107 template <
typename stream_type,
108 typename legal_alph_type,
bool seq_qual_combined,
116 qual_type & SEQAN3_DOXYGEN_ONLY(qualities))
121 read_id(stream_view, options,
id);
124 read_seq(stream_view, options, sequence);
128 template <
typename stream_type,
134 seq_type && sequence,
136 qual_type && SEQAN3_DOXYGEN_ONLY(qualities))
141 if constexpr (detail::decays_to_ignore_v<id_type>)
143 throw std::logic_error{
"The ID field may not be set to ignore when writing FASTA files."};
150 write_id(stream_it, options,
id);
154 if constexpr (detail::decays_to_ignore_v<seq_type>)
156 throw std::logic_error{
"The SEQ and SEQ_QUAL fields may not both be set to ignore when writing FASTA files."};
163 write_seq(stream_it, options, sequence);
170 template <
typename stream_view_t,
171 typename seq_legal_alph_type,
bool seq_qual_combined,
173 void read_id(stream_view_t & stream_view,
177 auto const is_id = is_char<'>
'> || is_char<';
'>; 179 if (!is_id(*begin(stream_view))) 180 throw parse_error{std::string{"Expected to be on beginning of ID, but "} + is_id.msg + 181 " evaluated to false on " + detail::make_printable(*begin(stream_view))}; 184 if constexpr (!detail::decays_to_ignore_v<id_type>) 186 if (options.truncate_ids) 188 #if SEQAN3_WORKAROUND_VIEW_PERFORMANCE 189 auto it = stream_view.begin(); 190 auto e = stream_view.end(); 191 for (; (it != e) && (is_id || is_blank)(*it); ++it) 194 bool at_delimiter = false; 195 for (; it != e; ++it) 197 if ((is_cntrl || is_blank)(*it)) 202 id.push_back(assign_char_to(*it, value_type_t<id_type>{})); 206 throw unexpected_end_of_input{"FastA ID line did not end in newline."}; 208 for (; (it != e) && ((!is_char<'\n
'>)(*it)); ++it) 211 #else // ↑↑↑ WORKAROUND | ORIGINAL ↓↓↓ 213 std::ranges::copy(stream_view | std::views::drop_while(is_id || is_blank) // skip leading > 214 | views::take_until_or_throw(is_cntrl || is_blank) // read ID until delimiter… 215 | views::char_to<value_type_t<id_type>>, 216 std::ranges::back_inserter(id)); // … ^A is old delimiter 218 // consume rest of line 219 detail::consume(stream_view | views::take_line_or_throw); 220 #endif // SEQAN3_WORKAROUND_VIEW_PERFORMANCE 225 #if SEQAN3_WORKAROUND_VIEW_PERFORMANCE 226 auto it = stream_view.begin(); 227 auto e = stream_view.end(); 228 for (; (it != e) && (is_id || is_blank)(*it); ++it) 231 bool at_delimiter = false; 232 for (; it != e; ++it) 234 if ((is_char<'\n
'>)(*it)) 239 id.push_back(assign_char_to(*it, value_type_t<id_type>{})); 243 throw unexpected_end_of_input{"FastA ID line did not end in newline."}; 245 #else // ↑↑↑ WORKAROUND | ORIGINAL ↓↓↓ 247 std::ranges::copy(stream_view | views::take_line_or_throw // read line 248 | std::views::drop_while(is_id || is_blank) // skip leading > 249 | views::char_to<value_type_t<id_type>>, 250 std::ranges::back_inserter(id)); 251 #endif // SEQAN3_WORKAROUND_VIEW_PERFORMANCE 256 detail::consume(stream_view | views::take_line_or_throw); 261 template <typename stream_view_t, 262 typename seq_legal_alph_type, bool seq_qual_combined, 264 void read_seq(stream_view_t & stream_view, 265 sequence_file_input_options<seq_legal_alph_type, seq_qual_combined> const &, 268 auto constexpr is_id = is_char<'>
'> || is_char<';
'>; 270 if constexpr (!detail::decays_to_ignore_v<seq_type>) 272 auto constexpr not_in_alph = !is_in_alphabet<seq_legal_alph_type>; 274 #if SEQAN3_WORKAROUND_VIEW_PERFORMANCE 275 auto it = stream_view.begin(); 276 auto e = stream_view.end(); 277 for (; (it != e) && ((!is_id)(*it)); ++it) 279 if ((is_space || is_digit)(*it)) 281 else if (not_in_alph(*it)) 283 throw parse_error{std::string{"Encountered an unexpected letter: "} + 285 " evaluated to true on " + 286 detail::make_printable(*it)}; 289 seq.push_back(assign_char_to(*it, value_type_t<seq_type>{})); 292 #else // ↑↑↑ WORKAROUND | ORIGINAL ↓↓↓ 294 std::ranges::copy(stream_view | views::take_until(is_id) // until next header (or end) 295 | std::views::filter(!(is_space || is_digit))// ignore whitespace and numbers 296 | std::views::transform([not_in_alph] (char const c) 300 throw parse_error{std::string{"Encountered an unexpected letter: "} + 302 " evaluated to false on " + 303 detail::make_printable(c)}; 306 }) // enforce legal alphabet 307 | views::char_to<value_type_t<seq_type>>, // convert to actual target alphabet 308 std::ranges::back_inserter(seq)); 309 #endif // SEQAN3_WORKAROUND_VIEW_PERFORMANCE 313 detail::consume(stream_view | views::take_until(is_id)); 318 template <typename stream_it_t, 320 void write_id(stream_it_t & stream_it, 321 sequence_file_output_options const & options, 324 if (options.fasta_legacy_id_marker) 329 if (options.fasta_blank_before_id) 332 std::ranges::copy(id, stream_it); 334 detail::write_eol(stream_it, options.add_carriage_return); 338 template <typename stream_it_t, 340 void write_seq(stream_it_t & stream_it, 341 sequence_file_output_options const & options, 344 if (options.fasta_letters_per_line > 0) 346 #if SEQAN3_WORKAROUND_VIEW_PERFORMANCE 350 stream_it = to_char(c); 351 if (++count % options.fasta_letters_per_line == 0) 352 detail::write_eol(stream_it, options.add_carriage_return); 354 if (count % options.fasta_letters_per_line != 0) 355 detail::write_eol(stream_it, options.add_carriage_return); 357 #else // ↑↑↑ WORKAROUND | ORIGINAL ↓↓↓ 359 //TODO: combining chunk and join is substantially faster than views::interleave (2.5x), why? 360 std::ranges::copy(seq | views::to_char 361 | ranges::view::chunk(options.fasta_letters_per_line) 362 | views::join(options.add_carriage_return 363 ? std::string_view{"\r\n"} 364 : std::string_view{"\n"}), 366 detail::write_eol(stream_it, options.add_carriage_return); 367 #endif // SEQAN3_WORKAROUND_VIEW_PERFORMANCE 371 // No performance workaround here, because transform views alone are fast 372 std::ranges::copy(seq | views::to_char, stream_it); 373 detail::write_eol(stream_it, options.add_carriage_return);
Provides seqan3::views::istreambuf.
Provides various shortcuts for common std::ranges functions.
::ranges::ostreambuf_iterator ostreambuf_iterator
Alias for ranges::ostreambuf_iterator. Writes successive characters onto the output stream from which...
Definition: iterator.hpp:204
Provides seqan3::detail::ignore_output_iterator for writing to null stream.
Provides seqan3::views::join.
Provides seqan3::views::take.
The main SeqAn3 namespace.
Provides seqan3::dna5, container aliases and string literals.
Provides seqan3::views::take_line and seqan3::views::take_line_or_throw.
Provides seqan3::sequence_file_output_options.
Provides seqan3::views::take_until and seqan3::views::take_until_or_throw.
Provides alphabet adaptations for standard char types.
Provides various utility functions.
Provides various utility functions.
Provides seqan3::views::char_to.
Adaptations of concepts from the Ranges TS.
Provides character predicates for tokenisation.
Provides seqan3::ostream and seqan3::ostreambuf iterator.
Adaptations of algorithms from the Ranges TS.
The options type defines various option members that influence the behaviour of all or some formats...
Definition: output_options.hpp:21
Provides seqan3::views::to_char.
Provides various transformation traits used by the range module.
Provides aliases for qualified.
constexpr auto istreambuf
A view factory that returns a view over the stream buffer of an input stream.
Definition: istreambuf.hpp:113
Provides seqan3::views::take_exactly and seqan3::views::take_exactly_or_throw.