A scheme for representing and computing scores against gap characters.
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#include <seqan3/alignment/scoring/gap_scheme.hpp>
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using | score_type = score_t |
| | The template parameter exposed as member type.
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(Note that these are not member functions.)
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| gap_scheme () -> gap_scheme< int8_t > |
| | Default constructed objects deduce to int8_t.
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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.
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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.
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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.
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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.
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template<arithmetic score_t = int8_t>
class seqan3::gap_scheme< score_t >
A scheme for representing and computing scores against gap characters.
- Template Parameters
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| score_type | Type of the score values saved internally. |
◆ gap_scheme() [1/2]
template<arithmetic score_t = int8_t>
template<arithmetic score_arg_t>
Constructor for the Affine gap costs model (delegates to set_affine()).
- Template Parameters
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| score_arg_t | The underlying type of the arguments. |
- Parameters
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- Exceptions
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The score for a sequence of n gap characters is computed as n * g + go.
- Attention
- This is the formula used most commonly in the literature, but it is different from SeqAn2 where the formula was
(n-1) * g + go.
◆ gap_scheme() [2/2]
template<arithmetic score_t = int8_t>
template<arithmetic score_arg_t>
Constructor for the Linear gap costs model (delegates to set_linear()).
- Template Parameters
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| score_arg_t | The underlying type of the argument. |
- Parameters
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- Exceptions
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The score for a sequence of n gap characters is computed as n * g. This is the same as the affine model with a gap open score of 0.
◆ get_gap_open_score()
template<arithmetic score_t = int8_t>
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.
- Deprecated:
- This type is deprecated and will be removed in SeqAn3.1.
- Template Parameters
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| score_type | The underlying type. |
- See also
- seqan3::gap_scheme
◆ get_gap_score()
template<arithmetic score_t = int8_t>
A strong type of underlying type score_type that represents the score of any character against a gap character.
- Deprecated:
- This type is deprecated and will be removed in SeqAn3.1.
- Template Parameters
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| score_type | The underlying type. |
- See also
- seqan3::gap_scheme
◆ score()
template<arithmetic score_t = int8_t>
| constexpr ptrdiff_t seqan3::gap_scheme< score_t >::score |
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size_t const |
number_of_consecutive_gaps | ) |
const |
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inlineconstexprnoexcept |
Compute the score of a stretch of gap characters.
- Parameters
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| number_of_consecutive_gaps | The number of consecutive gaps that you wish to know the score for. |
- Returns
- A signed integer (usually 64bit) that holds the score computed based on the selected scheme.
◆ set_affine()
template<arithmetic score_t = int8_t>
template<arithmetic score_arg_t>
Set the Affine gap costs model.
- Template Parameters
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| score_arg_t | The underlying type of the arguments. |
- Parameters
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- Exceptions
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The score for a sequence of n gap characters is computed as n * g + go.
- Attention
- This is the formula used most commonly in the literature, but it is different from SeqAn2 where the formula was
(n-1) * g + go.
◆ set_linear()
template<arithmetic score_t = int8_t>
template<arithmetic score_arg_t>
Set the Linear gap costs model.
- Template Parameters
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| score_arg_t | The underlying type of the argument. |
- Parameters
-
- Exceptions
-
The score for a sequence of n gap characters is computed as n * g. This is the same as the affine model with a gap open score of 0.
The documentation for this class was generated from the following file:
Inheritance diagram for seqan3::gap_scheme< score_t >:
1.9.1