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[MISC] Add typed test to kmerhash
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@MitraDarja
MitraDarja committed Apr 14, 2020
1 parent 332f4b3 commit 71dd793
Showing 1 changed file with 49 additions and 118 deletions.
167 changes: 49 additions & 118 deletions test/unit/range/views/view_kmer_hash_test.cpp
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Original file line number Diff line number Diff line change
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#include <seqan3/range/views/take_until.hpp>
#include <seqan3/range/views/to.hpp>

#include <seqan3/core/debug_stream.hpp>

#include <gtest/gtest.h>

using seqan3::operator""_dna4;
using seqan3::operator""_dna5;
using seqan3::operator""_shape;
using result_t = std::vector<size_t>;

static constexpr auto ungapped_view = seqan3::views::kmer_hash(seqan3::ungapped{3});
static constexpr auto gapped_view = seqan3::views::kmer_hash(0b101_shape);

template <typename T>
class kmer_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,
std::forward_list<seqan3::dna4>,
std::forward_list<seqan3::dna4> const>;

TYPED_TEST_SUITE(kmer_hash_properties_test, underlying_range_types, );

class kmer_hash_test : public ::testing::Test
{
protected:
using result_t = std::vector<size_t>;
std::vector<seqan3::dna4> text1{"AAAAA"_dna4};
result_t result1{0,0,0}; // Same for gapped and ungapped

static constexpr auto ungapped_view = seqan3::views::kmer_hash(seqan3::ungapped{3});
static constexpr auto gapped_view = seqan3::views::kmer_hash(0b101_shape);
std::vector<seqan3::dna4> text2{"AC"_dna4};
result_t result2{}; // Same for gapped and ungapped

std::vector<seqan3::dna4> text1{"AAAAA"_dna4};
std::vector<seqan3::dna4> const ctext1{"AAAAA"_dna4};
result_t ungapped1{0,0,0};
result_t gapped1{0,0,0};

std::vector<seqan3::dna4> text2{"ACGTAGC"_dna4};
std::vector<seqan3::dna4> const ctext2{"ACGTAGC"_dna4};
result_t ungapped2{6,27,44,50,9};
result_t gapped2{2, 7, 8, 14, 1};

std::vector<seqan3::dna4> text3{"AC"_dna4};
std::vector<seqan3::dna4> const ctext3{"AC"_dna4};
result_t ungapped3{};
result_t gapped3{ungapped3};

seqan3::bitcompressed_vector<seqan3::dna4> text4{"ACGTAGC"_dna4};
seqan3::bitcompressed_vector<seqan3::dna4> const ctext4{"ACGTAGC"_dna4};
result_t ungapped4{ungapped2};
result_t gapped4{gapped2};

std::list<seqan3::dna4> text5{'A'_dna4, 'C'_dna4, 'G'_dna4, 'T'_dna4, 'A'_dna4, 'G'_dna4, 'C'_dna4};
std::list<seqan3::dna4> const ctext5{'A'_dna4, 'C'_dna4, 'G'_dna4, 'T'_dna4, 'A'_dna4, 'G'_dna4, 'C'_dna4};
result_t ungapped5{ungapped2};
result_t gapped5{gapped2};

std::forward_list<seqan3::dna4> text6{'A'_dna4, 'C'_dna4, 'G'_dna4, 'T'_dna4, 'A'_dna4, 'G'_dna4, 'C'_dna4};
std::forward_list<seqan3::dna4> const ctext6{'A'_dna4, 'C'_dna4, 'G'_dna4, 'T'_dna4, 'A'_dna4, 'G'_dna4, 'C'_dna4};
result_t ungapped6{ungapped2};
result_t gapped6{gapped2};

std::vector<seqan3::dna4> text7{"ACG"_dna4};
std::vector<seqan3::dna4> const ctext7{"ACG"_dna4};
result_t ungapped7{6};
result_t gapped7{2};
std::vector<seqan3::dna4> text3{"ACG"_dna4};
result_t ungapped3{6};
result_t gapped3{2};
};

TYPED_TEST(kmer_hash_properties_test, combinability)
{
TypeParam text{'A'_dna4, 'C'_dna4, 'G'_dna4, 'T'_dna4, 'A'_dna4, 'G'_dna4, 'C'_dna4}; // ACGTAGC
result_t ungapped{6,27,44,50,9};
result_t gapped{2,7,8,14,1};
EXPECT_EQ(ungapped, text | ungapped_view | seqan3::views::to<result_t>);
EXPECT_EQ(gapped, text | gapped_view | seqan3::views::to<result_t>);

auto stop_at_t = seqan3::views::take_until([] (seqan3::dna4 x) { return x == 'T'_dna4; });
EXPECT_EQ(result_t{6}, text | stop_at_t | ungapped_view | seqan3::views::to<result_t>);
EXPECT_EQ(result_t{2}, text | stop_at_t | gapped_view | seqan3::views::to<result_t>);
}

TEST_F(kmer_hash_test, concepts)
TYPED_TEST(kmer_hash_properties_test, concepts)
{
auto v1 = text1 | ungapped_view;
TypeParam text{'A'_dna4, 'C'_dna4, 'G'_dna4, 'T'_dna4}; // ACGT
auto v1 = text | ungapped_view;
EXPECT_TRUE(std::ranges::input_range<decltype(v1)>);
EXPECT_TRUE(std::ranges::forward_range<decltype(v1)>);
EXPECT_TRUE(std::ranges::bidirectional_range<decltype(v1)>);
EXPECT_TRUE(std::ranges::random_access_range<decltype(v1)>);
EXPECT_EQ(std::ranges::bidirectional_range<decltype(text)>, std::ranges::bidirectional_range<decltype(v1)>);
EXPECT_EQ(std::ranges::random_access_range<decltype(text)>, std::ranges::random_access_range<decltype(v1)>);
EXPECT_TRUE(std::ranges::view<decltype(v1)>);
EXPECT_TRUE(std::ranges::sized_range<decltype(v1)>);
EXPECT_EQ(std::ranges::sized_range<decltype(text)>, std::ranges::sized_range<decltype(v1)>);
EXPECT_FALSE(std::ranges::common_range<decltype(v1)>);
EXPECT_TRUE(seqan3::const_iterable_range<decltype(v1)>);
EXPECT_FALSE((std::ranges::output_range<decltype(v1), size_t>));

auto v2 = text5 | ungapped_view;
EXPECT_TRUE(std::ranges::input_range<decltype(v2)>);
EXPECT_TRUE(std::ranges::forward_range<decltype(v2)>);
EXPECT_TRUE(std::ranges::bidirectional_range<decltype(v2)>);
EXPECT_FALSE(std::ranges::random_access_range<decltype(v2)>);
EXPECT_TRUE(std::ranges::view<decltype(v2)>);
EXPECT_FALSE(std::ranges::sized_range<decltype(v2)>);
EXPECT_FALSE(std::ranges::common_range<decltype(v2)>);
EXPECT_TRUE(seqan3::const_iterable_range<decltype(v2)>);
EXPECT_FALSE((std::ranges::output_range<decltype(v2), size_t>));

auto v3 = text6 | ungapped_view;
EXPECT_TRUE(std::ranges::input_range<decltype(v3)>);
EXPECT_TRUE(std::ranges::forward_range<decltype(v3)>);
EXPECT_FALSE(std::ranges::bidirectional_range<decltype(v3)>);
EXPECT_FALSE(std::ranges::random_access_range<decltype(v3)>);
EXPECT_TRUE(std::ranges::view<decltype(v3)>);
EXPECT_FALSE(std::ranges::sized_range<decltype(v3)>);
EXPECT_FALSE(std::ranges::common_range<decltype(v3)>);
EXPECT_TRUE(seqan3::const_iterable_range<decltype(v3)>);
EXPECT_FALSE((std::ranges::output_range<decltype(v3), size_t>));
}

TEST_F(kmer_hash_test, ungapped)
{
EXPECT_EQ(ungapped1, text1 | ungapped_view | seqan3::views::to<result_t>);
EXPECT_EQ(ungapped2, text2 | ungapped_view | seqan3::views::to<result_t>);
EXPECT_EQ(result1, text1 | ungapped_view | seqan3::views::to<result_t>);
EXPECT_EQ(result2, text2 | ungapped_view | seqan3::views::to<result_t>);
EXPECT_EQ(ungapped3, text3 | ungapped_view | seqan3::views::to<result_t>);
EXPECT_EQ(ungapped4, text4 | ungapped_view | seqan3::views::to<result_t>);
EXPECT_EQ(ungapped5, text5 | ungapped_view | seqan3::views::to<result_t>);
EXPECT_EQ(ungapped6, text6 | ungapped_view | seqan3::views::to<result_t>);
EXPECT_EQ(ungapped7, text7 | ungapped_view | seqan3::views::to<result_t>);
}

TEST_F(kmer_hash_test, gapped)
{
EXPECT_EQ(gapped1, text1 | gapped_view | seqan3::views::to<result_t>);
EXPECT_EQ(gapped2, text2 | gapped_view | seqan3::views::to<result_t>);
EXPECT_EQ(result1, text1 | gapped_view | seqan3::views::to<result_t>);
EXPECT_EQ(result2, text2 | gapped_view | seqan3::views::to<result_t>);
EXPECT_EQ(gapped3, text3 | gapped_view | seqan3::views::to<result_t>);
EXPECT_EQ(gapped4, text4 | gapped_view | seqan3::views::to<result_t>);
EXPECT_EQ(gapped5, text5 | gapped_view | seqan3::views::to<result_t>);
EXPECT_EQ(gapped6, text6 | gapped_view | seqan3::views::to<result_t>);
EXPECT_EQ(gapped7, text7 | gapped_view | seqan3::views::to<result_t>);
}

TEST_F(kmer_hash_test, const_ungapped)
{
EXPECT_EQ(ungapped1, ctext1 | ungapped_view | seqan3::views::to<result_t>);
EXPECT_EQ(ungapped2, ctext2 | ungapped_view | seqan3::views::to<result_t>);
EXPECT_EQ(ungapped3, ctext3 | ungapped_view | seqan3::views::to<result_t>);
EXPECT_EQ(ungapped4, ctext4 | ungapped_view | seqan3::views::to<result_t>);
EXPECT_EQ(ungapped5, ctext5 | ungapped_view | seqan3::views::to<result_t>);
EXPECT_EQ(ungapped6, ctext6 | ungapped_view | seqan3::views::to<result_t>);
EXPECT_EQ(ungapped7, ctext7 | ungapped_view | seqan3::views::to<result_t>);
}

TEST_F(kmer_hash_test, const_gapped)
{
EXPECT_EQ(gapped1, ctext1 | gapped_view | seqan3::views::to<result_t>);
EXPECT_EQ(gapped2, ctext2 | gapped_view | seqan3::views::to<result_t>);
EXPECT_EQ(gapped3, ctext3 | gapped_view | seqan3::views::to<result_t>);
EXPECT_EQ(gapped4, ctext4 | gapped_view | seqan3::views::to<result_t>);
EXPECT_EQ(gapped5, ctext5 | gapped_view | seqan3::views::to<result_t>);
EXPECT_EQ(gapped6, ctext6 | gapped_view | seqan3::views::to<result_t>);
EXPECT_EQ(gapped7, ctext7 | gapped_view | seqan3::views::to<result_t>);
}

TEST_F(kmer_hash_test, combinability)
{
auto stop_at_t = seqan3::views::take_until([] (seqan3::dna4 const x) { return x == 'T'_dna4; });
EXPECT_EQ(result_t{6}, text2 | stop_at_t | ungapped_view | seqan3::views::to<result_t>);
EXPECT_EQ(result_t{6}, text5 | stop_at_t | ungapped_view | seqan3::views::to<result_t>);
EXPECT_EQ(result_t{6}, text6 | stop_at_t | ungapped_view | seqan3::views::to<result_t>);

EXPECT_EQ(ungapped2 | std::views::reverse | seqan3::views::to<result_t>,
text2 | ungapped_view | std::views::reverse | seqan3::views::to<result_t>);

EXPECT_EQ(gapped2 | std::views::reverse | seqan3::views::to<result_t>,
text2 | gapped_view | std::views::reverse | seqan3::views::to<result_t>);

EXPECT_EQ(ungapped5 | std::views::reverse | seqan3::views::to<result_t>,
text5 | ungapped_view | std::views::reverse | seqan3::views::to<result_t>);

EXPECT_EQ(gapped5 | std::views::reverse | seqan3::views::to<result_t>,
text5 | gapped_view | std::views::reverse | seqan3::views::to<result_t>);
}

TEST_F(kmer_hash_test, invalid_sizes)
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