Merge pull request #1898 from smehringer/range_sequence_concept

[FEATURE] add the seqan3::sequence concept

include/seqan3/alignment/aligned_sequence/aligned_sequence_concept.hpp

@@ -14,6 +14,7 @@
 #pragma once
 
 #include <iomanip>
+#include <seqan3/std/ranges>
 #include <tuple>
 
 #include <range/v3/algorithm/for_each.hpp>
@@ -22,11 +23,11 @@
 #include <seqan3/alphabet/gap/gapped.hpp>
 #include <seqan3/core/concept/tuple.hpp>
 #include <seqan3/core/detail/debug_stream_type.hpp>
+#include <seqan3/range/concept.hpp>
 #include <seqan3/range/container/concept.hpp>
 #include <seqan3/range/views/slice.hpp>
 #include <seqan3/range/views/to_char.hpp>
 #include <seqan3/range/views/zip.hpp>
-#include <seqan3/std/ranges>
 
 // ---------------------------------------------------------------------------------------------------------------------
 // unaligned_seq transformation trait
@@ -202,8 +203,8 @@ namespace seqan3
 //!\cond
 template <typename t>
 SEQAN3_CONCEPT aligned_sequence =
+    sequence<t> &&
     std::ranges::forward_range<t> &&
-    alphabet<std::ranges::range_reference_t<t>> &&
     weakly_assignable_from<std::ranges::range_reference_t<t>, gap const &> &&
     requires { typename detail::unaligned_seq_t<t>; } &&
     requires (t v, detail::unaligned_seq_t<t> unaligned)

include/seqan3/alphabet/all.hpp

@@ -166,6 +166,7 @@
  *
  * We provide specialised containers with certain properties in the \ref range module.
  *
+ * A container over an seqan3::alphabet automatically models the seqan3::sequence concept.
  */
 
 #pragma once

include/seqan3/core/detail/debug_stream_range.hpp

@@ -12,12 +12,14 @@
 
 #pragma once
 
+#include <seqan3/std/ranges>
+
 #include <seqan3/alphabet/adaptation/char.hpp>
 #include <seqan3/alphabet/adaptation/uint.hpp>
 #include <seqan3/alphabet/concept.hpp>
 #include <seqan3/core/detail/debug_stream_type.hpp>
 #include <seqan3/core/type_traits/range.hpp>
-#include <seqan3/std/ranges>
+#include <seqan3/range/concept.hpp>
 
 namespace seqan3::detail
 {
@@ -96,34 +98,38 @@ inline debug_stream_type<char_t> & operator<<(debug_stream_type<char_t> & s, rng
     static_assert(detail::reference_type_is_streamable_v<rng_t, char_t>,
                   "The reference type of the passed range cannot be streamed into the debug_stream.");
 
-    if constexpr (alphabet<std::ranges::range_reference_t<rng_t>> &&
-                  !detail::is_uint_adaptation_v<remove_cvref_t<std::ranges::range_reference_t<rng_t>>>)
+    s << '[';
+    auto b = std::ranges::begin(r);
+    auto e = std::ranges::end(r);
+    if (b != e)
     {
-        for (auto && l : r)
-            s << l;
+        s << *b;
+        ++b;
     }
-    else
+    while (b != e)
     {
-        s << '[';
-        auto b = std::ranges::begin(r);
-        auto e = std::ranges::end(r);
-        if (b != e)
-        {
-            s << *b;
-            ++b;
-        }
-        while (b != e)
-        {
-            s << ',';
-            s << *b;
-            ++b;
-        }
-        s << ']';
+        s << ',';
+        s << *b;
+        ++b;
     }
+    s << ']';
 
     return s;
 }
 
+//!\overload
+template <sequence rng_t, typename char_t>
+inline debug_stream_type<char_t> & operator<<(debug_stream_type<char_t> & s, rng_t && r)
+//!\cond
+    requires detail::debug_stream_range_guard<rng_t> &&
+             !detail::is_uint_adaptation_v<remove_cvref_t<std::ranges::range_reference_t<rng_t>>>
+//!\endcond
+{
+    for (auto && l : r)
+        s << l;
+
+    return s;
+}
 //!\}
 
 } // namespace seqan3

include/seqan3/range/concept.hpp

@@ -14,7 +14,7 @@
 
 #include <seqan3/std/ranges>
 
-#include <seqan3/core/platform.hpp>
+#include <seqan3/alphabet/concept.hpp>
 
 namespace seqan3
 {
@@ -135,4 +135,23 @@ SEQAN3_CONCEPT pseudo_random_access_range =
     pseudo_random_access_iterator<std::ranges::iterator_t<rng_t>>;
 //!\endcond
 
+/*!\interface seqan3::sequence <>
+ * \brief The generic concept for a sequence.
+ * \ingroup range
+ * \extends std::ranges::input_range
+ *
+ * We define a range over an seqan3::alphabet as a *sequence*.
+ * A type models seqan3::sequence if it is at least an std::ranges::input_range
+ * and its references type models seqan3::alphabet.
+ *
+ * ### Concepts and doxygen
+ *
+ * The requirements for this concept are given as related functions and type traits.
+ * Types that model this concept are shown as "implementing this interface".
+ */
+//!\cond
+template <typename rng_t>
+SEQAN3_CONCEPT sequence = std::ranges::input_range<rng_t> && alphabet<std::ranges::range_reference_t<rng_t>>;
+//!\endcond
+
 } // namespace seqan3