SeqAn3 3.4.0-rc.1
The Modern C++ library for sequence analysis.
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seqan3::align_cfg Namespace Reference

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

Namespaces

namespace  detail
 

Classes

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...
 
class  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...
 
class  method_global
 Sets the global alignment method. More...
 
class  method_local
 Sets the local alignment method. More...
 
class  min_score
 Sets the minimal score (maximal errors) allowed during an distance computation e.g. edit distance. More...
 
class  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...
 
class  output_alignment
 Configures the alignment result to output the alignment. More...
 
class  output_begin_position
 Configures the alignment result to output the begin positions. More...
 
class  output_end_position
 Configures the alignment result to output the end position. More...
 
class  output_score
 Configures the alignment result to output the score. More...
 
class  output_sequence1_id
 Configures the alignment result to output the id of the first sequence. More...
 
class  output_sequence2_id
 Configures the alignment result to output the id of the second sequence. More...
 
class  score_type
 A configuration element to set the score type used in the alignment algorithm. More...
 
class  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...
 
class  vectorised
 Enables the vectorised alignment computation if possible for the current configuration. 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.
 

Functions

Type deduction guides
template<std::copy_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.
 

Detailed Description

A special sub namespace for the alignment configurations.

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