1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
|
// SPDX-FileCopyrightText: 2006-2025 Knut Reinert & Freie Universität Berlin
// SPDX-FileCopyrightText: 2016-2025 Knut Reinert & MPI für molekulare Genetik
// SPDX-License-Identifier: BSD-3-Clause
#include <gtest/gtest.h>
#include <algorithm>
#include <sstream>
#include <seqan3/alphabet/detail/debug_stream_alphabet.hpp>
#include <seqan3/alphabet/nucleotide/dna4.hpp>
#include <seqan3/io/record.hpp>
#include <seqan3/test/expect_range_eq.hpp>
#include <seqan3/test/expect_same_type.hpp>
#include <seqan3/utility/tuple/concept.hpp>
using seqan3::operator""_dna4;
using default_fields = seqan3::fields<seqan3::field::seq, seqan3::field::id, seqan3::field::qual>;
// This is needed for EXPECT_RANGE_EQ:
namespace seqan3
{
// TODO: This is only for the test. We might need to consider adding enumeration_names for the io fields to the library.
template <typename char_t>
inline debug_stream_type<char_t> & operator<<(debug_stream_type<char_t> & stream, field f)
{
stream << "<field: " << static_cast<size_t>(f) << ">";
return stream;
}
} // namespace seqan3
// ----------------------------------------------------------------------------
// fields
// ----------------------------------------------------------------------------
TEST(fields, usage)
{
std::array comp{seqan3::field::seq, seqan3::field::id, seqan3::field::qual};
EXPECT_RANGE_EQ(default_fields::as_array, comp);
EXPECT_EQ(default_fields::size, 3ul);
EXPECT_TRUE(default_fields::contains(seqan3::field::seq));
EXPECT_TRUE(default_fields::contains(seqan3::field::id));
EXPECT_TRUE(default_fields::contains(seqan3::field::qual));
EXPECT_FALSE(default_fields::contains(seqan3::field::user_defined_0));
EXPECT_EQ(default_fields::index_of(seqan3::field::seq), 0ul);
EXPECT_EQ(default_fields::index_of(seqan3::field::id), 1ul);
EXPECT_EQ(default_fields::index_of(seqan3::field::qual), 2ul);
EXPECT_EQ(default_fields::index_of(seqan3::field::user_defined_0), default_fields::npos);
}
// ----------------------------------------------------------------------------
// record
// ----------------------------------------------------------------------------
struct record : public ::testing::Test
{
using types = seqan3::type_list<std::string, seqan3::dna4_vector>;
using types_as_ids = seqan3::fields<seqan3::field::id, seqan3::field::seq>;
using record_type = seqan3::record<types, types_as_ids>;
};
TEST_F(record, definition_tuple_traits)
{
EXPECT_TRUE((std::is_same_v<typename record_type::base_type, std::tuple<std::string, seqan3::dna4_vector>>));
EXPECT_TRUE((std::is_same_v<std::tuple_element_t<0, record_type>, std::string>));
EXPECT_TRUE((std::is_same_v<std::tuple_element_t<1, record_type>, seqan3::dna4_vector>));
EXPECT_EQ(std::tuple_size_v<record_type>, 2ul);
EXPECT_TRUE(seqan3::tuple_like<record_type>);
}
TEST_F(record, construction)
{
[[maybe_unused]] record_type r{"MY ID", "ACGT"_dna4};
}
TEST_F(record, get_by_index)
{
record_type r{"MY ID", "ACGT"_dna4};
EXPECT_EQ(std::get<0>(r), "MY ID");
EXPECT_RANGE_EQ(std::get<1>(r), "ACGT"_dna4);
}
TEST_F(record, get_by_type)
{
record_type r{"MY ID", "ACGT"_dna4};
EXPECT_EQ(std::get<std::string>(r), "MY ID");
EXPECT_RANGE_EQ(std::get<seqan3::dna4_vector>(r), "ACGT"_dna4);
}
|
