95 template <
typename stream_type,
96 typename seq_legal_alph_type,
bool seq_qual_combined,
104 qual_type & SEQAN3_DOXYGEN_ONLY(qualities))
107 auto stream_it = std::ranges::begin(stream_view);
111 std::cpp20::back_inserter(idbuffer));
112 if (idbuffer !=
"ID")
113 throw parse_error{
"An entry has to start with the code word ID."};
115 if constexpr (!detail::decays_to_ignore_v<id_type>)
119 std::ranges::copy(idbuffer |
views::char_to<std::ranges::range_value_t<id_type>>, std::cpp20::back_inserter(
id));
124 std::cpp20::back_inserter(
id));
125 id.push_back(*stream_it);
127 }
while (*stream_it !=
'Q');
141 std::cpp20::back_inserter(
id));
147 std::cpp20::back_inserter(
id));
159 }
while (*stream_it !=
'Q');
164 auto constexpr is_end =
is_char<
'/'> ;
165 if constexpr (!detail::decays_to_ignore_v<seq_type>)
170 auto constexpr is_legal_alph = char_is_valid_for<seq_legal_alph_type>;
173 if (!is_legal_alph(c))
176 "char_is_valid_for<" +
177 detail::type_name_as_string<seq_legal_alph_type> +
178 "> evaluated to false on " +
179 detail::make_printable(c)};
184 std::cpp20::back_inserter(
sequence));
197 template <
typename stream_type,
205 qual_type && SEQAN3_DOXYGEN_ONLY(qualities))
207 seqan3::detail::fast_ostreambuf_iterator stream_it{*stream.rdbuf()};
209 [[maybe_unused]]
size_t sequence_size = 0;
211 if constexpr (!detail::decays_to_ignore_v<seq_type>)
212 sequence_size = std::ranges::distance(
sequence);
215 if constexpr (detail::decays_to_ignore_v<id_type>)
217 throw std::logic_error{
"The ID field may not be set to ignore when writing embl files."};
221 if (ranges::empty(
id))
226 stream_it.write_range(
id);
231 stream_it.write_range(
id);
233 stream_it.write_number(sequence_size);
239 if constexpr (detail::decays_to_ignore_v<seq_type>)
241 throw std::logic_error{
"The SEQ field may not be set to ignore when writing embl files."};
250 stream_it.write_number(sequence_size);
255 auto it = std::ranges::begin(char_sequence);
256 size_t written_chars{0};
257 uint8_t chunk_size{10u};
259 while (it != std::ranges::end(char_sequence))
261 auto current_end = it;
262 size_t steps = std::ranges::advance(current_end, chunk_size, std::ranges::end(char_sequence));
264 using subrange_t = std::ranges::subrange<decltype(it), decltype(it), std::ranges::subrange_kind::sized>;
265 it = stream_it.write_range(subrange_t{it, current_end, chunk_size - steps});
267 written_chars += chunk_size;
269 if (written_chars % 60 == 0)
271 stream_it.write_number(written_chars);
277 auto characters_in_last_line = sequence_size % 60;
278 auto number_of_padding_needed = 65 - characters_in_last_line - characters_in_last_line / chunk_size;
280 stream_it.write_number(sequence_size);
Adaptations of algorithms from the Ranges TS.
Core alphabet concept and free function/type trait wrappers.
Provides seqan3::views::char_to.
Provides seqan3::views::to_char.
Provides various transformation traits used by the range module.
Provides seqan3::dna5, container aliases and string literals.
Provides seqan3::detail::fast_ostreambuf_iterator.
constexpr auto is_blank
Checks whether c is a blank character.
Definition: predicate.hpp:161
constexpr auto is_digit
Checks whether c is a digital character.
Definition: predicate.hpp:285
constexpr auto is_char
Checks whether a given letter is the same as the template non-type argument.
Definition: predicate.hpp:81
constexpr auto is_space
Checks whether c is a space character.
Definition: predicate.hpp:144
constexpr auto is_cntrl
Checks whether c is a control character.
Definition: predicate.hpp:108
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:434
auto const to_char
A view that calls seqan3::to_char() on each element in the input range.
Definition: to_char.hpp:68
constexpr auto take_until_or_throw
A view adaptor that returns elements from the underlying range until the functor evaluates to true (t...
Definition: take_until.hpp:614
constexpr auto istreambuf
A view factory that returns a view over the stream buffer of an input stream.
Definition: istreambuf.hpp:114
constexpr auto take_until
A view adaptor that returns elements from the underlying range until the functor evaluates to true (o...
Definition: take_until.hpp:600
auto const char_to
A view over an alphabet, given a range of characters.
Definition: char_to.hpp:72
constexpr auto repeat_n
A view factory that repeats a given value n times.
Definition: repeat_n.hpp:95
constexpr auto take_line_or_throw
A view adaptor that returns a single line from the underlying range (throws if there is no end-of-lin...
Definition: take_line.hpp:90
The generic concept for a (biological) sequence.
Provides various utility functions.
Provides seqan3::views::istreambuf.
The main SeqAn3 namespace.
Definition: aligned_sequence_concept.hpp:29
SeqAn specific customisations in the standard namespace.
Provides various utility functions.
Adaptations of concepts from the Ranges TS.
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:22
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:39
bool embl_genbank_complete_header
Complete header given for embl or genbank.
Definition: output_options.hpp:42
Provides seqan3::views::take_line and seqan3::views::take_line_or_throw.
Provides seqan3::views::take_until and seqan3::views::take_until_or_throw.
Provides traits to inspect some information of a type, for example its name.
Provides character predicates for tokenisation.
Provides seqan3::views::repeat_n.