96 template <
typename stream_type,
97 typename seq_legal_alph_type,
98 typename stream_pos_type,
104 stream_pos_type & position_buffer,
107 qual_type & SEQAN3_DOXYGEN_ONLY(qualities))
109 auto stream_view = detail::istreambuf(stream);
110 auto stream_it = std::ranges::begin(stream_view);
113 position_buffer = stream.tellg();
116 std::ranges::copy(stream_view | detail::take_until_or_throw(
is_cntrl ||
is_blank),
117 std::cpp20::back_inserter(idbuffer));
118 if (idbuffer !=
"ID")
119 throw parse_error{
"An entry has to start with the code word ID."};
121 if constexpr (!detail::decays_to_ignore_v<id_type>)
125 std::ranges::copy(idbuffer |
views::char_to<std::ranges::range_value_t<id_type>>, std::cpp20::back_inserter(
id));
128 std::ranges::copy(stream_view | detail::take_until_or_throw(is_char<'S'>)
130 std::cpp20::back_inserter(
id));
131 id.push_back(*stream_it);
133 }
while (*stream_it !=
'Q');
140 detail::consume(stream_view | detail::take_until(!
is_blank));
145 std::ranges::copy(stream_view | detail::take_until_or_throw(
is_blank || is_char<';'> ||
is_cntrl)
147 std::cpp20::back_inserter(
id));
151 std::ranges::copy(stream_view | detail::take_until_or_throw(is_char<';'>)
153 std::cpp20::back_inserter(
id));
163 detail::consume(stream_view | detail::take_until_or_throw(is_char<'S'>));
165 }
while (*stream_it !=
'Q');
167 detail::consume(stream_view | detail::take_line_or_throw);
170 auto constexpr is_end =
is_char<
'/'> ;
171 if constexpr (!detail::decays_to_ignore_v<seq_type>)
174 | detail::take_until_or_throw(is_end);
176 auto constexpr is_legal_alph = char_is_valid_for<seq_legal_alph_type>;
179 if (!is_legal_alph(c))
182 "char_is_valid_for<" +
183 detail::type_name_as_string<seq_legal_alph_type> +
184 "> evaluated to false on " +
185 detail::make_printable(c)};
190 std::cpp20::back_inserter(
sequence));
194 detail::consume(stream_view | detail::take_until(is_end));
203 template <
typename stream_type,
211 qual_type && SEQAN3_DOXYGEN_ONLY(qualities))
213 seqan3::detail::fast_ostreambuf_iterator stream_it{*stream.rdbuf()};
215 [[maybe_unused]]
size_t sequence_size = 0;
217 if constexpr (!detail::decays_to_ignore_v<seq_type>)
218 sequence_size = std::ranges::distance(
sequence);
221 if constexpr (detail::decays_to_ignore_v<id_type>)
223 throw std::logic_error{
"The ID field may not be set to ignore when writing embl files."};
227 if (ranges::empty(
id))
232 stream_it.write_range(
id);
237 stream_it.write_range(
id);
239 stream_it.write_number(sequence_size);
245 if constexpr (detail::decays_to_ignore_v<seq_type>)
247 throw std::logic_error{
"The SEQ field may not be set to ignore when writing embl files."};
256 stream_it.write_number(sequence_size);
261 auto it = std::ranges::begin(char_sequence);
262 size_t written_chars{0};
263 uint8_t chunk_size{10u};
265 while (it != std::ranges::end(char_sequence))
267 auto current_end = it;
268 size_t steps = std::ranges::advance(current_end, chunk_size, std::ranges::end(char_sequence));
270 using subrange_t = std::ranges::subrange<
decltype(it),
decltype(it), std::ranges::subrange_kind::sized>;
271 it = stream_it.write_range(subrange_t{it, current_end, chunk_size - steps});
273 written_chars += chunk_size;
275 if (written_chars % 60 == 0)
277 stream_it.write_number(written_chars);
283 auto characters_in_last_line = sequence_size % 60;
284 auto number_of_padding_needed = 65 - characters_in_last_line - characters_in_last_line / chunk_size;
286 stream_it.write_number(sequence_size);
The <algorithm> header from C++20's standard library.
Core alphabet concept and free function/type trait wrappers.
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 is_blank
Checks whether c is a blank character.
Definition: predicate.hpp:145
constexpr auto is_digit
Checks whether c is a digital character.
Definition: predicate.hpp:269
constexpr auto is_char
Checks whether a given letter is the same as the template non-type argument.
Definition: predicate.hpp:65
constexpr auto is_space
Checks whether c is a space character.
Definition: predicate.hpp:128
constexpr auto is_cntrl
Checks whether c is a control character.
Definition: predicate.hpp:92
decltype(detail::transform< trait_t >(list_t{})) transform
Apply a transformation trait to every type in the list and return a seqan3::type_list of the results.
Definition: traits.hpp:495
constexpr auto repeat_n
A view factory that repeats a given value n times.
Definition: repeat_n.hpp:91
The generic concept for a (biological) sequence.
Provides various utility functions.
Provides seqan3::detail::istreambuf.
The main SeqAn3 namespace.
Definition: cleanup.hpp:4
SeqAn specific customisations in the standard namespace.
Provides character predicates for tokenisation.
The <ranges> header from C++20's standard library.
Provides seqan3::views::repeat_n.
Provides seqan3::sequence_file_output_options.
Thrown if there is a parse error, such as reading an unexpected character from an input stream.
Definition: exception.hpp:48
The options type defines various option members that influence the behaviour of all or some formats.
Definition: output_options.hpp:26
bool add_carriage_return
The default plain text line-ending is "\n", but on Windows an additional carriage return is recommend...
Definition: output_options.hpp:43
bool embl_genbank_complete_header
Complete header given for embl or genbank.
Definition: output_options.hpp:46
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.