SeqAn3  3.0.2
The Modern C++ library for sequence analysis.
seqan3::alignment_result< alignment_result_value_t > Class Template Reference

Stores the alignment results and gives access to score, alignment and the front and end positionss. More...

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

Public Member Functions

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 auto sequence1_end_position () const noexcept
 Returns the end position of the first sequence of the alignment. More...
 
constexpr auto sequence2_end_position () const noexcept
 Returns the end position of the second sequence of the alignment. More...
 
constexpr auto sequence1_begin_position () const noexcept
 Returns the begin position of the first sequence of the alignment. More...
 
constexpr auto sequence2_begin_position () const noexcept
 Returns the begin position of the second sequence of the alignment. More...
 
constexpr const alignment_t & alignment () const noexcept
 Returns the actual alignment, i.e. the base pair matching. More...
 

Constructors, destructor and assignment

 alignment_result ()=default
 
 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
 

Detailed Description

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

Stores the alignment results and gives access to score, alignment and the front and end positionss.

Template Parameters
alignment_result_value_tThe underlying value type containing the information from the alignment computation.

This class provides read-only access to the results of a pairwise 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.

Remarks
The template type argument is set internally by a result factory and depends on the configuration of the alignment result. For the general use of this class the concrete type information is not relevant and it suffices to know that this is a template class with one template type argument.

Constructor & Destructor Documentation

◆ alignment_result()

template<typename alignment_result_value_t >
seqan3::alignment_result< alignment_result_value_t >::alignment_result ( )
default

Defaulted.

◆ ~alignment_result()

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

Defaulted.

Member Function Documentation

◆ alignment()

template<typename alignment_result_value_t >
constexpr const alignment_t& seqan3::alignment_result< alignment_result_value_t >::alignment ( ) const
inlineconstexprnoexcept

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).

◆ id()

template<typename alignment_result_value_t >
constexpr id_t seqan3::alignment_result< alignment_result_value_t >::id ( ) const
inlineconstexprnoexcept

Returns the alignment identifier.

Returns
The id field.

◆ score()

template<typename alignment_result_value_t >
constexpr score_t seqan3::alignment_result< alignment_result_value_t >::score ( ) const
inlineconstexprnoexcept

Returns the alignment score.

Returns
The score field.

◆ sequence1_begin_position()

template<typename alignment_result_value_t >
constexpr auto seqan3::alignment_result< alignment_result_value_t >::sequence1_begin_position ( ) const
inlineconstexprnoexcept

Returns the begin position of the first sequence 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 sequence1_end_position().

Note
This function is only available if the begin position of the first sequence was requested via the alignment configuration (see seqan3::align_cfg::result).

◆ sequence1_end_position()

template<typename alignment_result_value_t >
constexpr auto seqan3::alignment_result< alignment_result_value_t >::sequence1_end_position ( ) const
inlineconstexprnoexcept

Returns the end position of the first sequence of the alignment.

Returns
The calculated alignment end of sequence 1 (inclusive).
Note
This function is only available if the end position of the first sequence was requested via the alignment configuration (see seqan3::align_cfg::result).

◆ sequence2_begin_position()

template<typename alignment_result_value_t >
constexpr auto seqan3::alignment_result< alignment_result_value_t >::sequence2_begin_position ( ) const
inlineconstexprnoexcept

Returns the begin position of the second sequence 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 sequence2_end_position().

Note
This function is only available if the begin position of the second sequence was requested via the alignment configuration (see seqan3::align_cfg::result).

◆ sequence2_end_position()

template<typename alignment_result_value_t >
constexpr auto seqan3::alignment_result< alignment_result_value_t >::sequence2_end_position ( ) const
inlineconstexprnoexcept

Returns the end position of the second sequence 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 end position of the second sequence was requested via the alignment configuration (see seqan3::align_cfg::result).

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