68 #ifdef SEQAN3_DEPRECATED_310
111 #ifdef SEQAN3_DEPRECATED_310
170 template <
field ...fs>
181 static constexpr
size_t size =
sizeof...(fs);
184 static constexpr
size_t index_of(
field f)
186 for (
size_t i = 0; i <
sizeof...(fs); ++i)
187 if (as_array[i] == f)
193 static constexpr
bool contains(
field f)
195 return index_of(f) != npos;
198 static_assert([] () constexpr
200 for (
size_t i = 0; i < as_array.
size(); ++i)
201 for (
size_t j = i + 1; j < as_array.
size(); ++j)
202 if (as_array[i] == as_array[j])
206 } (),
"You may not include a field twice into fields<>.");
233 template <
typename field_types,
typename field_
ids>
234 struct record : detail::transfer_template_args_onto_t<field_types, std::tuple>
238 template <
typename t>
240 requires requires (t & v) { v.
clear(); }
242 static constexpr
void clear_element(t & v) noexcept(noexcept(v.clear()))
248 template <
typename t>
249 static constexpr
void clear_element(t & v) noexcept(noexcept(std::declval<t &>() = t{}))
255 static constexpr
auto expander = [] (
auto & ...args) { (clear_element(args), ...); };
259 using base_type = detail::transfer_template_args_onto_t<field_types, std::tuple>;
272 using base_type::base_type;
276 "You must give as many IDs as types to seqan3::record.");
292 template <field f,
typename tuple_t>
293 static decltype(
auto) get_impl(field_constant<f>, tuple_t && record_as_tuple)
295 static_assert(
field_ids::contains(f),
"The record does not contain the field you wish to retrieve.");
296 #if SEQAN3_WORKAROUND_GCC_94967
299 if constexpr (!std::is_lvalue_reference_v<tuple_t> && std::is_const_v<tuple_t>)
302 using return_t = std::tuple_element_t<field_ids::index_of(f), tuple_t>;
303 return static_cast<return_t
const &&
>(std::get<field_ids::index_of(f)>(
std::move(record_as_tuple)));
307 return std::get<field_ids::index_of(f)>(std::forward<tuple_t>(record_as_tuple));
310 return std::get<field_ids::index_of(f)>(std::forward<tuple_t>(record_as_tuple));
325 template <
typename field_types,
typename field_
ids>
326 struct tuple_size<
seqan3::record<field_types, field_ids>>
327 : tuple_size<typename seqan3::record<field_types, field_ids>::base_type>
335 template <
size_t elem_no,
typename field_types,
typename field_
ids>
336 struct tuple_element<elem_no,
seqan3::record<field_types, field_ids>>
337 : tuple_element<elem_no, typename seqan3::record<field_types, field_ids>::base_type>
342 #ifdef SEQAN3_DEPRECATED_310
353 template <field f,
typename field_types,
typename field_
ids>
356 static_assert(
field_ids::contains(f),
"The record does not contain the field you wish to retrieve.");
357 return std::get<field_ids::index_of(f)>(r);
361 template <field f,
typename field_types,
typename field_
ids>
364 static_assert(
field_ids::contains(f),
"The record does not contain the field you wish to retrieve.");
365 return std::get<field_ids::index_of(f)>(r);
369 template <field f,
typename field_types,
typename field_
ids>
372 static_assert(
field_ids::contains(f),
"The record does not contain the field you wish to retrieve.");
373 return std::get<field_ids::index_of(f)>(
std::move(r));
377 template <field f,
typename field_types,
typename field_
ids>
380 static_assert(
field_ids::contains(f),
"The record does not contain the field you wish to retrieve.");
381 #if SEQAN3_WORKAROUND_GCC_94967
384 return static_cast<return_t
const &&
>(std::get<field_ids::index_of(f)>(
std::move(r)));
386 return std::get<field_ids::index_of(f)>(
std::move(r));
Provides type traits for working with templates.
field
An enumerator for the fields used in file formats.
Definition: record.hpp:63
@ 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 seqan3::field::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.
@ _seq_qual_deprecated
[DEPRECATED] Sequence and qualities combined in one range. Use field::seq and field::qual instead.
@ ref_offset
Sequence (seqan3::field::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 object that models seqan3::detail::pairwise_alignment.
@ cigar
The cigar vector (std::vector<seqan3::cigar>) representing the alignment in SAM/BAM format.
@ mapq
The mapping quality of the seqan3::field::seq alignment, usually a Phred-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 (seqan3::field::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
[DEPRECATED] Sequence and qualities combined in one range. Use field::seq and field::qual instead.
@ header_ptr
A pointer to the seqan3::sam_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 seqan3::field::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
[DEPRECATED] Sequence and qualities combined in one range. Use field::seq and field::qual instead.
@ 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 bool contains
Whether a type occurs in a type list or not.
Definition: traits.hpp:231
constexpr size_t size
The size of a type pack.
Definition: traits.hpp:151
auto const move
A view that turns lvalue-references into rvalue-references.
Definition: move.hpp:74
The main SeqAn3 namespace.
Definition: aligned_sequence_concept.hpp:29
SeqAn specific customisations in the standard namespace.
A class template that holds a choice of seqan3::field.
Definition: record.hpp:172
The class template that file records are based on; behaves like an std::tuple.
Definition: record.hpp:235
auto & get(record< field_types, field_ids > &r)
Free function get() for seqan3::record based on seqan3::field.
Definition: record.hpp:354
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:370
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:279
~record()=default
Defaulted.
detail::transfer_template_args_onto_t< field_types, std::tuple > base_type
A specialisation of std::tuple.
Definition: record.hpp:259
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:362
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:378
record(record const &)=default
Defaulted.