SeqAn3
The Modern C++ library for sequence analysis.
seqan3::alignment_result< alignment_result_traits > Class Template Reference

Stores the alignment results and gives access to score, alignment and the front and back coordinates. More...

#include <seqan3/alignment/pairwise/alignment_result.hpp>

Public Member Functions

Constructors, destructor and assignment
 alignment_result (alignment_result_traits value)
 Constructs a seqan3::alignment_result from an alignment_result_traits object. More...
 
 alignment_result ()=default
 Defaulted.
 
 alignment_result (alignment_result const &)=default
 Defaulted.
 
 alignment_result (alignment_result &&)=default
 Defaulted.
 
alignment_resultoperator= (alignment_result const &)=default
 Defaulted.
 
alignment_resultoperator= (alignment_result &&)=default
 Defaulted.
 
 ~alignment_result ()=default
 
Access functions

Functions to access elements of the alignment result type.

constexpr id_t id () const noexcept
 Returns the alignment identifier. More...
 
constexpr score_t score () const noexcept
 Returns the alignment score. More...
 
constexpr back_coord_t const & back_coordinate () const noexcept
 Returns the back coordinate of the alignment. More...
 
constexpr front_coord_t const & front_coordinate () const noexcept
 Returns the front coordinate of the alignment. More...
 
constexpr alignment_t const & alignment () const noexcept
 Returns the actual alignment, i.e. the base pair matching. More...
 

Detailed Description

template<typename alignment_result_traits>
class seqan3::alignment_result< alignment_result_traits >

Stores the alignment results and gives access to score, alignment and the front and back coordinates.

Template Parameters
alignment_result_traitsThe type of the traits object.

Objects of this class are the result of an alignment computation. It always contains an alignment identifier and the resulting score. Optionally – if the user requests – also the begin and end positions within the sequences and the alignment can be calculated. When accessing a field that has not been calculated, an assertion will fail during compilation.

Constructor & Destructor Documentation

◆ alignment_result()

template<typename alignment_result_traits >
seqan3::alignment_result< alignment_result_traits >::alignment_result ( alignment_result_traits  value)
inline

Constructs a seqan3::alignment_result from an alignment_result_traits object.

Parameters
[in]valueThe alignment results.

◆ ~alignment_result()

template<typename alignment_result_traits >
seqan3::alignment_result< alignment_result_traits >::~alignment_result ( )
default

Defaulted

Member Function Documentation

◆ alignment()

template<typename alignment_result_traits >
constexpr alignment_t const& seqan3::alignment_result< alignment_result_traits >::alignment ( ) const
inlinenoexcept

Returns the actual alignment, i.e. the base pair matching.

Returns
At least two aligned sequences, which represent the alignment.
Note
This function is only available if the alignment was requested via the alignment configuration (see seqan3::align_cfg::result).

◆ back_coordinate()

template<typename alignment_result_traits >
constexpr back_coord_t const& seqan3::alignment_result< alignment_result_traits >::back_coordinate ( ) const
inlinenoexcept

Returns the back coordinate of the alignment.

Returns
A pair of positions in the respective sequences, where the calculated alignment ends (inclusive).
Note
This function is only available if the back coordinate was requested via the alignment configuration (see seqan3::align_cfg::result).

◆ front_coordinate()

template<typename alignment_result_traits >
constexpr front_coord_t const& seqan3::alignment_result< alignment_result_traits >::front_coordinate ( ) const
inlinenoexcept

Returns the front coordinate of the alignment.

Returns
A pair of positions in the respective sequences, where the calculated alignment starts.

Guaranteed to be smaller than or equal to back_coordinate().

Note
This function is only available if the front coordinate was requested via the alignment configuration (see seqan3::align_cfg::result).

◆ id()

template<typename alignment_result_traits >
constexpr id_t seqan3::alignment_result< alignment_result_traits >::id ( ) const
inlinenoexcept

Returns the alignment identifier.

Returns
The id field.

◆ score()

template<typename alignment_result_traits >
constexpr score_t seqan3::alignment_result< alignment_result_traits >::score ( ) const
inlinenoexcept

Returns the alignment score.

Returns
The score field.

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