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Configuration
Sequence Alignment

Provides configuration elements for the pairwise alignment configuration. More...

Collaboration diagram for Configuration:

## Classes

class | seqan3::align_cfg::band_fixed_size
| Configuration element for setting a fixed size band. More...
struct | seqan3::align_cfg::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 | seqan3::align_cfg::free_end_gaps_sequence1_leading
| A strong type representing free_end_gaps_sequence1_leading of the seqan3::align_cfg::method_global. More...
struct | seqan3::align_cfg::free_end_gaps_sequence1_trailing
| A strong type representing free_end_gaps_sequence1_trailing of the seqan3::align_cfg::method_global. More...
struct | seqan3::align_cfg::free_end_gaps_sequence2_leading
| A strong type representing free_end_gaps_sequence2_leading of the seqan3::align_cfg::method_global. More...
struct | seqan3::align_cfg::free_end_gaps_sequence2_trailing
| A strong type representing free_end_gaps_sequence2_trailing of the seqan3::align_cfg::method_global. More...
class | seqan3::align_cfg::gap_cost_affine
| A configuration element for the affine gap cost scheme. More...
struct | seqan3::align_cfg::lower_diagonal
| A strong type representing the lower diagonal of the seqan3::align_cfg::band_fixed_size. More...
class | seqan3::align_cfg::method_global
| Sets the global alignment method. More...
class | seqan3::align_cfg::method_local
| Sets the local alignment method. More...
class | seqan3::align_cfg::min_score
| Sets the minimal score (maximal errors) allowed during an distance computation e.g. edit distance. More...
class | seqan3::align_cfg::on_result< callback_t >
| Configuration element to provide a user defined callback function for the alignment. More...
struct | seqan3::align_cfg::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 | seqan3::align_cfg::output_alignment
| Configures the alignment result to output the alignment. More...
class | seqan3::align_cfg::output_begin_position
| Configures the alignment result to output the begin positions. More...
class | seqan3::align_cfg::output_end_position
| Configures the alignment result to output the end position. More...
class | seqan3::align_cfg::output_score
| Configures the alignment result to output the score. More...
class | seqan3::align_cfg::output_sequence1_id
| Configures the alignment result to output the id of the first sequence. More...
class | seqan3::align_cfg::output_sequence2_id
| Configures the alignment result to output the id of the second sequence. More...
class | seqan3::align_cfg::detail::result_type< alignment_result_t >
| Configuration element capturing the configured seqan3::alignment_result for the alignment algorithm. More...
class | seqan3::align_cfg::score_type< score_t >
| A configuration element to set the score type used in the alignment algorithm. More...
class | seqan3::align_cfg::scoring_scheme< scoring_scheme_t >
| Sets the scoring scheme for the alignment algorithm. More...
struct | seqan3::align_cfg::upper_diagonal
| A strong type representing the upper diagonal of the seqan3::align_cfg::band_fixed_size. More...
class | seqan3::align_cfg::vectorised
| Enables the vectorised alignment computation if possible for the current configuration. More...

## Typedefs

using | seqan3::align_cfg::detail::debug
| Configuration element for debugging the alignment algorithm.
using | seqan3::align_cfg::parallel
| Enables the parallel execution of the alignment algorithm if possible for the given configuration.

## Variables

constexpr configuration | seqan3::align_cfg::edit_scheme
| Shortcut for edit distance configuration.

## Detailed Description

Provides configuration elements for the pairwise alignment configuration.

See the detailed Pairwise Alignments documentation for more details.

See also
  Pairwise Alignments

## Typedef Documentation

## debug

using seqan3::align_cfg::detail::debug

Initial value:
seqan3::detail::debug_mode<
std::integral_constant<seqan3::detail::align_config_id, seqan3::detail::align_config_id::debug>>
std::integral_constant

Configuration element for debugging the alignment algorithm.

Using this configuration allows to output the alignment matrices from the DP algorithm using the returned seqan3::alignment_result. The score matrix is always accessible, while the trace matrix can only be computed if an alignment was requested via the seqan3::align_cfg::output_alignment configuration.

Note
  This configuration is only useful for debugging purposes as it can have a significant impact on the performance.

## parallel

using seqan3::align_cfg::parallel

Initial value:
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.

SeqAn's pairwise sequence alignment algorithm is internally accelerated using multi-threading. The parallel execution can be selected by specifying the seqan3::align_cfg::parallel configuration element. This will enable the asynchronous execution of the alignments in the backend. For the user interface nothing changes as the returned seqan3::algorithm_result_generator_range will preserve the order of the computed alignment results, i.e. the first result corresponds to the first alignment given by the input range. By default, a thread pool with std::thread::hardware_concurrency many threads will be created on a call to seqan3::align_pairwise and destructed when all alignments have been processed and the seqan3::algorithm_result_generator_range goes out of scope. The configuration element seqan3::align_cfg::parallel can be initialised with a custom thread count which determines the number of threads that will be spawned in the background.
Note that only independent alignment computations can be executed in parallel, i.e. you use this method when computing a batch of alignments rather than executing them separately.
Depending on your processor architecture you can gain a significant speed-up.

The value represents the number of threads to be used and must be greater than 0.

### Example

// SPDX-FileCopyrightText: 2006-2025 Knut Reinert & Freie Universität Berlin
// SPDX-FileCopyrightText: 2016-2025 Knut Reinert & MPI für molekulare Genetik
// SPDX-License-Identifier: CC0-1.0
#include <thread>
#include <seqan3/alignment/configuration/align_config_parallel.hpp>
int main()
{
// Enables parallel computation with two threads.
seqan3::align_cfg::parallel cfg_2{2};
// Enables parallel computation with the number of concurrent threads supported by the current architecture.
seqan3::align_cfg::parallel cfg_n{std::thread::hardware_concurrency()};
;
}
align_config_parallel.hpp
Provides seqan3::align_cfg::parallel configuration.
seqan3::align_cfg::parallel
seqan3::detail::parallel_mode< std::integral_constant< seqan3::detail::align_config_id, seqan3::detail::align_config_id::parallel > > parallel
Enables the parallel execution of the alignment algorithm if possible for the given configuration.
Definition align_config_parallel.hpp:34
std::thread::hardware_concurrency
T hardware_concurrency(T... args)
thread

Remarks
  For a complete overview, take a look at Pairwise Alignments.

## Variable Documentation

## edit_scheme

configuration seqan3::align_cfg::edit_scheme

inline constexpr

Initial value:
=
scoring_scheme{hamming_scoring_scheme{}} | gap_cost_affine{open_score{0}, extension_score{-1}}
seqan3::align_cfg::scoring_scheme
Sets the scoring scheme for the alignment algorithm.
Definition align_config_scoring_scheme.hpp:42
seqan3::hamming_scoring_scheme
A scoring scheme that assigns a score of 0 to matching letters and -1 to mismatching letters.
Definition hamming_scoring_scheme.hpp:33

Shortcut for edit distance configuration.

The edit distance computation is a specific sub-problem of the alignment computation with the aim to count the number of edits to transform one sequence into another. An edit operation can be a substitution, an insertion, or a deletion. Accordingly, this algorithm uses a predefined scoring scheme as well as a gap scheme, where the score for a match is 0, for a mismatch -1, for a gap -1, and for a gap open 0.

### Performance

Under the hood SeqAn uses a fast bit-vector algorithm to compute the edit distance whenever possible. This depends on the final alignment configuration. Currently, the fast edit distance algorithm is only triggered for global alignments with the with free ends in the first sequence. So make sure to configure the seqan3::align_cfg::method_global configuration element accordingly (see class documentation).

The performance of the algorithm can further be improved if the number of maximal errors (edits) is known by using the align_cfg::min_score configuration.

// SPDX-FileCopyrightText: 2006-2025 Knut Reinert & Freie Universität Berlin
// SPDX-FileCopyrightText: 2016-2025 Knut Reinert & MPI für molekulare Genetik
// SPDX-License-Identifier: CC0-1.0
#include <seqan3/alignment/configuration/align_config_edit.hpp>
#include <seqan3/alignment/configuration/align_config_method.hpp>
#include <seqan3/alignment/configuration/align_config_min_score.hpp>
int main()
{
// Computes semi global edit distance using fast-bit vector algorithm.
auto cfg_fast = seqan3::align_cfg::method_global{seqan3::align_cfg::free_end_gaps_sequence1_leading{true},
seqan3::align_cfg::free_end_gaps_sequence2_leading{false},
seqan3::align_cfg::free_end_gaps_sequence1_trailing{true},
seqan3::align_cfg::free_end_gaps_sequence2_trailing{false}}
| seqan3::align_cfg::edit_scheme;
// Computes semi global edit distance using slower standard pairwise algorithm.
auto cfg_slow = seqan3::align_cfg::method_global{seqan3::align_cfg::free_end_gaps_sequence1_leading{false},
seqan3::align_cfg::free_end_gaps_sequence2_leading{true},
seqan3::align_cfg::free_end_gaps_sequence1_trailing{false},
seqan3::align_cfg::free_end_gaps_sequence2_trailing{true}}
| seqan3::align_cfg::edit_scheme;
// Computes global distance allowing a minimal score of 3 (Default: edit distance).
auto cfg_errors =
seqan3::align_cfg::method_global{} | seqan3::align_cfg::edit_scheme | seqan3::align_cfg::min_score{-3};
}
align_config_edit.hpp
Provides seqan3::align_cfg::edit_scheme.
align_config_method.hpp
Provides global and local alignment configurations.
align_config_min_score.hpp
Provides seqan3::align_cfg::min_score configuration.
seqan3::align_cfg::method_global
Sets the global alignment method.
Definition align_config_method.hpp:119
seqan3::align_cfg::min_score
Sets the minimal score (maximal errors) allowed during an distance computation e.g....
Definition align_config_min_score.hpp:36
seqan3::align_cfg::edit_scheme
constexpr configuration edit_scheme
Shortcut for edit distance configuration.
Definition align_config_edit.hpp:48
seqan3::align_cfg::free_end_gaps_sequence1_leading
A strong type representing free_end_gaps_sequence1_leading of the seqan3::align_cfg::method_global.
Definition align_config_method.hpp:65
seqan3::align_cfg::free_end_gaps_sequence1_trailing
A strong type representing free_end_gaps_sequence1_trailing of the seqan3::align_cfg::method_global.
Definition align_config_method.hpp:85
seqan3::align_cfg::free_end_gaps_sequence2_leading
A strong type representing free_end_gaps_sequence2_leading of the seqan3::align_cfg::method_global.
Definition align_config_method.hpp:75
seqan3::align_cfg::free_end_gaps_sequence2_trailing
A strong type representing free_end_gaps_sequence2_trailing of the seqan3::align_cfg::method_global.
Definition align_config_method.hpp:95

Attention
  If the edit distance configuration is combined with any other configuration element or setting, the algorithm falls back to the slower standard pairwise algorithm. For example the cfg_slow in the above example will trigger the slower algorithm which can handle the case if the ends are free in the second sequence instead of the first sequence.

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