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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
// -----------------------------------------------------------------------------------------------------
#include <forward_list>
#include <list>
#include <seqan3/alphabet/nucleotide/dna4.hpp>
#include <seqan3/range/container/bitcompressed_vector.hpp>
#include <seqan3/range/views/minimiser_hash.hpp>
#include <seqan3/range/views/take_until.hpp>
#include <seqan3/test/expect_range_eq.hpp>
#include <gtest/gtest.h>
#include "../iterator_test_template.hpp"
using seqan3::operator""_dna4;
using seqan3::operator""_shape;
using result_t = std::vector<size_t>;
using iterator_type = std::ranges::iterator_t<decltype(std::declval<seqan3::dna4_vector&>()
| seqan3::views::minimiser_hash(seqan3::ungapped{4},
seqan3::window_size{8},
seqan3::seed{0}))>;
static constexpr seqan3::shape ungapped_shape = seqan3::ungapped{4};
static constexpr seqan3::shape gapped_shape = 0b1001_shape;
static constexpr auto ungapped_view = seqan3::views::minimiser_hash(ungapped_shape,
seqan3::window_size{8},
seqan3::seed{0});
static constexpr auto gapped_view = seqan3::views::minimiser_hash(gapped_shape,
seqan3::window_size{8},
seqan3::seed{0});
template <>
struct iterator_fixture<iterator_type> : public ::testing::Test
{
using iterator_tag = std::forward_iterator_tag;
static constexpr bool const_iterable = false;
seqan3::dna4_vector text{"ACGGCGACGTTTAG"_dna4};
result_t expected_range{26, 97, 27, 6, 1};
using test_range_t = decltype(text | ungapped_view);
test_range_t test_range = text | ungapped_view;
};
using test_type = ::testing::Types<iterator_type>;
INSTANTIATE_TYPED_TEST_SUITE_P(iterator_fixture, iterator_fixture, test_type, );
template <typename T>
class minimiser_hash_properties_test: public ::testing::Test { };
using underlying_range_types = ::testing::Types<std::vector<seqan3::dna4>,
std::vector<seqan3::dna4> const,
seqan3::bitcompressed_vector<seqan3::dna4>,
seqan3::bitcompressed_vector<seqan3::dna4> const,
std::list<seqan3::dna4>,
std::list<seqan3::dna4> const>;
TYPED_TEST_SUITE(minimiser_hash_properties_test, underlying_range_types, );
class minimiser_hash_test : public ::testing::Test
{
protected:
std::vector<seqan3::dna4> text1{"AAAAAAAAAAAAAAAAAAA"_dna4};
std::vector<seqan3::dna4> text1_short{"AAAAAA"_dna4};
result_t result1{0, 0, 0}; // Same for ungapped and gapped
result_t ungapped_default_seed{0x8F3F73B5CF1C9A21, 0x8F3F73B5CF1C9A21, 0x8F3F73B5CF1C9A21};
result_t gapped_default_seed{0x8F3F73B5CF1C9AD1, 0x8F3F73B5CF1C9AD1, 0x8F3F73B5CF1C9AD1};
std::vector<seqan3::dna4> text2{"AC"_dna4};
result_t result2{};
std::vector<seqan3::dna4> text3{"ACGGCGACGTTTAG"_dna4};
result_t ungapped3{26, 97, 27, 6, 1}; // ACGG, CGAC, ACGT, aacg, aaac
result_t ungapped_stop_at_t3{26, 97}; // ACGG, CGAC
result_t gapped3{2, 5, 3, 2, 1}; // A--G, C--C, A--T, a--g, a--c "-" for gap
result_t gapped_stop_at_t3{2, 5}; // A--G, C--C "-" for gap
};
TYPED_TEST(minimiser_hash_properties_test, different_input_ranges)
{
TypeParam text{'A'_dna4, 'C'_dna4, 'G'_dna4, 'T'_dna4, 'C'_dna4, 'G'_dna4, 'A'_dna4, 'C'_dna4, 'G'_dna4, 'T'_dna4,
'T'_dna4, 'T'_dna4, 'A'_dna4, 'G'_dna4}; // ACGTCGACGTTTAG
result_t ungapped{27, 97, 27, 6, 1}; // ACGT, CGAC, ACGT, aacg, aaac
result_t gapped{3, 5, 3, 2, 1}; // A--T, C--C, A--T, a--g, a--c - "-" for gap
EXPECT_RANGE_EQ(ungapped, text | ungapped_view);
EXPECT_RANGE_EQ(gapped, text | gapped_view);
}
TEST_F(minimiser_hash_test, ungapped)
{
EXPECT_RANGE_EQ(result1, text1 | ungapped_view);
EXPECT_RANGE_EQ(result2, text2 | ungapped_view);
EXPECT_RANGE_EQ(ungapped3, text3 | ungapped_view);
auto stop_at_t = seqan3::views::take_until([] (seqan3::dna4 const x) { return x == 'T'_dna4; });
EXPECT_RANGE_EQ(ungapped_stop_at_t3, text3 | stop_at_t | ungapped_view);
}
TEST_F(minimiser_hash_test, gapped)
{
EXPECT_RANGE_EQ(result1, text1 | gapped_view);
EXPECT_RANGE_EQ(result2, text2 | gapped_view);
EXPECT_RANGE_EQ(gapped3, text3 | gapped_view);
auto stop_at_t = seqan3::views::take_until([] (seqan3::dna4 const x) { return x == 'T'_dna4; });
EXPECT_RANGE_EQ(gapped_stop_at_t3, text3 | stop_at_t | gapped_view);
}
TEST_F(minimiser_hash_test, seed)
{
EXPECT_RANGE_EQ(ungapped_default_seed,
text1 | seqan3::views::minimiser_hash(ungapped_shape, seqan3::window_size{8}));
EXPECT_RANGE_EQ(gapped_default_seed, text1 | seqan3::views::minimiser_hash(gapped_shape, seqan3::window_size{8}));
}
TEST_F(minimiser_hash_test, shape_bigger_than_window)
{
EXPECT_THROW(text1 | seqan3::views::minimiser_hash(ungapped_shape, seqan3::window_size{3}), std::invalid_argument);
EXPECT_THROW(text1 | seqan3::views::minimiser_hash(gapped_shape, seqan3::window_size{3}), std::invalid_argument);
}
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