SeqAn3  3.0.2
The Modern C++ library for sequence analysis.
record.hpp
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1 // -----------------------------------------------------------------------------------------------------
2 // Copyright (c) 2006-2020, Knut Reinert & Freie Universität Berlin
3 // Copyright (c) 2016-2020, 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 
13 #pragma once
14 
15 #include <tuple>
16 
17 #include <meta/meta.hpp>
18 
21 
22 namespace seqan3
23 {
24 
25 // ----------------------------------------------------------------------------
26 // enum field
27 // ----------------------------------------------------------------------------
28 
64 enum class field
65 {
66  // Fields used in multiple contexts ........................................
67  seq,
68  id,
69  qual,
70  seq_qual,
71  offset,
72 
73  // Fields unique to structure io ...........................................
74  bpp,
75  structure,
77  energy,
78  react,
79  react_err,
80  comment,
81 
82  // Fields unique to alignment io ...........................................
83  alignment,
84  ref_id,
85  ref_seq,
86  ref_offset,
87  header_ptr,
88 
89  flag,
90  mate,
91  mapq,
92  cigar,
93  tags,
94 
95  bit_score,
96  evalue,
97 
98  // User defined field aliases .. ...........................................
109 
110  // deprecated uppercase:
145 };
146 
147 // ----------------------------------------------------------------------------
148 // fields
149 // ----------------------------------------------------------------------------
150 
164 template <field ...fs>
165 struct fields
166 {
169  static constexpr std::array<field, sizeof...(fs)> as_array{fs...};
170 
172  static constexpr size_t npos = std::numeric_limits<size_t>::max();
173 
175  static constexpr size_t index_of(field f)
176  {
177  for (size_t i = 0; i < sizeof...(fs); ++i)
178  if (as_array[i] == f)
179  return i;
180  return npos;
181  }
182 
184  static constexpr bool contains(field f)
185  {
186  return index_of(f) != npos;
187  }
188 
189  static_assert([] () constexpr
190  {
191  for (size_t i = 0; i < as_array.size(); ++i)
192  for (size_t j = i + 1; j < as_array.size(); ++j)
193  if (as_array[i] == as_array[j])
194  return false;
195 
196  return true;
197  } (), "You may not include a field twice into fields<>.");
198 };
199 
200 // ----------------------------------------------------------------------------
201 // record
202 // ----------------------------------------------------------------------------
203 
224 template <typename field_types, typename field_ids>
225 struct record : detail::transfer_template_args_onto_t<field_types, std::tuple>
226 {
227 private:
229  template <typename t>
231  requires requires (t & v) { v.clear(); }
233  static constexpr void clear_element(t & v) noexcept(noexcept(v.clear()))
234  {
235  v.clear();
236  }
237 
239  template <typename t>
240  static constexpr void clear_element(t & v) noexcept(noexcept(std::declval<t &>() = t{}))
241  {
242  v = {};
243  }
244 
246  static constexpr auto expander = [] (auto & ...args) { (clear_element(args), ...); };
247 
248 public:
250  using base_type = detail::transfer_template_args_onto_t<field_types, std::tuple>;
251 
255  record() = default;
256  record(record const &) = default;
257  record & operator=(record const &) = default;
258  record(record &&) = default;
259  record & operator=(record &&) = default;
260  ~record() = default;
261 
263  using base_type::base_type;
265 
266  static_assert(field_types::size() == field_ids::as_array.size(),
267  "You must give as many IDs as types to seqan3::record.");
268 
270  void clear() noexcept(noexcept(std::apply(expander, std::declval<record &>())))
271  {
272  std::apply(expander, *this);
273  }
274 };
275 
276 } // namespace seqan3
277 
278 namespace std
279 {
280 
286 template <typename field_types, typename field_ids>
287 struct tuple_size<seqan3::record<field_types, field_ids>>
288 {
290  static constexpr size_t value = tuple_size_v<typename seqan3::record<field_types, field_ids>::base_type>;
291 };
292 
298 template <size_t elem_no, typename field_types, typename field_ids>
299 struct tuple_element<elem_no, seqan3::record<field_types, field_ids>>
300 {
302  using type = std::tuple_element_t<elem_no, typename seqan3::record<field_types, field_ids>::base_type>;
303 };
304 
305 } // namespace std
306 
307 namespace seqan3
308 {
309 
317 template <field f, typename field_types, typename field_ids>
319 {
320  static_assert(field_ids::contains(f), "The record does not contain the field you wish to retrieve.");
321  return std::get<field_ids::index_of(f)>(r);
322 }
323 
325 template <field f, typename field_types, typename field_ids>
326 auto const & get(record<field_types, field_ids> const & r)
327 {
328  static_assert(field_ids::contains(f), "The record does not contain the field you wish to retrieve.");
329  return std::get<field_ids::index_of(f)>(r);
330 }
331 
333 template <field f, typename field_types, typename field_ids>
335 {
336  static_assert(field_ids::contains(f), "The record does not contain the field you wish to retrieve.");
337  return std::get<field_ids::index_of(f)>(std::move(r));
338 }
339 
341 template <field f, typename field_types, typename field_ids>
342 auto const && get(record<field_types, field_ids> const && r)
343 {
344  static_assert(field_ids::contains(f), "The record does not contain the field you wish to retrieve.");
345  return std::get<field_ids::index_of(f)>(std::move(r));
346 }
348 
349 } // namespace seqan3
T apply(T... args)
field
An enumerator for the fields used in file formats.
Definition: record.hpp:65
@ energy
Energy of a folded sequence, represented by one float number.
@ comment
Comment field of arbitrary content, usually a string.
@ CIGAR
Please use the field name in lower case.
@ structure
Fixed interactions, usually a string of structure alphabet characters.
@ bpp
Base pair probability matrix of interactions, usually a matrix of float numbers.
@ FLAG
Please use the field name in lower case.
@ REF_SEQ
Please use the field name in lower case.
@ OFFSET
Please use the field name in lower case.
@ react
Reactivity values of the sequence characters given in a vector of float numbers.
@ flag
The alignment flag (bit information), uint16_t value.
@ USER_DEFINED_6
Please use the field name in lower case.
@ TAGS
Please use the field name in lower case.
@ react_err
Reactivity error values given in a vector corresponding to REACT.
@ QUAL
Please use the field name in lower case.
@ USER_DEFINED_8
Please use the field name in lower case.
@ MATE
Please use the field name in lower case.
@ ref_offset
Sequence (REF_SEQ) relative start position (0-based), unsigned value.
@ ref_seq
The (reference) "sequence" information, usually a range of nucleotides or amino acids.
@ SEQ
Please use the field name in lower case.
@ alignment
The (pairwise) alignment stored in an seqan3::alignment object.
@ cigar
The cigar vector (std::vector<seqan3::cigar>) representing the alignment in SAM/BAM format.
@ mapq
The mapping quality of the SEQ alignment, usually a ohred-scaled score.
@ user_defined_2
Identifier for user defined file formats and specialisations.
@ user_defined_5
Identifier for user defined file formats and specialisations.
@ STRUCTURE
Please use the field name in lower case.
@ USER_DEFINED_2
Please use the field name in lower case.
@ REACT_ERR
Please use the field name in lower case.
@ bit_score
The bit score (statistical significance indicator), unsigned value.
@ user_defined_0
Identifier for user defined file formats and specialisations.
@ user_defined_8
Identifier for user defined file formats and specialisations.
@ STRUCTURED_SEQ
Please use the field name in lower case.
@ user_defined_3
Identifier for user defined file formats and specialisations.
@ offset
Sequence (SEQ) relative start position (0-based), unsigned value.
@ MAPQ
Please use the field name in lower case.
@ mate
The mate pair information given as a std::tuple of reference name, offset and template length.
@ SEQ_QUAL
Please use the field name in lower case.
@ header_ptr
A pointer to the seqan3::alignment_file_header object storing header information.
@ user_defined_7
Identifier for user defined file formats and specialisations.
@ user_defined_4
Identifier for user defined file formats and specialisations.
@ ENERGY
Please use the field name in lower case.
@ ref_id
The identifier of the (reference) sequence that SEQ was aligned to.
@ BIT_SCORE
Please use the field name in lower case.
@ REACT
Please use the field name in lower case.
@ structured_seq
Sequence and fixed interactions combined in one range.
@ ALIGNMENT
Please use the field name in lower case.
@ HEADER_PTR
Please use the field name in lower case.
@ evalue
The e-value (length normalized bit score), double value.
@ ID
Please use the field name in lower case.
@ id
The identifier, usually a string.
@ USER_DEFINED_1
Please use the field name in lower case.
@ REF_OFFSET
Please use the field name in lower case.
@ user_defined_6
Identifier for user defined file formats and specialisations.
@ USER_DEFINED_3
Please use the field name in lower case.
@ seq_qual
Sequence and qualities combined in one range.
@ tags
The optional tags in the SAM format, stored in a dictionary.
@ user_defined_1
Identifier for user defined file formats and specialisations.
@ user_defined_9
Identifier for user defined file formats and specialisations.
@ seq
The "sequence", usually a range of nucleotides or amino acids.
@ USER_DEFINED_9
Please use the field name in lower case.
@ USER_DEFINED_5
Please use the field name in lower case.
@ USER_DEFINED_7
Please use the field name in lower case.
@ qual
The qualities, usually in phred-score notation.
@ BPP
Please use the field name in lower case.
@ COMMENT
Please use the field name in lower case.
@ EVALUE
Please use the field name in lower case.
@ REF_ID
Please use the field name in lower case.
@ USER_DEFINED_4
Please use the field name in lower case.
@ USER_DEFINED_0
Please use the field name in lower case.
constexpr size_t size
The size of a type pack.
Definition: traits.hpp:116
constexpr bool contains
Whether a type occurs in a pack or not.
Definition: traits.hpp:193
auto const move
A view that turns lvalue-references into rvalue-references.
Definition: move.hpp:68
T max(T... args)
The main SeqAn3 namespace.
Definition: aligned_sequence_concept.hpp:29
SeqAn specific customisations in the standard namespace.
#define SEQAN3_DEPRECATED_310
Deprecation message for SeqAn 3.1.0 release.
Definition: platform.hpp:194
T size(T... args)
A class template that holds a choice of seqan3::field.
Definition: record.hpp:166
The class template that file records are based on; behaves like an std::tuple.
Definition: record.hpp:226
auto & get(record< field_types, field_ids > &r)
Free function get() for seqan3::record based on seqan3::field.
Definition: record.hpp:318
auto && get(record< field_types, field_ids > &&r)
This is an overloaded member function, provided for convenience. It differs from the above function o...
Definition: record.hpp:334
record(record &&)=default
Defaulted.
record & operator=(record &&)=default
Defaulted.
void clear() noexcept(noexcept(std::apply(expander, std::declval< record & >())))
Clears containers that provide .clear() and (re-)initialises all other elements with = {}.
Definition: record.hpp:270
~record()=default
Defaulted.
detail::transfer_template_args_onto_t< field_types, std::tuple > base_type
A specialisation of std::tuple.
Definition: record.hpp:250
auto const & get(record< field_types, field_ids > const &r)
This is an overloaded member function, provided for convenience. It differs from the above function o...
Definition: record.hpp:326
record & operator=(record const &)=default
Defaulted.
record()=default
Defaulted.
auto const && get(record< field_types, field_ids > const &&r)
This is an overloaded member function, provided for convenience. It differs from the above function o...
Definition: record.hpp:342
record(record const &)=default
Defaulted.
std::tuple_element_t< elem_no, typename seqan3::record< field_types, field_ids >::base_type > type
The member type. Delegates to same type on base_type.
Definition: record.hpp:302
Provides seqan3::type_list and auxiliary type traits.
Provides seqan3::type_list.