|
|
constexpr | nucleotide_scoring_scheme () noexcept=default |
| The default constructor (delegates to set_hamming_distance()).
|
|
template<arithmetic score_arg_t> |
constexpr | nucleotide_scoring_scheme (match_score< score_arg_t > const ms, mismatch_score< score_arg_t > const mms) |
| Constructor for the simple scheme (delegates to set_simple_scheme()).
|
|
constexpr | nucleotide_scoring_scheme (matrix_type const &matrix) noexcept |
| Constructor for a custom scheme (delegates to set_custom_matrix()).
|
|
template<cereal_archive archive_t> |
void | serialize (archive_t &archive) |
| Serialisation support function.
|
|
constexpr | scoring_scheme_base (scoring_scheme_base const &) noexcept=default |
| Defaulted.
|
|
constexpr | scoring_scheme_base (scoring_scheme_base &&) noexcept=default |
| Defaulted.
|
|
constexpr scoring_scheme_base & | operator= (scoring_scheme_base const &) noexcept=default |
| Defaulted.
|
|
constexpr scoring_scheme_base & | operator= (scoring_scheme_base &&) noexcept=default |
| Defaulted.
|
|
| ~scoring_scheme_base () noexcept=default |
| Defaulted.
|
|
constexpr | scoring_scheme_base () noexcept |
| The default constructor (delegates to set_hamming_distance()).
|
|
template<arithmetic score_arg_t> |
constexpr | scoring_scheme_base (match_score< score_arg_t > const ms, mismatch_score< score_arg_t > const mms) |
| Constructor for the simple scheme (delegates to set_simple_scheme()).
|
|
constexpr | scoring_scheme_base (matrix_type const &matrix) noexcept |
| Constructor for a custom scheme (delegates to set_custom_matrix()).
|
|
constexpr void | set_hamming_distance () noexcept |
| Set the hamming scheme, a variant of the simple scheme where match is scored 0 and mismatch -1 .
|
|
template<arithmetic score_arg_t> |
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).
|
|
constexpr void | set_custom_matrix (matrix_type const &matrix) noexcept |
| Set a custom scheme by passing a full matrix with arbitrary content.
|
|
template<typename alph1_t , typename alph2_t >
requires explicitly_convertible_to<alph1_t, alphabet_t> && explicitly_convertible_to<alph2_t, alphabet_t> |
constexpr score_t & | score (alph1_t const alph1, alph2_t const alph2) noexcept |
| Score two letters (either two nucleotids or two amino acids).
|
|
template<typename alph1_t , typename alph2_t >
requires explicitly_convertible_to<alph1_t, alphabet_t> && explicitly_convertible_to<alph2_t, alphabet_t> |
constexpr score_t | score (alph1_t const alph1, alph2_t const alph2) const noexcept |
| Score two letters (either two nucleotids or two amino acids).
|
|
constexpr bool | operator== (derived_t const &rhs) const noexcept |
| Checks whether *this is equal to rhs .
|
|
constexpr bool | operator!= (derived_t const &rhs) const noexcept |
| Checks whether *this is not equal to rhs .
|
|
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;
for (
auto pair :
seqan3::views::zip(one, two))
}
A data structure for managing and computing the score of two nucleotides.
Definition nucleotide_scoring_scheme.hpp:35
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:175
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:214
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
The SeqAn namespace for literals.
The main SeqAn3 namespace.
Definition aligned_sequence_concept.hpp:26
constexpr auto const & get(configuration< configs_t... > const &config) noexcept
This is an overloaded member function, provided for convenience. It differs from the above function o...
Definition configuration.hpp:412
SeqAn specific customisations in the standard namespace.
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:38
A strong type of underlying type score_type that represents the score two different characters.
Definition scoring_scheme_base.hpp:63
Provides seqan3::views::zip.