107 template <
typename stream_type,
108 typename legal_alph_type,
109 typename stream_pos_type,
115 stream_pos_type & position_buffer,
118 qual_type & SEQAN3_DOXYGEN_ONLY(qualities))
123 position_buffer = stream.tellg();
125 auto stream_view = detail::istreambuf(stream);
128 read_id(stream_view, options,
id);
131 read_seq(stream_view, options,
sequence);
135 template <
typename stream_type,
143 qual_type && SEQAN3_DOXYGEN_ONLY(qualities))
145 seqan3::detail::fast_ostreambuf_iterator stream_it{*stream.rdbuf()};
148 if constexpr (detail::decays_to_ignore_v<id_type>)
150 throw std::logic_error{
"The ID field may not be set to ignore when writing FASTA files."};
154 if (std::ranges::empty(
id))
157 write_id(stream_it, options,
id);
161 if constexpr (detail::decays_to_ignore_v<seq_type>)
164 "The SEQ and SEQ_QUAL fields may not both be set to ignore when writing FASTA files."};
171 write_seq(stream_it, options,
sequence);
178 template <
typename stream_view_t,
typename seq_legal_alph_type,
typename id_type>
184 if (!is_id(*begin(stream_view)))
186 +
" evaluated to false on " + detail::make_printable(*begin(stream_view))};
188 if constexpr (detail::decays_to_ignore_v<id_type>)
190 detail::consume(stream_view | detail::take_line_or_throw);
196#if SEQAN3_WORKAROUND_VIEW_PERFORMANCE
197 auto it = stream_view.begin();
198 auto e = stream_view.end();
203 for (; (it != e) && (
is_blank)(*it); ++it)
207 bool at_delimiter =
false;
208 for (; it != e; ++it)
215 id.push_back(
assign_char_to(*it, std::ranges::range_value_t<id_type>{}));
219 throw unexpected_end_of_input{
"FASTA ID line did not end in newline."};
221 for (; (it != e) && ((!
is_char<
'\n'>)(*it)); ++it)
228 stream_view | std::views::drop(1)
237 stream_view | std::views::drop(1)
244 detail::consume(stream_view | detail::take_line_or_throw);
249#if SEQAN3_WORKAROUND_VIEW_PERFORMANCE
250 auto it = stream_view.begin();
251 auto e = stream_view.end();
256 for (; (it != e) && (
is_blank)(*it); ++it)
260 bool at_delimiter =
false;
261 for (; it != e; ++it)
268 id.push_back(
assign_char_to(*it, std::ranges::range_value_t<id_type>{}));
272 throw unexpected_end_of_input{
"FASTA ID line did not end in newline."};
277 std::ranges::copy(stream_view | detail::take_line_or_throw
278 | std::views::drop(1)
285 std::ranges::copy(stream_view | detail::take_line_or_throw
286 | std::views::drop(1)
296 template <
typename stream_view_t,
typename seq_legal_alph_type,
typename seq_type>
297 void read_seq(stream_view_t & stream_view, sequence_file_input_options<seq_legal_alph_type>
const &, seq_type &
seq)
301 if constexpr (!detail::decays_to_ignore_v<seq_type>)
303 constexpr auto is_legal_alph = char_is_valid_for<seq_legal_alph_type>;
305#if SEQAN3_WORKAROUND_VIEW_PERFORMANCE
306 auto it = stream_view.begin();
307 auto e = stream_view.end();
310 throw unexpected_end_of_input{
"No sequence information given!"};
312 for (; (it != e) && ((!is_id)(*it)); ++it)
318 else if (is_legal_alph(*it))
325 throw parse_error{
std::string{
"Encountered an unexpected letter: "} +
"char_is_valid_for<"
326 + detail::type_name_as_string<seq_legal_alph_type>
327 +
"> evaluated to false on " + detail::make_printable(*it)};
333 if (std::ranges::begin(stream_view) == std::ranges::end(stream_view))
334 throw unexpected_end_of_input{
"No sequence information given!"};
337 stream_view | detail::take_until(is_id)
339 | std::views::transform(
340 [is_legal_alph](
char const c)
342 if (!is_legal_alph(c))
344 throw parse_error{
std::string{
"Encountered an unexpected letter: "}
345 +
"char_is_valid_for<"
346 + detail::type_name_as_string<seq_legal_alph_type>
347 +
"> evaluated to false on " + detail::make_printable(c)};
357 detail::consume(stream_view | detail::take_until(is_id));
362 template <
typename stream_it_t,
typename id_type>
363 void write_id(stream_it_t & stream_it, sequence_file_output_options
const & options, id_type &&
id)
365 if (options.fasta_legacy_id_marker)
370 if (options.fasta_blank_before_id)
373 stream_it.write_range(
id);
374 stream_it.write_end_of_line(options.add_carriage_return);
378 template <
typename stream_it_t,
typename seq_type>
379 void write_seq(stream_it_t & stream_it, sequence_file_output_options
const & options, seq_type &&
seq)
383 if (options.fasta_letters_per_line > 0)
386 auto it = std::ranges::begin(char_sequence);
387 auto end = std::ranges::end(char_sequence);
392 auto current_end = it;
393 size_t steps = std::ranges::advance(current_end, options.fasta_letters_per_line, end);
394 using subrange_t = std::ranges::subrange<
decltype(it),
decltype(it), std::ranges::subrange_kind::sized>;
395 it = stream_it.write_range(subrange_t{it, current_end, (options.fasta_letters_per_line - steps)});
396 stream_it.write_end_of_line(options.add_carriage_return);
401 stream_it.write_range(char_sequence);
402 stream_it.write_end_of_line(options.add_carriage_return);
Provides aliases for qualified.
Core alphabet concept and free function/type trait wrappers.
T back_inserter(T... args)
Provides alphabet adaptations for standard char types.
Provides seqan3::views::char_to.
Provides various utility functions.
Provides various transformation traits used by the range module.
Provides seqan3::dna5, container aliases and string literals.
Provides seqan3::detail::fast_ostreambuf_iterator.
auto const to_char
A view that calls seqan3::to_char() on each element in the input range.
Definition to_char.hpp:63
auto const char_to
A view over an alphabet, given a range of characters.
Definition char_to.hpp:67
constexpr auto assign_char_to
Assign a character to an alphabet object.
Definition alphabet/concept.hpp:524
@ seq
The "sequence", usually a range of nucleotides or amino acids.
constexpr auto is_blank
Checks whether c is a blank character.
Definition predicate.hpp:142
constexpr auto is_digit
Checks whether c is a digital character.
Definition predicate.hpp:262
constexpr auto is_char
Checks whether a given letter is the same as the template non-type argument.
Definition predicate.hpp:63
constexpr auto is_space
Checks whether c is a space character.
Definition predicate.hpp:125
constexpr auto is_cntrl
Checks whether c is a control character.
Definition predicate.hpp:90
Provides seqan3::detail::ignore_output_iterator for writing to null stream.
The generic concept for a (biological) sequence.
Provides various utility functions.
Provides seqan3::detail::istreambuf.
The main SeqAn3 namespace.
Definition aligned_sequence_concept.hpp:29
SeqAn specific customisations in the standard namespace.
Provides character predicates for tokenisation.
Provides seqan3::sequence_file_output_options.
Thrown if there is a parse error, such as reading an unexpected character from an input stream.
Definition io/exception.hpp:48
The options type defines various option members that influence the behaviour of all or some formats.
Definition sequence_file/output_options.hpp:26
Provides seqan3::detail::take_line and seqan3::detail::take_line_or_throw.
Provides seqan3::views::take_until and seqan3::views::take_until_or_throw.
Provides seqan3::views::to_char.
Provides traits to inspect some information of a type, for example its name.