49template <
typename trace_t,
bool coordinate_only = false>
56 "Value type must either be a trace_directions object or a simd vector.");
126 template <std::ranges::forward_range first_sequence_t, std::ranges::forward_range second_sequence_t>
153 static_assert(!
coordinate_only,
"Requested trace but storing the trace was disabled!");
155 using matrix_iter_t = std::ranges::iterator_t<typename matrix_base_t::pool_type>;
157 using path_t = std::ranges::subrange<trace_iterator_t, std::default_sentinel_t>;
164 std::default_sentinel};
210 template <std::random_access_iterator iter_t>
215 return {*host_iter, std::ignore, std::ignore, std::ignore, std::ignore};
220 std::get<2>(*host_iter),
221 std::get<0>(*host_iter),
222 std::get<1>(*(host_iter + 1)),
223 std::get<1>(*host_iter),
Provides seqan3::detail::align_config_band.
Provides seqan3::detail::alignment_matrix_column_major_range_base.
Provides seqan3::detail::alignment_trace_matrix_base.
Provides seqan3::detail::alignment_trace_matrix_proxy.
Configuration element for setting a fixed size band.
Definition align_config_band.hpp:60
Represents a column within an alignment matrix.
Definition alignment_matrix_column_major_range_base.hpp:75
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 traceback matrix storing the entire banded traceback matrix.
Definition alignment_trace_matrix_full_banded.hpp:53
typename range_base_t::sentinel sentinel
The type of sentinel.
Definition alignment_trace_matrix_full_banded.hpp:91
int32_t band_size
The size of the band.
Definition alignment_trace_matrix_full_banded.hpp:172
advanceable_alignment_coordinate< advanceable_alignment_coordinate_state::row > coordinate_type
The coordinate type.
Definition alignment_trace_matrix_base.hpp:42
constexpr alignment_trace_matrix_full_banded(first_sequence_t &&first, second_sequence_t &&second, align_cfg::band_fixed_size const &band, trace_t const initial_value=trace_t{})
Construction from two ranges and a band.
Definition alignment_trace_matrix_full_banded.hpp:127
constexpr alignment_trace_matrix_full_banded(alignment_trace_matrix_full_banded const &)=default
Defaulted.
constexpr alignment_trace_matrix_full_banded()=default
Defaulted.
size_t size_type
The size type.
Definition alignment_trace_matrix_base.hpp:52
constexpr value_type make_proxy(iter_t host_iter) noexcept
Creates the proxy value returned when dereferencing the alignment-column-iterator.
Definition alignment_trace_matrix_full_banded.hpp:211
int32_t band_col_index
The column index where the upper bound of the band passes through.
Definition alignment_trace_matrix_full_banded.hpp:168
~alignment_trace_matrix_full_banded()=default
Defaulted.
typename range_base_t::iterator iterator
The type of the iterator.
Definition alignment_trace_matrix_full_banded.hpp:89
auto trace_path(matrix_coordinate const &trace_begin)
Returns a trace path starting from the given coordinate and ending in the cell with seqan3::detail::t...
Definition alignment_trace_matrix_full_banded.hpp:151
int32_t band_row_index
The row index where the lower bound of the band passes through.
Definition alignment_trace_matrix_full_banded.hpp:170
constexpr alignment_trace_matrix_full_banded & operator=(alignment_trace_matrix_full_banded const &)=default
Defaulted.
constexpr alignment_trace_matrix_full_banded(alignment_trace_matrix_full_banded &&)=default
Defaulted.
alignment_trace_matrix_proxy< coordinate_type, std::conditional_t< coordinate_only, detail::ignore_t const, trace_t > > value_type
The proxy type of an alignment matrix.
Definition alignment_trace_matrix_full_banded.hpp:85
constexpr alignment_column_type initialise_column(size_type const column_index) noexcept
Returns the current alignment-column at the given column_index.
Definition alignment_trace_matrix_full_banded.hpp:176
friend range_base_t
Befriend the range base class.
Definition alignment_trace_matrix_full_banded.hpp:64
constexpr alignment_trace_matrix_full_banded & operator=(alignment_trace_matrix_full_banded &&)=default
Defaulted.
constexpr iterator begin() noexcept
Returns an iterator pointing to the first element of the matrix.
Definition two_dimensional_matrix.hpp:270
@ band
ID for the band option.
seqan::stl::views::zip zip
A view adaptor that takes several views and returns tuple-like values from every i-th element of each...
Definition zip.hpp:24
The internal SeqAn3 namespace.
Definition aligned_sequence_concept.hpp:26
A crtp-base class for alignment traceback matrices.
Definition alignment_trace_matrix_base.hpp:36
advanceable_alignment_coordinate< advanceable_alignment_coordinate_state::row > coordinate_type
The coordinate type.
Definition alignment_trace_matrix_base.hpp:42
std::conditional_t< detail::simd_concept< trace_t >, aligned_allocator< element_type, sizeof(element_type)>, std::allocator< element_type > > allocator_type
The allocator type. Uses seqan3::aligned_allocator if storing seqan3::detail::simd_concepttypes.
Definition alignment_trace_matrix_base.hpp:48
size_t size_type
The size type.
Definition alignment_trace_matrix_base.hpp:52
std::vector< element_type, allocator_type > cache_left
Internal cache for the trace values to the left.
Definition alignment_trace_matrix_base.hpp:58
size_type num_rows
The number of num_rows.
Definition alignment_trace_matrix_base.hpp:64
element_type cache_up
Internal cache for the last trace value above.
Definition alignment_trace_matrix_base.hpp:60
trace_t element_type
The actual element type.
Definition alignment_trace_matrix_base.hpp:44
size_type num_cols
The number of columns.
Definition alignment_trace_matrix_base.hpp:62
pool_type data
The linearised matrix storing the trace data in column-major-order.
Definition alignment_trace_matrix_base.hpp:56
two_dimensional_matrix< element_type, allocator_type, matrix_major_order::column > pool_type
The type of the underlying memory pool.
Definition alignment_trace_matrix_base.hpp:50
A proxy type for a unified access to the traceback matrix during alignment computation.
Definition alignment_trace_matrix_proxy.hpp:33
A strong type for designated initialisation of the column index of a matrix.
Definition matrix_coordinate.hpp:29
A representation of a location or offset within a two-dimensional matrix.
Definition matrix_coordinate.hpp:87
Strong type for setting the row dimension of a matrix.
Definition two_dimensional_matrix.hpp:37
A strong type for designated initialisation of the row index of a matrix.
Definition matrix_coordinate.hpp:58
Provides seqan3::detail::trace_iterator_banded.
Provides seqan3::views::zip.