19namespace seqan3::detail
23template <
typename configuration_t>
24 requires seqan3::detail::is_type_specialisation_of_v<configuration_t, configuration>
25class policy_alignment_result_builder;
39template <
typename sequence1_id_t,
40 typename sequence2_id_t,
47struct alignment_result_value_type
50 sequence1_id_t sequence1_id{};
52 sequence2_id_t sequence2_id{};
56 end_positions_t end_positions{};
58 begin_positions_t begin_positions{};
63 score_debug_matrix_t score_debug_matrix{};
65 trace_debug_matrix_t trace_debug_matrix{};
76template <
typename sequence1_
id_t,
typename sequence2_
id_t,
typename score_t>
77alignment_result_value_type(sequence1_id_t, sequence2_id_t, score_t)
78 -> alignment_result_value_type<sequence1_id_t, sequence2_id_t, score_t>;
81template <
typename sequence1_
id_t,
typename sequence2_
id_t,
typename score_t,
typename end_positions_t>
82alignment_result_value_type(sequence1_id_t, sequence2_id_t, score_t, end_positions_t)
83 -> alignment_result_value_type<sequence1_id_t, sequence2_id_t, score_t, end_positions_t>;
86template <
typename sequence1_id_t,
87 typename sequence2_id_t,
89 typename end_positions_t,
90 typename begin_positions_t>
91alignment_result_value_type(sequence1_id_t, sequence2_id_t, score_t, end_positions_t, begin_positions_t)
92 -> alignment_result_value_type<sequence1_id_t, sequence2_id_t, score_t, end_positions_t, begin_positions_t>;
95template <
typename sequence1_id_t,
96 typename sequence2_id_t,
98 typename end_positions_t,
99 typename begin_positions_t,
100 typename alignment_t>
101alignment_result_value_type(sequence1_id_t, sequence2_id_t, score_t, end_positions_t, begin_positions_t, alignment_t)
102 -> alignment_result_value_type<sequence1_id_t,
111template <
typename result_t>
112struct alignment_result_value_type_accessor;
142template <
typename alignment_result_value_t>
143 requires detail::is_type_specialisation_of_v<alignment_result_value_t, detail::alignment_result_value_type>
148 alignment_result_value_t data{};
155 using sequence1_id_t =
decltype(data.sequence1_id);
157 using sequence2_id_t =
decltype(data.sequence2_id);
159 using score_t =
decltype(data.score);
161 using end_positions_t =
decltype(data.end_positions);
163 using begin_positions_t =
decltype(data.begin_positions);
165 using alignment_t =
decltype(data.alignment);
169 template <
typename configuration_t>
170 requires seqan3::detail::is_type_specialisation_of_v<configuration_t, configuration>
205 static_assert(!std::is_same_v<sequence1_id_t, std::nullopt_t *>,
206 "Trying to access the id of the first sequence, although it was not requested in the"
207 " alignment configuration.");
208 return data.sequence1_id;
216 static_assert(!std::is_same_v<sequence2_id_t, std::nullopt_t *>,
217 "Trying to access the id of the second sequence, although it was not requested in the"
218 " alignment configuration.");
219 return data.sequence2_id;
225 constexpr score_t
score() const noexcept
227 static_assert(!std::is_same_v<score_t, std::nullopt_t *>,
228 "Trying to access the score, although it was not requested in the alignment configuration.");
248 static_assert(!std::is_same_v<end_positions_t, std::nullopt_t *>,
249 "Trying to access the end position of the first sequence, although it was not requested in the"
250 " alignment configuration.");
251 return data.end_positions.first;
270 static_assert(!std::is_same_v<end_positions_t, std::nullopt_t *>,
271 "Trying to access the end position of the second sequence, although it was not requested in the"
272 " alignment configuration.");
273 return data.end_positions.second;
294 static_assert(!std::is_same_v<begin_positions_t, std::nullopt_t *>,
295 "Trying to access the begin position of the first sequence, although it was not requested in the"
296 " alignment configuration.");
297 return data.begin_positions.first;
318 static_assert(!std::is_same_v<begin_positions_t, std::nullopt_t *>,
319 "Trying to access the begin position of the second sequence, although it was not requested in the"
320 " alignment configuration.");
321 return data.begin_positions.second;
330 constexpr alignment_t
const &
alignment() const noexcept
332 static_assert(!std::is_same_v<alignment_t, std::nullopt_t *>,
333 "Trying to access the alignment, although it was not requested in the alignment configuration.");
334 return data.alignment;
350 constexpr auto const & score_matrix() const noexcept
354 "Trying to access the score matrix, although it was not requested in the alignment configuration.");
355 return data.score_debug_matrix;
369 constexpr auto const & trace_matrix() const noexcept
373 "Trying to access the trace matrix, although it was not requested in the alignment configuration.");
374 return data.trace_debug_matrix;
380namespace seqan3::detail
392template <
typename result_value_t>
393struct alignment_result_value_type_accessor<alignment_result<result_value_t>>
396 using type = result_value_t;
412template <
typename char_t,
typename alignment_result_t>
413 requires detail::is_type_specialisation_of_v<std::remove_cvref_t<alignment_result_t>, alignment_result>
414inline debug_stream_type<char_t> &
operator<<(debug_stream_type<char_t> & stream, alignment_result_t && result)
417 using result_data_t =
418 typename detail::alignment_result_value_type_accessor<std::remove_cvref_t<alignment_result_t>>::type;
420 constexpr bool has_sequence1_id = !std::is_same_v<decltype(std::declval<result_data_t>().sequence1_id), disabled_t>;
421 constexpr bool has_sequence2_id = !std::is_same_v<decltype(std::declval<result_data_t>().sequence2_id), disabled_t>;
422 constexpr bool has_score = !std::is_same_v<decltype(std::declval<result_data_t>().score), disabled_t>;
423 constexpr bool has_end_positions =
424 !std::is_same_v<decltype(std::declval<result_data_t>().end_positions), disabled_t>;
425 constexpr bool has_begin_positions =
426 !std::is_same_v<decltype(std::declval<result_data_t>().begin_positions), disabled_t>;
427 constexpr bool has_alignment = !std::is_same_v<decltype(std::declval<result_data_t>().alignment), disabled_t>;
429 bool prepend_comma =
false;
430 auto append_to_stream = [&](
auto &&... args)
432 ((stream << (prepend_comma ?
std::string{
", "} :
std::string{})) << ... << std::forward<decltype(args)>(args));
433 prepend_comma =
true;
437 if constexpr (has_sequence1_id)
438 append_to_stream(
"sequence1 id: ", result.sequence1_id());
439 if constexpr (has_sequence2_id)
440 append_to_stream(
"sequence2 id: ", result.sequence2_id());
441 if constexpr (has_score)
442 append_to_stream(
"score: ", result.score());
443 if constexpr (has_begin_positions)
444 append_to_stream(
"begin: (", result.sequence1_begin_position(),
",", result.sequence2_begin_position(),
")");
445 if constexpr (has_end_positions)
446 append_to_stream(
"end: (", result.sequence1_end_position(),
",", result.sequence2_end_position(),
")");
447 if constexpr (has_alignment)
448 append_to_stream(
"\nalignment:\n", result.alignment());
Stores the alignment results and gives access to score, alignment and the front and end positions.
Definition alignment_result.hpp:145
constexpr sequence2_id_t sequence2_id() const noexcept
Returns the alignment identifier of the second sequence.
Definition alignment_result.hpp:214
alignment_result & operator=(alignment_result &&)=default
Defaulted.
alignment_result & operator=(alignment_result const &)=default
Defaulted.
constexpr sequence1_id_t sequence1_id() const noexcept
Returns the alignment identifier of the first sequence.
Definition alignment_result.hpp:203
constexpr auto sequence2_end_position() const noexcept
Returns the end position of the second sequence of the alignment.
Definition alignment_result.hpp:268
constexpr auto sequence1_begin_position() const noexcept
Returns the begin position of the first sequence of the alignment.
Definition alignment_result.hpp:292
alignment_result(alignment_result const &)=default
Defaulted.
constexpr alignment_t const & alignment() const noexcept
Returns the actual alignment, i.e. the base pair matching.
Definition alignment_result.hpp:330
friend class detail::policy_alignment_result_builder
Befriend alignment result builder.
Definition alignment_result.hpp:171
constexpr auto sequence2_begin_position() const noexcept
Returns the begin position of the second sequence of the alignment.
Definition alignment_result.hpp:316
~alignment_result()=default
Defaulted.
constexpr score_t score() const noexcept
Returns the alignment score.
Definition alignment_result.hpp:225
constexpr auto sequence1_end_position() const noexcept
Returns the end position of the first sequence of the alignment.
Definition alignment_result.hpp:246
alignment_result()=default
alignment_result(alignment_result &&)=default
Defaulted.
Provides seqan3::configuration and utility functions.
Provides seqan3::debug_stream and related types.
debug_stream_type< char_t > & operator<<(debug_stream_type< char_t > &stream, alignment_t &&alignment)
Stream operator for alignments, which are represented as tuples of aligned sequences.
Definition debug_stream_alignment.hpp:107
@ alignment
The (pairwise) alignment stored in an object that models seqan3::detail::pairwise_alignment.
The main SeqAn3 namespace.
Definition aligned_sequence_concept.hpp:26
SeqAn specific customisations in the standard namespace.
Provides type traits for working with templates.