Stores the alignment results and gives access to score, alignment and the front and end positionss. More...
#include <seqan3/alignment/pairwise/alignment_result.hpp>
Public Member Functions | |
constexpr auto const & | score_matrix () const noexcept |
Returns the score matrix used to compute the alignment. More... | |
constexpr auto const & | trace_matrix () const noexcept |
Returns the trace matrix used to compute the alignment. More... | |
Access functions | |
Functions to access elements of the alignment result type. | |
constexpr sequence1_id_t | sequence1_id () const noexcept |
Returns the alignment identifier of the first sequence. More... | |
constexpr sequence2_id_t | sequence2_id () const noexcept |
Returns the alignment identifier of the second sequence. More... | |
constexpr score_t | score () const noexcept |
Returns the alignment score. More... | |
constexpr auto | sequence1_end_position () const noexcept |
Returns the end position of the first sequence of the alignment. More... | |
constexpr auto | sequence2_end_position () const noexcept |
Returns the end position of the second sequence of the alignment. More... | |
constexpr auto | sequence1_begin_position () const noexcept |
Returns the begin position of the first sequence of the alignment. More... | |
constexpr auto | sequence2_begin_position () const noexcept |
Returns the begin position of the second sequence of the alignment. More... | |
constexpr alignment_t const & | alignment () const noexcept |
Returns the actual alignment, i.e. the base pair matching. More... | |
Private Types | |
Member types | |
Local definition of the types contained in the | |
using | sequence1_id_t = decltype(data.sequence1_id) |
The type for the alignment identifier for the first sequence. | |
using | sequence2_id_t = decltype(data.sequence2_id) |
The type for the alignment identifier for the second sequence. | |
using | score_t = decltype(data.score) |
The type for the resulting score. | |
using | end_positions_t = decltype(data.end_positions) |
The type for the end positions. | |
using | begin_positions_t = decltype(data.begin_positions) |
The type for the begin positions. | |
using | alignment_t = decltype(data.alignment) |
The type for the alignment. | |
Private Attributes | |
alignment_result_value_t | data {} |
Object that stores the computed alignment results. | |
Friends | |
template<typename configuration_t > | |
class | detail::policy_alignment_result_builder |
Befriend alignment result builder. | |
Constructors, destructor and assignment | |
alignment_result (alignment_result_value_t value) | |
Constructs a seqan3::alignment_result from an value_type object. More... | |
alignment_result ()=default | |
alignment_result (alignment_result const &)=default | |
Defaulted. | |
alignment_result (alignment_result &&)=default | |
Defaulted. | |
alignment_result & | operator= (alignment_result const &)=default |
Defaulted. | |
alignment_result & | operator= (alignment_result &&)=default |
Defaulted. | |
~alignment_result ()=default | |
Defaulted. | |
Stores the alignment results and gives access to score, alignment and the front and end positionss.
alignment_result_value_t | The underlying value type containing the information from the alignment computation. |
This class provides read-only access to the results of a pairwise alignment computation. It always contains an alignment identifier and the resulting score. Optionally – if the user requests – also the begin and end positions within the sequences and the alignment can be calculated. When accessing a field that has not been calculated, an assertion will fail during compilation.
To access the type of the passed alignment result value use the seqan3::detail::alignment_result_value_type_accessor transformation trait. The seqan3::detail::policy_alignment_result_builder is used to set the respective values. This class is befriended with this class to allow access to the private data member.
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inlineprivate |
Constructs a seqan3::alignment_result from an value_type
object.
[in] | value | The alignment results. |
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default |
Defaulted.
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inlineconstexprnoexcept |
Returns the actual alignment, i.e. the base pair matching.
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inlineconstexprnoexcept |
Returns the alignment score.
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inlineconstexprnoexcept |
Returns the score matrix used to compute the alignment.
This function is only used for debugging such that performance can be affected significantly when enabling seqan3::align_cfg::detail::debug.
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inlineconstexprnoexcept |
Returns the begin position of the first sequence of the alignment.
Guaranteed to be smaller than or equal to sequence1_end_position()
.
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inlineconstexprnoexcept |
Returns the end position of the first sequence of the alignment.
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inlineconstexprnoexcept |
Returns the alignment identifier of the first sequence.
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inlineconstexprnoexcept |
Returns the begin position of the second sequence of the alignment.
Guaranteed to be smaller than or equal to sequence2_end_position()
.
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inlineconstexprnoexcept |
Returns the end position of the second sequence of the alignment.
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inlineconstexprnoexcept |
Returns the alignment identifier of the second sequence.
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inlineconstexprnoexcept |
Returns the trace matrix used to compute the alignment.
This function is only used for debugging such that performance can be affected significantly when enabling seqan3::align_cfg::detail::debug.