score_matrix_proxy< score_t > value_type
The proxy type of an alignment matrix.
Definition alignment_score_matrix_one_column.hpp:67
constexpr value_type make_proxy(iter_t host_iter) noexcept
Creates the proxy value returned when dereferencing the alignment-column-iterator.
Definition alignment_score_matrix_one_column.hpp:129
size_t size_type
The size type.
Definition alignment_score_matrix_one_column_base.hpp:48
constexpr alignment_score_matrix_one_column & operator=(alignment_score_matrix_one_column const &)=default
Defaulted.
constexpr alignment_score_matrix_one_column(first_sequence_t &&first, second_sequence_t &&second, score_t const initial_value=score_t{})
Construction from two ranges.
Definition alignment_score_matrix_one_column.hpp:108
constexpr alignment_score_matrix_one_column(alignment_score_matrix_one_column &&)=default
Defaulted.
constexpr void on_column_iterator_creation(iter_t host_iter) noexcept
Allows additional initialisations when calling begin on an alignment-column.
Definition alignment_score_matrix_one_column.hpp:140
constexpr void after_column_iterator_increment(iter_t host_iter) noexcept
Allows to perform additional steps after incrementing the alignment-column-iterator.
Definition alignment_score_matrix_one_column.hpp:156
constexpr alignment_score_matrix_one_column()=default
Defaulted.
typename range_base_t::iterator iterator
The type of the iterator.
Definition alignment_score_matrix_one_column.hpp:71
friend range_base_t
Befriend the range base class.
Definition alignment_score_matrix_one_column.hpp:52
constexpr void before_column_iterator_increment(iter_t host_iter) noexcept
Allows to perform additional steps before incrementing the alignment-column-iterator.
Definition alignment_score_matrix_one_column.hpp:148
typename range_base_t::sentinel sentinel
The type of sentinel.
Definition alignment_score_matrix_one_column.hpp:73
constexpr alignment_column_type initialise_column(size_type const column_index) noexcept
Returns the current alignment-column at the given column_index.
Definition alignment_score_matrix_one_column.hpp:120
std::tuple< underlying_type, underlying_type > element_type
The actual element type.
Definition alignment_score_matrix_one_column_base.hpp:42
constexpr alignment_score_matrix_one_column(alignment_score_matrix_one_column const &)=default
Defaulted.
constexpr alignment_score_matrix_one_column & operator=(alignment_score_matrix_one_column &&)=default
Defaulted.
~alignment_score_matrix_one_column()=default
Defaulted.
The internal SeqAn3 namespace.
Definition aligned_sequence_concept.hpp:26
A base class for alignment score matrices using only one column to compute the matrix.
Definition alignment_score_matrix_one_column_base.hpp:34
std::array< underlying_type, 3 > cache
Internal cache for the last diagonal and vertical value during the alignment computation.
Definition alignment_score_matrix_one_column_base.hpp:54
pool_type pool
The linearised memory pool storing only one column of the matrix.
Definition alignment_score_matrix_one_column_base.hpp:52
size_t size_type
The size type.
Definition alignment_score_matrix_one_column_base.hpp:48
score_t underlying_type
The underlying type of the scores.
Definition alignment_score_matrix_one_column_base.hpp:40
size_type num_rows
The number of num_rows.
Definition alignment_score_matrix_one_column_base.hpp:58
std::tuple< underlying_type, underlying_type > element_type
The actual element type.
Definition alignment_score_matrix_one_column_base.hpp:42
aligned_allocator< element_type, sizeof(element_type)> allocator_type
The allocator type.
Definition alignment_score_matrix_one_column_base.hpp:44
size_type num_cols
The number of columns.
Definition alignment_score_matrix_one_column_base.hpp:56
Provides concepts that do not have equivalents in C++20.
Provides seqan3::simd::simd_concept.