SeqAn3  3.0.3
The Modern C++ library for sequence analysis.
alignment_result.hpp
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1 // -----------------------------------------------------------------------------------------------------
2 // Copyright (c) 2006-2021, Knut Reinert & Freie Universität Berlin
3 // Copyright (c) 2016-2021, Knut Reinert & MPI für molekulare Genetik
4 // This file may be used, modified and/or redistributed under the terms of the 3-clause BSD-License
5 // shipped with this file and also available at: https://github.com/seqan/seqan3/blob/master/LICENSE.md
6 // -----------------------------------------------------------------------------------------------------
7 
14 #pragma once
15 
16 #include <optional>
17 
21 
22 namespace seqan3::detail
23 {
24 
25 // forward declaration for friend declaration in alignment_result.
26 template <typename configuration_t>
27 #if !SEQAN3_WORKAROUND_GCC_93467
29  requires is_type_specialisation_of_v<configuration_t, configuration>
31 #endif // !SEQAN3_WORKAROUND_GCC_93467
32 class policy_alignment_result_builder;
33 
46 template <typename sequence1_id_t,
47  typename sequence2_id_t,
48  typename score_t,
49  typename end_positions_t = std::nullopt_t *,
50  typename begin_positions_t = std::nullopt_t *,
51  typename alignment_t = std::nullopt_t *,
52  typename score_debug_matrix_t = std::nullopt_t *,
53  typename trace_debug_matrix_t = std::nullopt_t *>
54 struct alignment_result_value_type
55 {
57  sequence1_id_t sequence1_id{};
59  sequence2_id_t sequence2_id{};
61  score_t score{};
63  end_positions_t end_positions{};
65  begin_positions_t begin_positions{};
67  alignment_t alignment{};
68 
70  score_debug_matrix_t score_debug_matrix{};
72  trace_debug_matrix_t trace_debug_matrix{};
73 };
74 
80 alignment_result_value_type()
81  -> alignment_result_value_type<std::nullopt_t *, std::nullopt_t *, std::nullopt_t *>;
82 
84 template <typename sequence1_id_t, typename sequence2_id_t, typename score_t>
85 alignment_result_value_type(sequence1_id_t, sequence2_id_t, score_t)
86  -> alignment_result_value_type<sequence1_id_t, sequence2_id_t, score_t>;
87 
89 template <typename sequence1_id_t, typename sequence2_id_t, typename score_t, typename end_positions_t>
90 alignment_result_value_type(sequence1_id_t, sequence2_id_t, score_t, end_positions_t)
91  -> alignment_result_value_type<sequence1_id_t, sequence2_id_t, score_t, end_positions_t>;
92 
94 template <typename sequence1_id_t,
95  typename sequence2_id_t,
96  typename score_t,
97  typename end_positions_t,
98  typename begin_positions_t>
99 alignment_result_value_type(sequence1_id_t, sequence2_id_t, score_t, end_positions_t, begin_positions_t)
100  -> alignment_result_value_type<sequence1_id_t, sequence2_id_t, score_t, end_positions_t, begin_positions_t>;
101 
103 template <typename sequence1_id_t,
104  typename sequence2_id_t,
105  typename score_t,
106  typename end_positions_t,
107  typename begin_positions_t,
108  typename alignment_t>
109 alignment_result_value_type(sequence1_id_t, sequence2_id_t, score_t, end_positions_t, begin_positions_t, alignment_t)
110  -> alignment_result_value_type<sequence1_id_t,
111  sequence2_id_t,
112  score_t,
113  end_positions_t,
114  begin_positions_t,
115  alignment_t>;
117 
119 template <typename result_t>
120 struct alignment_result_value_type_accessor;
122 } // namespace seqan3::detail
123 
124 namespace seqan3
125 {
126 
150 template <typename alignment_result_value_t>
152  requires detail::is_type_specialisation_of_v<alignment_result_value_t, detail::alignment_result_value_type>
155 {
156 private:
158  alignment_result_value_t data{};
159 
165  using sequence1_id_t = decltype(data.sequence1_id);
167  using sequence2_id_t = decltype(data.sequence2_id);
169  using score_t = decltype(data.score);
171  using end_positions_t = decltype(data.end_positions);
173  using begin_positions_t = decltype(data.begin_positions);
175  using alignment_t = decltype(data.alignment);
177 
179  template <typename configuration_t>
180  #if !SEQAN3_WORKAROUND_GCC_93467
182  requires detail::is_type_specialisation_of_v<configuration_t, configuration>
184  #endif // !SEQAN3_WORKAROUND_GCC_93467
185  friend class detail::policy_alignment_result_builder;
186 
187 public:
193 
196  alignment_result(alignment_result_value_t value) : data(std::move(value))
197  {}
198 
200  alignment_result() = default;
201  alignment_result(alignment_result const &) = default;
205  ~alignment_result() = default;
206 
208 
217  constexpr sequence1_id_t sequence1_id() const noexcept
218  {
219  static_assert(!std::is_same_v<sequence1_id_t, std::nullopt_t *>,
220  "Trying to access the id of the first sequence, although it was not requested in the"
221  " alignment configuration.");
222  return data.sequence1_id;
223  }
224 
228  constexpr sequence2_id_t sequence2_id() const noexcept
229  {
230  static_assert(!std::is_same_v<sequence2_id_t, std::nullopt_t *>,
231  "Trying to access the id of the second sequence, although it was not requested in the"
232  " alignment configuration.");
233  return data.sequence2_id;
234  }
235 
239  constexpr score_t score() const noexcept
240  {
241  static_assert(!std::is_same_v<score_t, std::nullopt_t *>,
242  "Trying to access the score, although it was not requested in the alignment configuration.");
243  return data.score;
244  }
245 
252  constexpr auto sequence1_end_position() const noexcept
253  {
254  static_assert(!std::is_same_v<end_positions_t, std::nullopt_t *>,
255  "Trying to access the end position of the first sequence, although it was not requested in the"
256  " alignment configuration.");
257  return data.end_positions.first;
258  }
259 
266  constexpr auto sequence2_end_position() const noexcept
267  {
268  static_assert(!std::is_same_v<end_positions_t, std::nullopt_t *>,
269  "Trying to access the end position of the second sequence, although it was not requested in the"
270  " alignment configuration.");
271  return data.end_positions.second;
272  }
273 
284  constexpr auto sequence1_begin_position() const noexcept
285  {
286  static_assert(!std::is_same_v<begin_positions_t, std::nullopt_t *>,
287  "Trying to access the begin position of the first sequence, although it was not requested in the"
288  " alignment configuration.");
289  return data.begin_positions.first;
290  }
291 
302  constexpr auto sequence2_begin_position() const noexcept
303  {
304  static_assert(!std::is_same_v<begin_positions_t, std::nullopt_t *>,
305  "Trying to access the begin position of the second sequence, although it was not requested in the"
306  " alignment configuration.");
307  return data.begin_positions.second;
308  }
309 
316  constexpr alignment_t const & alignment() const noexcept
317  {
318  static_assert(!std::is_same_v<alignment_t, std::nullopt_t *>,
319  "Trying to access the alignment, although it was not requested in the alignment configuration.");
320  return data.alignment;
321  }
323 
325 
336  constexpr auto const & score_matrix() const noexcept
337  {
338  static_assert(!std::is_same_v<decltype(data.score_debug_matrix), std::nullopt_t *>,
339  "Trying to access the score matrix, although it was not requested in the alignment configuration.");
340  return data.score_debug_matrix;
341  }
342 
354  constexpr auto const & trace_matrix() const noexcept
355  {
356  static_assert(!std::is_same_v<decltype(data.trace_debug_matrix), std::nullopt_t *>,
357  "Trying to access the trace matrix, although it was not requested in the alignment configuration.");
358  return data.trace_debug_matrix;
359  }
361 };
362 } // namespace seqan3
363 
364 namespace seqan3::detail
365 {
376 template <typename result_value_t>
377 struct alignment_result_value_type_accessor<alignment_result<result_value_t>>
378 {
380  using type = result_value_t;
381 };
382 
383 } // namespace seqan3::detail
384 
385 namespace seqan3
386 {
396 template <typename char_t, typename alignment_result_t>
398  requires detail::is_type_specialisation_of_v<std::remove_cvref_t<alignment_result_t>, alignment_result>
400 inline debug_stream_type<char_t> & operator<<(debug_stream_type<char_t> & stream, alignment_result_t && result)
401 {
402  using disabled_t = std::nullopt_t *;
403  using result_data_t =
404  typename detail::alignment_result_value_type_accessor<std::remove_cvref_t<alignment_result_t>>::type;
405 
406  constexpr bool has_sequence1_id = !std::is_same_v<decltype(std::declval<result_data_t>().sequence1_id), disabled_t>;
407  constexpr bool has_sequence2_id = !std::is_same_v<decltype(std::declval<result_data_t>().sequence2_id), disabled_t>;
408  constexpr bool has_score = !std::is_same_v<decltype(std::declval<result_data_t>().score), disabled_t>;
409  constexpr bool has_end_positions = !std::is_same_v<decltype(std::declval<result_data_t>().end_positions),
410  disabled_t>;
411  constexpr bool has_begin_positions = !std::is_same_v<decltype(std::declval<result_data_t>().begin_positions),
412  disabled_t>;
413  constexpr bool has_alignment = !std::is_same_v<decltype(std::declval<result_data_t>().alignment), disabled_t>;
414 
415  bool prepend_comma = false;
416  auto append_to_stream = [&] (auto && ...args)
417  {
418  ((stream << (prepend_comma ? std::string{", "} : std::string{})) << ... << std::forward<decltype(args)>(args));
419  prepend_comma = true;
420  };
421 
422  stream << '{';
423  if constexpr (has_sequence1_id)
424  append_to_stream("sequence1 id: ", result.sequence1_id());
425  if constexpr (has_sequence2_id)
426  append_to_stream("sequence2 id: ", result.sequence2_id());
427  if constexpr (has_score)
428  append_to_stream("score: ", result.score());
429  if constexpr (has_begin_positions)
430  append_to_stream("begin: (", result.sequence1_begin_position(), ",", result.sequence2_begin_position(), ")");
431  if constexpr (has_end_positions)
432  append_to_stream("end: (", result.sequence1_end_position(), ",", result.sequence2_end_position(), ")");
433  if constexpr (has_alignment)
434  append_to_stream("\nalignment:\n", result.alignment());
435  stream << '}';
436 
437  return stream;
438 }
439 } // namespace seqan3
Stores the alignment results and gives access to score, alignment and the front and end positionss.
Definition: alignment_result.hpp:155
constexpr sequence2_id_t sequence2_id() const noexcept
Returns the alignment identifier of the second sequence.
Definition: alignment_result.hpp:228
constexpr alignment_t const & alignment() const noexcept
Returns the actual alignment, i.e. the base pair matching.
Definition: alignment_result.hpp:316
alignment_result & operator=(alignment_result &&)=default
Defaulted.
constexpr sequence1_id_t sequence1_id() const noexcept
Returns the alignment identifier of the first sequence.
Definition: alignment_result.hpp:217
constexpr auto sequence2_end_position() const noexcept
Returns the end position of the second sequence of the alignment.
Definition: alignment_result.hpp:266
constexpr auto sequence1_begin_position() const noexcept
Returns the begin position of the first sequence of the alignment.
Definition: alignment_result.hpp:284
alignment_result(alignment_result const &)=default
Defaulted.
constexpr auto sequence2_begin_position() const noexcept
Returns the begin position of the second sequence of the alignment.
Definition: alignment_result.hpp:302
~alignment_result()=default
Defaulted.
constexpr score_t score() const noexcept
Returns the alignment score.
Definition: alignment_result.hpp:239
constexpr auto sequence1_end_position() const noexcept
Returns the end position of the first sequence of the alignment.
Definition: alignment_result.hpp:252
alignment_result & operator=(alignment_result const &)=default
Defaulted.
alignment_result(alignment_result &&)=default
Defaulted.
Provides seqan3::configuration and utility functions.
Provides seqan3::debug_stream and related types.
Provides type traits for working with templates.
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:101
@ alignment
The (pairwise) alignment stored in an object that models seqan3::detail::pairwise_alignment.
auto const move
A view that turns lvalue-references into rvalue-references.
Definition: move.hpp:74
T is_same_v
The main SeqAn3 namespace.
Definition: aligned_sequence_concept.hpp:29