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
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
|
// -----------------------------------------------------------------------------------------------------
// 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 <gtest/gtest.h>
#include <meta/meta.hpp>
#include <tuple>
#include <type_traits>
#include <utility>
#include <vector>
#include <seqan3/alignment/pairwise/alignment_result.hpp>
#include <seqan3/alphabet/gap/gapped.hpp>
#include <seqan3/alphabet/nucleotide/all.hpp>
#include <seqan3/core/type_traits/template_inspection.hpp>
#include <seqan3/range/views/persist.hpp>
#include <seqan3/range/views/to_char.hpp>
#include <seqan3/range/views/to.hpp>
using seqan3::operator""_dna4;
using seqan3::operator""_rna5;
using aligned_seq_type = std::vector<seqan3::gapped<seqan3::dna4>>;
template <typename T>
struct alignment_result_test : public ::testing::Test
{};
using alignment_result_test_types = ::testing::Types
<seqan3::detail::alignment_result_value_type<uint32_t, uint32_t, int32_t,
std::pair<size_t, size_t>, std::pair<size_t, size_t>,
std::pair<aligned_seq_type, aligned_seq_type>>,
seqan3::detail::alignment_result_value_type<uint32_t, uint32_t, int32_t,
std::pair<size_t, size_t>, std::pair<size_t, size_t>,
std::tuple<aligned_seq_type, aligned_seq_type>>,
seqan3::detail::alignment_result_value_type<uint32_t, uint32_t, int32_t,
std::pair<size_t, size_t>, std::pair<size_t, size_t>,
std::vector<aligned_seq_type>>,
seqan3::detail::alignment_result_value_type<uint32_t, uint32_t, float,
std::pair<size_t, size_t>, std::pair<size_t, size_t>,
std::pair<aligned_seq_type, aligned_seq_type>>,
seqan3::detail::alignment_result_value_type<uint32_t, uint32_t, float,
std::pair<size_t, size_t>, std::pair<size_t, size_t>,
std::tuple<aligned_seq_type, aligned_seq_type>>,
seqan3::detail::alignment_result_value_type<uint32_t, uint32_t, float,
std::pair<size_t, size_t>, std::pair<size_t, size_t>,
std::vector<aligned_seq_type>>>;
TYPED_TEST_SUITE(alignment_result_test, alignment_result_test_types, );
TYPED_TEST(alignment_result_test, type_specialisation)
{
EXPECT_TRUE((seqan3::detail::is_type_specialisation_of_v<TypeParam, seqan3::detail::alignment_result_value_type>));
}
TYPED_TEST(alignment_result_test, constructor)
{
EXPECT_TRUE((std::is_default_constructible_v<seqan3::alignment_result<TypeParam>>));
EXPECT_TRUE((std::is_copy_constructible_v<seqan3::alignment_result<TypeParam>>));
EXPECT_TRUE((std::is_move_constructible_v<seqan3::alignment_result<TypeParam>>));
EXPECT_TRUE((std::is_copy_assignable_v<seqan3::alignment_result<TypeParam>>));
EXPECT_TRUE((std::is_move_assignable_v<seqan3::alignment_result<TypeParam>>));
EXPECT_TRUE((std::is_destructible_v<seqan3::alignment_result<TypeParam>>));
}
TYPED_TEST(alignment_result_test, get_id)
{
using id1_t = decltype(std::declval<TypeParam>().sequence1_id);
using id2_t = decltype(std::declval<TypeParam>().sequence2_id);
aligned_seq_type seq{'A'_dna4, 'T'_dna4, seqan3::gap{}, 'C'_dna4, seqan3::gap{}, seqan3::gap{}, 'A'_dna4};
{
seqan3::alignment_result<TypeParam> tmp{TypeParam{1u, 2u, 0, {10ul, 10ul}, {0ul, 0ul}, {seq, seq}}};
EXPECT_TRUE((std::is_same_v<decltype(tmp.sequence1_id()), id1_t>));
EXPECT_TRUE((std::is_same_v<decltype(tmp.sequence2_id()), id2_t>));
EXPECT_TRUE((std::is_same_v<decltype(std::move(tmp).sequence1_id()), id1_t>));
EXPECT_TRUE((std::is_same_v<decltype(std::move(tmp).sequence2_id()), id2_t>));
EXPECT_EQ(tmp.sequence1_id(), 1u);
EXPECT_EQ(tmp.sequence2_id(), 2u);
}
{
seqan3::alignment_result<TypeParam> const tmp{TypeParam{1u, 2u, 0, {10ul, 10ul}, {0ul, 0ul}, {seq, seq}}};
EXPECT_EQ(tmp.sequence1_id(), 1u);
EXPECT_EQ(tmp.sequence2_id(), 2u);
EXPECT_TRUE((std::is_same_v<decltype(tmp.sequence1_id()), id1_t>));
EXPECT_TRUE((std::is_same_v<decltype(tmp.sequence2_id()), id2_t>));
EXPECT_TRUE((std::is_same_v<decltype(std::move(tmp).sequence1_id()), id1_t>));
EXPECT_TRUE((std::is_same_v<decltype(std::move(tmp).sequence2_id()), id2_t>));
}
}
TYPED_TEST(alignment_result_test, get_score)
{
using score_t = decltype(std::declval<TypeParam>().score);
aligned_seq_type seq{'A'_dna4, 'T'_dna4, seqan3::gap{}, 'C'_dna4, seqan3::gap{}, seqan3::gap{}, 'A'_dna4};
{
seqan3::alignment_result<TypeParam> tmp{TypeParam{1u, 2u, 0, {10ul, 10ul}, {0ul, 0ul}, {seq, seq}}};
EXPECT_EQ(tmp.score(), 0);
EXPECT_TRUE((std::is_same_v<decltype(tmp.score()), score_t>));
EXPECT_TRUE((std::is_same_v<decltype(std::move(tmp).score()), score_t>));
}
{
seqan3::alignment_result<TypeParam> const tmp{TypeParam{1u, 2u, 0, {10ul, 10ul}, {0ul, 0ul}, {seq, seq}}};
EXPECT_EQ(tmp.score(), 0);
EXPECT_TRUE((std::is_same_v<decltype(tmp.score()), score_t>));
EXPECT_TRUE((std::is_same_v<decltype(std::move(tmp).score()), score_t>));
}
}
TYPED_TEST(alignment_result_test, end_positions)
{
aligned_seq_type seq{'A'_dna4, 'T'_dna4, seqan3::gap{}, 'C'_dna4, seqan3::gap{}, seqan3::gap{}, 'A'_dna4};
{
seqan3::alignment_result<TypeParam> tmp{TypeParam{1u, 2u, 0, {10ul, 10ul}, {0ul, 0ul}, {seq, seq}}};
EXPECT_EQ(tmp.sequence1_end_position(), 10ul);
EXPECT_EQ(tmp.sequence2_end_position(), 10ul);
EXPECT_TRUE((std::is_same_v<decltype(tmp.sequence1_end_position()), size_t>));
EXPECT_TRUE((std::is_same_v<decltype(tmp.sequence2_end_position()), size_t>));
EXPECT_TRUE((std::is_same_v<decltype(std::move(tmp).sequence1_end_position()), size_t>));
EXPECT_TRUE((std::is_same_v<decltype(std::move(tmp).sequence2_end_position()), size_t>));
}
{
seqan3::alignment_result<TypeParam> const tmp{TypeParam{1u, 2u, 0, {10ul, 10ul}, {0ul, 0ul}, {seq, seq}}};
EXPECT_EQ(tmp.sequence1_end_position(), 10ul);
EXPECT_EQ(tmp.sequence2_end_position(), 10ul);
EXPECT_TRUE((std::is_same_v<decltype(tmp.sequence1_end_position()), size_t>));
EXPECT_TRUE((std::is_same_v<decltype(tmp.sequence2_end_position()), size_t>));
EXPECT_TRUE((std::is_same_v<decltype(std::move(tmp).sequence1_end_position()), size_t>));
EXPECT_TRUE((std::is_same_v<decltype(std::move(tmp).sequence2_end_position()), size_t>));
}
}
TYPED_TEST(alignment_result_test, begin_positions)
{
aligned_seq_type seq{'A'_dna4, 'T'_dna4, seqan3::gap{}, 'C'_dna4, seqan3::gap{}, seqan3::gap{}, 'A'_dna4};
{
seqan3::alignment_result<TypeParam> tmp{TypeParam{1u, 2u, 0, {10ul, 10ul}, {0ul, 0ul}, {seq, seq}}};
EXPECT_EQ(tmp.sequence1_begin_position(), 0ul);
EXPECT_EQ(tmp.sequence2_begin_position(), 0ul);
EXPECT_TRUE((std::is_same_v<decltype(tmp.sequence1_begin_position()), size_t>));
EXPECT_TRUE((std::is_same_v<decltype(tmp.sequence2_begin_position()), size_t>));
EXPECT_TRUE((std::is_same_v<decltype(std::move(tmp).sequence1_begin_position()), size_t>));
EXPECT_TRUE((std::is_same_v<decltype(std::move(tmp).sequence2_begin_position()), size_t>));
}
{
seqan3::alignment_result<TypeParam> const tmp{TypeParam{1u, 2u, 0, {10ul, 10ul}, {0ul, 0ul}, {seq, seq}}};
EXPECT_EQ(tmp.sequence1_begin_position(), 0ul);
EXPECT_EQ(tmp.sequence2_begin_position(), 0ul);
EXPECT_TRUE((std::is_same_v<decltype(tmp.sequence1_begin_position()), size_t>));
EXPECT_TRUE((std::is_same_v<decltype(tmp.sequence2_begin_position()), size_t>));
EXPECT_TRUE((std::is_same_v<decltype(std::move(tmp).sequence1_begin_position()), size_t>));
EXPECT_TRUE((std::is_same_v<decltype(std::move(tmp).sequence2_begin_position()), size_t>));
}
}
TYPED_TEST(alignment_result_test, alignment)
{
using alignment_t = decltype(std::declval<TypeParam>().alignment);
aligned_seq_type seq{'A'_dna4, 'T'_dna4, seqan3::gap{}, 'C'_dna4, seqan3::gap{}, seqan3::gap{}, 'A'_dna4};
{
seqan3::alignment_result<TypeParam> tmp{TypeParam{1u, 2u, 0, {10ul, 10ul}, {0ul, 0ul}, {seq, seq}}};
EXPECT_EQ(tmp.alignment(), (alignment_t{seq, seq}));
EXPECT_TRUE((std::is_same_v<decltype(tmp.alignment()), alignment_t const &>));
EXPECT_TRUE((std::is_same_v<decltype(std::move(tmp).alignment()), alignment_t const &>));
}
{
seqan3::alignment_result<TypeParam> const tmp{TypeParam{1u, 2u, 0, {10ul, 10ul}, {0ul, 0ul}, {seq, seq}}};
EXPECT_EQ(tmp.alignment(), (alignment_t{seq, seq}));
EXPECT_TRUE((std::is_same_v<decltype(tmp.alignment()), alignment_t const &>));
EXPECT_TRUE((std::is_same_v<decltype(std::move(tmp).alignment()), alignment_t const &>));
}
if constexpr (seqan3::tuple_like<alignment_t>)
{
seqan3::alignment_result<TypeParam> tmp{TypeParam{1u, 2u, 0, {10ul, 10ul}, {0ul, 0ul}, {seq, seq}}};
EXPECT_EQ(std::get<0>(tmp.alignment()) | seqan3::views::persist
| seqan3::views::to_char
| seqan3::views::to<std::string>,
std::string{"AT-C--A"});
EXPECT_EQ(std::get<1>(tmp.alignment()) | seqan3::views::persist
| seqan3::views::to_char
| seqan3::views::to<std::string>,
std::string{"AT-C--A"});
}
else
{
seqan3::alignment_result<TypeParam> tmp{TypeParam{1u, 2u, 0, {10ul, 10ul}, {0ul, 0ul}, {seq, seq}}};
EXPECT_EQ(tmp.alignment()[0] | seqan3::views::persist | seqan3::views::to_char | seqan3::views::to<std::string>,
"AT-C--A");
EXPECT_EQ(tmp.alignment()[1] | seqan3::views::persist | seqan3::views::to_char | seqan3::views::to<std::string>,
"AT-C--A");
}
}
TEST(alignment_result_test, reduced_type)
{
{
seqan3::detail::alignment_result_value_type tr{2u, 4u, 5};
seqan3::alignment_result tmp(tr);
EXPECT_EQ(tmp.sequence1_id(), 2u);
EXPECT_EQ(tmp.sequence2_id(), 4u);
EXPECT_EQ(tmp.score(), 5);
}
{
seqan3::detail::alignment_result_value_type tr{2, 4u, 5.0f, std::pair<int, int>{1, -1}};
seqan3::alignment_result tmp(tr);
EXPECT_EQ(tmp.sequence1_id(), 2);
EXPECT_EQ(tmp.sequence2_id(), 4u);
EXPECT_FLOAT_EQ(tmp.score(), 5.0f);
EXPECT_EQ((tmp.sequence1_end_position()), 1);
EXPECT_EQ((tmp.sequence2_end_position()), -1);
}
{
seqan3::detail::alignment_result_value_type tr{2,
4u,
5.0f,
std::pair<int, int>{1, -1},
std::pair<int, int>{10, -10}};
seqan3::alignment_result tmp(tr);
EXPECT_EQ(tmp.sequence1_id(), 2);
EXPECT_EQ(tmp.sequence2_id(), 4u);
EXPECT_FLOAT_EQ(tmp.score(), 5.0f);
EXPECT_EQ((tmp.sequence1_end_position()), 1);
EXPECT_EQ((tmp.sequence2_end_position()), -1);
EXPECT_EQ((tmp.sequence1_begin_position()), 10);
EXPECT_EQ((tmp.sequence2_begin_position()), -10);
}
}
TEST(alignment_result_test, type_deduction)
{
{
using coord_t = std::pair<int, int>;
std::vector<seqan3::gapped<seqan3::rna5>> seq{'A'_rna5,
'U'_rna5,
seqan3::gap{},
'C'_rna5,
seqan3::gap{},
seqan3::gap{},
'A'_rna5};
seqan3::detail::alignment_result_value_type tr{2, 4, 5.0, coord_t{1, -1}, coord_t{10,-10}, seq};
seqan3::alignment_result tmp(tr);
EXPECT_TRUE((std::is_same_v<decltype(tmp.sequence1_id()), int>));
EXPECT_TRUE((std::is_same_v<decltype(tmp.sequence2_id()), int>));
EXPECT_TRUE((std::is_same_v<decltype(tmp.score()), double>));
EXPECT_TRUE((std::is_same_v<decltype(tmp.sequence1_end_position()), int>));
EXPECT_TRUE((std::is_same_v<decltype(tmp.sequence2_end_position()), int>));
EXPECT_TRUE((std::is_same_v<decltype(tmp.sequence1_begin_position()), int>));
EXPECT_TRUE((std::is_same_v<decltype(tmp.sequence2_begin_position()), int>));
EXPECT_TRUE((std::is_same_v<decltype(tmp.alignment()), std::vector<seqan3::gapped<seqan3::rna5>> const &>));
EXPECT_EQ(tmp.sequence1_id(), 2);
EXPECT_EQ(tmp.sequence2_id(), 4);
EXPECT_DOUBLE_EQ(tmp.score(), 5.0);
EXPECT_EQ((tmp.sequence1_end_position()), 1);
EXPECT_EQ((tmp.sequence2_end_position()), -1);
EXPECT_EQ((tmp.sequence1_begin_position()), 10);
EXPECT_EQ((tmp.sequence2_begin_position()), -10);
EXPECT_EQ(tmp.alignment(), seq);
}
{
using coord_t = std::pair<int, int>;
seqan3::detail::alignment_result_value_type tr{2, 4, 5.0, coord_t{1, -1}};
seqan3::alignment_result tmp(tr);
EXPECT_TRUE((std::is_same_v<decltype(tmp.sequence1_id()), int>));
EXPECT_TRUE((std::is_same_v<decltype(tmp.sequence2_id()), int>));
EXPECT_TRUE((std::is_same_v<decltype(tmp.score()), double>));
EXPECT_TRUE((std::is_same_v<decltype(tmp.sequence1_end_position()), int>));
EXPECT_TRUE((std::is_same_v<decltype(tmp.sequence2_end_position()), int>));
}
{
seqan3::detail::alignment_result_value_type tr{2, 3, 5.0};
seqan3::alignment_result tmp(tr);
EXPECT_TRUE((std::is_same_v<decltype(tmp.sequence1_id()), int>));
EXPECT_TRUE((std::is_same_v<decltype(tmp.sequence2_id()), int>));
EXPECT_TRUE((std::is_same_v<decltype(tmp.score()), double>));
}
}
TEST(alignment_result_test, empty_type)
{
seqan3::detail::alignment_result_value_type tr{};
seqan3::alignment_result tmp(tr);
// members must not be accessed
}
TEST(alignment_result_test, access_result_value_type)
{
seqan3::detail::alignment_result_value_type result_value{2u, 4u, 5};
seqan3::alignment_result result(result_value);
using result_value_t = typename seqan3::detail::alignment_result_value_type_accessor<decltype(result)>::type;
EXPECT_TRUE((std::same_as<result_value_t, decltype(result_value)>));
}
|
