diff --git a/include/seqan3/alphabet/nucleotide/dna16sam.hpp b/include/seqan3/alphabet/nucleotide/dna16sam.hpp index 6ed8337ae9..3b51f7283c 100644 --- a/include/seqan3/alphabet/nucleotide/dna16sam.hpp +++ b/include/seqan3/alphabet/nucleotide/dna16sam.hpp @@ -217,3 +217,24 @@ constexpr std::array dna16sam::complement_tab }; } // namespace seqan3 + +namespace seqan3 +{ +//!\deprecated Please use seqan3::dna16sam instead. +using sam_dna16 SEQAN3_DEPRECATED_310 = seqan3::dna16sam; + +//!\deprecated Please use seqan3::dna16sam_vector instead. +using sam_dna16_vector SEQAN3_DEPRECATED_310 = dna16sam_vector; + +//!\deprecated Please use seqan3::operator""_dna16sam instead. +SEQAN3_DEPRECATED_310 constexpr dna16sam operator""_sam_dna16(char const c) noexcept +{ + return seqan3::operator""_dna16sam(c); +} + +//!\deprecated Please use seqan3::operator""_dna16sam instead. +SEQAN3_DEPRECATED_310 inline dna16sam_vector operator""_sam_dna16(char const * s, size_t n) +{ + return seqan3::operator""_dna16sam(s, n); +} +} // namespace seqan3 diff --git a/include/seqan3/alphabet/nucleotide/sam_dna16.hpp b/include/seqan3/alphabet/nucleotide/sam_dna16.hpp index 2e0aea9d89..bbbdb91deb 100644 --- a/include/seqan3/alphabet/nucleotide/sam_dna16.hpp +++ b/include/seqan3/alphabet/nucleotide/sam_dna16.hpp @@ -15,11 +15,5 @@ #include -namespace seqan3 -{ -//!\deprecated Please use seqan3::dna16sam instead. -using sam_dna16 SEQAN3_DEPRECATED_310 = seqan3::dna16sam; -} // namespace seqan3 - SEQAN3_DEPRECATED_HEADER( "This header is deprecated and will be removed in SeqAn-3.1.0; Please #include instead.") diff --git a/include/seqan3/alphabet/quality/phred68legacy.hpp b/include/seqan3/alphabet/quality/phred68legacy.hpp index 7bb3df2795..21bfd19301 100644 --- a/include/seqan3/alphabet/quality/phred68legacy.hpp +++ b/include/seqan3/alphabet/quality/phred68legacy.hpp @@ -16,11 +16,5 @@ #include -namespace seqan3 -{ -//!\deprecated Please use seqan3::phred68solexa instead. -using phred68legacy SEQAN3_DEPRECATED_310 = seqan3::phred68solexa; -} // namespace seqan3 - SEQAN3_DEPRECATED_HEADER( "This header is deprecated and will be removed in SeqAn-3.1.0; Please #include instead.") diff --git a/include/seqan3/alphabet/quality/phred68solexa.hpp b/include/seqan3/alphabet/quality/phred68solexa.hpp index b05e0afc74..64131884d8 100644 --- a/include/seqan3/alphabet/quality/phred68solexa.hpp +++ b/include/seqan3/alphabet/quality/phred68solexa.hpp @@ -125,3 +125,21 @@ inline std::vector operator""_phred68solexa(char const * s, std:: //!\} } // namespace seqan3 + +namespace seqan3 +{ +//!\deprecated Please use seqan3::phred68solexa instead. +using phred68legacy SEQAN3_DEPRECATED_310 = seqan3::phred68solexa; + +//!\deprecated Please use seqan3::operator""_phred68solexa instead. +SEQAN3_DEPRECATED_310 constexpr phred68solexa operator""_phred68legacy(char const c) noexcept +{ + return seqan3::operator""_phred68solexa(c); +} + +//!\deprecated Please use seqan3::operator""_phred68solexa instead. +SEQAN3_DEPRECATED_310 inline std::vector operator""_phred68legacy(char const * s, size_t n) +{ + return seqan3::operator""_phred68solexa(s, n); +} +} // namespace seqan3 diff --git a/include/seqan3/search/dream_index/interleaved_bloom_filter.hpp b/include/seqan3/search/dream_index/interleaved_bloom_filter.hpp index eb63d46212..fac2ee6281 100644 --- a/include/seqan3/search/dream_index/interleaved_bloom_filter.hpp +++ b/include/seqan3/search/dream_index/interleaved_bloom_filter.hpp @@ -592,7 +592,9 @@ class interleaved_bloom_filter::membership_agent * \private * \param ibf The seqan3::interleaved_bloom_filter. */ - membership_agent(ibf_t const & ibf) : ibf_ptr(std::addressof(ibf)), result_buffer(ibf.bin_count()) {} + explicit membership_agent(ibf_t const & ibf) : + ibf_ptr(std::addressof(ibf)), result_buffer(ibf.bin_count()) + {} //!\} //!\brief Stores the result of bulk_contains(). @@ -679,7 +681,9 @@ class interleaved_bloom_filter::membership_agent::binning_bitv ~binning_bitvector() = default; //!< Defaulted. //!\brief Construct with given size. - binning_bitvector(size_t const size) : data(size) {} + explicit binning_bitvector(size_t const size) : + data(size) + {} //!\} //!\brief Returns the number of elements. @@ -730,6 +734,36 @@ class interleaved_bloom_filter::membership_agent::binning_bitv { return !(lhs == rhs); } + +#ifdef SEQAN3_DEPRECATED_310 + //!\brief Test for equality. + //!\deprecated Use binning_bitvector.raw_data() == rhs + SEQAN3_DEPRECATED_310 friend bool operator==(binning_bitvector const & lhs, sdsl::bit_vector const & rhs) noexcept + { + return lhs.data == rhs; + } + + //!\brief Test for equality. + //!\deprecated Use lhs == binning_bitvector.raw_data() + SEQAN3_DEPRECATED_310 friend bool operator==(sdsl::bit_vector const & lhs, binning_bitvector const & rhs) noexcept + { + return lhs == rhs.data; + } + + //!\brief Test for inequality. + //!\deprecated Use binning_bitvector.raw_data() != rhs + SEQAN3_DEPRECATED_310 friend bool operator!=(binning_bitvector const & lhs, sdsl::bit_vector const & rhs) noexcept + { + return !(lhs.data == rhs); + } + + //!\brief Test for inequality. + //!\deprecated Use lhs != binning_bitvector.raw_data() + SEQAN3_DEPRECATED_310 friend bool operator!=(sdsl::bit_vector const & lhs, binning_bitvector const & rhs) noexcept + { + return !(lhs == rhs.data); + } +#endif // SEQAN3_DEPRECATED_310 //!\} /*!\name Access @@ -916,7 +950,7 @@ class interleaved_bloom_filter::counting_agent_type * \private * \param ibf The seqan3::interleaved_bloom_filter. */ - counting_agent_type(ibf_t const & ibf) : + explicit counting_agent_type(ibf_t const & ibf) : ibf_ptr(std::addressof(ibf)), membership_agent(ibf), result_buffer(ibf.bin_count()) {} //!\} diff --git a/test/api_stability/3.0.2/0023-NOAPI-INCLUDE-add-missing-includes-seqan3-views-pers.patch b/test/api_stability/3.0.2/0023-NOAPI-INCLUDE-add-missing-includes-seqan3-views-pers.patch new file mode 100644 index 0000000000..e9f1fdda2c --- /dev/null +++ b/test/api_stability/3.0.2/0023-NOAPI-INCLUDE-add-missing-includes-seqan3-views-pers.patch @@ -0,0 +1,38 @@ +From 12b7805b266a7477492657756fa77dda9b8f5fe5 Mon Sep 17 00:00:00 2001 +From: marehr +Date: Sun, 25 Apr 2021 18:12:55 +0200 +Subject: [PATCH 23/24] [NOAPI] [INCLUDE] add missing includes + seqan3::views::persist + +--- + .../pairwise_alignment/pairwise_alignment_solution_6.cpp | 1 + + .../fm_index_cursor/bi_fm_index_cursor_collection_test.cpp | 1 + + 2 files changed, 2 insertions(+) + +diff --git a/doc/tutorial/pairwise_alignment/pairwise_alignment_solution_6.cpp b/doc/tutorial/pairwise_alignment/pairwise_alignment_solution_6.cpp +index 1ed35c8cd..32b6077d2 100644 +--- a/doc/tutorial/pairwise_alignment/pairwise_alignment_solution_6.cpp ++++ b/doc/tutorial/pairwise_alignment/pairwise_alignment_solution_6.cpp +@@ -6,6 +6,7 @@ + #include + #include + #include ++#include + #include + + using seqan3::operator""_dna4; +diff --git a/test/unit/search/fm_index_cursor/bi_fm_index_cursor_collection_test.cpp b/test/unit/search/fm_index_cursor/bi_fm_index_cursor_collection_test.cpp +index 48be041bc..5d055adb9 100644 +--- a/test/unit/search/fm_index_cursor/bi_fm_index_cursor_collection_test.cpp ++++ b/test/unit/search/fm_index_cursor/bi_fm_index_cursor_collection_test.cpp +@@ -9,6 +9,7 @@ + + #include + #include ++#include + #include + #include + #include +-- +2.31.1 + diff --git a/test/api_stability/3.0.2/0024-NOAPI-INCLUDE-add-missing-includes-std-isnan.patch b/test/api_stability/3.0.2/0024-NOAPI-INCLUDE-add-missing-includes-std-isnan.patch new file mode 100644 index 0000000000..1a5b30704a --- /dev/null +++ b/test/api_stability/3.0.2/0024-NOAPI-INCLUDE-add-missing-includes-std-isnan.patch @@ -0,0 +1,24 @@ +From ccf8a01d614f20c114d384003092a60366056be8 Mon Sep 17 00:00:00 2001 +From: marehr +Date: Sun, 25 Apr 2021 18:13:15 +0200 +Subject: [PATCH 24/24] [NOAPI] [INCLUDE] add missing includes std::isnan + +--- + test/unit/std/charconv_float_test.cpp | 1 + + 1 file changed, 1 insertion(+) + +diff --git a/test/unit/std/charconv_float_test.cpp b/test/unit/std/charconv_float_test.cpp +index 123f2e3d8..654d2a8c2 100644 +--- a/test/unit/std/charconv_float_test.cpp ++++ b/test/unit/std/charconv_float_test.cpp +@@ -7,6 +7,7 @@ + + #include + ++#include + #include + #include + +-- +2.31.1 +