seqan3::align_cfg::mode< mode_type > Struct Template Reference

Sets the alignment mode. More...

#include <seqan3/alignment/configuration/align_config_mode.hpp>

Inheritance diagram for seqan3::align_cfg::mode< mode_type >:

Public Attributes
mode_type	value
	The stored config value.

Related Functions
(Note that these are not member functions.)
Type deduction guides
template<typename mode_type >
	mode (mode_type) -> mode< mode_type >
	Deduces the alignment mode from the given constructor argument.

Detailed Description

template<typename mode_type>
struct seqan3::align_cfg::mode< mode_type >

Sets the alignment mode.

Template Parameters

mode_type

The type of the alignment mode.

The alignment algorithm can be categorised in different modes. For example, the local and the global alignment are two different modes, while the semi-global alignment is a variation of the global alignment. This differentiation makes it possible to define a subset of configurations that can work with a particular mode. Since it is not possible to guess what the desired mode for a user is, this configuration must be provided for the alignment algorithm and cannot be defaulted.

Example

#include <seqan3/alignment/configuration/align_config_mode.hpp>
#include <seqan3/alignment/configuration/align_config_scoring.hpp>
#include <seqan3/alignment/pairwise/align_pairwise.hpp>
#include <seqan3/alignment/scoring/nucleotide_scoring_scheme.hpp>
#include <seqan3/alphabet/nucleotide/dna4.hpp>
#include <seqan3/core/debug_stream.hpp>

using namespace seqan3;

int main()
{
    auto min_cfg = align_cfg::mode{global_alignment} |
                   align_cfg::scoring{nucleotide_scoring_scheme{match_score{4}, mismatch_score{-5}}};

    auto seq1 = "ACGT"_dna4;
    auto seq2 = "ACCT"_dna4;
    for (auto res : align_pairwise(std::tie(seq1, seq2), min_cfg))
        debug_stream << res.score() << '\n';
}

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The documentation for this struct was generated from the following file:

• seqan3/alignment/configuration/align_config_mode.hpp