[MISC] Reintroduce seqan3::literals (#2568)

* [MISC] Introduce literals namespace in aminoacids * [MISC] Introduce literals namespace in nucleotides * [MISC] Introduce literals namespace in quality * [MISC] Introduce literals namespace in structure * [MISC] Introduce literals namespace in cigar * [MISC] Introduce literals namespace in sam_tag_dictionary * [MISC] Introduce literals namespace in shape * [MISC] Use literals namespace in snippets * [MISC] Use literals namespace in tutorials * [MISC] Add changelog entry * [DOC] Properly document namespace * Update test/snippet/alphabet/composite/alphabet_tuple_base_subtype_construction.cpp * Update test/snippet/alphabet/cigar/cigar_operation.cpp Co-authored-by: Lydia Buntrock <irallia@chrigelyra.de> Co-authored-by: Lydia Buntrock <irallia@chrigelyra.de>
seqan · Apr 28, 2021 · 9472019 · 9472019 · vercel · Apr 28, 2021
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -136,6 +136,10 @@ regression test suite and patches at https://github.com/seqan/seqan3/tree/master
     `seqan3::phred68legacy(phred_type)`.
 * Renamed `seqan3::quality_base` to `seqan3::phred_base`
   ([\#2539](https://github.com/seqan/seqan3/pull/2539)).
+* Added the `seqan3::literals` namespace containing all literals. This adds the option to use
+  `using namespace seqan3::literals` to import literal operators. The old way of explicitly importing specific
+  operators via `using seqan3::operator""_{dna4, rna4, ...}` is not affected by this change
+  ([\#2568](https://github.com/seqan/seqan3/pull/2568)).
 
 #### Argument Parser
 

diff --git a/doc/tutorial/alphabet/alphabet_gc_content.cpp b/doc/tutorial/alphabet/alphabet_gc_content.cpp
@@ -8,10 +8,11 @@
 #include <seqan3/core/debug_stream.hpp>
 #include <seqan3/range/views/all.hpp>       // optional: use views to convert the input string to a dna5 sequence
 
-using seqan3::operator""_dna5;
 
 int main (int argc, char * argv[])
 {
+    using namespace seqan3::literals;
+
     std::string input{};
     seqan3::argument_parser parser("GC-Content", argc, argv);
     parser.add_positional_option(input, "Specify an input sequence.");

diff --git a/doc/tutorial/alphabet/alphabet_main.cpp b/doc/tutorial/alphabet/alphabet_main.cpp
@@ -8,10 +8,10 @@
 //! [create]
 #include <seqan3/alphabet/all.hpp> // for working with alphabets directly
 
-using seqan3::operator""_dna4;
-
 int main ()
 {
+    using namespace seqan3::literals;
+
     // Two objects of seqan3::dna4 alphabet constructed with a char literal.
     seqan3::dna4 ade = 'A'_dna4;
     seqan3::dna4 gua = 'G'_dna4;
@@ -79,8 +79,7 @@ int main ()
     assert(some_nucl == "AGT"_dna4);
 
 //! [phred]
-    using seqan3::operator""_dna4;
-    using seqan3::operator""_phred42;
+    using namespace seqan3::literals;
 
     seqan3::phred42 phred;
     phred.assign_phred(2);
@@ -98,7 +97,7 @@ int main ()
     // Assign a gap symbol to a gapped RNA alphabet.
     seqan3::gapped<seqan3::rna5> sym = seqan3::gap{};                         // => -
 
-    using seqan3::operator""_rna5;
+    using namespace seqan3::literals;
     // Each seqan3::rna5 symbol is still valid.
     sym = 'U'_rna5;                                   // => U
 
@@ -108,7 +107,7 @@ int main ()
     assert(size2 == 6u);
 
 //! [containers]
-    using seqan3::operator""_dna5;
+    using namespace seqan3::literals;
 
     // Examples of different container types with SeqAn's alphabets.
     std::vector<seqan3::dna5> dna_sequence{"GATTANAG"_dna5};

diff --git a/doc/tutorial/concepts/index.md b/doc/tutorial/concepts/index.md
@@ -170,13 +170,12 @@ Write a small program, similar to the one above with the following "skeleton":
 ```cpp
 // which includes?
 
-using seqan3::operator""_dna5;
-using seqan3::operator""_aa27;
-
 // Add one or more `void print` function template(s) here //
 
 int main()
 {
+    using namespace seqan3::literals;
+
     auto d = 'A'_dna5;
     auto a = 'L'_aa27;
     auto g = seqan3::gap{};

diff --git a/doc/tutorial/concepts/overloading_solution1.cpp b/doc/tutorial/concepts/overloading_solution1.cpp
@@ -7,11 +7,11 @@ void print(t const v)
     std::cout << "I am an alphabet and my value as char is: " << seqan3::to_char(v) << '\n';
 }
 
-using seqan3::operator""_dna5;
-using seqan3::operator""_aa27;
 
 int main()
 {
+    using namespace seqan3::literals;
+
     auto d = 'A'_dna5;
     auto a = 'L'_aa27;
     auto g = seqan3::gap{};

diff --git a/doc/tutorial/concepts/overloading_solution2.cpp b/doc/tutorial/concepts/overloading_solution2.cpp
@@ -14,11 +14,10 @@ void print(t const v)
               << " and my complement is: " << seqan3::to_char(seqan3::complement(v)) << '\n';
 }
 
-using seqan3::operator""_dna5;
-using seqan3::operator""_aa27;
-
 int main()
 {
+    using namespace seqan3::literals;
+
     auto d = 'A'_dna5;
     auto a = 'L'_aa27;
     auto g = seqan3::gap{};

diff --git a/doc/tutorial/introduction/index.md b/doc/tutorial/introduction/index.md
@@ -155,7 +155,7 @@ to learn more.
 \note
 We encourage you to avoid declaring `using namespace seqan3;`. This has the additional benefit of easily distinguishing
 between library features and standard C++. The only exception are string literals, where we often use
-`using seqan3::operator""_dna4;` for convenience.
+`using namespace seqan3::literals` for convenience.
 
 \note
 We use a lot of Modern C++ in SeqAn so some things might look alien at first,

diff --git a/doc/tutorial/introduction/introduction_align.cpp b/doc/tutorial/introduction/introduction_align.cpp
@@ -13,14 +13,14 @@
 
 int main()
 {
+    using namespace seqan3::literals;
+
     auto tmp_dir = std::filesystem::temp_directory_path();
     std::string filename{tmp_dir/"seq.fasta"};
     {
         // Create a /tmp/seq.fasta file.
         seqan3::sequence_file_output file_out{filename};
 
-        using seqan3::operator""_dna5;
-
         file_out.emplace_back("ACGTGATG"_dna5, std::string{"seq1"});
         file_out.emplace_back("AGTGATACT"_dna5, std::string{"seq2"});
     }

diff --git a/doc/tutorial/pairwise_alignment/configurations.cpp b/doc/tutorial/pairwise_alignment/configurations.cpp
@@ -47,8 +47,7 @@ int main()
 
 {
 //! [scoring_scheme]
-using seqan3::operator""_dna4;
-using seqan3::operator""_aa27;
+using namespace seqan3::literals;
 
 // Define a simple scoring scheme with match and mismatch cost and get the score.
 seqan3::nucleotide_scoring_scheme nc_scheme{seqan3::match_score{4}, seqan3::mismatch_score{-5}};

diff --git a/doc/tutorial/pairwise_alignment/pa_assignment_3_solution.cpp b/doc/tutorial/pairwise_alignment/pa_assignment_3_solution.cpp
@@ -7,10 +7,10 @@
 #include <seqan3/alphabet/all.hpp>
 #include <seqan3/core/debug_stream.hpp>
 
-using seqan3::operator""_aa27;
-
 int main()
 {
+    using namespace seqan3::literals;
+
     std::vector vec{"MANLGYZW"_aa27,
                     "LCKRLGNM"_aa27,
                     "KPSKPRDYEDG"_aa27,

diff --git a/doc/tutorial/pairwise_alignment/pairwise_alignment_first_global.cpp b/doc/tutorial/pairwise_alignment/pairwise_alignment_first_global.cpp
@@ -5,10 +5,10 @@
 #include <seqan3/alphabet/nucleotide/dna4.hpp>
 #include <seqan3/core/debug_stream.hpp>
 
-using seqan3::operator""_dna4;
-
 int main()
 {
+    using namespace seqan3::literals;
+
     seqan3::dna4_vector s1 = "ACGTGAACTGACT"_dna4;
     seqan3::dna4_vector s2 = "ACGAAGACCGAT"_dna4;
 

diff --git a/doc/tutorial/pairwise_alignment/pairwise_alignment_solution_1.cpp b/doc/tutorial/pairwise_alignment/pairwise_alignment_solution_1.cpp
@@ -7,10 +7,10 @@
 #include <seqan3/core/debug_stream.hpp>
 #include <seqan3/range/views/pairwise_combine.hpp>
 
-using seqan3::operator""_dna4;
-
 int main()
 {
+    using namespace seqan3::literals;
+
     std::vector vec{"ACGTGAACTGACT"_dna4,
                     "ACGAAGACCGAT"_dna4,
                     "ACGTGACTGACT"_dna4,

diff --git a/doc/tutorial/pairwise_alignment/pairwise_alignment_solution_2.cpp b/doc/tutorial/pairwise_alignment/pairwise_alignment_solution_2.cpp
@@ -7,10 +7,10 @@
 #include <seqan3/core/debug_stream.hpp>
 #include <seqan3/range/views/pairwise_combine.hpp>
 
-using seqan3::operator""_dna4;
-
 int main()
 {
+    using namespace seqan3::literals;
+
     std::vector vec{"ACGTGAACTGACT"_dna4,
                     "ACGAAGACCGAT"_dna4,
                     "ACGTGACTGACT"_dna4,

diff --git a/doc/tutorial/pairwise_alignment/pairwise_alignment_solution_3.cpp b/doc/tutorial/pairwise_alignment/pairwise_alignment_solution_3.cpp
@@ -4,10 +4,10 @@
 #include <seqan3/alphabet/aminoacid/aa27.hpp>       // for seqan3::operator""_aa27
 #include <seqan3/core/debug_stream.hpp>
 
-using seqan3::operator""_aa27;
-
 int main()
 {
+    using namespace seqan3::literals;
+
     auto seq1 = "QFSEEILSDIYCWMLQCGQERAV"_aa27;
     auto seq2 = "AFLPGWQEENKLSKIWMKDCGCLW"_aa27;
 

diff --git a/doc/tutorial/pairwise_alignment/pairwise_alignment_solution_4.cpp b/doc/tutorial/pairwise_alignment/pairwise_alignment_solution_4.cpp
@@ -5,10 +5,10 @@
 #include <seqan3/alphabet/nucleotide/dna4.hpp>
 #include <seqan3/core/debug_stream.hpp>
 
-using seqan3::operator""_dna4;
-
 int main()
 {
+    using namespace seqan3::literals;
+
     auto seq1 = "TTACGTACGGACTAGCTACAACATTACGGACTAC"_dna4;
     auto seq2 = "GGACGACATGACGTACGACTTTACGTACGACTAGC"_dna4;
 

diff --git a/doc/tutorial/pairwise_alignment/pairwise_alignment_solution_5.cpp b/doc/tutorial/pairwise_alignment/pairwise_alignment_solution_5.cpp
@@ -5,10 +5,10 @@
 #include <seqan3/alphabet/nucleotide/dna4.hpp>
 #include <seqan3/core/debug_stream.hpp>
 
-using seqan3::operator""_dna4;
-
 int main()
 {
+    using namespace seqan3::literals;
+
     auto seq1 = "TTACGTACGGACTAGCTACAACATTACGGACTAC"_dna4;
     auto seq2 = "GGACGACATGACGTACGACTTTACGTACGACTAGC"_dna4;
 

diff --git a/doc/tutorial/pairwise_alignment/pairwise_alignment_solution_6.cpp b/doc/tutorial/pairwise_alignment/pairwise_alignment_solution_6.cpp
@@ -8,10 +8,10 @@
 #include <seqan3/core/debug_stream.hpp>
 #include <seqan3/range/views/pairwise_combine.hpp>
 
-using seqan3::operator""_dna4;
-
 int main()
 {
+    using namespace seqan3::literals;
+
     std::vector vec{"ACGTGACTGACT"_dna4,
                     "ACGAAGACCGAT"_dna4,
                     "ACGTGACTGACT"_dna4,

diff --git a/doc/tutorial/ranges/range_solution4.cpp b/doc/tutorial/ranges/range_solution4.cpp
@@ -5,10 +5,10 @@
 #include <seqan3/core/debug_stream.hpp>                         // for debug_stream
 #include <seqan3/range/container/bitcompressed_vector.hpp>      // include bitcompressed vector
 
-using seqan3::operator""_dna4;
-
 int main(int argc, char ** argv)
 {
+    using namespace seqan3::literals;
+
     seqan3::argument_parser myparser("Vector-implementations-comparison", argc, argv);
     size_t size{};
     bool use_bitvector{};

diff --git a/doc/tutorial/sam_file/sam_file_snippets.cpp b/doc/tutorial/sam_file/sam_file_snippets.cpp
@@ -111,7 +111,7 @@ int main()
 
 {
 //![alignments_with_ref]
-    using seqan3::operator""_dna5;
+    using namespace seqan3::literals;
 
     auto filename = std::filesystem::temp_directory_path()/"example.sam";
 

diff --git a/doc/tutorial/sam_file/sam_file_solution3.cpp b/doc/tutorial/sam_file/sam_file_solution3.cpp
@@ -3,10 +3,10 @@
 #include <seqan3/alphabet/nucleotide/dna4.hpp>
 #include <seqan3/io/sam_file/all.hpp>
 
-using seqan3::operator""_dna4;
-
 int main()
 {
+    using namespace seqan3::literals;
+
     std::vector<std::string> ids = {"read1", "read2"};
     std::vector<std::vector<seqan3::dna4>> seqs = {"ACGATCGACTAGCTACGATCAGCTAGCAG"_dna4,
                                                    "AGAAAGAGCGAGGCTATTTTAGCGAGTTA"_dna4};

diff --git a/doc/tutorial/search/search_solution1.cpp b/doc/tutorial/search/search_solution1.cpp
@@ -10,10 +10,10 @@ seqan3::cleanup index_file{"index.file"};
 
 #include <seqan3/search/fm_index/fm_index.hpp>
 
-using seqan3::operator""_dna4;
-
 int main()
 {
+    using namespace seqan3::literals;
+
     seqan3::dna4_vector
                 text{"CGCTGTCTGAAGGATGAGTGTCAGCCAGTGTAACCCGATGAGCTACCCAGTAGTCGAACTGGGCCAGACAACCCGGCGCTAATGCACTCA"_dna4};
     seqan3::fm_index index{text};

diff --git a/doc/tutorial/search/search_solution2.cpp b/doc/tutorial/search/search_solution2.cpp
@@ -3,7 +3,7 @@
 #include <seqan3/search/search.hpp>
 #include <seqan3/search/fm_index/fm_index.hpp>
 
-using seqan3::operator""_dna4;
+using namespace seqan3::literals;
 
 void run_text_single()
 {

diff --git a/doc/tutorial/search/search_solution3.cpp b/doc/tutorial/search/search_solution3.cpp
@@ -4,10 +4,10 @@
 #include <seqan3/search/fm_index/fm_index.hpp>
 #include <seqan3/std/span>
 
-using seqan3::operator""_dna4;
-
 int main()
 {
+    using namespace seqan3::literals;
+
     seqan3::dna4_vector
                 text{"CGCTGTCTGAAGGATGAGTGTCAGCCAGTGTAACCCGATGAGCTACCCAGTAGTCGAACTGGGCCAGACAACCCGGCGCTAATGCACTCA"_dna4};
     seqan3::fm_index index{text};

diff --git a/doc/tutorial/search/search_solution4.cpp b/doc/tutorial/search/search_solution4.cpp
@@ -3,10 +3,10 @@
 #include <seqan3/search/search.hpp>
 #include <seqan3/search/fm_index/fm_index.hpp>
 
-using seqan3::operator""_dna4;
-
 int main()
 {
+    using namespace seqan3::literals;
+
     seqan3::dna4_vector
                 text{"CGCTGTCTGAAGGATGAGTGTCAGCCAGTGTAACCCGATGAGCTACCCAGTAGTCGAACTGGGCCAGACAACCCGGCGCTAATGCACTCA"_dna4};
     seqan3::dna4_vector query{"GCT"_dna4};

diff --git a/doc/tutorial/search/search_solution5.cpp b/doc/tutorial/search/search_solution5.cpp
@@ -6,7 +6,7 @@
 #include <seqan3/search/fm_index/fm_index.hpp>
 #include <seqan3/std/span>
 
-using seqan3::operator""_dna4;
+using namespace seqan3::literals;
 
 // Define the pairwise alignment configuration globally.
 inline constexpr auto align_config = seqan3::align_cfg::method_global{

diff --git a/doc/tutorial/search/views/minimiser/minimiser_snippets.cpp b/doc/tutorial/search/views/minimiser/minimiser_snippets.cpp
@@ -6,7 +6,7 @@
 #include <seqan3/search/views/kmer_hash.hpp>
 #include <seqan3/search/views/minimiser.hpp>
 
-using seqan3::operator""_dna4;
+using namespace seqan3::literals;
 
 int main()
 {

diff --git a/doc/tutorial/search/views/minimiser/minimiser_solution1.cpp b/doc/tutorial/search/views/minimiser/minimiser_solution1.cpp
@@ -2,7 +2,7 @@
 #include <seqan3/core/debug_stream.hpp>
 #include <seqan3/search/views/minimiser_hash.hpp>
 
-using seqan3::operator""_dna4;
+using namespace seqan3::literals;
 
 int main()
 {

diff --git a/doc/tutorial/search/views/minimiser/minimiser_solution2.cpp b/doc/tutorial/search/views/minimiser/minimiser_solution2.cpp
@@ -2,8 +2,7 @@
 #include <seqan3/core/debug_stream.hpp>
 #include <seqan3/search/views/minimiser_hash.hpp>
 
-using seqan3::operator""_dna4;
-using seqan3::operator""_shape;
+using namespace seqan3::literals;
 
 int main()
 {

diff --git a/doc/tutorial/search/views/minimiser/minimiser_solution3.cpp b/doc/tutorial/search/views/minimiser/minimiser_solution3.cpp
@@ -3,8 +3,7 @@
 #include <seqan3/search/views/kmer_hash.hpp>
 #include <seqan3/search/views/minimiser.hpp>
 
-using seqan3::operator""_dna4;
-using seqan3::operator""_shape;
+using namespace seqan3::literals;
 
 int main()
 {

diff --git a/doc/tutorial/search/views/minimiser/seed_example.cpp b/doc/tutorial/search/views/minimiser/seed_example.cpp
@@ -2,7 +2,7 @@
 #include <seqan3/core/debug_stream.hpp>
 #include <seqan3/search/views/minimiser_hash.hpp>
 
-using seqan3::operator""_dna4;
+using namespace seqan3::literals;
 
 int main()
 {