SeqAn3  3.0.3
The Modern C++ library for sequence analysis.
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_globaloperator= (method_global const &)=default
 Defaulted.
 
method_globaloperator= (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 Description

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, this configuration must be provided for the alignment algorithm and cannot be defaulted.

Example

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 
)
inlineconstexprnoexcept

Construct method_global with a specific free end gap configuration.

Parameters
[in]free_sequence1_leadingAn 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_leadingAn 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_trailingAn 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_trailingAn instance of seqan3::align_cfg::free_end_gaps_sequence2_trailing that indicates whether trailing gaps in sequence2 should be free (not penalised).

The documentation for this class was generated from the following file:
debug_stream.hpp
Provides seqan3::debug_stream and related types.
dna4.hpp
Provides seqan3::dna4, container aliases and string literals.
align_pairwise.hpp
Provides pairwise alignment function.
align_config_method.hpp
Provides global and local alignment configurations.
seqan3::align_cfg::method_local
Sets the local alignment method.
Definition: align_config_method.hpp:43
align_config_scoring_scheme.hpp
Provides seqan3::align_cfg::scoring_scheme.
seqan3::nucleotide_scoring_scheme
A data structure for managing and computing the score of two nucleotides.
Definition: nucleotide_scoring_scheme.hpp:38
nucleotide_scoring_scheme.hpp
Provides seqan3::nucleotide_scoring_scheme.
seqan3::align_pairwise
constexpr auto align_pairwise(sequence_t &&seq, alignment_config_t const &config)
Computes the pairwise alignment for a pair of sequences or a range over sequence pairs.
Definition: align_pairwise.hpp:138
std::tie
T tie(T... args)
seqan3::mismatch_score
A strong type of underlying type score_type that represents the score two different characters.
Definition: scoring_scheme_base.hpp:66
seqan3::align_cfg::scoring_scheme
Sets the scoring scheme for the alignment algorithm.
Definition: align_config_scoring_scheme.hpp:45
seqan3::debug_stream
debug_stream_type debug_stream
A global instance of seqan3::debug_stream_type.
Definition: debug_stream.hpp:42
seqan3::match_score
A strong type of underlying type score_type that represents the score of two matching characters.
Definition: scoring_scheme_base.hpp:41