FEATURE: add seqan3::default_printer

This PR will resolve seqan/product_backlog#63. This issue is a long-standing regret of mine. I hope that you can take it over and push it over the finishing line. The state of the current PR is just a draft of an idea. I'll comment on multiple code locations to point out the advantages of the new design. # The old design The major idea of the design is due to the following observation: > We use overload resolution and in particular overload ordering via concepts to determine the order in which we should print Just to give a small example (the more down, the more specialized): ```cpp std::cout //-printable [1] < seqan3::tuple_like // [4] < std::ranges::input_range // [2] < std::vector<uint8_t> // [3] < seqan3::sequence // [3] < char * // [2] std::cout //-printable [1] < char // [5] < seqan3::tuple_like // [4] < seqan3::alphabet // [5] < seqan3::mask // [6] ``` NOTE: that using concepts as overload resolution always uses a partially ordered set, which can be depicted by as a [Hasse Diagram](https://en.wikipedia.org/wiki/Hasse_diagram), and by using the except clauses via `requires` we give it a total order. # The new design ### Before anything, note that the new design does not break any existing code. As existing `seqan3::debugstream << ` overloads, still take place in overload resolution (). The idea is simple: * Have a list of printers. * The order of the printers dictates in which order an object should be printed. * We allow that multiple printers might be viable to print a type. * Each `printer<type>` either has a function object / lambda `print` or not; depending on whether the `printer` can print that `type` or not (implemented by [template specialization](https://en.cppreference.com/w/cpp/language/template_specialization) ) So put together: For a given type, ask every printer in order whether it can print that type and the first one to answer yes, is the selected printer. ---- [1] If all overloads do not work, use `std::ostream` https://github.com/seqan/seqan3/blob/6b681fb2eae5ab2997d293e99fc6a7f869a20316/include/seqan3/core/debug_stream/debug_stream_type.hpp#L242-L247 [2] Use this for all `std::ranges::input_range`s except if type is something like `std::filesystem` (type == range_value_t) or `char *` https://github.com/seqan/seqan3/blob/6b681fb2eae5ab2997d293e99fc6a7f869a20316/include/seqan3/core/debug_stream/range.hpp#L96-L98 https://github.com/seqan/seqan3/blob/6b681fb2eae5ab2997d293e99fc6a7f869a20316/include/seqan3/core/debug_stream/range.hpp#L38-L45 [3] Same as [2] where value_type is an alphabet but only if the alphabet is not an `unsigned int` (this condition has no test case?!) https://github.com/seqan/seqan3/blob/6b681fb2eae5ab2997d293e99fc6a7f869a20316/include/seqan3/core/debug_stream/range.hpp#L138-L141 [4] Use this for all `std::tuple`-like types except if it is a `std::ranges::input_range` (what is a tuple and ranges at the same time?!) and an `seqan3::alphabet` (basically `seqan3::alphabet_tuple_base` derived types) https://github.com/seqan/seqan3/blob/6b681fb2eae5ab2997d293e99fc6a7f869a20316/include/seqan3/core/debug_stream/tuple.hpp#L53-L56 [5] Use this for all `seqan3::alphabet`s except if it can be printed by `std::cout` (like `char`) https://github.com/seqan/seqan3/blob/6b681fb2eae5ab2997d293e99fc6a7f869a20316/include/seqan3/alphabet/detail/debug_stream_alphabet.hpp#L30-L32 [6] Type must be `seqan3::semialphabet` and `seqan3::mask` https://github.com/seqan/seqan3/blob/6b681fb2eae5ab2997d293e99fc6a7f869a20316/include/seqan3/alphabet/detail/debug_stream_alphabet.hpp#L46-L48
marehr · Jan 1, 2024 · f3dcea4 · f3dcea4
1 parent 6b681fb
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diff --git a/include/seqan3/alignment/aligned_sequence/debug_stream_alignment.hpp b/include/seqan3/alignment/aligned_sequence/debug_stream_alignment.hpp
@@ -104,17 +104,30 @@ namespace seqan3
  *
  * \return The given stream to which the alignment representation is appended.
  */
+#if 0
 template <typename char_t, typename alignment_t>
     requires (detail::debug_streamable_tuple<alignment_t>
               && detail::all_model_aligned_seq<detail::tuple_type_list_t<std::remove_cvref_t<alignment_t>>>)
 inline debug_stream_type<char_t> & operator<<(debug_stream_type<char_t> & stream, alignment_t && alignment)
 {
+#else
+template <typename alignment_t>
+    requires (tuple_like<std::remove_cvref_t<alignment_t>> && detail::all_model_aligned_seq<detail::tuple_type_list_t<std::remove_cvref_t<alignment_t>>>)
+struct alignment_printer<alignment_t>
+{
+    constexpr static auto print = [](auto & stream, auto && alignment)
+    {
     constexpr size_t sequence_count = std::tuple_size_v<std::remove_cvref_t<alignment_t>>;
 
     static_assert(sequence_count >= 2, "An alignment requires at least two sequences.");
 
     detail::stream_alignment(stream, alignment, std::make_index_sequence<sequence_count - 1>{});
+    };
+};
+#endif
+#if 0
     return stream;
 }
+#endif
 
 } // namespace seqan3
diff --git a/include/seqan3/alignment/matrix/detail/advanceable_alignment_coordinate.hpp b/include/seqan3/alignment/matrix/detail/advanceable_alignment_coordinate.hpp
@@ -307,13 +307,27 @@ namespace seqan3
  *
  * Prints the alignment coordinate as a tuple.
  */
+#if 0
 template <typename char_t, typename coordinate_type>
     requires detail::is_value_specialisation_of_v<std::remove_cvref_t<coordinate_type>,
                                                   detail::advanceable_alignment_coordinate>
 inline debug_stream_type<char_t> & operator<<(debug_stream_type<char_t> & s, coordinate_type && c)
 {
+#else
+template <typename coordinate_type>
+    requires detail::is_value_specialisation_of_v<std::remove_cvref_t<coordinate_type>,
+                                                  detail::advanceable_alignment_coordinate>
+struct advanceable_alignment_coordinate_printer<coordinate_type>
+{
+    constexpr static auto print = [](auto & s, coordinate_type const & c)
+    {
     s << std::tie(c.first, c.second);
+    };
+};
+#endif
+#if 0
     return s;
 }
+#endif
 
 } // namespace seqan3
diff --git a/include/seqan3/alignment/matrix/detail/debug_matrix.hpp b/include/seqan3/alignment/matrix/detail/debug_matrix.hpp
@@ -479,23 +479,38 @@ namespace seqan3
  *
  * This prints out an alignment matrix which can be a score matrix or a trace matrix.
  */
+#if 0
 template <typename char_t, detail::matrix alignment_matrix_t>
 inline debug_stream_type<char_t> & operator<<(debug_stream_type<char_t> & s, alignment_matrix_t && matrix)
 {
+#else
+template <typename alignment_matrix_t>
+    requires detail::matrix<std::remove_cvref_t<alignment_matrix_t>>
+struct alignment_matrix_printer<alignment_matrix_t>
+{
+    constexpr static auto print = [](auto & s, auto && matrix)
+    {
     detail::debug_matrix debug{std::forward<alignment_matrix_t>(matrix)};
 
     std::stringstream sstream{};
     debug.stream_matrix(sstream, s.flags2());
     s << sstream.str();
+    };
+};
+#endif
+#if 0
     return s;
 }
+#endif
 
+#if 0
 //!\overload
 template <typename char_t, std::ranges::input_range alignment_matrix_t>
     requires detail::debug_stream_range_guard<alignment_matrix_t> && detail::matrix<alignment_matrix_t>
 inline debug_stream_type<char_t> & operator<<(debug_stream_type<char_t> & s, alignment_matrix_t && matrix)
 {
     return s << detail::debug_matrix{std::forward<alignment_matrix_t>(matrix)};
 }
+#endif
 
 } // namespace seqan3
diff --git a/include/seqan3/alignment/matrix/detail/trace_directions.hpp b/include/seqan3/alignment/matrix/detail/trace_directions.hpp
@@ -75,9 +75,17 @@ constexpr bool add_enum_bitwise_operators<seqan3::detail::trace_directions> = tr
  * | seqan3::detail::trace_directions::left_open | ←    | L     |
  * | seqan3::detail::trace_directions::left      | ⇠    | l     |
  */
+#if 0
 template <typename char_t>
 inline debug_stream_type<char_t> & operator<<(debug_stream_type<char_t> & s, detail::trace_directions const trace)
 {
+#else
+template <typename trace_directions_t>
+    requires std::is_same_v<std::remove_cvref_t<trace_directions_t>, detail::trace_directions>
+struct trace_directions_printer<trace_directions_t>
+{
+    constexpr static auto print = [](auto & s, detail::trace_directions const trace)
+    {
     static char const * unicode[32]{"↺",   "↖",    "↑",   "↖↑",  "⇡",    "↖⇡",   "↑⇡",  "↖↑⇡",  "←",    "↖←",   "↑←",
                                     "↖↑←", "⇡←",   "↖⇡←", "↑⇡←", "↖↑⇡←", "⇠",    "↖⇠",  "↑⇠",   "↖↑⇠",  "⇡⇠",   "↖⇡⇠",
                                     "↑⇡⇠", "↖↑⇡⇠", "←⇠",  "↖←⇠", "↑←⇠",  "↖↑←⇠", "⇡←⇠", "↖⇡←⇠", "↑⇡←⇠", "↖↑⇡←⇠"};
@@ -90,7 +98,12 @@ inline debug_stream_type<char_t> & operator<<(debug_stream_type<char_t> & s, det
     auto const & trace_dir = is_unicode ? unicode : csv;
 
     s << trace_dir[static_cast<size_t>(trace)];
+    };
+};
+#endif
+#if 0
     return s;
 }
+#endif
 
 } // namespace seqan3
diff --git a/include/seqan3/alignment/pairwise/alignment_result.hpp b/include/seqan3/alignment/pairwise/alignment_result.hpp
@@ -384,10 +384,24 @@ namespace seqan3
  * \param[in] result The alignment result to print.
  * \relates seqan3::debug_stream_type
  */
+#if 0
 template <typename char_t, typename alignment_result_t>
     requires detail::is_type_specialisation_of_v<std::remove_cvref_t<alignment_result_t>, alignment_result>
 inline debug_stream_type<char_t> & operator<<(debug_stream_type<char_t> & stream, alignment_result_t && result)
 {
+#else
+template <typename T>
+    requires (!std::is_same_v<T, std::remove_cvref_t<T>>)
+struct alignment_result_printer<T> : public alignment_result_printer<std::remove_cvref_t<T>>
+{
+};
+
+template <typename result_value_t>
+struct alignment_result_printer<alignment_result<result_value_t>>
+{
+    constexpr static auto print = [](auto & stream, alignment_result<result_value_t> const & result)
+    {
+    using alignment_result_t = alignment_result<result_value_t>;
     using disabled_t = std::nullopt_t *;
     using result_data_t =
         typename detail::alignment_result_value_type_accessor<std::remove_cvref_t<alignment_result_t>>::type;
@@ -423,6 +437,11 @@ inline debug_stream_type<char_t> & operator<<(debug_stream_type<char_t> & stream
         append_to_stream("\nalignment:\n", result.alignment());
     stream << '}';
 
+    };
+};
+#endif
+#if 0
     return stream;
 }
+#endif
 } // namespace seqan3
diff --git a/include/seqan3/alphabet/cigar/cigar.hpp b/include/seqan3/alphabet/cigar/cigar.hpp
@@ -210,13 +210,15 @@ class cigar : public alphabet_tuple_base<cigar, uint32_t, exposition_only::cigar
     //!\}
 };
 
+#if 1
 //!\brief Overload for the seqan3::debug_stream's operator.
 template <typename char_t>
 inline debug_stream_type<char_t> & operator<<(debug_stream_type<char_t> & s, cigar const c)
 {
     s << c.to_string();
     return s;
 }
+#endif
 
 inline namespace literals
 {

diff --git a/include/seqan3/alphabet/detail/debug_stream_alphabet.hpp b/include/seqan3/alphabet/detail/debug_stream_alphabet.hpp
@@ -18,6 +18,7 @@
 
 namespace seqan3
 {
+#if 0
 /*!\name Formatted output overloads
  * \{
  */
@@ -33,10 +34,22 @@ inline debug_stream_type<char_t> & operator<<(debug_stream_type<char_t> & s, alp
 {
     return s << to_char(l);
 }
+#else
+template <typename alphabet_t>
+    requires alphabet<alphabet_t>
+struct alphabet_printer<alphabet_t>
+{
+    constexpr static auto print = [](auto & s, alphabet_t l)
+    {
+        s << to_char(l);
+    };
+};
+#endif
 
 // forward declare seqan3::mask
 class mask;
 
+#if 0
 /*!\brief Overload for the seqan3::mask alphabet.
  * \tparam char_t Type char type of the debug_stream.
  * \param s The seqan3::debug_stream.
@@ -51,5 +64,16 @@ inline debug_stream_type<char_t> & operator<<(debug_stream_type<char_t> & s, alp
 }
 
 //!\}
+#else
+template <typename alphabet_t>
+    requires std::same_as<std::remove_cvref_t<alphabet_t>, mask>
+struct mask_printer<alphabet_t>
+{
+    constexpr static auto print = [](auto & s, alphabet_t const l)
+    {
+        s << (l == std::remove_cvref_t<alphabet_t>{} ? "UNMASKED" : "MASKED");
+    };
+};
+#endif
 
 } // namespace seqan3
diff --git a/include/seqan3/argument_parser/auxiliary.hpp b/include/seqan3/argument_parser/auxiliary.hpp
@@ -222,6 +222,7 @@ concept argument_parser_compatible_option =
  * This searches the seqan3::enumeration_names of the respective type for the value \p op and prints the
  * respective string if found or '\<UNKNOWN_VALUE\>' if the value cannot be found in the map.
  */
+#if 1
 template <typename char_t, typename option_type>
     requires named_enumeration<std::remove_cvref_t<option_type>>
 inline debug_stream_type<char_t> & operator<<(debug_stream_type<char_t> & s, option_type && op)
@@ -234,6 +235,7 @@ inline debug_stream_type<char_t> & operator<<(debug_stream_type<char_t> & s, opt
 
     return s << "<UNKNOWN_VALUE>";
 }
+#endif
 //!\}
 
 /*!\brief Used to further specify argument_parser options/flags.

diff --git a/include/seqan3/core/debug_stream/byte.hpp b/include/seqan3/core/debug_stream/byte.hpp
@@ -28,13 +28,15 @@ namespace seqan3
  * \param[in] arg           The std::byte.
  * \relates seqan3::debug_stream_type
  */
+#if 1
 template <typename char_t, typename byte_type>
     requires std::same_as<std::remove_cvref_t<byte_type>, std::byte>
 inline debug_stream_type<char_t> & operator<<(debug_stream_type<char_t> & s, byte_type && arg)
 {
     s << std::to_integer<uint8_t>(arg);
     return s;
 }
+#endif
 
 //!\}