Iterator for calculating hash values via a given seqan3::shape. More...

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

Inheritance diagram for seqan3::detail::kmer_hash_view< urng_t >::basic_iterator< const_range >:

Public Types
Associated types
using	difference_type = typename std::iter_difference_t< it_t >
	Type for distances between iterators.

using	value_type = size_t
	Value type of this iterator.

using	pointer = void
	The pointer type.

using	reference = value_type
	Reference to `value_type`.

using	iterator_concept = std::conditional_t< std::contiguous_iterator< it_t >, typename std::random_access_iterator_tag, detail::iterator_concept_tag_t< it_t > >
	Tag this class depending on which concept `it_t` models.

Public Types inherited from seqan3::detail::maybe_iterator_category< maybe_const_iterator_t< const_range, urng_t > >
using	iterator_category = MAYBE_PRESENT(std::iterator_traits< maybe_const_iterator_t< const_range, urng_t > >::iterator_category)
	The iterator category tag. (not always present!)

Public Member Functions
value_type	operator* () const noexcept
	Return the hash value.

basic_iterator	operator+ (difference_type const skip) const noexcept
	Forward copy of this iterator.

basic_iterator &	operator++ () noexcept
	Pre-increment.

basic_iterator	operator++ (int) noexcept
	Post-increment.

basic_iterator &	operator+= (difference_type const skip) noexcept
	Forward this iterator.

basic_iterator	operator- (difference_type const skip) const noexcept
	Return decremented copy of this iterator.

basic_iterator &	operator-- () noexcept
	Pre-decrement.

basic_iterator	operator-- (int) noexcept
	Post-decrement.

basic_iterator &	operator-= (difference_type const skip) noexcept
	Decrement iterator by `skip`.

reference	operator[] (difference_type const n) const
	Move the iterator by a given offset and return the corresponding hash value.

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

constexpr	basic_iterator (basic_iterator const &)=default
	Defaulted.

constexpr	basic_iterator (basic_iterator &&)=default
	Defaulted.

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

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

	~basic_iterator ()=default
	Defaulted.

constexpr	basic_iterator (basic_iterator<!const_range > const &it) noexcept
	Allow iterator on a const range to be constructible from an iterator over a non-const range.

	basic_iterator (it_t it_start, sentinel_t it_end, shape s_)
	Construct from a given iterator on the text and a seqan3::shape. /param[in] it_start Iterator pointing to the first position of the text. /param[in] it_end Sentinel pointing to the end of the text. /param[in] s_ The seqan3::shape that determines which positions participate in hashing.

	basic_iterator (it_t it_start, sentinel_t it_end, shape s_, bool is_end)
	Construct from a given iterator on the text and a seqan3::shape. /param[in] it_start Iterator pointing to the first position of the text. /param[in] it_end Sentinel pointing to the end of the text. /param[in] s_ The seqan3::shape that determines which positions participate in hashing. /param[in] is_end Indicates that this iterator should point to the end of the text.

Private Types
using	alphabet_t = std::iter_value_t< it_t >
	The alphabet type of the passed iterator.

using	it_t = maybe_const_iterator_t< const_range, urng_t >
	The iterator type of the underlying range.

using	sentinel_t = maybe_const_sentinel_t< const_range, urng_t >
	The sentinel type of the underlying range.

Private Member Functions
void	hash_backward ()
	Decrements iterator by 1.

void	hash_backward (difference_type const skip)
	Decrements iterator by `skip`.

void	hash_forward ()
	Increments iterator by 1.

void	hash_forward (difference_type const skip)
	Increments iterator by `skip`.

void	hash_full ()
	Calculates a hash value by explicitly looking at each position.

void	hash_roll_backward ()
	Calculates the previous hash value via rolling hash.

void	hash_roll_forward ()
	Calculates the next hash value via rolling hash.

Private Attributes
size_t	hash_value {0}
	The hash value.

size_t	roll_factor {0}
	The factor for the left most position of the hash value.

shape	shape_
	The shape to use.

it_t	text_left
	Iterator to the leftmost position of the k-mer.

it_t	text_right
	Iterator to the rightmost position of the k-mer.

Static Private Attributes
static constexpr auto const	sigma {alphabet_size<alphabet_t>}
	The alphabet size.

Friends
basic_iterator	operator+ (difference_type const skip, basic_iterator const &it) noexcept
	Non-member operator+ delegates to non-friend operator+.

difference_type	operator- (basic_iterator const &lhs, basic_iterator const &rhs) noexcept
	Return offset between two iterator's positions.

difference_type	operator- (basic_iterator const &lhs, sentinel_t const &rhs) noexcept
	Return offset this and remote sentinel's position.

basic_iterator	operator- (difference_type const skip, basic_iterator const &it) noexcept
	Non-member operator- delegates to non-friend operator-.

difference_type	operator- (sentinel_t const &lhs, basic_iterator const &rhs) noexcept
	Return offset between remote sentinel's position and this.

Comparison operators

bool	operator== (basic_iterator const &lhs, sentinel_t const &rhs) noexcept
	Compare to iterator on text.

bool	operator== (sentinel_t const &lhs, basic_iterator const &rhs) noexcept
	Compare to iterator on text.

bool	operator== (basic_iterator const &lhs, basic_iterator const &rhs) noexcept
	Compare to another basic_iterator.

bool	operator!= (basic_iterator const &lhs, sentinel_t const &rhs) noexcept
	Compare to iterator on text.

bool	operator!= (sentinel_t const &lhs, basic_iterator const &rhs) noexcept
	Compare to iterator on text.

bool	operator!= (basic_iterator const &lhs, basic_iterator const &rhs) noexcept
	Compare to another basic_iterator.

bool	operator< (basic_iterator const &lhs, basic_iterator const &rhs) noexcept
	Compare to another basic_iterator.

bool	operator> (basic_iterator const &lhs, basic_iterator const &rhs) noexcept
	Compare to another basic_iterator.

bool	operator<= (basic_iterator const &lhs, basic_iterator const &rhs) noexcept
	Compare to another basic_iterator.

bool	operator>= (basic_iterator const &lhs, basic_iterator const &rhs) noexcept
	Compare to another basic_iterator.

Detailed Description

template<std::ranges::view urng_t>
template<bool const_range>
class seqan3::detail::kmer_hash_view< urng_t >::basic_iterator< const_range >

Iterator for calculating hash values via a given seqan3::shape.

Template Parameters

urng_t Type of the text. Must model std::forward_range. Reference type must model seqan3::semialphabet.

The basic_iterator can be used to iterate over the hash values of a text. The basic_iterator needs an iterator of the text and a seqan3::shape that defines how to hash the text.

Depending on the type of the iterator passed to the basic_iterator, different functionality is available:

Concept modelled by passed text iterator	Available functions
std::forward_iterator	Comparison operators Pre-increment (++it) Post-increment (it++) Indirection operator (*it)
std::bidirectional_iterator	Pre-decrement (--it) Post-decrement (it--)
std::random_access_iterator	Forward (it +=) Forward copy (it +) Decrement(it -=) Decrement copy (it -) Difference (it1 - it2) Subscript (it[])

When using a gapped seqan3::shape, the 0s of the seqan3::shape are virtually removed from the hashed k-mer. Note that any shape is expected to start with a 1 and end with a 1.

This entity is experimental and subject to change in the future.

Implementation detail

To avoid dereferencing the sentinel when iterating, the basic_iterator computes the hash value up until the second to last position and performs the addition of the last position upon access (operator* and operator[]).

Constructor & Destructor Documentation

◆ basic_iterator() [1/2]

template<std::ranges::view urng_t>

template<bool const_range>

seqan3::detail::kmer_hash_view< urng_t >::basic_iterator< const_range >::basic_iterator	(	it_t	it_start,
		sentinel_t	it_end,
		shape	s_
	)

inline

Construct from a given iterator on the text and a seqan3::shape. /param[in] it_start Iterator pointing to the first position of the text. /param[in] it_end Sentinel pointing to the end of the text. /param[in] s_ The seqan3::shape that determines which positions participate in hashing.

Complexity

Linear in size of shape.

◆ basic_iterator() [2/2]

template<std::ranges::view urng_t>

template<bool const_range>

seqan3::detail::kmer_hash_view< urng_t >::basic_iterator< const_range >::basic_iterator	(	it_t	it_start,
		sentinel_t	it_end,
		shape	s_,
		bool	is_end
	)

inline

Construct from a given iterator on the text and a seqan3::shape. /param[in] it_start Iterator pointing to the first position of the text. /param[in] it_end Sentinel pointing to the end of the text. /param[in] s_ The seqan3::shape that determines which positions participate in hashing. /param[in] is_end Indicates that this iterator should point to the end of the text.

If we have a common_range as underlying range, we want to preserve this property. This means that we need to have a basic_iterator that can act as end for the kmer_hash_view, i.e. the text_right iterator is equal to the end iterator of the underlying range. However, we still need to do some initialisation via hash_full: When using std::views::reverse, we start iterating from the end and decrement the iterator. After calling hash_full, we need to reset our text_right iterator to point to the end again.

Another difference to the other constructor is that we need to do some work to determine the position of the text_left iterator. Note that we use std::ranges::next instead of std::ranges::prev because the latter only works for bidirectional ranges. *

Complexity

Linear in size of shape.

Member Function Documentation

◆ hash_backward() [1/2]

template<std::ranges::view urng_t>

template<bool const_range>

void seqan3::detail::kmer_hash_view< urng_t >::basic_iterator< const_range >::hash_backward ( )

inlineprivate

Decrements iterator by 1.

Attention: This function is only available if it_t models std::bidirectional_iterator.

◆ hash_backward() [2/2]

template<std::ranges::view urng_t>

template<bool const_range>

void seqan3::detail::kmer_hash_view< urng_t >::basic_iterator< const_range >::hash_backward ( difference_type const skip )

inlineprivate

Decrements iterator by skip.

Parameters

skip	Amount to decrement.

Attention: This function is only available if it_t models std::bidirectional_iterator.

◆ hash_forward()

template<std::ranges::view urng_t>

template<bool const_range>

void seqan3::detail::kmer_hash_view< urng_t >::basic_iterator< const_range >::hash_forward ( difference_type const skip )

inlineprivate

Increments iterator by skip.

Parameters

skip	Amount to increment.

Attention: This function is only available if it_t models std::random_access_iterator.

◆ hash_roll_backward()

template<std::ranges::view urng_t>

template<bool const_range>

void seqan3::detail::kmer_hash_view< urng_t >::basic_iterator< const_range >::hash_roll_backward ( )

inlineprivate

Calculates the previous hash value via rolling hash.

Attention: This function is only available if it_t models std::bidirectional_iterator.

◆ operator+()

template<std::ranges::view urng_t>

template<bool const_range>

basic_iterator seqan3::detail::kmer_hash_view< urng_t >::basic_iterator< const_range >::operator+ ( difference_type const skip ) const

inlinenoexcept

Forward copy of this iterator.

Attention: This function is only available if it_t models std::random_access_iterator.

◆ operator+=()

template<std::ranges::view urng_t>

template<bool const_range>

basic_iterator & seqan3::detail::kmer_hash_view< urng_t >::basic_iterator< const_range >::operator+= ( difference_type const skip )

inlinenoexcept

Forward this iterator.

Attention: This function is only available if it_t models std::random_access_iterator.

◆ operator-()

template<std::ranges::view urng_t>

template<bool const_range>

basic_iterator seqan3::detail::kmer_hash_view< urng_t >::basic_iterator< const_range >::operator- ( difference_type const skip ) const

inlinenoexcept

Return decremented copy of this iterator.

Attention: This function is only available if it_t models std::random_access_iterator.

◆ operator--() [1/2]

template<std::ranges::view urng_t>

template<bool const_range>

basic_iterator & seqan3::detail::kmer_hash_view< urng_t >::basic_iterator< const_range >::operator-- ( )

inlinenoexcept

Pre-decrement.

Attention: This function is only available if it_t models std::bidirectional_iterator.

◆ operator--() [2/2]

template<std::ranges::view urng_t>

template<bool const_range>

basic_iterator seqan3::detail::kmer_hash_view< urng_t >::basic_iterator< const_range >::operator-- ( int )

inlinenoexcept

Post-decrement.

Attention: This function is only available if it_t models std::bidirectional_iterator.

◆ operator-=()

template<std::ranges::view urng_t>

template<bool const_range>

basic_iterator & seqan3::detail::kmer_hash_view< urng_t >::basic_iterator< const_range >::operator-= ( difference_type const skip )

inlinenoexcept

Decrement iterator by skip.

Attention: This function is only available if it_t models std::random_access_iterator.

◆ operator[]()

template<std::ranges::view urng_t>

template<bool const_range>

reference seqan3::detail::kmer_hash_view< urng_t >::basic_iterator< const_range >::operator[] ( difference_type const n ) const

inline

Move the iterator by a given offset and return the corresponding hash value.

Attention: This function is only available if it_t models std::random_access_iterator.

Friends And Related Symbol Documentation

◆ operator+

template<std::ranges::view urng_t>

template<bool const_range>

basic_iterator operator+	(	difference_type const	skip,
		basic_iterator< const_range > const &	it
	)

friend

Non-member operator+ delegates to non-friend operator+.

Attention: This function is only available if it_t models std::random_access_iterator.

◆ operator- [1/4]

template<std::ranges::view urng_t>

template<bool const_range>

difference_type operator-	(	basic_iterator< const_range > const &	lhs,
		basic_iterator< const_range > const &	rhs
	)

friend

Return offset between two iterator's positions.

Attention: This function is only available if it_t models std::random_access_iterator.

◆ operator- [2/4]

template<std::ranges::view urng_t>

template<bool const_range>

difference_type operator-	(	basic_iterator< const_range > const &	lhs,
		sentinel_t const &	rhs
	)

friend

Return offset this and remote sentinel's position.

Attention: This function is only available if it_t and sentinel_t model std::sized_sentinel_for.

◆ operator- [3/4]

template<std::ranges::view urng_t>

template<bool const_range>

basic_iterator operator-	(	difference_type const	skip,
		basic_iterator< const_range > const &	it
	)

friend

Non-member operator- delegates to non-friend operator-.

Attention: This function is only available if it_t models std::random_access_iterator.

◆ operator- [4/4]

template<std::ranges::view urng_t>

template<bool const_range>

difference_type operator-	(	sentinel_t const &	lhs,
		basic_iterator< const_range > const &	rhs
	)

friend

Return offset between remote sentinel's position and this.

Attention: This function is only available if sentinel_t and it_t model std::sized_sentinel_for.

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

kmer_hash.hpp

Public Types

Public Member Functions

Private Types

Private Member Functions

Private Attributes

Static Private Attributes

Friends

Detailed Description

Implementation detail

Constructor & Destructor Documentation

◆ basic_iterator() [1/2]

Complexity

◆ basic_iterator() [2/2]

Complexity

Member Function Documentation

◆ hash_backward() [1/2]

◆ hash_backward() [2/2]

◆ hash_forward()

◆ hash_roll_backward()

◆ operator+()

◆ operator+=()

◆ operator-()

◆ operator--() [1/2]

◆ operator--() [2/2]

◆ operator-=()

◆ operator[]()

Friends And Related Symbol Documentation

◆ operator+

◆ operator- [1/4]

◆ operator- [2/4]

◆ operator- [3/4]

◆ operator- [4/4]