seqan3::shape Class Reference

A class that defines which positions of a pattern to hash. More...

#include <seqan3/search/kmer_index/shape.hpp>

Inheritance diagram for seqan3::shape:

Public Member Functions
Constructors, destructor and assignment
constexpr	shape () noexcept=default
	Defaulted.
constexpr	shape (shape const &) noexcept=default
	Defaulted.
constexpr	shape (shape &&) noexcept=default
	Defaulted.
constexpr shape &	operator= (shape const &) noexcept=default
	Defaulted.
constexpr shape &	operator= (shape &&) noexcept=default
	Defaulted.
	~shape () noexcept=default
	Defaulted.
constexpr	shape (ungapped k) noexcept
	Construct an ungapped shape from a given size.
constexpr	shape (bin_literal const literal) noexcept
	Construct from a given seqan3::bin_literal.
Public Member Functions inherited from seqan3::dynamic_bitset< 58 >
constexpr	dynamic_bitset () noexcept=default
	Defaulted.
constexpr	dynamic_bitset (dynamic_bitset const &) noexcept=default
	Defaulted.
constexpr	dynamic_bitset (dynamic_bitset &&) noexcept=default
	Defaulted.
constexpr	dynamic_bitset (uint64_t const value)
	Construct from an uint64_t.
constexpr	dynamic_bitset (begin_it_type begin_it, end_it_type end_it) noexcept
	Construct from two iterators.
constexpr	dynamic_bitset (other_range_t &&range) noexcept
	Construct from a different range.
constexpr	dynamic_bitset (size_type const n, value_type const value) noexcept
	Construct with n times value.
constexpr	dynamic_bitset (char const(&lit)[N])
	Construction from literal.
constexpr dynamic_bitset &	operator= (dynamic_bitset const &) noexcept=default
	Defaulted.
constexpr dynamic_bitset &	operator= (dynamic_bitset &&) noexcept=default
	Defaulted.
constexpr dynamic_bitset &	operator= (std::initializer_list< value_type > const ilist) noexcept
	Assign from std::initializer_list.
constexpr dynamic_bitset &	operator= (char const(&lit)[N])
	Assign from literal.
	~dynamic_bitset () noexcept=default
	Defaulted.
constexpr void	assign (char const(&lit)[N])
	Assign from literal.
constexpr void	assign (std::initializer_list< value_type > const ilist) noexcept
	Assign from std::initializer_list.
constexpr void	assign (size_type const count, value_type const value) noexcept
	Assign with count times value.
constexpr void	assign (other_range_t &&range) noexcept
	Assign from a different range.
constexpr void	assign (begin_it_type begin_it, end_it_type end_it) noexcept
	Assign from pair of iterators.
constexpr iterator	begin () noexcept
	Returns the begin to the dynamic_bitset.
constexpr const_iterator	begin () const noexcept
	Returns the begin to the dynamic_bitset.
constexpr const_iterator	cbegin () const noexcept
	Returns the begin to the dynamic_bitset.
constexpr iterator	end () noexcept
	Returns iterator past the end of the dynamic_bitset.
constexpr const_iterator	end () const noexcept
	Returns iterator past the end of the dynamic_bitset.
constexpr const_iterator	cend () const noexcept
	Returns iterator past the end of the dynamic_bitset.
constexpr dynamic_bitset &	operator&= (dynamic_bitset const &rhs) noexcept
	Sets the bits to the result of binary AND on corresponding pairs of bits of *this and rhs.
constexpr dynamic_bitset &	operator|= (dynamic_bitset const &rhs) noexcept
	Sets the bits to the result of binary OR on corresponding pairs of bits of *this and rhs.
constexpr dynamic_bitset &	operator^= (dynamic_bitset const &rhs) noexcept
	Sets the bits to the result of binary XOR on corresponding pairs of bits of *this and rhs.
constexpr dynamic_bitset	operator~ () const noexcept
	Returns a temporary copy of *this with all bits flipped (binary NOT).
constexpr dynamic_bitset &	operator<<= (size_t const count) noexcept
	Performs binary shift left on the current object.
constexpr dynamic_bitset &	operator>>= (size_t const count) noexcept
	Performs binary shift right on the current object.
constexpr dynamic_bitset	operator>> (size_t const count) const noexcept
	Performs binary shift right.
constexpr dynamic_bitset	operator<< (size_t const count) const noexcept
	Performs binary shift left.
constexpr dynamic_bitset &	set () noexcept
	Sets all bits to 1.
constexpr dynamic_bitset &	set (size_t const i, bool const value=true)
	Sets the i'th bit to value.
constexpr dynamic_bitset &	reset () noexcept
	Sets all bits to 0.
constexpr dynamic_bitset &	reset (size_t const i)
	Sets the i'th bit to false.
constexpr dynamic_bitset &	flip () noexcept
	Flips all bits (binary NOT).
constexpr dynamic_bitset &	flip (size_t const i)
	Flips the i'th bit (binary NOT).
constexpr bool	all () const noexcept
	Checks if all bit are set.
constexpr bool	any () const noexcept
	Checks if any bit is set.
constexpr bool	none () const noexcept
	Checks if no bit is set.
constexpr size_type	count () const noexcept
	Returns the number of set bits.
constexpr reference	at (size_t const i)
	Returns the i-th element.
constexpr const_reference	at (size_t const i) const
	Returns the i-th element.
constexpr const_reference	test (size_t const i) const
	Returns the i-th element.
constexpr reference	operator[] (size_t const i) noexcept
	Returns the i-th element.
constexpr const_reference	operator[] (size_t const i) const noexcept
	Returns the i-th element.
constexpr reference	front () noexcept
	Returns the first element.
constexpr const_reference	front () const noexcept
	Returns the first element.
constexpr reference	back () noexcept
	Returns the last element.
constexpr const_reference	back () const noexcept
	Returns the last element.
constexpr bitfield *	raw_data () noexcept
	Direct access to the underlying bit field.
constexpr bitfield const *	raw_data () const noexcept
	Direct access to the underlying bit field.
constexpr bool	empty () const noexcept
	Checks whether the container is empty.
constexpr size_type	size () const noexcept
	Returns the number of elements in the container, i.e. std::distance(begin(), end()).
constexpr size_type	max_size () const noexcept
	Returns the maximum number of elements the container is able to hold and resolves to bit_capacity.
constexpr size_type	capacity () const noexcept
	Returns the number of elements that the container is able to hold and resolves to bit_capacity.
constexpr void	reserve (size_t) const noexcept
	Since the capacity is fixed on compile time, this is a no-op.
constexpr void	shrink_to_fit () const noexcept
	Since the capacity is fixed on compile time, this is a no-op.
constexpr void	clear () noexcept
	Removes all elements from the container.
constexpr iterator	insert (const_iterator pos, value_type const value) noexcept
	Inserts value before pos in the container.
constexpr iterator	insert (const_iterator pos, size_type const count, value_type const value) noexcept
	Inserts count copies of value before position in the container.
constexpr iterator	insert (const_iterator pos, begin_it_type begin_it, end_it_type end_it) noexcept
	Inserts elements from range [begin_it, end_it) before pos in the container.
constexpr iterator	insert (const_iterator pos, std::initializer_list< value_type > const &ilist) noexcept
	Inserts elements from initializer list before pos in the container.
constexpr iterator	erase (const_iterator begin_it, const_iterator end_it) noexcept
	Removes specified elements from the container.
constexpr iterator	erase (const_iterator pos) noexcept
	Removes specified elements from the container.
constexpr void	push_back (value_type const value) noexcept
	Appends the given element value to the end of the container.
constexpr void	pop_back () noexcept
	Removes the last element of the container.
constexpr void	resize (size_type const count, value_type const value=false) noexcept
	Resizes the container to contain count elements.
constexpr void	swap (dynamic_bitset &rhs) noexcept
	Swap contents with another instance.
constexpr void	swap (dynamic_bitset &&rhs) noexcept
	This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.
std::string	to_string (char_t zero=char_t{ '0'}, char_t one=char_t{ '1'}) const
	Converts the dynamic_bitset to a std::string.
constexpr unsigned long	to_ulong () const
	Converts the dynamic_bitset to an unsigned long integer.
constexpr unsigned long long	to_ullong () const
	Converts the dynamic_bitset to an unsigned long long integer.

Related Symbols
(Note that these are not member symbols.)
Other literals
constexpr shape	operator""_shape (unsigned long long const value)
	The seqan3::shape literal.

Additional Inherited Members
Public Types inherited from seqan3::dynamic_bitset< 58 >
using	value_type = bool
	Equals bool.
using	reference = reference_proxy_type
	A proxy type that enables assignment.
using	const_reference = bool
	Equals the value_type.
using	iterator = detail::random_access_iterator< dynamic_bitset >
	The iterator type of this container (a random access iterator).
using	const_iterator = detail::random_access_iterator< dynamic_bitset const >
	The const_iterator type of this container (a random access iterator).
using	difference_type = ptrdiff_t
	A std::ptrdiff_t.
using	size_type = detail::min_viable_uint_t< bit_capacity >
	An unsigned integer type (usually std::size_t).

Detailed Description

A class that defines which positions of a pattern to hash.

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

When hashing a sequence, there may be positions that do not count towards the final hash value. A shape offers an easy way to define such patterns. Given a k-mer length k (0 < k <= 58), a shape represents a binary sequence where a 0 encodes a "don't care position", i.e. a position that is not taken into account when computing the hash value. A 1 therefore translates to a position that is used to compute the hash value.

Example

// SPDX-FileCopyrightText: 2006-2025 Knut Reinert & Freie Universität Berlin
// SPDX-FileCopyrightText: 2016-2025 Knut Reinert & MPI für molekulare Genetik
// SPDX-License-Identifier: CC0-1.0
 
#include <ranges> // For std::ranges::size()
 
#include <seqan3/core/debug_stream.hpp>       // For seqan3::debug_stream
#include <seqan3/search/kmer_index/shape.hpp> // For seqan3::shape
 
using namespace seqan3::literals;
 
int main()
{
    seqan3::shape s0{seqan3::ungapped{5}};                 // represents "11111", i.e. ungapped 5-mer
    seqan3::debug_stream << s0 << '\n';                    // prints "[1,1,1,1,1]"
    seqan3::debug_stream << std::ranges::size(s0) << '\n'; // prints "5"
 
    seqan3::shape s1{seqan3::bin_literal{0b101}};          // represents "101", i.e. gapped 3-mer
    seqan3::debug_stream << s1 << '\n';                    // prints "[1,0,1]"
    seqan3::debug_stream << std::ranges::size(s1) << '\n'; // prints "3"
 
    seqan3::shape s2{0b101_shape};                         // Same as previous
    seqan3::debug_stream << s2 << '\n';                    // prints "[1,0,1]"
    seqan3::debug_stream << std::ranges::size(s2) << '\n'; // prints "3"
}

Attention

0 < size <= 58

Constructor & Destructor Documentation

shape() [1/2]

constexpr seqan3::shape::shape ( ungapped  k )

inlineconstexprnoexcept

Construct an ungapped shape from a given size.

Complexity

Linear in k.

Exceptions

No-throw guarantee.

Attention

The size must be in the interval [1, 58]. In Debug mode, an assertion will check this constraint.

shape() [2/2]

constexpr seqan3::shape::shape ( bin_literal const  literal )

inlineconstexprnoexcept

Construct from a given seqan3::bin_literal.

Complexity

Linear in the size of the bin_literal.

Exceptions

No-throw guarantee.

Attention

The size of the bin_literal must be in the interval [1, 58].

Friends And Related Symbol Documentation

operator""_shape()

constexpr shape operator""_shape ( unsigned long long const  value )

related

The seqan3::shape literal.

Parameters

[in]

value

The unsigned integer to assign.

Returns

seqan3::shape

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

• shape.hpp