[MISC] introduce new concepts seqan3::detail::(writable_)pairwise_ali…

…gnment

This PR finishes task seqan/product_backlog#60
by implementing seqan3::detail::(writable_)pairwise_alignment.

include/seqan3/alignment/aligned_sequence/aligned_sequence_concept.hpp

@@ -510,16 +510,4 @@ inline bool constexpr all_model_aligned_seq = (aligned_sequence<elems> && ...);
  */
 template <typename ...elems>
 inline bool constexpr all_model_aligned_seq<type_list<elems...>> = all_model_aligned_seq<elems...>;
-
-/*!\brief True, if each type models seqan3::writable_aligned_sequence; false otherwise.
- * \tparam elems The pack of types to be tested.
- */
-template <typename ...elems>
-inline bool constexpr all_model_writable_aligned_seq = (writable_aligned_sequence<elems> && ...);
-
-/*!\brief True, if each type in the seqan3::type_list models seqan3::writable_aligned_sequence; false otherwise.
- * \tparam elems The pack of types to be tested.
- */
-template <typename ...elems>
-inline bool constexpr all_model_writable_aligned_seq<type_list<elems...>> = all_model_writable_aligned_seq<elems...>;
 } // namespace seqan3::detail

include/seqan3/alignment/detail/pairwise_alignment_concept.hpp

@@ -0,0 +1,54 @@
+// -----------------------------------------------------------------------------------------------------
+// Copyright (c) 2006-2020, Knut Reinert & Freie Universität Berlin
+// Copyright (c) 2016-2020, Knut Reinert & MPI für molekulare Genetik
+// This file may be used, modified and/or redistributed under the terms of the 3-clause BSD-License
+// shipped with this file and also available at: https://github.com/seqan/seqan3/blob/master/LICENSE.md
+// -----------------------------------------------------------------------------------------------------
+
+/*!\file
+ * \brief Provides seqan3::detail::pairwise_alignment and seqan3::detail::writable_pairwise_alignment.
+ * \author Marcel Ehrhardt <marcel.ehrhardt AT fu-berlin.de>
+ */
+
+#pragma once
+
+#include <seqan3/alignment/aligned_sequence/aligned_sequence_concept.hpp>
+
+namespace seqan3::detail
+{
+
+/*!\interface seqan3::detail::pairwise_alignment < >
+ * \extends seqan3::pair_like
+ * \ingroup alignment
+ * \brief A concept that models a pairwise alignment type.
+ *
+ * \details
+ *
+ * A pairwise alignment is a seqan3::pair_like of two seqan3::aligned_sequence's.
+ */
+//!\cond
+template <typename pairwise_alignment_t>
+SEQAN3_CONCEPT pairwise_alignment =
+    pair_like<pairwise_alignment_t> &&
+    aligned_sequence<std::tuple_element_t<0, std::remove_reference_t<pairwise_alignment_t>>> &&
+    aligned_sequence<std::tuple_element_t<1, std::remove_reference_t<pairwise_alignment_t>>>;
+//!\endcond
+
+/*!\interface seqan3::detail::writable_pairwise_alignment < >
+ * \extends seqan3::detail::pairwise_alignment
+ * \ingroup alignment
+ * \brief A concept that models a writable pairwise alignment type.
+ *
+ * \details
+ *
+ * A writable pairwise alignment is a seqan3::pair_like of two seqan3::writable_aligned_sequence's.
+ */
+//!\cond
+template <typename pairwise_alignment_t>
+SEQAN3_CONCEPT writable_pairwise_alignment =
+    pairwise_alignment<pairwise_alignment_t> &&
+    writable_aligned_sequence<std::tuple_element_t<0, std::remove_reference_t<pairwise_alignment_t>>> &&
+    writable_aligned_sequence<std::tuple_element_t<1, std::remove_reference_t<pairwise_alignment_t>>>;
+//!\endcond
+
+} // namespace seqan3::detail

include/seqan3/io/alignment_file/detail.hpp

@@ -18,7 +18,7 @@
 #include <seqan3/std/ranges>
 #include <sstream>
 
-#include <seqan3/alignment/aligned_sequence/aligned_sequence_concept.hpp>
+#include <seqan3/alignment/detail/pairwise_alignment_concept.hpp>
 #include <seqan3/alphabet/cigar/cigar.hpp>
 #include <seqan3/core/debug_stream/detail/to_string.hpp>
 #include <seqan3/range/views/single_pass_input.hpp>
@@ -328,11 +328,7 @@ template <std::ranges::forward_range ref_seq_type, std::ranges::forward_range qu
  * ATGCCCCGTTG--C
  * ```
  */
-template <tuple_like alignment_type>
-//!\cond
-    requires (std::tuple_size_v<std::remove_cvref_t<alignment_type>> == 2) &&
-             detail::all_model_writable_aligned_seq<detail::tuple_type_list_t<alignment_type>>
-//!\endcond
+template <seqan3::detail::writable_pairwise_alignment alignment_type>
 inline void alignment_from_cigar(alignment_type & alignment, std::vector<cigar> const & cigar_vector)
 {
     using std::get;

include/seqan3/io/record.hpp

@@ -77,7 +77,7 @@ enum class field
     comment,        //!< Comment field of arbitrary content, usually a string.
 
     // Fields unique to alignment io ...........................................
-    alignment,      //!< The (pairwise) alignment stored in an seqan3::alignment object.
+    alignment,      //!< The (pairwise) alignment stored in an object that models seqan3::detail::pairwise_alignment.
     ref_id,         //!< The identifier of the (reference) sequence that SEQ was aligned to.
     ref_seq,        //!< The (reference) "sequence" information, usually a range of nucleotides or amino acids.
     ref_offset,     //!< Sequence (REF_SEQ) relative start position (0-based), unsigned value.

test/unit/alignment/detail/CMakeLists.txt

@@ -0,0 +1 @@
+seqan3_test(pairwise_alignment_concept_test.cpp)

test/unit/alignment/detail/pairwise_alignment_concept_test.cpp

@@ -0,0 +1,109 @@
+// -----------------------------------------------------------------------------------------------------
+// Copyright (c) 2006-2020, Knut Reinert & Freie Universität Berlin
+// Copyright (c) 2016-2020, Knut Reinert & MPI für molekulare Genetik
+// This file may be used, modified and/or redistributed under the terms of the 3-clause BSD-License
+// shipped with this file and also available at: https://github.com/seqan/seqan3/blob/master/LICENSE.md
+// -----------------------------------------------------------------------------------------------------
+
+#include <gtest/gtest.h>
+
+#include <seqan3/alignment/detail/pairwise_alignment_concept.hpp>
+#include <seqan3/alphabet/gap/gapped.hpp>
+#include <seqan3/alphabet/nucleotide/dna4.hpp>
+#include <seqan3/alphabet/nucleotide/dna5.hpp>
+
+TEST(pairwise_alignment_concept, std_pair_gapped_sequences)
+{
+    using gapped_sequence1_t = std::vector<seqan3::gapped<seqan3::dna4>>;
+    using gapped_sequence2_t = std::vector<seqan3::gapped<seqan3::dna4>>;
+    using alignment_t = std::pair<gapped_sequence1_t, gapped_sequence2_t>;
+
+    EXPECT_FALSE((seqan3::detail::pairwise_alignment<gapped_sequence1_t>));
+    EXPECT_FALSE((seqan3::detail::pairwise_alignment<gapped_sequence2_t>));
+    EXPECT_TRUE((seqan3::detail::pairwise_alignment<alignment_t>));
+    EXPECT_TRUE((seqan3::detail::pairwise_alignment<alignment_t const>));
+    EXPECT_TRUE((seqan3::detail::pairwise_alignment<alignment_t &>));
+    EXPECT_TRUE((seqan3::detail::pairwise_alignment<alignment_t const &>));
+    EXPECT_TRUE((seqan3::detail::pairwise_alignment<alignment_t &&>));
+    EXPECT_TRUE((seqan3::detail::pairwise_alignment<alignment_t const &&>));
+}
+
+TEST(pairwise_alignment_concept, std_tuple_gapped_sequences)
+{
+    using gapped_sequence1_t = std::vector<seqan3::gapped<seqan3::dna4>> const;
+    using gapped_sequence2_t = std::vector<seqan3::gapped<seqan3::dna5>>;
+    using alignment_t = std::tuple<gapped_sequence1_t, gapped_sequence2_t>;
+
+    EXPECT_FALSE((seqan3::detail::pairwise_alignment<gapped_sequence1_t>));
+    EXPECT_FALSE((seqan3::detail::pairwise_alignment<gapped_sequence2_t>));
+    EXPECT_TRUE((seqan3::detail::pairwise_alignment<alignment_t>));
+    EXPECT_TRUE((seqan3::detail::pairwise_alignment<alignment_t const>));
+    EXPECT_TRUE((seqan3::detail::pairwise_alignment<alignment_t &>));
+    EXPECT_TRUE((seqan3::detail::pairwise_alignment<alignment_t const &>));
+    EXPECT_TRUE((seqan3::detail::pairwise_alignment<alignment_t &&>));
+    EXPECT_TRUE((seqan3::detail::pairwise_alignment<alignment_t const &&>));
+}
+
+TEST(pairwise_alignment_concept, std_tuple_gap_sequence)
+{
+    using gap_sequence1_t = std::vector<seqan3::gap> const;
+    using gap_sequence2_t = std::vector<seqan3::gap>;
+    using alignment_t = std::tuple<gap_sequence1_t, gap_sequence2_t>;
+
+    EXPECT_FALSE((seqan3::detail::pairwise_alignment<gap_sequence1_t>));
+    EXPECT_FALSE((seqan3::detail::pairwise_alignment<gap_sequence2_t>));
+    EXPECT_TRUE((seqan3::detail::pairwise_alignment<alignment_t>));
+    EXPECT_TRUE((seqan3::detail::pairwise_alignment<alignment_t const>));
+    EXPECT_TRUE((seqan3::detail::pairwise_alignment<alignment_t &>));
+    EXPECT_TRUE((seqan3::detail::pairwise_alignment<alignment_t const &>));
+    EXPECT_TRUE((seqan3::detail::pairwise_alignment<alignment_t &&>));
+    EXPECT_TRUE((seqan3::detail::pairwise_alignment<alignment_t const &&>));
+}
+
+TEST(writable_pairwise_alignment_concept, std_pair_gapped_sequences)
+{
+    using gapped_sequence1_t = std::vector<seqan3::gapped<seqan3::dna4>>;
+    using gapped_sequence2_t = std::vector<seqan3::gapped<seqan3::dna4>>;
+    using alignment_t = std::pair<gapped_sequence1_t, gapped_sequence2_t>;
+
+    EXPECT_FALSE((seqan3::detail::writable_pairwise_alignment<gapped_sequence1_t>));
+    EXPECT_FALSE((seqan3::detail::writable_pairwise_alignment<gapped_sequence2_t>));
+    EXPECT_TRUE((seqan3::detail::writable_pairwise_alignment<alignment_t>));
+    EXPECT_FALSE((seqan3::detail::writable_pairwise_alignment<alignment_t const>));
+    EXPECT_TRUE((seqan3::detail::writable_pairwise_alignment<alignment_t &>));
+    EXPECT_FALSE((seqan3::detail::writable_pairwise_alignment<alignment_t const &>));
+    EXPECT_TRUE((seqan3::detail::writable_pairwise_alignment<alignment_t &&>));
+    EXPECT_FALSE((seqan3::detail::writable_pairwise_alignment<alignment_t const &&>));
+}
+
+TEST(writable_pairwise_alignment_concept, std_tuple_gapped_sequences)
+{
+    using gapped_sequence1_t = std::vector<seqan3::gapped<seqan3::dna4>>;
+    using gapped_sequence2_t = std::vector<seqan3::gapped<seqan3::dna5>> const;
+    using alignment_t = std::tuple<gapped_sequence1_t, gapped_sequence2_t>;
+
+    EXPECT_FALSE((seqan3::detail::writable_pairwise_alignment<gapped_sequence1_t>));
+    EXPECT_FALSE((seqan3::detail::writable_pairwise_alignment<gapped_sequence2_t>));
+    EXPECT_FALSE((seqan3::detail::writable_pairwise_alignment<alignment_t>));
+    EXPECT_FALSE((seqan3::detail::writable_pairwise_alignment<alignment_t const>));
+    EXPECT_FALSE((seqan3::detail::writable_pairwise_alignment<alignment_t &>));
+    EXPECT_FALSE((seqan3::detail::writable_pairwise_alignment<alignment_t const &>));
+    EXPECT_FALSE((seqan3::detail::writable_pairwise_alignment<alignment_t &&>));
+    EXPECT_FALSE((seqan3::detail::writable_pairwise_alignment<alignment_t const &&>));
+}
+
+TEST(writable_pairwise_alignment_concept, std_tuple_gap_sequence)
+{
+    using gap_sequence1_t = std::vector<seqan3::gap>;
+    using gap_sequence2_t = std::vector<seqan3::gap> const;
+    using alignment_t = std::tuple<gap_sequence1_t, gap_sequence2_t>;
+
+    EXPECT_FALSE((seqan3::detail::writable_pairwise_alignment<gap_sequence1_t>));
+    EXPECT_FALSE((seqan3::detail::writable_pairwise_alignment<gap_sequence2_t>));
+    EXPECT_FALSE((seqan3::detail::writable_pairwise_alignment<alignment_t>));
+    EXPECT_FALSE((seqan3::detail::writable_pairwise_alignment<alignment_t const>));
+    EXPECT_FALSE((seqan3::detail::writable_pairwise_alignment<alignment_t &>));
+    EXPECT_FALSE((seqan3::detail::writable_pairwise_alignment<alignment_t const &>));
+    EXPECT_FALSE((seqan3::detail::writable_pairwise_alignment<alignment_t &&>));
+    EXPECT_FALSE((seqan3::detail::writable_pairwise_alignment<alignment_t const &&>));
+}