implicit conversion of dna4 from rna4.

[marehr]

Tasks

• implicit conversion between rna* and dna* should only accept our types

From 2a9acf73da20842103cbfd5d010f17b5f2ba5dfc Mon Sep 17 00:00:00 2001
From: marehr <[email protected]>
Date: Thu, 11 Mar 2021 12:47:42 +0100
Subject: [PATCH 10/12] TODO: [DOC] implicit conversion of dna4 from rna4.

---
 include/seqan3/alphabet/nucleotide/dna4.hpp   | 28 +++++++++++++++++--
 include/seqan3/alphabet/nucleotide/rna4.hpp   |  2 +-
 .../dna4_implicit_conversion_from_rna4.cpp    | 11 ++++++++
 ..._implicit_conversion_from_rna4_inherit.cpp | 18 ++++++++++++
 ...4_implicit_conversion_from_rna4_vector.cpp | 19 +++++++++++++
 5 files changed, 74 insertions(+), 4 deletions(-)
 create mode 100644 test/snippet/alphabet/nucleotide/dna4_implicit_conversion_from_rna4.cpp
 create mode 100644 test/snippet/alphabet/nucleotide/dna4_implicit_conversion_from_rna4_inherit.cpp
 create mode 100644 test/snippet/alphabet/nucleotide/dna4_implicit_conversion_from_rna4_vector.cpp

diff --git a/include/seqan3/alphabet/nucleotide/dna4.hpp b/include/seqan3/alphabet/nucleotide/dna4.hpp
index 57140e826..de13a1bd1 100644
--- a/include/seqan3/alphabet/nucleotide/dna4.hpp
+++ b/include/seqan3/alphabet/nucleotide/dna4.hpp
@@ -76,9 +76,31 @@ public:
 
     using base_t::base_t;
 
-    //!\brief Allow implicit construction from dna/rna of the same size.
-    template <std::same_as<rna4> t>    // Accept incomplete type
-    constexpr dna4(t const & r) noexcept
+    /*!\brief Allow implicit construction from dna/rna of the same size.
+     * \details
+     *
+     * Normally, we don't allow implicit conversion of single argument constructors, but in this case we allow it,
+     * because seqan3::dna4 and seqan3::rna4 are interchangeable as they behave nearly the same (e.g. same ranks,
+     * same char to rank conversion).
+     *
+     * \include test/snippet/alphabet/nucleotide/dna4_implicit_conversion_from_rna4.cpp
+     *
+     * seqan3::sequence's (e.g. seqan3::dna4_vector) in general aren't implicitly convertible and must be
+     * explicitly copied to be converted:
+     *
+     * \include test/snippet/alphabet/nucleotide/dna4_implicit_conversion_from_rna4_vector.cpp
+     *
+     * You can avoid this copy by using std::ranges::view's:
+     *
+     * This only allows converting seqan3::rna4 to seqan3::dna4. Other alphabets that inherit from seqan3::rna4 will not
+     * be implicitly convertible to seqan3::dna4.
+     *
+     * \include test/snippet/alphabet/nucleotide/dna4_implicit_conversion_from_rna4_inherit.cpp
+     *
+     * \stableapi{Since version 3.1.}
+     */
+    template <std::same_as<rna4> t> // template parameter t to accept incomplete type
+    constexpr dna4(t const & r) noexcept // TODO check what breaks if explicit
     {
         assign_rank(r.to_rank());
     }
diff --git a/include/seqan3/alphabet/nucleotide/rna4.hpp b/include/seqan3/alphabet/nucleotide/rna4.hpp
index 4ecf8083f..ef91e183c 100644
--- a/include/seqan3/alphabet/nucleotide/rna4.hpp
+++ b/include/seqan3/alphabet/nucleotide/rna4.hpp
@@ -71,7 +71,7 @@ public:
     using base_t::base_t;
 
     //!\brief Allow implicit construction from dna/rna of the same size.
-    constexpr rna4(dna4 const & r) noexcept
+    constexpr rna4(dna4 const & r) noexcept // TODO: should behave the same as seqan3::dna4
 #if SEQAN3_WORKAROUND_GCC_90897
         requires true
 #endif
diff --git a/test/snippet/alphabet/nucleotide/dna4_implicit_conversion_from_rna4.cpp b/test/snippet/alphabet/nucleotide/dna4_implicit_conversion_from_rna4.cpp
new file mode 100644
index 000000000..f3c7e49e7
--- /dev/null
+++ b/test/snippet/alphabet/nucleotide/dna4_implicit_conversion_from_rna4.cpp
@@ -0,0 +1,11 @@
+#include <seqan3/alphabet/nucleotide/dna4.hpp>
+#include <seqan3/alphabet/nucleotide/rna4.hpp>
+
+int main()
+{
+    using seqan3::operator""_rna4;
+
+    seqan3::dna4 letter1 = 'C'_rna4; // implicitly converted
+    seqan3::dna4 letter2{};
+    letter2 = 'C'_rna4; // implicitly converted
+}
diff --git a/test/snippet/alphabet/nucleotide/dna4_implicit_conversion_from_rna4_inherit.cpp b/test/snippet/alphabet/nucleotide/dna4_implicit_conversion_from_rna4_inherit.cpp
new file mode 100644
index 000000000..8e1a3ef5d
--- /dev/null
+++ b/test/snippet/alphabet/nucleotide/dna4_implicit_conversion_from_rna4_inherit.cpp
@@ -0,0 +1,18 @@
+#include <seqan3/alphabet/nucleotide/dna4.hpp>
+#include <seqan3/alphabet/nucleotide/rna4.hpp>
+
+struct my_dna4 : public seqan3::dna4
+{
+    // using seqan3::dna4::dna4; // uncomment to import implicit conversion shown by letter1
+};
+
+struct my_rna4 : public seqan3::rna4
+{};
+
+int main()
+{
+    using seqan3::operator""_rna4;
+
+    // my_dna4 letter1 = 'C'_rna4; // NO automatic implicit conversion!
+    // seqan3::dna4 letter2 = my_rna4{}; // seqan3::dna4 only allows implicit conversion from seqan3::rna4!
+}
diff --git a/test/snippet/alphabet/nucleotide/dna4_implicit_conversion_from_rna4_vector.cpp b/test/snippet/alphabet/nucleotide/dna4_implicit_conversion_from_rna4_vector.cpp
new file mode 100644
index 000000000..e052fa5ee
--- /dev/null
+++ b/test/snippet/alphabet/nucleotide/dna4_implicit_conversion_from_rna4_vector.cpp
@@ -0,0 +1,19 @@
+#include <vector>
+
+#include <seqan3/alphabet/nucleotide/dna4.hpp>
+#include <seqan3/alphabet/nucleotide/rna4.hpp>
+
+int main()
+{
+    using seqan3::operator""_rna4;
+
+    seqan3::dna4_vector vector{'A'_rna4, 'C'_rna4, 'G'_rna4}; // (element-wise) implicit conversion
+
+    // but this won't work:
+    // seqan3::dna4_vector dna4_vector{"ACGT"_rna4};
+
+    // as a workaround you can use:
+    // side note: this would also work without the implicit conversion.
+    seqan3::rna4_vector rna4_vector = "ACGT"_rna4;
+    seqan3::dna4_vector dna4_vector{rna4_vector.begin(), rna4_vector.end()};
+}
-- 
2.31.1

[marehr]

fixed by seqan/seqan3#2656