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[FIX] Missing seqan3 namespace identifier in gap_decorator_test.cpp (#…
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…1769)
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@wvdtoorn
wvdtoorn authored Apr 28, 2020
1 parent 4e2f1cc commit f5278f7
Showing 1 changed file with 42 additions and 40 deletions.
82 changes: 42 additions & 40 deletions test/unit/range/decorator/gap_decorator_test.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -21,12 +21,13 @@
#include "../iterator_test_template.hpp"
#include "../../alignment/aligned_sequence_test_template.hpp"

using decorator_t = gap_decorator<std::vector<dna4> const &>;
using decorator_t = seqan3::gap_decorator<std::vector<seqan3::dna4> const &>;

std::vector<dna4> const dummy_obj{}; // dummy lvalue for type declaration of views
using decorator_t2 = gap_decorator<
std::vector<seqan3::dna4> const dummy_obj{}; // dummy lvalue for type declaration of views
using decorator_t2 = seqan3::gap_decorator<
decltype(std::ranges::subrange<decltype(dummy_obj.begin()),
decltype(dummy_obj.begin())>{dummy_obj.begin(), dummy_obj.end()})>;
decltype(dummy_obj.begin())>{dummy_obj.begin(),
dummy_obj.end()})>;


using test_types = ::testing::Types<decorator_t, decorator_t2>;
Expand All @@ -36,21 +37,22 @@ using test_types = ::testing::Types<decorator_t, decorator_t2>;
// ---------------------------------------------------------------------------------------------------------------------

template <typename inner_type_>
class aligned_sequence_<gap_decorator<inner_type_>> : public ::testing::Test
class aligned_sequence_<seqan3::gap_decorator<inner_type_>> : public ::testing::Test
{
public:
// Initialiser function is needed for the typed test because the gapped_decorator
// will be initialised differently than the naive vector<gapped<dna>>.
void initialise_typed_test_container(decorator_t & container_, dna4_vector const & target)
// will be initialised differently than the naive vector<seqan3::gapped<seqan3::dna>>.
void initialise_typed_test_container(decorator_t & container_, seqan3::dna4_vector const & target)
{
container_ = target;
}

// Initialiser function is needed for the typed test because the gapped_decorator
// will be initialised differently than the naive vector<gapped<dna>>.
void initialise_typed_test_container(decorator_t2 & container_, dna4_vector const & target)
// will be initialised differently than the naive vector<seqan3::gapped<seqan3::dna>>.
void initialise_typed_test_container(decorator_t2 & container_, seqan3::dna4_vector const & target)
{
container_ = std::ranges::subrange<decltype(target.begin()), decltype(target.end())>{target.begin(), target.end()};
container_ = std::ranges::subrange<decltype(target.begin()),
decltype(target.end())>{target.begin(), target.end()};
}
};

Expand All @@ -62,7 +64,7 @@ struct iterator_fixture<std::ranges::iterator_t<decorator_t>> : public ::testing
using iterator_tag = std::bidirectional_iterator_tag;
static constexpr bool const_iterable = true;

std::vector<dna4> const vec{"ACTGACTG"_dna4};
std::vector<seqan3::dna4> const vec{"ACTGACTG"_dna4};

template <typename t>
static void initialise_with_gaps(t & v)
Expand All @@ -73,9 +75,9 @@ struct iterator_fixture<std::ranges::iterator_t<decorator_t>> : public ::testing
insert_gap(v, v.begin(), 5);
}

std::vector<gapped<dna4>> expected_range = [this] ()
std::vector<seqan3::gapped<seqan3::dna4>> expected_range = [this] ()
{
std::vector<gapped<dna4>> tmp{};
std::vector<seqan3::gapped<seqan3::dna4>> tmp{};
assign_unaligned(tmp, vec);
initialise_with_gaps(tmp);
return tmp;
Expand Down Expand Up @@ -130,7 +132,7 @@ TYPED_TEST(gap_decorator_f, concept_checks)

EXPECT_FALSE((std::ranges::view<TypeParam>));

EXPECT_TRUE((aligned_sequence<TypeParam>));
EXPECT_TRUE((seqan3::aligned_sequence<TypeParam>));
}

TYPED_TEST(gap_decorator_f, construction_general)
Expand Down Expand Up @@ -182,31 +184,31 @@ TYPED_TEST(gap_decorator_f, construction_general)
TEST(gap_decorator, construction_from_ungapped_sequence)
{
{
std::vector<dna4> v{"ACTG"_dna4};
std::vector<dna4> const v_const{"ACTG"_dna4};
std::vector<seqan3::dna4> v{"ACTG"_dna4};
std::vector<seqan3::dna4> const v_const{"ACTG"_dna4};

// non-const version
gap_decorator dec{v};
seqan3::gap_decorator dec{v};
EXPECT_EQ('A'_dna4, dec[0]);
EXPECT_EQ('C'_dna4, dec[1]);

// const version
gap_decorator const dec2(v_const);
seqan3::gap_decorator const dec2(v_const);
EXPECT_EQ('A'_dna4, dec2[0]);
EXPECT_EQ('C'_dna4, dec2[1]);
}

{
std::vector<dna4> v{"ACTG"_dna4};
std::vector<dna4> const v_const{"ACTG"_dna4};
std::vector<seqan3::dna4> v{"ACTG"_dna4};
std::vector<seqan3::dna4> const v_const{"ACTG"_dna4};

// non-const version
gap_decorator dec = v;
seqan3::gap_decorator dec = v;
EXPECT_EQ('A'_dna4, dec[0]);
EXPECT_EQ('C'_dna4, dec[1]);

// const version
gap_decorator const dec2 = v_const;
seqan3::gap_decorator const dec2 = v_const;
EXPECT_EQ('A'_dna4, dec2[0]);
EXPECT_EQ('C'_dna4, dec2[1]);
}
Expand All @@ -215,11 +217,11 @@ TEST(gap_decorator, construction_from_ungapped_sequence)
TEST(gap_decorator, assignment_from_ungapped_sequence)
{
{
std::vector<dna4> v{"TT"_dna4};
std::vector<dna4> v2{"ACTG"_dna4};
std::vector<dna4> const v_const{"TGCC"_dna4};
std::vector<seqan3::dna4> v{"TT"_dna4};
std::vector<seqan3::dna4> v2{"ACTG"_dna4};
std::vector<seqan3::dna4> const v_const{"TGCC"_dna4};

gap_decorator dec{v};
seqan3::gap_decorator dec{v};
dec = v2;
EXPECT_EQ('A'_dna4, dec[0]);
EXPECT_EQ('C'_dna4, dec[1]);
Expand All @@ -242,10 +244,10 @@ TEST(gap_decorator, assignment_from_ungapped_sequence)

TEST(gap_decorator, comparison)
{
std::vector<dna4> v{"ACTG"_dna4};
std::vector<seqan3::dna4> v{"ACTG"_dna4};

gap_decorator dec{v};
gap_decorator dec2{v};
seqan3::gap_decorator dec{v};
seqan3::gap_decorator dec2{v};

EXPECT_EQ(dec, dec2);
EXPECT_LE(dec, dec2);
Expand All @@ -268,17 +270,17 @@ TEST(gap_decorator, comparison)
EXPECT_LT(dec, dec2);
EXPECT_LE(dec, dec2);

std::vector<dna4> v2{"TCTG"_dna4};
gap_decorator decNE{v2};
std::vector<seqan3::dna4> v2{"TCTG"_dna4};
seqan3::gap_decorator decNE{v2};
EXPECT_NE(dec, decNE);
}

TEST(gap_decorator, begin_and_end)
{
std::vector<dna4> v{"ACTG"_dna4};
std::vector<seqan3::dna4> v{"ACTG"_dna4};

gap_decorator dec{v};
gap_decorator const dec_const{v};
seqan3::gap_decorator dec{v};
seqan3::gap_decorator const dec_const{v};

EXPECT_EQ(*dec.begin(), 'A'_dna4);
EXPECT_EQ(*dec.cbegin(), 'A'_dna4);
Expand All @@ -291,10 +293,10 @@ TEST(gap_decorator, begin_and_end)

TEST(gap_decorator, decorator_on_views)
{
std::vector<dna4> v{"ACTG"_dna4};
std::vector<seqan3::dna4> v{"ACTG"_dna4};

auto sub = std::ranges::subrange<decltype(v.begin()), decltype(v.begin())>{v.begin()+1, v.begin()+3};
gap_decorator dec{sub};
seqan3::gap_decorator dec{sub};

EXPECT_EQ(dec.size(), 2u);
EXPECT_EQ(*dec.begin(), 'C'_dna4);
Expand All @@ -304,16 +306,16 @@ TEST(gap_decorator, decorator_on_views)

EXPECT_EQ(dec.size(), 4u);
EXPECT_EQ(*dec.begin(), 'C'_dna4);
EXPECT_EQ(*(std::next(dec.begin(), 1)), gap{});
EXPECT_EQ(*it, gap{});
EXPECT_EQ(*(std::next(dec.begin(), 1)), seqan3::gap{});
EXPECT_EQ(*it, seqan3::gap{});

// auto v_char = v | seqan3::views::to_char;
gap_decorator dec2{v | seqan3::views::to_char};
seqan3::gap_decorator dec2{v | seqan3::views::to_char};
EXPECT_EQ(dec2.size(), 4u);
EXPECT_EQ(*dec2.begin(), 'A');
EXPECT_EQ(*++dec2.begin(), 'C');

auto dec3 = dec | std::views::filter([] (auto chr) { return chr != gap{}; });
auto dec3 = dec | std::views::filter([] (auto chr) { return chr != seqan3::gap{}; });
EXPECT_EQ(*dec3.begin(), 'C'_dna4);
EXPECT_EQ(*(std::next(dec3.begin())), 'T'_dna4);
}

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