109 #ifdef SEQAN3_DEPRECATED_310
110 template <
typename stream_type,
111 typename legal_alph_type,
bool seq_qual_combined,
119 qual_type & SEQAN3_DOXYGEN_ONLY(qualities))
121 template <
typename stream_type,
122 typename legal_alph_type,
130 qual_type & SEQAN3_DOXYGEN_ONLY(qualities))
133 auto stream_view = detail::istreambuf(stream);
136 read_id(stream_view, options,
id);
139 read_seq(stream_view, options,
sequence);
143 template <
typename stream_type,
151 qual_type && SEQAN3_DOXYGEN_ONLY(qualities))
153 seqan3::detail::fast_ostreambuf_iterator stream_it{*stream.rdbuf()};
156 if constexpr (detail::decays_to_ignore_v<id_type>)
158 throw std::logic_error{
"The ID field may not be set to ignore when writing FASTA files."};
162 if (std::ranges::empty(
id))
165 write_id(stream_it, options,
id);
169 if constexpr (detail::decays_to_ignore_v<seq_type>)
171 throw std::logic_error{
"The SEQ and SEQ_QUAL fields may not both be set to ignore when writing FASTA files."};
178 write_seq(stream_it, options,
sequence);
185 #ifdef SEQAN3_DEPRECATED_310
186 template <
typename stream_view_t,
187 typename seq_legal_alph_type,
bool seq_qual_combined,
189 void read_id(stream_view_t & stream_view,
193 template <
typename stream_view_t,
194 typename seq_legal_alph_type,
196 void read_id(stream_view_t & stream_view,
201 auto const is_id = is_char<'>
'> || is_char<';
'>;
203 if (!is_id(*begin(stream_view)))
204 throw parse_error{std::string{"Expected to be on beginning of ID, but "} + is_id.msg +
205 " evaluated to false on " + detail::make_printable(*begin(stream_view))};
208 if constexpr (!detail::decays_to_ignore_v<id_type>)
210 if (options.truncate_ids)
212 #if SEQAN3_WORKAROUND_VIEW_PERFORMANCE
213 auto it = stream_view.begin();
214 auto e = stream_view.end();
215 for (; (it != e) && (is_id || is_blank)(*it); ++it)
218 bool at_delimiter = false;
219 for (; it != e; ++it)
221 if ((is_cntrl || is_blank)(*it))
226 id.push_back(assign_char_to(*it, std::ranges::range_value_t<id_type>{}));
230 throw unexpected_end_of_input{"FastA ID line did not end in newline."};
232 for (; (it != e) && ((!is_char<'\n
'>)(*it)); ++it)
235 #else // ↑↑↑ WORKAROUND | ORIGINAL ↓↓↓
237 std::ranges::copy(stream_view | std::views::drop_while(is_id || is_blank) // skip leading >
238 | detail::take_until_or_throw(is_cntrl || is_blank) // read ID until delimiter…
239 | views::char_to<std::ranges::range_value_t<id_type>>,
240 std::cpp20::back_inserter(id)); // … ^A is old delimiter
242 // consume rest of line
243 detail::consume(stream_view | detail::take_line_or_throw);
244 #endif // SEQAN3_WORKAROUND_VIEW_PERFORMANCE
249 #if SEQAN3_WORKAROUND_VIEW_PERFORMANCE
250 auto it = stream_view.begin();
251 auto e = stream_view.end();
252 for (; (it != e) && (is_id || is_blank)(*it); ++it)
255 bool at_delimiter = false;
256 for (; it != e; ++it)
258 if ((is_char<'\n
'>)(*it))
263 id.push_back(assign_char_to(*it, std::ranges::range_value_t<id_type>{}));
267 throw unexpected_end_of_input{"FastA ID line did not end in newline."};
269 #else // ↑↑↑ WORKAROUND | ORIGINAL ↓↓↓
271 std::ranges::copy(stream_view | detail::take_line_or_throw // read line
272 | std::views::drop_while(is_id || is_blank) // skip leading >
273 | views::char_to<std::ranges::range_value_t<id_type>>,
274 std::cpp20::back_inserter(id));
275 #endif // SEQAN3_WORKAROUND_VIEW_PERFORMANCE
280 detail::consume(stream_view | detail::take_line_or_throw);
285 #ifdef SEQAN3_DEPRECATED_310
286 template <typename stream_view_t,
287 typename seq_legal_alph_type, bool seq_qual_combined,
289 void read_seq(stream_view_t & stream_view,
290 sequence_file_input_options<seq_legal_alph_type, seq_qual_combined> const &,
292 #else // ^^^ before seqan 3.1 / after seqan 3.1 vvv
293 template <typename stream_view_t,
294 typename seq_legal_alph_type,
296 void read_seq(stream_view_t & stream_view,
297 sequence_file_input_options<seq_legal_alph_type> const &,
299 #endif // SEQAN3_DEPRECATED_310
301 auto constexpr is_id = is_char<'>
'> || is_char<';
'>;
303 if constexpr (!detail::decays_to_ignore_v<seq_type>)
305 auto constexpr is_legal_alph = char_is_valid_for<seq_legal_alph_type>;
307 #if SEQAN3_WORKAROUND_VIEW_PERFORMANCE
308 auto it = stream_view.begin();
309 auto e = stream_view.end();
312 throw unexpected_end_of_input{"No sequence information given!"};
314 for (; (it != e) && ((!is_id)(*it)); ++it)
316 if ((is_space || is_digit)(*it))
318 else if (!is_legal_alph(*it))
320 throw parse_error{std::string{"Encountered an unexpected letter: "} +
321 "char_is_valid_for<" +
322 detail::type_name_as_string<seq_legal_alph_type> +
323 "> evaluated to false on " +
324 detail::make_printable(*it)};
327 seq.push_back(assign_char_to(*it, std::ranges::range_value_t<seq_type>{}));
330 #else // ↑↑↑ WORKAROUND | ORIGINAL ↓↓↓
332 if (std::ranges::begin(stream_view) == std::ranges::end(stream_view))
333 throw unexpected_end_of_input{"No sequence information given!"};
335 std::ranges::copy(stream_view | detail::take_until(is_id) // until next header (or end)
336 | std::views::filter(!(is_space || is_digit))// ignore whitespace and numbers
337 | std::views::transform([is_legal_alph] (char const c)
339 if (!is_legal_alph(c))
341 throw parse_error{std::string{"Encountered an unexpected letter: "} +
342 "char_is_valid_for<" +
343 detail::type_name_as_string<seq_legal_alph_type> +
344 "> evaluated to false on " +
345 detail::make_printable(c)};
348 }) // enforce legal alphabet
349 | views::char_to<std::ranges::range_value_t<seq_type>>, // convert to actual target alphabet
350 std::cpp20::back_inserter(seq));
351 #endif // SEQAN3_WORKAROUND_VIEW_PERFORMANCE
355 detail::consume(stream_view | detail::take_until(is_id));
360 template <typename stream_it_t, typename id_type>
361 void write_id(stream_it_t & stream_it, sequence_file_output_options const & options, id_type && id)
363 if (options.fasta_legacy_id_marker)
368 if (options.fasta_blank_before_id)
371 stream_it.write_range(id);
372 stream_it.write_end_of_line(options.add_carriage_return);
376 template <typename stream_it_t, typename seq_type>
377 void write_seq(stream_it_t & stream_it, sequence_file_output_options const & options, seq_type && seq)
379 auto char_sequence = seq | views::to_char;
381 if (options.fasta_letters_per_line > 0)
383 /* Using `views::interleave` is probably the way to go but that needs performance-tuning.*/
384 auto it = std::ranges::begin(char_sequence);
385 auto end = std::ranges::end(char_sequence);
389 /* Note: This solution is slightly suboptimal for sized but non-random-access ranges.*/
390 auto current_end = it;
391 size_t steps = std::ranges::advance(current_end, options.fasta_letters_per_line, end);
392 using subrange_t = std::ranges::subrange<decltype(it), decltype(it), std::ranges::subrange_kind::sized>;
393 it = stream_it.write_range(subrange_t{it, current_end, (options.fasta_letters_per_line - steps)});
394 stream_it.write_end_of_line(options.add_carriage_return);
399 stream_it.write_range(char_sequence);
400 stream_it.write_end_of_line(options.add_carriage_return);
Adaptations of algorithms from the Ranges TS.
Provides aliases for qualified.
Core alphabet concept and free function/type trait wrappers.
Provides seqan3::views::char_to.
Provides seqan3::views::to_char.
Provides alphabet adaptations for standard char types.
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.
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.
Adaptations of concepts from the Ranges TS.
Provides seqan3::sequence_file_output_options.
The options type defines various option members that influence the behaviour of all or some formats.
Definition: output_options.hpp:22
Provides seqan3::views::take_exactly and seqan3::views::take_exactly_or_throw.
Provides seqan3::detail::take_line and seqan3::detail::take_line_or_throw.
Provides seqan3::views::take_until and seqan3::views::take_until_or_throw.
[DEPRECATED] Provides seqan3::views::take.
Provides traits to inspect some information of a type, for example its name.
Provides character predicates for tokenisation.