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[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.
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include/seqan3/alignment/detail/pairwise_alignment_concept.hpp
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| // ----------------------------------------------------------------------------------------------------- | ||
| // 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 | ||
| // ----------------------------------------------------------------------------------------------------- | ||
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| /*!\file | ||
| * \brief Provides seqan3::detail::pairwise_alignment and seqan3::detail::writable_pairwise_alignment. | ||
| * \author Marcel Ehrhardt <marcel.ehrhardt AT fu-berlin.de> | ||
| */ | ||
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| #pragma once | ||
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| #include <seqan3/alignment/aligned_sequence/aligned_sequence_concept.hpp> | ||
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| namespace seqan3::detail | ||
| { | ||
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| /*!\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 | ||
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| /*!\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 | ||
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| } // namespace seqan3::detail |
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| seqan3_test(pairwise_alignment_concept_test.cpp) |
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test/unit/alignment/detail/pairwise_alignment_concept_test.cpp
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| // ----------------------------------------------------------------------------------------------------- | ||
| // 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 | ||
| // ----------------------------------------------------------------------------------------------------- | ||
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| #include <gtest/gtest.h> | ||
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| #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> | ||
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| 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>; | ||
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| 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 &&>)); | ||
| } | ||
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| 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>; | ||
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| 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 &&>)); | ||
| } | ||
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| 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>; | ||
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| 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 &&>)); | ||
| } | ||
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| 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>; | ||
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| 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 &&>)); | ||
| } | ||
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| 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>; | ||
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| 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 &&>)); | ||
| } | ||
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| 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>; | ||
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| 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 &&>)); | ||
| } |