41template <std::ranges::input_range score_matrix_t, std::ranges::input_range trace_matrix_t>
42 requires (std::ranges::input_range<std::ranges::range_reference_t<score_matrix_t>>
43 && std::ranges::input_range<std::ranges::range_reference_t<trace_matrix_t>>)
54 score_matrix_t score_matrix{};
56 trace_matrix_t trace_matrix{};
91 template <std::
integral column_index_t, std::
integral row_index_t>
96 score_matrix_t tmp_score_matrix{};
97 tmp_score_matrix.resize(column_count, row_count, initial_score);
99 trace_matrix_t tmp_trace_matrix{};
100 tmp_trace_matrix.resize(column_count, row_count);
102 score_matrix = std::move(tmp_score_matrix);
103 trace_matrix = std::move(tmp_trace_matrix);
112 return iterator{score_matrix.begin(), trace_matrix.begin()};
121 return sentinel{score_matrix.end()};
136 auto trace_path(matrix_coordinate
const & from_coordinate)
const
138 return trace_matrix.trace_path(from_coordinate);
153template <std::ranges::input_range score_matrix_t, std::ranges::input_range trace_matrix_t>
154 requires (std::ranges::input_range<std::ranges::range_reference_t<score_matrix_t>>
155 && std::ranges::input_range<std::ranges::range_reference_t<trace_matrix_t>>)
164 static_assert(std::ranges::viewable_range<score_matrix_reference_type>);
165 static_assert(std::ranges::viewable_range<trace_matrix_reference_type>);
169 decltype(
views::zip(std::declval<score_matrix_reference_type>(), std::declval<trace_matrix_reference_type>()));
176 template <std::ranges::input_range other_score_matrix_t, std::ranges::input_range other_trace_matrix_t>
177 requires (std::ranges::input_range<std::ranges::range_reference_t<other_score_matrix_t>>
178 && std::ranges::input_range<std::ranges::range_reference_t<other_trace_matrix_t>>)
182 static constexpr auto transform_to_combined_matrix_cell = std::views::transform(
185 using fwd_tuple_t =
decltype(tpl);
199 using value_type =
decltype(std::declval<combined_column_type>() | transform_to_combined_matrix_cell);
226 score_matrix_it{std::move(score_matrix_it)},
227 trace_matrix_it{std::move(trace_matrix_it)}
237 return views::zip(*score_matrix_it, *trace_matrix_it) | transform_to_combined_matrix_cell;
267template <std::ranges::input_range score_matrix_t, std::ranges::input_range trace_matrix_t>
268 requires (std::ranges::input_range<std::ranges::range_reference_t<score_matrix_t>>
269 && std::ranges::input_range<std::ranges::range_reference_t<trace_matrix_t>>)
295 score_matrix_sentinel{std::move(score_matrix_sentinel)}
305 return rhs.equal(lhs);
317 return !(lhs == rhs);
323 return !(lhs == rhs);
339 return iter.score_matrix_it == score_matrix_sentinel;
Provides seqan3::detail::affine_cell_proxy.
A proxy for an affine score matrix cell.
Definition affine_cell_proxy.hpp:114
Combined score and trace matrix iterator for the pairwise sequence alignment.
Definition combined_score_and_trace_matrix.hpp:157
void operator++(int)
Advance the iterator to the next alignment matrix column.
Definition combined_score_and_trace_matrix.hpp:253
iterator(iterator const &)=default
Defaulted.
std::ranges::iterator_t< trace_matrix_t > trace_matrix_iter_type
The type of the trace matrix iterator.
Definition combined_score_and_trace_matrix.hpp:173
iterator & operator=(iterator &&)=default
Defaulted.
iterator & operator++()
Advance the iterator to the next alignment matrix column.
Definition combined_score_and_trace_matrix.hpp:245
value_type reference
The reference type.
Definition combined_score_and_trace_matrix.hpp:201
reference operator*() const
Returns the range over the current column.
Definition combined_score_and_trace_matrix.hpp:235
void pointer
The pointer type.
Definition combined_score_and_trace_matrix.hpp:203
std::ranges::range_reference_t< score_matrix_t > score_matrix_reference_type
The reference type of the score matrix.
Definition combined_score_and_trace_matrix.hpp:160
iterator & operator=(iterator const &)=default
Defaulted.
iterator(iterator &&)=default
Defaulted.
iterator()=default
Defaulted.
decltype(std::declval< combined_column_type >()|transform_to_combined_matrix_cell) value_type
The value type.
Definition combined_score_and_trace_matrix.hpp:199
score_matrix_iter_type score_matrix_it
The current iterator over the score matrix.
Definition combined_score_and_trace_matrix.hpp:190
std::ranges::iterator_t< score_matrix_t > score_matrix_iter_type
The type of the score matrix iterator.
Definition combined_score_and_trace_matrix.hpp:171
iterator(score_matrix_iter_type score_matrix_it, trace_matrix_iter_type trace_matrix_it) noexcept
Initialises the iterator from the underlying matrix.
Definition combined_score_and_trace_matrix.hpp:225
std::ranges::range_reference_t< trace_matrix_t > trace_matrix_reference_type
The reference type of the trace matrix.
Definition combined_score_and_trace_matrix.hpp:162
~iterator()=default
Defaulted.
trace_matrix_iter_type trace_matrix_it
The current iterator over the trace matrix.
Definition combined_score_and_trace_matrix.hpp:192
decltype(views::zip(std::declval< score_matrix_reference_type >(), std::declval< trace_matrix_reference_type >())) combined_column_type
The combined column type.
Definition combined_score_and_trace_matrix.hpp:169
The sentinel type for the seqan3::detail::combined_score_and_trace_matrix.
Definition combined_score_and_trace_matrix.hpp:271
friend bool operator==(iterator const &lhs, sentinel const &rhs) noexcept
Checks if the iterator reached the end of the matrix.
Definition combined_score_and_trace_matrix.hpp:303
friend bool operator!=(iterator const &lhs, sentinel const &rhs) noexcept
Checks if the iterator did not reach the end of the matrix.
Definition combined_score_and_trace_matrix.hpp:315
~sentinel()=default
Defaulted.
constexpr bool equal(iterator const &iter) const noexcept
Compares the stored score matrix sentinel with the given iterator.
Definition combined_score_and_trace_matrix.hpp:337
friend bool operator!=(sentinel const &lhs, iterator const &rhs) noexcept
Checks if the iterator did not reach the end of the matrix.
Definition combined_score_and_trace_matrix.hpp:321
sentinel(sentinel &&)=default
Defaulted.
sentinel & operator=(sentinel const &)=default
Defaulted.
friend bool operator==(sentinel const &lhs, iterator const &rhs) noexcept
Checks if the iterator reached the end of the matrix.
Definition combined_score_and_trace_matrix.hpp:309
sentinel(sentinel const &)=default
Defaulted.
sentinel(score_matrix_sentinel_type score_matrix_sentinel) noexcept
Initialises the sentinel from the underlying matrix.
Definition combined_score_and_trace_matrix.hpp:294
sentinel & operator=(sentinel &&)=default
Defaulted.
std::ranges::sentinel_t< score_matrix_t > score_matrix_sentinel_type
The sentinel type of the underlying score matrix.
Definition combined_score_and_trace_matrix.hpp:274
sentinel()=default
Defaulted.
An alignment matrix that combines a score matrix with a trace matrix into a common interface.
Definition combined_score_and_trace_matrix.hpp:45
sentinel end() const =delete
This alignment matrix is not const-iterable.
auto trace_path(matrix_coordinate const &from_coordinate) const
Returns a trace path starting from the given coordinate and ending in the cell with seqan3::detail::t...
Definition combined_score_and_trace_matrix.hpp:136
combined_score_and_trace_matrix & operator=(combined_score_and_trace_matrix const &)=default
Defaulted.
void resize(column_index_type< column_index_t > const column_count, row_index_type< row_index_t > const row_count, score_type const initial_score=score_type{})
Resizes the matrix.
Definition combined_score_and_trace_matrix.hpp:92
~combined_score_and_trace_matrix()=default
Defaulted.
combined_score_and_trace_matrix()=default
Defaulted.
combined_score_and_trace_matrix(combined_score_and_trace_matrix &&)=default
Defaulted.
iterator begin()
Returns the iterator pointing to the first alignment column.
Definition combined_score_and_trace_matrix.hpp:110
combined_score_and_trace_matrix & operator=(combined_score_and_trace_matrix &&)=default
Defaulted.
combined_score_and_trace_matrix(combined_score_and_trace_matrix const &)=default
Defaulted.
iterator begin() const =delete
This score matrix is not const-iterable.
sentinel end()
Returns the sentinel pointing behind the last alignment column.
Definition combined_score_and_trace_matrix.hpp:119
Provides various transformation traits used by the range module.
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
Provides seqan3::detail::matrix_index, seqan3::detail::matrix_coordinate and associated strong types.
The internal SeqAn3 namespace.
Definition aligned_sequence_concept.hpp:26
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
Provides concepts that do not have equivalents in C++20.
Provides seqan3::views::zip.