A CRTP-base class for trace iterator implementations for the alignment algorithms. More...

#include <seqan3/alignment/matrix/detail/trace_iterator_base.hpp>

Inheritance diagram for seqan3::detail::trace_iterator_base< derived_t, matrix_iter_t >:

Public Types
Associated types
using	value_type = trace_directions
	The value type.

using	reference = trace_directions const &
	The reference type.

using	pointer = value_type const *
	The pointer type.

using	difference_type = std::ptrdiff_t
	The difference type.

using	iterator_category = std::forward_iterator_tag

Public Member Functions
Element access
reference	operator* () const noexcept
	Returns the current trace direction.

pointer	operator-> () const noexcept
	Returns a pointer to the current trace direction.

constexpr matrix_coordinate	coordinate () const noexcept
	Returns the current coordinate in two-dimensional space.

Arithmetic operators
constexpr derived_t &	operator++ () noexcept
	Advances the iterator by one.

constexpr derived_t	operator++ (int) noexcept
	Returns an iterator advanced by one.

Private Member Functions
constexpr derived_t const &	derived () const noexcept
	This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.

constexpr derived_t &	derived () noexcept
	Cast this object to its derived type.

void	set_trace_direction (trace_directions const dir) noexcept
	Updates the current trace direction.

Constructors, destructor and assignment
constexpr	trace_iterator_base ()=default
	Defaulted.

constexpr	trace_iterator_base (trace_iterator_base const &)=default
	Defaulted.

constexpr	trace_iterator_base (trace_iterator_base &&)=default
	Defaulted.

constexpr trace_iterator_base &	operator= (trace_iterator_base const &)=default
	Defaulted.

constexpr trace_iterator_base &	operator= (trace_iterator_base &&)=default
	Defaulted.

	~trace_iterator_base ()=default
	Defaulted.

constexpr	trace_iterator_base (matrix_iter_t const matrix_iter) noexcept
	Constructs from the underlying trace matrix iterator indicating the start of the trace path.

template<typename other_derived_t , two_dimensional_matrix_iterator other_matrix_iter_t> requires std::constructible_from<matrix_iter_t, other_matrix_iter_t>
constexpr	trace_iterator_base (trace_iterator_base< other_derived_t, other_matrix_iter_t > const &other) noexcept
	Constructs from the underlying trace matrix iterator indicating the start of the trace path.

Overload functions
These functions can be overloaded by the derived class to customise the iterator.
constexpr void	go_left (matrix_iter_t &iter) const noexcept
	Moves iterator to previous left cell.

constexpr void	go_up (matrix_iter_t &iter) const noexcept
	Moves iterator to previous up cell.

constexpr void	go_diagonal (matrix_iter_t &iter) const noexcept
	Moves iterator to previous diagonal cell.

Private Attributes
trace_directions	current_direction {}
	The current trace direction.

friend	derived_t
	Befriend the derived iterator class to allow calling the private constructors.

matrix_iter_t	matrix_iter {}
	The underlying matrix iterator.

Friends
template<typename other_derived_t , two_dimensional_matrix_iterator other_matrix_iter_t>
class	trace_iterator_base
	Befriend with corresponding const_iterator.

Comparison operators
constexpr friend bool	operator== (derived_t const &lhs, derived_t const &rhs) noexcept
	Returns `true` if both iterators are equal, `false` otherwise.

constexpr friend bool	operator== (derived_t const &lhs, std::default_sentinel_t const &) noexcept
	Returns `true` if the pointed-to-element is seqan3::detail::trace_directions::none.

constexpr friend bool	operator== (std::default_sentinel_t const &, derived_t const &rhs) noexcept
	copydoc operator==()

constexpr friend bool	operator!= (derived_t const &lhs, derived_t const &rhs) noexcept
	Returns `true` if both iterators are not equal, `false` otherwise.

constexpr friend bool	operator!= (derived_t const &lhs, std::default_sentinel_t const &) noexcept
	Returns `true` if the pointed-to-element is not seqan3::detail::trace_directions::none.

constexpr friend bool	operator!= (std::default_sentinel_t const &, derived_t const &rhs) noexcept
	copydoc operator!=()

Detailed Description

template<typename derived_t, two_dimensional_matrix_iterator matrix_iter_t>
class seqan3::detail::trace_iterator_base< derived_t, matrix_iter_t >

A CRTP-base class for trace iterator implementations for the alignment algorithms.

Template Parameters

derived_t	The derived iterator type.
matrix_iter_t	The wrapped matrix iterator; must model seqan3::detail::two_dimensional_matrix_iterator and the iterator's value type must be the same as seqan3::detail::trace_directions, i.e. `std::same_as<std::iter_value_t<matrix_iter_t>, trace_directions>` must evaluate to `true`.

This iterator follows the trace path generated by the alignment algorithm. It wraps an underlying seqan3::detail::two_dimensional_matrix_iterator over a trace matrix, whose value type is seqan3::detail::trace_directions. The iterator moves along the trace path until it finds a cell with seqan3::detail::trace_directions::none. Accordingly, when advancing this iterator, it actually moves from right to left and from bottom to top in the underlying matrix. When the iterator is dereferenced, it outputs any of the following direction: seqan3::detail::trace_directions::diagonal, seqan3::detail::trace_directions::up, or seqan3::detail::trace_directions::left.

In addition, the iterator provides an additional member to access the current position as a seqan3::detail::matrix_coordinate.

This iterator also models the Cpp17ForwardIterator. Note, it does not directly dereference the actual trace direction stored in the underlying matrix. Thus, it cannot be used as an output iterator.

Overloading the behaviour

The behaviour of following a trace direction can be customised through the derived type by overloading the functions

In the default implementation they move along an unbanded matrix. This means, they go to the previous cell in the respective direction.

Member Typedef Documentation

◆ iterator_category

template<typename derived_t , two_dimensional_matrix_iterator matrix_iter_t>

using seqan3::detail::trace_iterator_base< derived_t, matrix_iter_t >::iterator_category = std::forward_iterator_tag

Forward iterator tag.

Constructor & Destructor Documentation

◆ trace_iterator_base() [1/2]

template<typename derived_t , two_dimensional_matrix_iterator matrix_iter_t>

constexpr seqan3::detail::trace_iterator_base< derived_t, matrix_iter_t >::trace_iterator_base ( matrix_iter_t const matrix_iter )

inlineconstexprprivatenoexcept

Constructs from the underlying trace matrix iterator indicating the start of the trace path.

Parameters

[in] matrix_iter The underlying matrix iterator.

◆ trace_iterator_base() [2/2]

template<typename derived_t , two_dimensional_matrix_iterator matrix_iter_t>

template<typename other_derived_t , two_dimensional_matrix_iterator other_matrix_iter_t>
requires std::constructible_from<matrix_iter_t, other_matrix_iter_t>

constexpr seqan3::detail::trace_iterator_base< derived_t, matrix_iter_t >::trace_iterator_base ( trace_iterator_base< other_derived_t, other_matrix_iter_t > const & other )

inlineconstexprprivatenoexcept

Constructs from the underlying trace matrix iterator indicating the start of the trace path.

Template Parameters

other_matrix_iter_t The underlying matrix iterator type of other; the condition std::constructible_from<matrix_iter_t, other_matrix_iter_t> must evaluate to true.

Parameters

[in] other The underlying matrix iterator.

Allows the conversion of non-const to const iterator.

The documentation for this class was generated from the following file:

trace_iterator_base.hpp

Public Types

Public Member Functions

Private Member Functions

Private Attributes

Friends

Detailed Description

Overloading the behaviour

Member Typedef Documentation

◆ iterator_category

Constructor & Destructor Documentation

◆ trace_iterator_base() [1/2]

◆ trace_iterator_base() [2/2]