seqan3::detail::minimiser_view< urng1_t, urng2_t >::basic_iterator< const_range > Class Template Reference

Iterator for calculating minimisers. More...

#include <seqan3/search/views/minimiser.hpp>

Public Types
Associated types
using	difference_type = std::ranges::range_difference_t< urng1_t >
	Type for distances between iterators.
using	value_type = std::ranges::range_value_t< urng1_t >
	Value type of this iterator.
using	pointer = void
	The pointer type.
using	reference = value_type
	Reference to value_type.
using	iterator_category = std::forward_iterator_tag
	Tag this class as a forward iterator.
using	iterator_concept = iterator_category
	Tag this class as a forward iterator.

Public Member Functions
constexpr urng1_iterator_t	base () &&
	Return the underlying iterator. It will point to the last element in the current window.
constexpr urng1_iterator_t const &	base () const &noexcept
	Return the underlying iterator. It will point to the last element in the current window.
value_type	operator* () const noexcept
	Return the minimiser.
basic_iterator &	operator++ () noexcept
	Pre-increment.
basic_iterator	operator++ (int) noexcept
	Post-increment.
Constructors, destructor and assignment
	basic_iterator ()=default
	Defaulted.
	basic_iterator (basic_iterator const &)=default
	Defaulted.
	basic_iterator (basic_iterator &&)=default
	Defaulted.
basic_iterator &	operator= (basic_iterator const &)=default
	Defaulted.
basic_iterator &	operator= (basic_iterator &&)=default
	Defaulted.
	~basic_iterator ()=default
	Defaulted.
	basic_iterator (basic_iterator<!const_range > const &it)
	Allow iterator on a const range to be constructible from an iterator over a non-const range.
	basic_iterator (urng1_iterator_t urng1_iterator_, urng1_sentinel_t urng1_sentinel_, urng2_iterator_t urng2_iterator_, size_t window_size)
	Construct from begin and end iterators of a given range over std::totally_ordered values, and the number of values per window.

Private Types
using	urng1_iterator_t = maybe_const_iterator_t< const_range, urng1_t >
	The iterator type of the first underlying range.
using	urng1_sentinel_t = maybe_const_sentinel_t< const_range, urng1_t >
	The sentinel type of the first underlying range.
using	urng2_iterator_t = maybe_const_iterator_t< const_range, urng2_t >
	The iterator type of the second underlying range.

Private Member Functions
void	advance_window ()
	Advances the window to the next position.
bool	next_minimiser ()
	Calculates the next minimiser value.
void	next_unique_minimiser ()
	Increments iterator by 1.
void	window_first (size_t const window_size)
	Calculates minimisers for the first window.
auto	window_value () const
	Returns new window value.

Private Attributes
size_t	minimiser_position_offset {}
	The offset relative to the beginning of the window where the minimizer value is found.
value_type	minimiser_value {}
	The minimiser value.
urng1_iterator_t	urng1_iterator {}
	Iterator to the rightmost value of one window.
urng1_sentinel_t	urng1_sentinel {}
	brief Iterator to last element in range.
urng2_iterator_t	urng2_iterator {}
	Iterator to the rightmost value of one window of the second range.
std::deque< value_type >	window_values {}
	Stored values per window. It is necessary to store them, because a shift can remove the current minimiser.

Friends
Comparison operators
bool	operator== (basic_iterator const &lhs, basic_iterator const &rhs)
	Compare to another basic_iterator.
bool	operator!= (basic_iterator const &lhs, basic_iterator const &rhs)
	Compare to another basic_iterator.
bool	operator== (basic_iterator const &lhs, sentinel const &)
	Compare to the sentinel of the minimiser_view.
bool	operator== (sentinel const &lhs, basic_iterator const &rhs)
	Compare to the sentinel of the minimiser_view.
bool	operator!= (sentinel const &lhs, basic_iterator const &rhs)
	Compare to the sentinel of the minimiser_view.
bool	operator!= (basic_iterator const &lhs, sentinel const &rhs)
	Compare to the sentinel of the minimiser_view.

Detailed Description

template<std::ranges::view urng1_t, std::ranges::view urng2_t = std::ranges::empty_view<seqan3::detail::empty_type>>
template<bool const_range>
class seqan3::detail::minimiser_view< urng1_t, urng2_t >::basic_iterator< const_range >

Iterator for calculating minimisers.

Constructor & Destructor Documentation

basic_iterator()

template<std::ranges::view urng1_t, std::ranges::view urng2_t = std::ranges::empty_view<seqan3::detail::empty_type>>

template<bool const_range>

seqan3::detail::minimiser_view< urng1_t, urng2_t >::basic_iterator< const_range >::basic_iterator ( urng1_iterator_t  urng1_iterator_, urng1_sentinel_t  urng1_sentinel_, urng2_iterator_t  urng2_iterator_, size_t  window_size  )

inline

Construct from begin and end iterators of a given range over std::totally_ordered values, and the number of values per window.

Parameters

[in]	urng1_iterator_	Iterator pointing to the first position of the first std::totally_ordered range.
[in]	urng1_sentinel_	Iterator pointing to the last position of the first std::totally_ordered range.
[in]	urng2_iterator_	Iterator pointing to the first position of the second std::totally_ordered range.
[in]	window_size	The number of values in one window.

Looks at the number of values per window in two ranges, returns the smallest between both as minimiser and shifts then by one to repeat this action. If a minimiser in consecutive windows is the same, it is returned only once.

Member Function Documentation

next_minimiser()

template<std::ranges::view urng1_t, std::ranges::view urng2_t = std::ranges::empty_view<seqan3::detail::empty_type>>

template<bool const_range>

bool seqan3::detail::minimiser_view< urng1_t, urng2_t >::basic_iterator< const_range >::next_minimiser ( )

inlineprivate

Calculates the next minimiser value.

Returns

True, if new minimiser is found or end is reached. Otherwise returns false.

For the following windows, we remove the first window value (is now not in window_values) and add the new value that results from the window shifting.

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

• minimiser.hpp