[DEPRECATED] A scheme for representing and computing scores against gap characters.
More...
|
template<cereal_archive archive_t> |
void | serialize (archive_t &archive) |
| Serialisation support function. More...
|
|
|
constexpr | gap_scheme () noexcept=default |
| Defaulted.
|
|
constexpr | gap_scheme (gap_scheme const &) noexcept=default |
| Defaulted.
|
|
constexpr | gap_scheme (gap_scheme &&) noexcept=default |
| Defaulted.
|
|
constexpr gap_scheme & | operator= (gap_scheme const &) noexcept=default |
| Defaulted.
|
|
constexpr gap_scheme & | operator= (gap_scheme &&) noexcept=default |
| Defaulted.
|
|
| ~gap_scheme () noexcept=default |
| Defaulted.
|
|
template<arithmetic score_arg_t> |
constexpr | gap_scheme (gap_score< score_arg_t > const g, gap_open_score< score_arg_t > const go) |
| Constructor for the Affine gap costs model (delegates to set_affine()). More...
|
|
template<arithmetic score_arg_t> |
constexpr | gap_scheme (gap_score< score_arg_t > const g) |
| Constructor for the Linear gap costs model (delegates to set_linear()). More...
|
|
|
template<arithmetic score_arg_t> |
constexpr void | set_affine (gap_score< score_arg_t > const g, gap_open_score< score_arg_t > const go) |
| Set the Affine gap costs model. More...
|
|
template<arithmetic score_arg_t> |
constexpr void | set_linear (gap_score< score_arg_t > const g) |
| Set the Linear gap costs model. More...
|
|
|
constexpr score_t & | get_gap_score () noexcept |
| Return the gap score.
|
|
constexpr score_t | get_gap_score () const noexcept |
| [DEPRECATED] A strong type of underlying type score_type that represents the score of any character against a gap character. More...
|
|
constexpr score_t & | get_gap_open_score () noexcept |
| Return the gap open score.
|
|
constexpr score_t | get_gap_open_score () const noexcept |
| [DEPRECATED] A strong type of underlying type score_type that represents an additional score (usually negative) that is incurred once additionaly per stretch of consecutive gaps. More...
|
|
constexpr ptrdiff_t | score (size_t const number_of_consecutive_gaps) const noexcept |
| Compute the score of a stretch of gap characters. More...
|
|
|
constexpr bool | operator== (gap_scheme const &rhs) const noexcept |
| Checks whether *this is equal to rhs .
|
|
constexpr bool | operator!= (gap_scheme const &rhs) const noexcept |
| Checks whether *this is not equal to rhs .
|
|
|
(Note that these are not member functions.)
|
|
| gap_scheme () -> gap_scheme< int8_t > |
| Default constructed objects deduce to int8_t .
|
|
template<floating_point score_arg_type> |
| gap_scheme (gap_score< score_arg_type >, gap_open_score< score_arg_type >) -> gap_scheme< float > |
| Attention: This guide does not actually deduce from the underlying type, but always defaults to float for floating point types. To use a larger type, specify the template argument manually.
|
|
template<floating_point score_arg_type> |
| gap_scheme (gap_score< score_arg_type >) -> gap_scheme< float > |
| Attention: This guide does not actually deduce from the underlying type, but always defaults to float for floating point types. To use a larger type, specify the template argument manually.
|
|
template<arithmetic score_arg_type> |
| gap_scheme (gap_score< score_arg_type >, gap_open_score< score_arg_type >) -> gap_scheme< int8_t > |
| Attention: This guide does not actually deduce from the underlying type, but always defaults to int8_t for integer types. To use a larger type, specify the template argument manually.
|
|
template<arithmetic score_arg_type> |
| gap_scheme (gap_score< score_arg_type >) -> gap_scheme< int8_t > |
| Attention: This guide does not actually deduce from the underlying type, but always defaults to int8_t for integer types. To use a larger type, specify the template argument manually.
|
|
template<arithmetic score_t = int8_t>
class seqan3::gap_scheme< score_t >
[DEPRECATED] A scheme for representing and computing scores against gap characters.
- Template Parameters
-
score_type | Type of the score values saved internally. |
- Deprecated:
- This type is deprecated and will be removed in SeqAn3.1.