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(Note that these are not member functions.)
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| nucleotide_scoring_scheme () -> nucleotide_scoring_scheme< int8_t > |
| Default constructed objects deduce to int8_t .
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template<arithmetic score_arg_type> |
| nucleotide_scoring_scheme (match_score< score_arg_type >, mismatch_score< score_arg_type >) -> nucleotide_scoring_scheme< int8_t > |
| Attention: This guide does not actually deduce from the underlying type, but always defaults to int8_t . To use a larger type, specify the template argument manually.
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template<arithmetic score_arg_type> |
| nucleotide_scoring_scheme (std::array< std::array< score_arg_type, 15 >, 15 >) -> nucleotide_scoring_scheme< score_arg_type > |
| Deduce the score type from the provided matrix.
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using | score_type = score_t |
| Type of the score values.
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using | alphabet_type = alphabet_t |
| Type of the underlying alphabet.
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using | matrix_size_type = std::remove_const_t< decltype(alphabet_size< alphabet_t >)> |
| Size type that can hold the dimension of the matrix (i.e. size of the alphabet).
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using | matrix_type = std::array< std::array< score_type, matrix_size >, matrix_size > |
| Type of the internal matrix (a two-dimensional array).
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static constexpr matrix_size_type | matrix_size |
| Size of the matrix dimensions (i.e. size of the alphabet).
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template<
arithmetic score_type = int8_t>
class seqan3::nucleotide_scoring_scheme< score_type >
A data structure for managing and computing the score of two nucleotides.
- Template Parameters
-
score_type | The underlying type. |
You can use an instance of this class to score two nucleotides, the nucleotides need not be of the same type. Different scoring behaviour can be set via the member functions.
Example
int main()
{
<< "\n";
<< "\n";
<< "\n";
scheme2.
score(
'A'_dna15,
'G'_dna15) = 3;
score += scheme3.
score(std::get<0>(pair), std::get<1>(pair));
}
A data structure for managing and computing the score of two nucleotides.
Definition: nucleotide_scoring_scheme.hpp:38
constexpr void set_simple_scheme(match_score< score_arg_t > const ms, mismatch_score< score_arg_t > const mms)
Set the simple scheme (everything is either match or mismatch).
Definition: scoring_scheme_base.hpp:178
constexpr score_t & score(alph1_t const alph1, alph2_t const alph2) noexcept
Score two letters (either two nucleotids or two amino acids).
Definition: scoring_scheme_base.hpp:217
Provides seqan3::debug_stream and related types.
Provides seqan3::dna5, container aliases and string literals.
debug_stream_type debug_stream
A global instance of seqan3::debug_stream_type.
Definition: debug_stream.hpp:37
constexpr auto zip
A view adaptor that takes several views and returns tuple-like values from every i-th element of each...
Definition: zip.hpp:573
The SeqAn namespace for literals.
Provides seqan3::nucleotide_scoring_scheme.
Provides seqan3::rna15, container aliases and string literals.
A strong type of underlying type score_type that represents the score of two matching characters.
Definition: scoring_scheme_base.hpp:41
A strong type of underlying type score_type that represents the score two different characters.
Definition: scoring_scheme_base.hpp:66
Provides seqan3::views::zip.