seqan3::align_cfg::method_global Class Reference

Sets the global alignment method. More...

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

Inheritance diagram for seqan3::align_cfg::method_global:

Public Member Functions
Constructors, destructor and assignment
	method_global ()=default
	Defaulted.
	method_global (method_global const &)=default
	Defaulted.
	method_global (method_global &&)=default
	Defaulted.
method_global &	operator= (method_global const &)=default
	Defaulted.
method_global &	operator= (method_global &&)=default
	Defaulted.
	~method_global ()=default
	Defaulted.
constexpr	method_global (seqan3::align_cfg::free_end_gaps_sequence1_leading free_sequence1_leading, seqan3::align_cfg::free_end_gaps_sequence2_leading free_sequence2_leading, seqan3::align_cfg::free_end_gaps_sequence1_trailing free_sequence1_trailing, seqan3::align_cfg::free_end_gaps_sequence2_trailing free_sequence2_trailing) noexcept
	Construct method_global with a specific free end gap configuration. More...

Public Attributes
bool	free_end_gaps_sequence1_leading {false}
	If set to true, leading gaps in sequence1 are not penalised when computing the optimal alignment.
bool	free_end_gaps_sequence1_trailing {false}
	If set to true, trailing gaps in sequence1 are not penalised when computing the optimal alignment.
bool	free_end_gaps_sequence2_leading {false}
	If set to true, leading gaps in sequence2 are not penalised when computing the optimal alignment.
bool	free_end_gaps_sequence2_trailing {false}
	If set to true, trailing gaps in sequence2 are not penalised when computing the optimal alignment.

Detailed Descriptionno-api

Sets the global alignment method.

The alignment algorithm can be categorised in different methods. For example, the local and the global alignment are two different methods, 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 method. Since it is not possible to guess what the desired method for a user is, there is no default and this configuration must always be provided for the alignment algorithm.

Example

#include <seqan3/alignment/configuration/align_config_method.hpp>
#include <seqan3/alignment/configuration/align_config_scoring_scheme.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::literals;
 
int main()
{
    auto min_cfg = seqan3::align_cfg::method_local{} |
                   seqan3::align_cfg::scoring_scheme{seqan3::nucleotide_scoring_scheme{seqan3::match_score{4},
                                                                                       seqan3::mismatch_score{-5}}};
 
    auto seq1 = "TCGT"_dna4;
    auto seq2 = "ACGA"_dna4;
    for (auto res : align_pairwise(std::tie(seq1, seq2), min_cfg))
        seqan3::debug_stream << res.score() << '\n';
}

Constructor & Destructor Documentation

method_global()

constexpr seqan3::align_cfg::method_global::method_global ( seqan3::align_cfg::free_end_gaps_sequence1_leading  free_sequence1_leading, seqan3::align_cfg::free_end_gaps_sequence2_leading  free_sequence2_leading, seqan3::align_cfg::free_end_gaps_sequence1_trailing  free_sequence1_trailing, seqan3::align_cfg::free_end_gaps_sequence2_trailing  free_sequence2_trailing  )

no-apiinlineconstexprnoexcept

Construct method_global with a specific free end gap configuration.

Parameters

[in]	free_sequence1_leading	An instance of seqan3::align_cfg::free_end_gaps_sequence1_leading that indicates whether leading gaps in sequence1 should be free (not penalised).
[in]	free_sequence2_leading	An instance of seqan3::align_cfg::free_end_gaps_sequence2_leading that indicates whether leading gaps in sequence2 should be free (not penalised).
[in]	free_sequence1_trailing	An instance of seqan3::align_cfg::free_end_gaps_sequence1_trailing that indicates whether trailing gaps in sequence1 should be free (not penalised).
[in]	free_sequence2_trailing	An instance of seqan3::align_cfg::free_end_gaps_sequence2_trailing that indicates whether trailing gaps in sequence2 should be free (not penalised).

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

• seqan3/alignment/configuration/align_config_method.hpp