SeqAn3
seqan3::align_cfg Namespace Reference

A special sub namespace for the alignment configurations. More...

Enumerations

enum  id : uint8_t {
  id::gap, id::sequence_ends, id::score, id::global,
  id::output, id::max_error, id::DEV
}
 Specifies an id for every configuration element. More...
 

Variables

constexpr detail::align_config_band_adaptor< seqan3::band_staticband_static
 A configuration adaptor for a static band.
 
constexpr detail::configuration edit
 Shortcut for edit distance configuration. More...
 
constexpr detail::align_config_gap_adaptor< seqan3::detail::align_config_gap > gap
 A configuration adaptor for gaps.
 
constexpr detail::align_config_global_adaptor global
 A configuration adaptor for global alignment.
 
constexpr detail::align_config_max_error_adaptor max_error
 A configuration adaptor for maximal errors.
 
template<align_result_key e>
constexpr detail::align_config_output_adaptor< e > output
 A configuration adaptor for alignment output.
 
constexpr detail::align_config_score_adaptor score
 A configuration adaptor for alignment scoring.
 
template<free_ends_at val = free_ends_at::none>
constexpr detail::align_config_sequence_ends_adaptor< val > sequence_ends
 A configuration adaptor for gaps at the sequence ends. More...
 

Detailed Description

A special sub namespace for the alignment configurations.

Variable Documentation

◆ edit

constexpr detail::configuration seqan3::align_cfg::edit
inline
Initial value:
= global |
gap(gap_scheme{gap_score{-1}})
constexpr detail::align_config_gap_adaptor< seqan3::detail::align_config_gap > gap
A configuration adaptor for gaps.
Definition: align_config_gap.hpp:162
nucleotide_scoring_scheme(match_score< score_arg_type >, mismatch_score< score_arg_type >) -> nucleotide_scoring_scheme< int8_t >
Attention: This guide does not actually deduce from the underlying type, but always defaults to int8_...
score_type score(alph1_t const alph1, alph2_t const alph2)
Compute the score of two letters.
constexpr detail::align_config_global_adaptor global
A configuration adaptor for global alignment.
Definition: align_config_global.hpp:108
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...

Shortcut for edit distance configuration.