diff --git a/doc/tutorial/07_sequence_file/index.md b/doc/tutorial/07_sequence_file/index.md index 3f67df4503..84a25c8340 100644 --- a/doc/tutorial/07_sequence_file/index.md +++ b/doc/tutorial/07_sequence_file/index.md @@ -249,7 +249,7 @@ If no 10 records are available any more, it will just print the remaining record On some occasions, you are only interested in sequence records that fulfill a certain criteria, e.g. having a minimum sequence length or a minimum average quality. -Just like in the example with *ranges::view::chunk* you can use *std::ranges::filter* for this purpose: +Just like in the example with *seqan3::views::chunk* you can use *std::ranges::filter* for this purpose: \snippet doc/tutorial/07_sequence_file/sequence_file_quality_filter.cpp main diff --git a/include/seqan3/alignment/pairwise/edit_distance_unbanded.hpp b/include/seqan3/alignment/pairwise/edit_distance_unbanded.hpp index df0e57ed33..6ae3df7795 100644 --- a/include/seqan3/alignment/pairwise/edit_distance_unbanded.hpp +++ b/include/seqan3/alignment/pairwise/edit_distance_unbanded.hpp @@ -874,8 +874,8 @@ class edit_distance_unbanded : query{std::forward(_query)}, config{std::forward(_config)}, _score{static_cast(std::ranges::size(query))}, - database_it{ranges::begin(database)}, - database_it_end{ranges::end(database)} + database_it{std::ranges::begin(database)}, + database_it_end{std::ranges::end(database)} { static constexpr size_t alphabet_size_ = alphabet_size; diff --git a/include/seqan3/alphabet/range/hash.hpp b/include/seqan3/alphabet/range/hash.hpp index af1990c1c7..7951f77138 100644 --- a/include/seqan3/alphabet/range/hash.hpp +++ b/include/seqan3/alphabet/range/hash.hpp @@ -26,7 +26,7 @@ namespace std * \details * \experimentalapi{Experimental since version 3.1.} */ -template +template requires seqan3::semialphabet> struct hash { @@ -38,7 +38,7 @@ struct hash * \details * \experimentalapi{Experimental since version 3.1.} */ - template + template requires seqan3::semialphabet> size_t operator()(urng2_t && range) const noexcept { diff --git a/include/seqan3/core/detail/persist_view.hpp b/include/seqan3/core/detail/persist_view.hpp index 598574a78e..813552f7d6 100644 --- a/include/seqan3/core/detail/persist_view.hpp +++ b/include/seqan3/core/detail/persist_view.hpp @@ -39,7 +39,7 @@ namespace seqan3::detail * * \details * - * Note that most members of this class are generated by ranges::view_interface which is not yet documented here. + * Note that most members of this class are generated by std::ranges::view_interface which is not yet documented here. */ template class view_persist : public std::ranges::view_interface> diff --git a/include/seqan3/io/sam_file/format_sam.hpp b/include/seqan3/io/sam_file/format_sam.hpp index 50a22989ba..a669ea7e60 100644 --- a/include/seqan3/io/sam_file/format_sam.hpp +++ b/include/seqan3/io/sam_file/format_sam.hpp @@ -958,7 +958,7 @@ inline void format_sam::read_sam_dict_vector(seqan3::detail::sam_tag_variant & v value_type value) { std::vector tmp_vector; - while (std::ranges::begin(stream_view) != ranges::end(stream_view)) // not fully consumed yet + while (std::ranges::begin(stream_view) != std::ranges::end(stream_view)) // not fully consumed yet { read_arithmetic_field(stream_view | detail::take_until(is_char<','>), value); tmp_vector.push_back(value); @@ -988,7 +988,7 @@ inline void format_sam::read_sam_byte_vector(seqan3::detail::sam_tag_variant & v std::vector tmp_vector; std::byte value; - while (std::ranges::begin(stream_view) != ranges::end(stream_view)) // not fully consumed yet + while (std::ranges::begin(stream_view) != std::ranges::end(stream_view)) // not fully consumed yet { try { diff --git a/include/seqan3/io/sequence_file/format_embl.hpp b/include/seqan3/io/sequence_file/format_embl.hpp index 22e8deec81..a5c1458594 100644 --- a/include/seqan3/io/sequence_file/format_embl.hpp +++ b/include/seqan3/io/sequence_file/format_embl.hpp @@ -228,7 +228,7 @@ class format_embl } else { - if (ranges::empty(id)) //[[unlikely]] + if (std::ranges::empty(id)) //[[unlikely]] throw std::runtime_error{"The ID field may not be empty when writing embl files."}; if (options.embl_genbank_complete_header) diff --git a/include/seqan3/io/sequence_file/format_genbank.hpp b/include/seqan3/io/sequence_file/format_genbank.hpp index 05b12383fc..4ca60848a2 100644 --- a/include/seqan3/io/sequence_file/format_genbank.hpp +++ b/include/seqan3/io/sequence_file/format_genbank.hpp @@ -201,14 +201,14 @@ class format_genbank size_t sequence_size{0}; [[maybe_unused]] char buffer[50]; if constexpr (!detail::decays_to_ignore_v) - sequence_size = ranges::size(sequence); + sequence_size = std::ranges::size(sequence); // ID if constexpr (detail::decays_to_ignore_v) { throw std::logic_error{"The ID field may not be set to ignore when writing genbank files."}; } - else if (ranges::empty(id)) //[[unlikely]] + else if (std::ranges::empty(id)) //[[unlikely]] { throw std::runtime_error{"The ID field may not be empty when writing genbank files."}; } diff --git a/include/seqan3/io/views/detail/take_exactly_view.hpp b/include/seqan3/io/views/detail/take_exactly_view.hpp index 895ddf4aa8..1ea4f48cc0 100644 --- a/include/seqan3/io/views/detail/take_exactly_view.hpp +++ b/include/seqan3/io/views/detail/take_exactly_view.hpp @@ -46,7 +46,7 @@ namespace seqan3::detail * * \details * - * Note that most members of this class are generated by ranges::view_interface which is not yet documented here. + * Note that most members of this class are generated by std::ranges::view_interface which is not yet documented here. */ template class view_take_exactly : public std::ranges::view_interface> diff --git a/include/seqan3/io/views/detail/take_until_view.hpp b/include/seqan3/io/views/detail/take_until_view.hpp index b47c3494ab..bac1434e59 100644 --- a/include/seqan3/io/views/detail/take_until_view.hpp +++ b/include/seqan3/io/views/detail/take_until_view.hpp @@ -45,7 +45,7 @@ namespace seqan3::detail * * \details * - * Note that most members of this class are generated by ranges::view_interface which is not yet documented here. + * Note that most members of this class are generated by std::ranges::view_interface which is not yet documented here. */ template class view_take_until : public std::ranges::view_interface> diff --git a/include/seqan3/search/views/kmer_hash.hpp b/include/seqan3/search/views/kmer_hash.hpp index 1d1e92311b..764d6e0db8 100644 --- a/include/seqan3/search/views/kmer_hash.hpp +++ b/include/seqan3/search/views/kmer_hash.hpp @@ -33,7 +33,7 @@ namespace seqan3::detail * * \details * - * Note that most members of this class are generated by ranges::view_interface which is not yet documented here. + * Note that most members of this class are generated by std::ranges::view_interface which is not yet documented here. */ template class kmer_hash_view : public std::ranges::view_interface> diff --git a/include/seqan3/search/views/minimiser.hpp b/include/seqan3/search/views/minimiser.hpp index 98d470bbe9..fd9717f477 100644 --- a/include/seqan3/search/views/minimiser.hpp +++ b/include/seqan3/search/views/minimiser.hpp @@ -114,7 +114,7 @@ class minimiser_view : public std::ranges::view_interface requires (std::ranges::viewable_range - && std::constructible_from>>) + && std::constructible_from>>) minimiser_view(other_urng1_t && urange1, size_t const window_size) : urange1{std::views::all(std::forward(urange1))}, urange2{default_urng2_t{}}, diff --git a/include/seqan3/utility/views/interleave.hpp b/include/seqan3/utility/views/interleave.hpp index 65bb585163..577dea893b 100644 --- a/include/seqan3/utility/views/interleave.hpp +++ b/include/seqan3/utility/views/interleave.hpp @@ -41,7 +41,7 @@ namespace seqan3::detail * * \details * - * Note that most members of this class are generated by ranges::view_interface which is not yet documented here. + * Note that most members of this class are generated by std::ranges::view_interface which is not yet documented here. */ template requires std::ranges::view && std::ranges::sized_range && std::ranges::view @@ -65,13 +65,13 @@ class view_interleave : public std::ranges::view_interface; //!\brief The reference_type. - using reference = ranges::common_reference_t, - std::ranges::range_reference_t>; + using reference = + std::common_reference_t, std::ranges::range_reference_t>; //!\brief The const_reference type is equal to the reference type. - using const_reference = detail::transformation_trait_or_t< - ranges::common_reference, - std::ranges::range_reference_t>, - void>; + using const_reference = + detail::transformation_trait_or_t, + std::ranges::range_reference_t>, + void>; //!\brief The value_type (which equals the reference_type with any references removed). using value_type = std::ranges::range_value_t; //!\brief A signed integer type, usually std::ptrdiff_t. diff --git a/include/seqan3/utility/views/repeat.hpp b/include/seqan3/utility/views/repeat.hpp index 3b7be28ec6..1a707f11a8 100644 --- a/include/seqan3/utility/views/repeat.hpp +++ b/include/seqan3/utility/views/repeat.hpp @@ -38,7 +38,7 @@ namespace seqan3::detail * This class models an infinite range over a given value, although "infinity" is limited by the maximum value of * `difference_type` of which the iterator stores a member variable to represent distances. * - * Note that most members of this class are generated by ranges::view_interface which is not yet documented here. + * Note that most members of this class are generated by std::ranges::view_interface which is not yet documented here. */ template class repeat_view : public std::ranges::view_interface>