58template <
typename value_t,
71 template <
bool const_range>
83 using pointer =
typename storage_type::pointer;
118 template <std::ranges::forward_range entries_t>
119 requires (std::convertible_to<std::ranges::range_value_t<entries_t>,
value_type>)
124 static_assert(std::move_constructible<std::ranges::range_value_t<entries_t>>,
125 "The value type must be moveable.");
127 assert(
static_cast<size_t>(std::ranges::distance(entries)) == (
row_dim.get() *
col_dim.get()));
137 assert(
static_cast<size_t>(std::ranges::distance(entries)) == (
row_dim.get() *
col_dim.get()));
166 template <
typename other_value_t,
typename other_allocator_t, matrix_major_order other_order>
167 requires std::assignable_from<other_value_t &, value_t &>
172 for (
size_t i = 0; i <
cols(); ++i)
174 for (
size_t j = 0; j <
rows(); ++j)
177 (*this)[coord] =
matrix[coord];
188 assert(coordinate.col <
cols());
189 assert(coordinate.row <
rows());
199 assert(coordinate.col <
cols());
200 assert(coordinate.row <
rows());
210 if (coordinate.col >=
cols())
211 throw std::invalid_argument{
"Column index is out of range. Please check the dimensions of the matrix."};
212 if (coordinate.row >=
rows())
213 throw std::invalid_argument{
"Row index is out of range. Please check the dimensions of the matrix."};
215 return (*
this)[coordinate];
221 if (coordinate.col >=
cols())
222 throw std::invalid_argument{
"Column index is out of range. Please check the dimensions of the matrix."};
223 if (coordinate.row >=
rows())
224 throw std::invalid_argument{
"Row index is out of range. Please check the dimensions of the matrix."};
226 return (*
this)[coordinate];
319template <
typename value_t,
typename allocator_t, matrix_major_order order>
320template <
bool const_range>
332 template <
typename derived_t, matrix_major_order other_order>
336 template <
bool other_const_range>
351 using pointer =
typename storage_iterator::pointer;
378 : matrix_ptr{other.matrix_ptr}, host_iter{other.host_iter}
383 using base_t::operator+=;
388 assert(matrix_ptr !=
nullptr);
392 host_iter += (
offset.col * matrix_ptr->rows());
398 host_iter += (
offset.row * matrix_ptr->cols());
406 assert(matrix_ptr !=
nullptr);
408 auto diff = *
this - matrix_ptr->begin();
Defines the requirements of a matrix (e.g. score matrices, trace matrices).
Definition matrix_concept.hpp:58
CRTP base class to declare a strong typedef for a regular type to avoid ambiguous parameter settings ...
Definition strong_type.hpp:174
constexpr value_t & get() &noexcept
Returns the underlying value.
Definition strong_type.hpp:201
constexpr strong_type() noexcept=default
Defaulted.
A two-dimensional matrix iterator.
Definition two_dimensional_matrix.hpp:323
constexpr basic_iterator(parent_t &matrix, storage_iterator iter)
Construction from the underlying matrix and the iterator over actual storage.
Definition two_dimensional_matrix.hpp:372
matrix_coordinate coordinate() const noexcept
Returns the current position of the iterator as a two-dimensional matrix coordinate.
Definition two_dimensional_matrix.hpp:404
constexpr basic_iterator & operator+=(matrix_offset const &offset) noexcept
Advances the iterator by the given offset.
Definition two_dimensional_matrix.hpp:386
constexpr basic_iterator(basic_iterator &&)=default
Defaulted.
constexpr basic_iterator & operator=(basic_iterator &&)=default
Defaulted.
detail::maybe_const_iterator_t< const_range, storage_type > storage_iterator
The iterator of the underlying storage.
Definition two_dimensional_matrix.hpp:340
typename storage_iterator::pointer pointer
The pointer type.
Definition two_dimensional_matrix.hpp:351
constexpr basic_iterator & operator=(basic_iterator const &)=default
Defaulted.
constexpr basic_iterator()=default
Defaulted.
~basic_iterator()=default
Defaulted.
constexpr basic_iterator(basic_iterator const &)=default
Defaulted.
constexpr basic_iterator(basic_iterator<!const_range > const &other) noexcept
Construction of cons-iterator from non-const-iterator.
Definition two_dimensional_matrix.hpp:376
A crtp-base class for iterators over seqan3::detail::two_dimensional_matrix.
Definition two_dimensional_matrix_iterator_base.hpp:74
A two dimensional matrix used inside of alignment algorithms.
Definition two_dimensional_matrix.hpp:62
size_type row_dim
The number of rows in the matrix.
Definition two_dimensional_matrix.hpp:307
two_dimensional_matrix(number_rows const row_dim, number_cols const col_dim)
Constructs the matrix by the given dimensions.
Definition two_dimensional_matrix.hpp:105
constexpr iterator begin() noexcept
Returns an iterator pointing to the first element of the matrix.
Definition two_dimensional_matrix.hpp:270
typename storage_type::reference reference
The reference type.
Definition two_dimensional_matrix.hpp:81
typename storage_type::pointer pointer
The pointer type.
Definition two_dimensional_matrix.hpp:83
constexpr const_reference operator[](matrix_coordinate const &coordinate) const noexcept
Returns a reference to the element at the given coordinate.
Definition two_dimensional_matrix.hpp:197
constexpr two_dimensional_matrix(two_dimensional_matrix< other_value_t, other_allocator_t, other_order > const &matrix)
Explicit construction from the other major-order.
Definition two_dimensional_matrix.hpp:168
constexpr const_iterator begin() const noexcept
Returns an iterator pointing to the first element of the matrix.
Definition two_dimensional_matrix.hpp:275
two_dimensional_matrix & operator=(two_dimensional_matrix &&)=default
Defaulted.
two_dimensional_matrix()=default
Defaulted.
size_type col_dim
The number of columns in the matrix.
Definition two_dimensional_matrix.hpp:308
void resize(number_rows const row_dim, number_cols const col_dim)
Resizes the underlying matrix storage to the given matrix dimensions.
Definition two_dimensional_matrix.hpp:234
constexpr const_pointer data() const noexcept
Returns a pointer to the data.
Definition two_dimensional_matrix.hpp:260
typename storage_type::const_reference const_reference
The const reference type.
Definition two_dimensional_matrix.hpp:82
constexpr const_iterator cbegin() const noexcept
Returns an iterator pointing to the first element of the matrix.
Definition two_dimensional_matrix.hpp:281
two_dimensional_matrix(two_dimensional_matrix const &)=default
Defaulted.
constexpr pointer data() noexcept
Returns a pointer to the data.
Definition two_dimensional_matrix.hpp:254
constexpr reference operator[](matrix_coordinate const &coordinate) noexcept
Returns a reference to the element at the given coordinate.
Definition two_dimensional_matrix.hpp:186
storage_type storage
The matrix as a one-dimensional (flattened) vector of entries.
Definition two_dimensional_matrix.hpp:306
two_dimensional_matrix(number_rows const row_dim, number_cols const col_dim, entries_t entries)
Constructs the matrix by the given dimensions and initialises it with the given range.
Definition two_dimensional_matrix.hpp:120
~two_dimensional_matrix()=default
Defaulted.
constexpr const_iterator cend() const noexcept
Returns an iterator pointing behind-the-end of the matrix.
Definition two_dimensional_matrix.hpp:299
size_t cols() const noexcept
The number of columns in the matrix.
Definition two_dimensional_matrix.hpp:248
constexpr const_reference at(matrix_coordinate const &coordinate) const
A reference to the entry of the matrix at the given coordinate.
Definition two_dimensional_matrix.hpp:219
typename storage_type::value_type value_type
The value type.
Definition two_dimensional_matrix.hpp:80
two_dimensional_matrix(number_rows const row_dim, number_cols const col_dim, storage_type entries)
This is an overloaded member function, provided for convenience. It differs from the above function o...
Definition two_dimensional_matrix.hpp:133
typename storage_type::const_pointer const_pointer
The pointer type.
Definition two_dimensional_matrix.hpp:84
constexpr iterator end() noexcept
Returns an iterator pointing behind-the-end of the matrix.
Definition two_dimensional_matrix.hpp:287
constexpr reference at(matrix_coordinate const &coordinate)
A reference to the entry of the matrix at the given coordinate.
Definition two_dimensional_matrix.hpp:208
two_dimensional_matrix(two_dimensional_matrix &&)=default
Defaulted.
two_dimensional_matrix & operator=(two_dimensional_matrix const &)=default
Defaulted.
constexpr const_iterator end() const noexcept
Returns an iterator pointing behind-the-end of the matrix.
Definition two_dimensional_matrix.hpp:293
typename storage_type::size_type size_type
The difference type.
Definition two_dimensional_matrix.hpp:86
size_t rows() const noexcept
The number of rows in the matrix.
Definition two_dimensional_matrix.hpp:242
typename storage_type::difference_type difference_type
The difference type.
Definition two_dimensional_matrix.hpp:85
Provides various transformation traits used by the range module.
Provides seqan3::detail::deferred_crtp_base.
matrix_major_order
Selects the major order of the matrix.
Definition two_dimensional_matrix_iterator_base.hpp:36
@ column
Accesses matrix in column major order.
@ row
Accesses matrix in row major order.
std::ranges::iterator_t< maybe_const_range_t< const_range, range_t > > maybe_const_iterator_t
Returns the const iterator of range_t if const_range is true; otherwise the non-const iterator.
Definition core/range/type_traits.hpp:41
@ offset
Sequence (seqan3::field::seq) relative start position (0-based), unsigned value.
Provides seqan3::detail::matrix_index, seqan3::detail::matrix_coordinate and associated strong types.
The internal SeqAn3 namespace.
Definition aligned_sequence_concept.hpp:26
constexpr auto const & get(configuration< configs_t... > const &config) noexcept
This is an overloaded member function, provided for convenience. It differs from the above function o...
Definition configuration.hpp:412
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 column dimension of a matrix.
Definition two_dimensional_matrix.hpp:29
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 type traits for working with templates.
Provides seqan3::detail::two_dimensional_matrix_iterator_base.