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[FIX] Add size() to kmer_hash_view
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@MitraDarja
MitraDarja committed May 4, 2020
1 parent 786c90d commit d12333c
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4 changes: 2 additions & 2 deletions CHANGELOG.md
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Expand Up @@ -64,6 +64,8 @@ Note that 3.1.0 will be the first API stable release and interfaces in this rele
* The `seqan3::begin()`, `seqan3::end()`, `seqan3::cbegin()`, `seqan3::cend()`, `seqan3::size()`, `seqan3::empty()`
functions have been deprecated:
Use `std::ranges::{begin|end|cbegin|cend|size|empty}()` instead ([\#1663](https://github.com/seqan/seqan3/pull/1663)).
* Added size() function to `seqan3::views::kmer_hash`
([\#1722](https://github.com/seqan/seqan3/pull/1722)).

#### Search

Expand Down Expand Up @@ -175,8 +177,6 @@ Note that 3.1.0 will be the first API stable release and interfaces in this rele
([\#1410](https://github.com/seqan/seqan3/pull/1410)).
* Renamed `seqan3::views::all` to `seqan3::views::type_reduce`
([\#1410](https://github.com/seqan/seqan3/pull/1410)).
* Added size() function to `seqan3::views::kmer_hash`
([\#1722](https://github.com/seqan/seqan3/pull/1722)).

#### Search

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8 changes: 4 additions & 4 deletions include/seqan3/range/views/kmer_hash.hpp
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Expand Up @@ -179,12 +179,12 @@ class kmer_hash_view : public std::ranges::view_interface<kmer_hash_view<urng_t>
* \returns Size of range.
*/
auto size() const
//!\cond
requires std::ranges::sized_range<urng_t>
//!\endcond
{
auto range_size{std::ranges::size(urange)};
if (range_size >= shape_.size())
return range_size - shape_.size() + 1;
return decltype(range_size){0};
using size_type = decltype(std::ranges::size(urange));
return std::max<size_type>(std::ranges::size(urange) + 1, shape_.size()) - shape_.size();
}
};

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112 changes: 67 additions & 45 deletions test/unit/range/views/view_kmer_hash_test.cpp
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Expand Up @@ -30,7 +30,10 @@ static constexpr auto prefix_until_first_thymine = seqan3::views::take_until([]
{ return x == 'T'_dna4; });

template <typename T>
class kmer_hash_test: public ::testing::Test {};
class kmer_hash_ungapped_test: public ::testing::Test {};

template <typename T>
class kmer_hash_gapped_test: public ::testing::Test {};

using underlying_range_types = ::testing::Types<std::vector<seqan3::dna4>,
std::vector<seqan3::dna4> const,
Expand All @@ -41,74 +44,88 @@ using underlying_range_types = ::testing::Types<std::vector<seqan3::dna4>,
std::forward_list<seqan3::dna4>,
std::forward_list<seqan3::dna4> const>;

TYPED_TEST_SUITE(kmer_hash_test, underlying_range_types, );
TYPED_TEST_SUITE(kmer_hash_ungapped_test, underlying_range_types, );
TYPED_TEST_SUITE(kmer_hash_gapped_test, underlying_range_types, );

TYPED_TEST(kmer_hash_test, ungapped_combined_with_container)
TYPED_TEST(kmer_hash_ungapped_test, combined_with_container)
{
TypeParam text1{'A'_dna4, 'C'_dna4, 'G'_dna4, 'T'_dna4, 'A'_dna4, 'G'_dna4, 'C'_dna4}; // ACGTAGC
result_t ungapped1{6, 27, 44, 50, 9};
TypeParam text2{'A'_dna4, 'A'_dna4, 'A'_dna4, 'A'_dna4, 'A'_dna4}; // AAAAA
result_t ungapped2{0,0,0};
TypeParam text3{'A'_dna4, 'C'_dna4}; // AC
result_t ungapped3{};
TypeParam text4{'A'_dna4, 'C'_dna4, 'G'_dna4}; // AC
result_t ungapped4{6};

EXPECT_EQ(ungapped1, text1 | ungapped_view | seqan3::views::to<result_t>);
EXPECT_EQ(ungapped2, 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(ungapped4, text1 | prefix_until_first_thymine | ungapped_view | seqan3::views::to<result_t>);
{
TypeParam text1{'A'_dna4, 'C'_dna4, 'G'_dna4, 'T'_dna4, 'A'_dna4, 'G'_dna4, 'C'_dna4}; // ACGTAGC
result_t ungapped1{6, 27, 44, 50, 9};
EXPECT_EQ(ungapped1, text1 | ungapped_view | seqan3::views::to<result_t>);
EXPECT_EQ(result_t{6}, text1 | prefix_until_first_thymine | ungapped_view | seqan3::views::to<result_t>);
}
{
TypeParam text2{'A'_dna4, 'A'_dna4, 'A'_dna4, 'A'_dna4, 'A'_dna4}; // AAAAA
result_t ungapped2{0, 0, 0};
EXPECT_EQ(ungapped2, text2 | ungapped_view | seqan3::views::to<result_t>);
}
{
TypeParam text3{'A'_dna4, 'C'_dna4}; // AC
EXPECT_EQ(result_t{}, text3 | ungapped_view | seqan3::views::to<result_t>);
}
{
TypeParam text4{'A'_dna4, 'C'_dna4, 'G'_dna4}; // AC
EXPECT_EQ(result_t{6}, text4 | ungapped_view | seqan3::views::to<result_t>);
}
}

TYPED_TEST(kmer_hash_test, gapped_combined_with_container)
TYPED_TEST(kmer_hash_gapped_test, combined_with_container)
{
TypeParam text1{'A'_dna4, 'C'_dna4, 'G'_dna4, 'T'_dna4, 'A'_dna4, 'G'_dna4, 'C'_dna4}; // ACGTAGC
result_t gapped1{2, 7, 8, 14, 1};
TypeParam text2{'A'_dna4, 'A'_dna4, 'A'_dna4, 'A'_dna4, 'A'_dna4}; // AAAAA
result_t gapped2{0,0,0};
TypeParam text3{'A'_dna4, 'C'_dna4}; // AC
result_t gapped3{};
TypeParam text4{'A'_dna4, 'C'_dna4, 'G'_dna4}; // AC
result_t gapped4{2};
EXPECT_EQ(gapped1, text1 | gapped_view | seqan3::views::to<result_t>);
EXPECT_EQ(gapped2, 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(gapped4, text1 | prefix_until_first_thymine| gapped_view | seqan3::views::to<result_t>);
{
TypeParam text1{'A'_dna4, 'C'_dna4, 'G'_dna4, 'T'_dna4, 'A'_dna4, 'G'_dna4, 'C'_dna4}; // ACGTAGC
result_t gapped1{2, 7, 8, 14, 1};
EXPECT_EQ(gapped1, text1 | gapped_view | seqan3::views::to<result_t>);
EXPECT_EQ(result_t{2}, text1 | prefix_until_first_thymine| gapped_view | seqan3::views::to<result_t>);
}
{
TypeParam text2{'A'_dna4, 'A'_dna4, 'A'_dna4, 'A'_dna4, 'A'_dna4}; // AAAAA
result_t gapped2{0, 0, 0};
EXPECT_EQ(gapped2, text2 | gapped_view | seqan3::views::to<result_t>);
}
{
TypeParam text3{'A'_dna4, 'C'_dna4}; // AC
EXPECT_EQ(result_t{}, text3 | gapped_view | seqan3::views::to<result_t>);
}
{
TypeParam text4{'A'_dna4, 'C'_dna4, 'G'_dna4}; // AC
EXPECT_EQ(result_t{2}, text4 | gapped_view | seqan3::views::to<result_t>);
}
}

TYPED_TEST(kmer_hash_test, ungapped_concepts)
TYPED_TEST(kmer_hash_ungapped_test, concepts)
{
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_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_FALSE(std::ranges::contiguous_range<decltype(v1)>);
EXPECT_TRUE(std::ranges::view<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>));
}

TYPED_TEST(kmer_hash_test, gapped_concepts)
TYPED_TEST(kmer_hash_gapped_test, concepts)
{
TypeParam text{'A'_dna4, 'C'_dna4, 'G'_dna4, 'T'_dna4}; // ACGT
auto v1 = text | gapped_view;
EXPECT_TRUE(std::ranges::input_range<decltype(v1)>);
EXPECT_TRUE(std::ranges::forward_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_FALSE(std::ranges::contiguous_range<decltype(v1)>);
EXPECT_TRUE(std::ranges::view<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>));
}

TYPED_TEST(kmer_hash_test, invalid_sizes)
TYPED_TEST(kmer_hash_ungapped_test, invalid_sizes)
{
TypeParam text1{'A'_dna4, 'A'_dna4, 'A'_dna4, 'A'_dna4, 'A'_dna4};
EXPECT_NO_THROW(text1 | seqan3::views::kmer_hash(seqan3::ungapped{32}));
Expand All @@ -129,15 +146,15 @@ TYPED_TEST(kmer_hash_test, invalid_sizes)
}

// https://github.com/seqan/seqan3/issues/1614
TEST(kmer_hash_test, issue1614)
TEST(kmer_hash_ungapped_test, issue1614)
{
std::vector<seqan3::dna5> sequence{"TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT"_dna5};
EXPECT_EQ(sequence | seqan3::views::kmer_hash(seqan3::ungapped{25}) | seqan3::views::to<std::vector<size_t>>,
seqan3::views::repeat_n(298023223876953124, 26) | seqan3::views::to<std::vector<size_t>>);
}

// https://github.com/seqan/seqan3/issues/1643
TEST(kmer_hash_test, issue1643)
TEST(kmer_hash_ungapped_test, issue1643)
{
std::vector<seqan3::dna4> text_23_elements{"ACGATCGATCGTAGCTACTGAGC"_dna4};

Expand All @@ -153,14 +170,19 @@ TEST(kmer_hash_test, issue1643)
}

// https://github.com/seqan/seqan3/issues/1719
TEST(kmer_hash_test, issue1719)
TYPED_TEST(kmer_hash_ungapped_test, issue1719)
{
uint64_t const expected = 0;
std::vector<seqan3::dna5> sequence{""_dna5};
auto v = sequence | seqan3::views::kmer_hash(seqan3::ungapped{25});
EXPECT_EQ(expected, v.size());

std::vector<seqan3::dna5> sequence2{"ACGATCGATCGTAGCTACTGAGC"_dna5};
auto v2 = sequence2 | seqan3::views::kmer_hash(seqan3::ungapped{25});
EXPECT_EQ(expected, v2.size());
if constexpr (std::ranges::sized_range<TypeParam>)
{
TypeParam sequence{};
auto v = sequence | seqan3::views::kmer_hash(seqan3::ungapped{8});
EXPECT_EQ(0u, v.size());

TypeParam sequence2{'A'_dna4, 'C'_dna4, 'G'_dna4, 'T'_dna4, 'A'_dna4, 'G'_dna4, 'C'_dna4};
auto v2 = sequence2 | seqan3::views::kmer_hash(seqan3::ungapped{8});
EXPECT_EQ(0u, v2.size());

auto v3 = sequence2 | seqan3::views::kmer_hash(seqan3::ungapped{4});
EXPECT_EQ(4u, v3.size());
}
}

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