[FEATURE] introduce new concepts seqan3::detail::(writable_)pairwise_…

…alignment This PR finishes task seqan/product_backlog#60 by implementing seqan3::detail::(writable_)pairwise_alignment.
marehr · Feb 2, 2021 · e0d0420 · e0d0420
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diff --git a/include/seqan3/alignment/detail/pairwise_alignment_concept.hpp b/include/seqan3/alignment/detail/pairwise_alignment_concept.hpp
@@ -0,0 +1,94 @@
+// -----------------------------------------------------------------------------------------------------
+// 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 <tuple>
+
+#include <seqan3/alignment/aligned_sequence/aligned_sequence_concept.hpp>
+#if SEQAN3_WORKAROUND_ISSUE_286
+#include <seqan3/core/detail/transfer_type_modifier_onto.hpp>
+#endif // SEQAN3_WORKAROUND_ISSUE_286
+
+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> &&
+#if SEQAN3_WORKAROUND_ISSUE_286
+    aligned_sequence<
+        // simulate that tuple_element transfers const over to it's inner members.
+        transfer_type_modifier_onto_t<
+            std::remove_reference_t<pairwise_alignment_t>,
+            std::tuple_element_t<0, std::remove_cvref_t<pairwise_alignment_t>>
+        >
+    > &&
+    aligned_sequence<
+        // simulate that tuple_element transfers const over to it's inner members.
+        transfer_type_modifier_onto_t<
+            std::remove_reference_t<pairwise_alignment_t>,
+            std::tuple_element_t<1, std::remove_cvref_t<pairwise_alignment_t>>
+        >
+    >;
+#else // ^^^ workaround / no workaround vvv
+    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>>>;
+#endif // SEQAN3_WORKAROUND_ISSUE_286
+
+//!\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> &&
+#if SEQAN3_WORKAROUND_ISSUE_286
+    writable_aligned_sequence<
+        // simulate that tuple_element transfers const over to it's inner members.
+        transfer_type_modifier_onto_t<
+            std::remove_reference_t<pairwise_alignment_t>,
+            std::tuple_element_t<0, std::remove_cvref_t<pairwise_alignment_t>>
+        >
+    > &&
+    writable_aligned_sequence<
+        // simulate that tuple_element transfers const over to it's inner members.
+        transfer_type_modifier_onto_t<
+            std::remove_reference_t<pairwise_alignment_t>,
+            std::tuple_element_t<1, std::remove_cvref_t<pairwise_alignment_t>>
+        >
+    >;
+#else // ^^^ workaround / no workaround vvv
+    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>>>;
+#endif // SEQAN3_WORKAROUND_ISSUE_286
+//!\endcond
+
+} // namespace seqan3::detail
diff --git a/include/seqan3/core/platform.hpp b/include/seqan3/core/platform.hpp
@@ -223,6 +223,15 @@
 #   define SEQAN3_WORKAROUND_VIEW_PERFORMANCE 1
 #endif
 
+//!\brief See https://github.com/seqan/product_backlog/issues/286
+#ifndef SEQAN3_WORKAROUND_ISSUE_286
+#   if defined(__GNUC__) && (__GNUC__ <= 9)
+#       define SEQAN3_WORKAROUND_ISSUE_286 1
+#   else
+#       define SEQAN3_WORKAROUND_ISSUE_286 0
+#   endif
+#endif
+
 //!\brief See https://gcc.gnu.org/bugzilla/show_bug.cgi?id=87113
 #ifndef SEQAN3_WORKAROUND_GCC_87113
 #   if defined(__GNUC_MINOR__) && ((__GNUC__ == 7) || ((__GNUC__ == 8) && (__GNUC_MINOR__ < 3)))

diff --git a/test/unit/alignment/detail/CMakeLists.txt b/test/unit/alignment/detail/CMakeLists.txt
@@ -0,0 +1 @@
+seqan3_test(pairwise_alignment_concept_test.cpp)
diff --git a/test/unit/alignment/detail/pairwise_alignment_concept_test.cpp b/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 &&>));
+}