A scheme for representing and computing scores against gap characters.
More...
#include <seqan3/alignment/scoring/gap_scheme.hpp>


using  score_type = score_t 
 The template parameter exposed as member type.



(Note that these are not member functions.)


 gap_scheme () > gap_scheme< int8_t > 
 Default constructed objects deduce to int8_t .


template<floating_point score_arg_type> 
 gap_scheme (gap_score< score_arg_type >, gap_open_score< score_arg_type >) > gap_scheme< float > 
 Attention: This guide does not actually deduce from the underlying type, but always defaults to float for floating point types. To use a larger type, specify the template argument manually.


template<floating_point score_arg_type> 
 gap_scheme (gap_score< score_arg_type >) > gap_scheme< float > 
 Attention: This guide does not actually deduce from the underlying type, but always defaults to float for floating point types. To use a larger type, specify the template argument manually.


template<arithmetic score_arg_type> 
 gap_scheme (gap_score< score_arg_type >, gap_open_score< score_arg_type >) > gap_scheme< int8_t > 
 Attention: This guide does not actually deduce from the underlying type, but always defaults to int8_t for integer types. To use a larger type, specify the template argument manually.


template<arithmetic score_arg_type> 
 gap_scheme (gap_score< score_arg_type >) > gap_scheme< int8_t > 
 Attention: This guide does not actually deduce from the underlying type, but always defaults to int8_t for integer types. To use a larger type, specify the template argument manually.


template<arithmetic score_t = int8_t>
class seqan3::gap_scheme< score_t >
A scheme for representing and computing scores against gap characters.
 Template Parameters

score_type  Type of the score values saved internally. 
◆ gap_scheme() [1/2]
template<arithmetic score_t = int8_t>
template<arithmetic score_arg_t>
Constructor for the Affine gap costs model (delegates to set_affine()).
 Template Parameters

score_arg_t  The underlying type of the arguments. 
 Parameters

 Exceptions

The score for a sequence of n
gap characters is computed as n * g + go
.
 Attention
 This is the formula used most commonly in the literature, but it is different from SeqAn2 where the formula was
(n1) * g + go
.
◆ gap_scheme() [2/2]
template<arithmetic score_t = int8_t>
template<arithmetic score_arg_t>
Constructor for the Linear gap costs model (delegates to set_linear()).
 Template Parameters

score_arg_t  The underlying type of the argument. 
 Parameters

 Exceptions

The score for a sequence of n
gap characters is computed as n * g
. This is the same as the affine model with a gap open score of 0
.
◆ get_gap_open_score()
template<arithmetic score_t = int8_t>
A strong type of underlying type score_type
that represents an additional score (usually negative) that is incurred once additionaly per stretch of consecutive gaps.
 Template Parameters

score_type  The underlying type. 
 See also
 seqan3::gap_scheme
◆ get_gap_score()
template<arithmetic score_t = int8_t>
A strong type of underlying type score_type
that represents the score of any character against a gap character.
 Template Parameters

score_type  The underlying type. 
 See also
 seqan3::gap_scheme
◆ score()
template<arithmetic score_t = int8_t>
constexpr ptrdiff_t seqan3::gap_scheme< score_t >::score 
( 
size_t const 
number_of_consecutive_gaps  ) 
const 

inlinenoexcept 
Compute the score of a stretch of gap characters.
 Parameters

number_of_consecutive_gaps  The number of consecutive gaps that you wish to know the score for. 
 Returns
 A signed integer (usually 64bit) that holds the score computed based on the selected scheme.
◆ set_affine()
template<arithmetic score_t = int8_t>
template<arithmetic score_arg_t>
Set the Affine gap costs model.
 Template Parameters

score_arg_t  The underlying type of the arguments. 
 Parameters

 Exceptions

The score for a sequence of n
gap characters is computed as n * g + go
.
 Attention
 This is the formula used most commonly in the literature, but it is different from SeqAn2 where the formula was
(n1) * g + go
.
◆ set_linear()
template<arithmetic score_t = int8_t>
template<arithmetic score_arg_t>
Set the Linear gap costs model.
 Template Parameters

score_arg_t  The underlying type of the argument. 
 Parameters

 Exceptions

The score for a sequence of n
gap characters is computed as n * g
. This is the same as the affine model with a gap open score of 0
.
The documentation for this class was generated from the following file: