seqan3::alignment_coordinate Class Reference

Represents the begin/end of the pairwise alignment in the respective sequences. More...

#include <seqan3/alignment/matrix/alignment_coordinate.hpp>

Inheritance diagram for seqan3::alignment_coordinate:

Public Member Functions
Constructors, destructor and assignment
constexpr	alignment_coordinate ()=default
	Defaulted.
constexpr	alignment_coordinate (alignment_coordinate const &)=default
	Defaulted.
constexpr	alignment_coordinate (alignment_coordinate &&)=default
	Defaulted.
constexpr alignment_coordinate &	operator= (alignment_coordinate const &)=default
	Defaulted.
constexpr alignment_coordinate &	operator= (alignment_coordinate &&)=default
	Defaulted.
	~alignment_coordinate ()=default
	Defaulted.
constexpr	alignment_coordinate (base_t const &base)
	Constructs from the seqan3::detail::advanceable_alignment_coordinate base class.
constexpr	alignment_coordinate (base_t &&base)
	Constructs from the seqan3::detail::advanceable_alignment_coordinate base class.
Public Member Functions inherited from seqan3::detail::advanceable_alignment_coordinate< detail::advanceable_alignment_coordinate_state::none >
constexpr	advanceable_alignment_coordinate () noexcept=default
constexpr	advanceable_alignment_coordinate (advanceable_alignment_coordinate const &) noexcept=default
	Defaulted.
constexpr	advanceable_alignment_coordinate (advanceable_alignment_coordinate &&) noexcept=default
constexpr	advanceable_alignment_coordinate (advanceable_alignment_coordinate< other_state > const &other)
	Copy-constructs from another advanceable_alignment_coordinate with a different policy.
constexpr	advanceable_alignment_coordinate (advanceable_alignment_coordinate< other_state > &&other)
	Move-constructs from another advanceable_alignment_coordinate with a different policy.
constexpr	advanceable_alignment_coordinate (column_index_type< size_t > const c_idx, row_index_type< size_t > const r_idx) noexcept
	Construction from the respective column and row indices. More...
constexpr advanceable_alignment_coordinate &	operator= (advanceable_alignment_coordinate const &) noexcept=default
	Defaulted.
constexpr advanceable_alignment_coordinate &	operator= (advanceable_alignment_coordinate &&) noexcept=default
	Defaulted.
	~advanceable_alignment_coordinate () noexcept=default
	Defaulted.
constexpr advanceable_alignment_coordinate &	operator++ () noexcept
	Increments the coordinate depending on the set policy by one. More...
constexpr advanceable_alignment_coordinate	operator++ (int) noexcept
	Post-increments the coordinate depending on the set policy by one. More...
constexpr advanceable_alignment_coordinate &	operator-- () noexcept
	Decrements the coordinate depending on the set policy by one. More...
constexpr advanceable_alignment_coordinate	operator-- (int) noexcept
	Post-decrements the coordinate depending on the set policy by one. More...
constexpr advanceable_alignment_coordinate &	operator+= (difference_type const offset) noexcept
	Returns the coordinate which is advanced depending on the set policy by offset. More...
constexpr advanceable_alignment_coordinate &	operator-= (difference_type const offset) noexcept
	Returns the coordinate which is advanced depending on the set policy by -offset. More...
constexpr advanceable_alignment_coordinate	operator+ (difference_type const offset) const noexcept
	Returns a new coordinate which is advanced depending on the set policy by offset. More...
constexpr advanceable_alignment_coordinate	operator- (difference_type const offset) const noexcept
	Returns a new coordinate which is advanced depending on the set policy by -offset. More...
constexpr difference_type	operator- (advanceable_alignment_coordinate const &other) const noexcept
	Returns the difference of this and another coordinate depending on the set policy. More...

Public Attributes
size_t	first
	The begin/end position of the alignment in the first sequence.
size_t	second
	The begin/end position of the alignment in the second sequence.
Public Attributes inherited from seqan3::detail::advanceable_alignment_coordinate< detail::advanceable_alignment_coordinate_state::none >
size_t	first
	The front/back position of the alignment in the first sequence.
size_t	second
	The front/back position of the alignment in the second sequence.

Private Types
using	base_t = detail::advanceable_alignment_coordinate< detail::advanceable_alignment_coordinate_state::none >
	The type of the base class.

Private Member Functions
constexpr	operator detail::matrix_coordinate () const
	Implicit conversion to seqan3::detail::matrix_coordinate.

Additional Inherited Members
Public Types inherited from seqan3::detail::advanceable_alignment_coordinate< detail::advanceable_alignment_coordinate_state::none >
using	difference_type = std::make_signed_t< size_t >
	Defines the difference type to model the std::weakly_incrementable concept.

Detailed Description

Represents the begin/end of the pairwise alignment in the respective sequences.

This class only gives access to the respective positions of the sequences and is meant for the user interface. The additional complexity of an advanceable coordinate using the seqan3::detail::advanceable_alignment_coordinate is only necessary for the implementation of the pairwise alignment algorithm. Within in the algorithm the coordinate is used in combination with a seqan3::views::iota to keep track of the current position within the alignment matrix. For the user, however, this interface adds no benefit as they are only interested in the front/back coordinates for the respective alignment.

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

• seqan3/alignment/matrix/alignment_coordinate.hpp