aligned_sequence_concept.hpp File Reference

Includes the aligned_sequence and the related insert_gap and erase_gap functions to enable stl container support. More...

#include <algorithm>
#include <ranges>
#include <seqan3/alignment/exception.hpp>
#include <seqan3/alphabet/gap/gapped.hpp>
#include <seqan3/alphabet/range/sequence.hpp>
#include <seqan3/utility/container/concept.hpp>

Include dependency graph for aligned_sequence_concept.hpp:

This graph shows which files directly or indirectly include this file:

Go to the source code of this file.

Classes
struct	seqan3::detail::unaligned_seq< t >
	Default transformation trait that shall expose the unaligned sequence type of t when specialised. More...
struct	seqan3::detail::unaligned_seq< t >
	Exposes the unaligned sequence type given an aligned sequence container type. More...

Namespaces
namespace	seqan3
	The main SeqAn3 namespace.
namespace	seqan3::detail
	The internal SeqAn3 namespace.

Typedefs
template<typename t >
using	seqan3::detail::unaligned_seq_t = typename unaligned_seq< t >::type
	Helper type that delegates to seqan3::detail::unaligned_seq::type.

Functions
template<template< typename... > typename container_type, template< typename... > typename allocator_type, typename seq_alph_t , typename... rest_t> requires container<container_type<gapped<seq_alph_t>, allocator_type<gapped<seq_alph_t>>, rest_t...>>
constexpr auto	seqan3::detail::remove_gap_from_value_type (container_type< gapped< seq_alph_t >, allocator_type< gapped< seq_alph_t > >, rest_t... >) -> container_type< seq_alph_t, allocator_type< seq_alph_t >, rest_t... >
	This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.
template<template< typename... > typename container_type, typename seq_alph_t , typename... rest_t> requires container<container_type<gapped<seq_alph_t>, rest_t...>>
constexpr auto	seqan3::detail::remove_gap_from_value_type (container_type< gapped< seq_alph_t >, rest_t... >) -> container_type< seq_alph_t, rest_t... >
	Helper function to deduce the unaligned sequence type from an aligned sequence container.

Variables
template<typename... elems>
constexpr bool	seqan3::detail::all_model_aligned_seq = (aligned_sequence<elems> && ...)
	True, if each type models seqan3::aligned_sequence; false otherwise.
template<typename... elems>
constexpr bool	seqan3::detail::all_model_aligned_seq< type_list< elems... > > = all_model_aligned_seq<elems...>
	True, if each type in the seqan3::type_list models seqan3::aligned_sequence; false otherwise.

Detailed Description

Includes the aligned_sequence and the related insert_gap and erase_gap functions to enable stl container support.

Author

Svenja Mehringer <svenja.mehringer AT fu-berlin.de>