seqan3::detail::aligned_sequence_builder< fst_sequence_t, sec_sequence_t > Class Template Reference

Builds the alignment for a given pair of sequences and the respective trace. More...

#include <seqan3/alignment/matrix/detail/aligned_sequence_builder.hpp>

Classes
struct	result_type
	The result type when building the aligned sequences. More...

Public Types
using	alignment_type = typename make_pairwise_alignment_type< fst_sequence_t, sec_sequence_t >::type
	The pairwise alignment type of the two sequences.

Public Member Functions
template<std::ranges::input_range trace_path_t>
result_type	operator() (trace_path_t &&trace_path)
	Builds the aligned sequences from the given trace path.
Constructors, destructor and assignment
constexpr	aligned_sequence_builder ()=default
	Defaulted.
constexpr	aligned_sequence_builder (aligned_sequence_builder const &)=default
	Defaulted.
constexpr	aligned_sequence_builder (aligned_sequence_builder &&)=default
	Defaulted.
constexpr aligned_sequence_builder &	operator= (aligned_sequence_builder const &)=default
	Defaulted.
constexpr aligned_sequence_builder &	operator= (aligned_sequence_builder &&)=default
	Defaulted.
	~aligned_sequence_builder ()=default
	Defaulted.
constexpr	aligned_sequence_builder (fst_sequence_t fst_rng, sec_sequence_t sec_rng)
	Construction from the underlying sequences.

Private Member Functions
template<typename reverse_traces_t , typename fst_aligned_t , typename sec_aligned_t >
void	fill_aligned_sequence (reverse_traces_t &&rev_traces, fst_aligned_t &fst_aligned, sec_aligned_t &sec_aligned) const
	Fills the sequences with gaps according to the given trace segments.

Private Attributes
type_reduce_t< fst_sequence_t >	fst_rng
	A view over the first range.
type_reduce_t< sec_sequence_t >	sec_rng
	A view over the second range.

Related Symbols
(Note that these are not member symbols.)
Type deduction guides
template<std::ranges::viewable_range fst_sequence_t, std::ranges::viewable_range sec_sequence_t>
	aligned_sequence_builder (fst_sequence_t &&, sec_sequence_t &&) -> aligned_sequence_builder< fst_sequence_t, sec_sequence_t >
	Deduces the type from the passed constructor arguments.

Detailed Description

template<std::ranges::viewable_range fst_sequence_t, std::ranges::viewable_range sec_sequence_t>
class seqan3::detail::aligned_sequence_builder< fst_sequence_t, sec_sequence_t >

Builds the alignment for a given pair of sequences and the respective trace.

Template Parameters

fst_sequence_t	The first sequence of the pairwise alignment; must model std::ranges::viewable_range.
sec_sequence_t	The second sequence of the pairwise alignment; must model std::ranges::viewable_range.

This class builds the alignment from a given trace path over the specified sequences. Use the interface seqan3::detail::aligned_sequence_builder::operator() to get the actual alignment. The returned seqan3::writable_aligned_sequence type is determined by the input types fst_sequence_t and sec_sequence_t.

See the seqan3::detail::make_aligned_sequence_type transformation trait for more information about the selected type.

Depending on the used alignment algorithm the computed alignment might only cover a subrange over the original sequences. Accordingly, the returned alignment covers only the part of the sequences that are part of the given trace path. One can use the seqan3::detail::aligned_sequence_builder::result_type to access the build alignment and also to access the actual slice positions over which the alignment was built for the first sequence and respectively the second sequence.

Constructor & Destructor Documentation

aligned_sequence_builder()

template<std::ranges::viewable_range fst_sequence_t, std::ranges::viewable_range sec_sequence_t>

constexpr seqan3::detail::aligned_sequence_builder< fst_sequence_t, sec_sequence_t >::aligned_sequence_builder ( fst_sequence_t  fst_rng, sec_sequence_t  sec_rng  )

inlineconstexpr

Construction from the underlying sequences.

Parameters

[in]	fst_rng	The first range to build the aligned sequence for.
[in]	sec_rng	The second range to build the aligned sequence for.

Member Function Documentation

fill_aligned_sequence()

template<std::ranges::viewable_range fst_sequence_t, std::ranges::viewable_range sec_sequence_t>

template<typename reverse_traces_t , typename fst_aligned_t , typename sec_aligned_t >

void seqan3::detail::aligned_sequence_builder< fst_sequence_t, sec_sequence_t >::fill_aligned_sequence ( reverse_traces_t &&  rev_traces, fst_aligned_t &  fst_aligned, sec_aligned_t &  sec_aligned  ) const

inlineprivate

Fills the sequences with gaps according to the given trace segments.

Template Parameters

reverse_traces_t

The type storing the reverse trace.

Parameters

[in]	rev_traces	The trace segments in order from source to sink in the trace matrix.
[in,out]	fst_aligned	The first aligned sequence to insert gaps into.
[in,out]	sec_aligned	The second aligned sequence to insert gaps into.

operator()()

template<std::ranges::viewable_range fst_sequence_t, std::ranges::viewable_range sec_sequence_t>

template<std::ranges::input_range trace_path_t>

result_type seqan3::detail::aligned_sequence_builder< fst_sequence_t, sec_sequence_t >::operator() ( trace_path_t &&  trace_path )

inline

Builds the aligned sequences from the given trace path.

Template Parameters

trace_path_t

The type of the trace path; must model std::ranges::input_range and std::same_as<std::ranges::range_value_t<trace_path_t>, seqan3::detail::trace_directions> must evaluate to true.

Parameters

[in]

trace_path

The trace path.

Returns

seqan3::detail::aligned_sequence_builder::result_type with the built alignment.

From the given trace path this function builds the aligned sequences for the first and the second target sequence. The return type seqan3::detail::aligned_sequence_builder::result_type is an aggregate type containing the begin and end coordinates with the respective sequence positions and the respective alignment over the sliced sequences.

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

• aligned_sequence_builder.hpp