SeqAn3  3.0.2
The Modern C++ library for sequence analysis.
seqan3::align_cfg Namespace Reference

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

Classes

struct  aligned_ends
 The configuration for aligned sequence ends. More...
 
class  band_fixed_size
 Configuration element for setting a fixed size band. More...
 
struct  extension_score
 A strong type of underlying type int32_t that represents the score (usually negative) of any character against a gap character. More...
 
struct  free_end_gaps_sequence1_leading
 A strong type representing free_end_gaps_sequence1_leading of the seqan3::align_cfg::method_global. More...
 
struct  free_end_gaps_sequence1_trailing
 A strong type representing free_end_gaps_sequence1_trailing of the seqan3::align_cfg::method_global. More...
 
struct  free_end_gaps_sequence2_leading
 A strong type representing free_end_gaps_sequence2_leading of the seqan3::align_cfg::method_global. More...
 
struct  free_end_gaps_sequence2_trailing
 A strong type representing free_end_gaps_sequence2_trailing of the seqan3::align_cfg::method_global. More...
 
struct  gap_cost_affine
 A configuration element for the affine gap cost scheme. More...
 
struct  lower_diagonal
 A strong type representing the lower diagonal of the seqan3::align_cfg::band_fixed_size. More...
 
struct  method_global
 Sets the global alignment method. More...
 
struct  min_score
 Sets the minimal score (maximal errors) allowed during an distance computation e.g. edit distance. More...
 
struct  on_result
 Configuration element to provide a user defined callback function for the alignment. More...
 
struct  open_score
 A strong type of underlying type int32_t that represents a score (usually negative) that is incurred once per stretch of consecutive gaps. More...
 
struct  output_alignment_tag
 Tag representing alignment output for the alignment algorithms. More...
 
struct  output_begin_position_tag
 Tag representing begin position output for the alignment algorithms. More...
 
struct  output_end_position_tag
 Tag representing end position output for the alignment algorithms. More...
 
struct  output_score_tag
 Tag representing score output for the alignment algorithms. More...
 
struct  output_sequence1_id_tag
 Tag representing sequence1 id output for the alignment algorithms. More...
 
struct  output_sequence2_id_tag
 Tag representing sequence2 id output for the alignment algorithms. More...
 
struct  score_type_tag
 Tag to configure the score type of the alignment algorithm. More...
 
struct  scoring_scheme
 Sets the scoring scheme for the alignment algorithm. More...
 
struct  upper_diagonal
 A strong type representing the upper diagonal of the seqan3::align_cfg::band_fixed_size. More...
 

Typedefs

using parallel = seqan3::detail::parallel_mode< std::integral_constant< seqan3::detail::align_config_id, seqan3::detail::align_config_id::parallel > >
 Enables the parallel execution of the alignment algorithm if possible for the given configuration. More...
 

Functions

Type deduction guides
template<std::move_constructible callback_t>
 on_result (callback_t &&) -> on_result< std::decay_t< callback_t >>
 Deduces the callback type from a forwarding constructor argument.
 

Variables

constexpr configuration edit_scheme
 Shortcut for edit distance configuration. More...
 
constexpr seqan3::detail::method_local_tag method_local {}
 Sets the local alignment method. More...
 
constexpr output_alignment_tag output_alignment {}
 Configures the alignment result to output the alignment. More...
 
constexpr output_begin_position_tag output_begin_position {}
 Configures the alignment result to output the begin positions. More...
 
constexpr output_end_position_tag output_end_position {}
 Configures the alignment result to output the end position. More...
 
constexpr output_score_tag output_score {}
 Configures the alignment result to output the score. More...
 
constexpr output_sequence1_id_tag output_sequence1_id {}
 Configures the alignment result to output the id of the first sequence. More...
 
constexpr output_sequence2_id_tag output_sequence2_id {}
 Configures the alignment result to output the id of the second sequence. More...
 
template<arithmetic score_t>
constexpr score_type_tag< score_t > score_type {}
 A configuration element to set the score type used in the alignment algorithm. More...
 
constexpr seqan3::detail::vectorised_tag vectorised {}
 Enables the vectorised alignment computation if possible for the current configuration. More...
 

Detailed Description

A special sub namespace for the alignment configurations.