aligned_sequence Interface Reference

The generic concept for an aligned sequence. More...

#include <seqan3/alignment/aligned_sequence/aligned_sequence_concept.hpp>

Inheritance diagram for aligned_sequence:

Related Functions
(Note that these are not member functions.)
Requirements for seqan3::aligned_sequence
You can expect these functions on all types that model seqan3::aligned_sequence.
std::ranges::iterator_t< aligned_seq_t >	insert_gap (aligned_seq_t &aligned_seq, typename aligned_seq_t::const_iterator pos_it)
	Insert a seqan3::gap into an aligned sequence. More...
std::ranges::iterator_t< aligned_seq_t >	insert_gap (aligned_seq_t &aligned_seq, typename aligned_seq_t::const_iterator pos_it, typename aligned_seq_t::size_type size)
	Insert multiple seqan3::gap into an aligned sequence. More...
std::ranges::iterator_t< aligned_seq_t >	erase_gap (aligned_seq_t &aligned_seq, typename aligned_seq_t::const_iterator pos_it)
	Erase a seqan3::gap from an aligned sequence. More...
std::ranges::iterator_t< aligned_seq_t >	erase_gap (aligned_seq_t &aligned_seq, typename aligned_seq_t::const_iterator first, typename aligned_seq_t::const_iterator last)
	Erase multiple seqan3::gap from an aligned sequence. More...
void	assign_unaligned (aligned_seq_t &aligned_seq, unaligned_sequence_type &&unaligned_seq)
	Assign an ungapped sequence to a gapped sequence. More...

Detailed Description

The generic concept for an aligned sequence.

This concept describes the requirements a sequence must fulfil in order to be used inside of the alignment algorithm to store the final alignment.

Concepts and doxygen

The requirements for this concept are given as related functions and type traits. Types that model this concept are shown as "implementing this interface".

Friends And Related Function Documentation

assign_unaligned()

void assign_unaligned ( aligned_seq_t &  aligned_seq, unaligned_sequence_type &&  unaligned_seq  )

related

Assign an ungapped sequence to a gapped sequence.

Template Parameters

aligned_seq_t	Type of the container to reassign; must model seqan3::aligned_sequence.
unaligned_seq_t	Type of the container to assign from; must correspond to the aligned type without gap information (see details.)

Parameters

[in,out]	aligned_seq	The gapped sequence container to assign to.
[in,out]	unaligned_seq	The unaligned sequence container to assign from.

An aligned sequence has to be assignable from its unaligned counter part. For example a std::vector<seqan3::gapped<seqan3::dna4>> as well as a seqan3::gap_decorator<std::vector<seqan3::dna4>> can be assigned from s std::vector<seqan3::dna4> via seqan3::assign_unaligned.

Attention

This is a concept requirement, not an actual function (however types modelling this concept will provide an implementation).

erase_gap() [1/2]

std::ranges::iterator_t< aligned_seq_t > erase_gap ( aligned_seq_t &  aligned_seq, typename aligned_seq_t::const_iterator  first, typename aligned_seq_t::const_iterator  last  )

related

Erase multiple seqan3::gap from an aligned sequence.

Template Parameters

aligned_seq_t

Type of the range to modify; must model seqan3::aligned_sequence.

Parameters

[in,out]	aligned_seq	The aligned sequence to modify.
[in]	first	The iterator pointing to the position where to start erasing gaps.
[in]	last	The iterator pointing to the position where to stop erasing gaps.

Returns

An iterator following the last removed element. If the iterator last refers to the last element, the std::ranges::end() iterator is returned.

Exceptions

seqan3::gap_erase_failure

if one of the characters in [first, last) no seqan3::gap.

Note

This may cause reallocations and thus invalidates all iterators and references. Use the returned iterator.

Attention

This is a concept requirement, not an actual function (however types modelling this concept will provide an implementation).

erase_gap() [2/2]

std::ranges::iterator_t< aligned_seq_t > erase_gap ( aligned_seq_t &  aligned_seq, typename aligned_seq_t::const_iterator  pos_it  )

related

Erase a seqan3::gap from an aligned sequence.

Template Parameters

aligned_seq_t

Type of the range to modify; must model seqan3::aligned_sequence.

Parameters

[in,out]	aligned_seq	The aligned sequence to modify.
[in]	pos_it	The iterator pointing to the position where to erase a gap.

Returns

An iterator following the removed element. If the iterator pos_it refers to the last element, the std::ranges::end() iterator is returned.

Exceptions

seqan3::gap_erase_failure

if there is no seqan3::gap at pos_it.

Note

This may cause reallocations and thus invalidates all iterators and references. Use the returned iterator.

Attention

This is a concept requirement, not an actual function (however types modelling this concept will provide an implementation).

insert_gap() [1/2]

std::ranges::iterator_t< aligned_seq_t > insert_gap ( aligned_seq_t &  aligned_seq, typename aligned_seq_t::const_iterator  pos_it  )

related

Insert a seqan3::gap into an aligned sequence.

Template Parameters

aligned_seq_t

Type of the range to modify; must model seqan3::aligned_sequence.

Parameters

[in,out]	aligned_seq	The aligned sequence to modify.
[in]	pos_it	The iterator pointing to the position where to insert a gap.

Returns

An iterator pointing to the inserted gap.

Note

This may cause reallocations and thus invalidates all iterators and references. Use the returned iterator.

Attention

This is a concept requirement, not an actual function (however types modelling this concept will provide an implementation).

insert_gap() [2/2]

std::ranges::iterator_t< aligned_seq_t > insert_gap ( aligned_seq_t &  aligned_seq, typename aligned_seq_t::const_iterator  pos_it, typename aligned_seq_t::size_type  size  )

related

Insert multiple seqan3::gap into an aligned sequence.

Template Parameters

aligned_seq_t

Type of the range to modify; must model seqan3::aligned_sequence.

Parameters

[in,out]	aligned_seq	The aligned sequence to modify.
[in]	pos_it	The iterator pointing to the position where to insert a gaps.
[in]	size	The number of gap symbols to insert (will result in a gap of length size).

Returns

An iterator pointing to the first inserted gap or pos_it if size == 0.

Note

This may cause reallocations and thus invalidates all iterators and references. Use the returned iterator.

Attention

This is a concept requirement, not an actual function (however types modelling this concept will provide an implementation).

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

• seqan3/alignment/aligned_sequence/aligned_sequence_concept.hpp