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
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
|
// -----------------------------------------------------------------------------------------------------
// 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 <range/v3/range_traits.hpp>
#include <seqan3/alphabet/nucleotide/dna4.hpp>
#include <seqan3/range/container/bitcompressed_vector.hpp>
#include <seqan3/range/container/concatenated_sequences.hpp>
#include <seqan3/test/cereal.hpp>
#include <seqan3/test/expect_range_eq.hpp>
#include <seqan3/test/pretty_printing.hpp>
using seqan3::operator""_dna4;
template <typename T>
class container_of_container : public ::testing::Test
{};
using container_of_container_types =
::testing::Types<std::vector<std::vector<seqan3::dna4>>,
seqan3::concatenated_sequences<std::vector<seqan3::dna4>>,
seqan3::concatenated_sequences<seqan3::bitcompressed_vector<seqan3::dna4>>>;
TYPED_TEST_SUITE(container_of_container, container_of_container_types, );
TYPED_TEST(container_of_container, concepts)
{
EXPECT_TRUE(seqan3::container<TypeParam>);
EXPECT_TRUE(seqan3::container<std::ranges::range_value_t<TypeParam>>);
}
TYPED_TEST(container_of_container, construction)
{
TypeParam t1;
TypeParam t2{};
EXPECT_EQ(t1, t2);
// initializer list
TypeParam t3{"ACGT"_dna4, "ACGT"_dna4, "GAGGA"_dna4};
TypeParam t4 = {"ACGT"_dna4, "ACGT"_dna4, "GAGGA"_dna4};
EXPECT_EQ(t3, t4);
// n * value
TypeParam t5{2, "ACGT"_dna4};
// from another TypeParam's sub-range
TypeParam t6{t3.begin(), t3.begin() + 2};
EXPECT_EQ(t5, t6);
std::vector<std::vector<seqan3::dna4>> other_vector{"ACGT"_dna4, "ACGT"_dna4, "GAGGA"_dna4};
// direct from another container-of-container
TypeParam t7{other_vector};
// from another container-of-container's sub-range
TypeParam t8{other_vector.cbegin(), other_vector.cend()};
EXPECT_EQ(t3, t7);
EXPECT_EQ(t7, t8);
}
TYPED_TEST(container_of_container, assign)
{
TypeParam t1{"ACGT"_dna4, "ACGT"_dna4, "GAGGA"_dna4};
TypeParam t2{"ACGT"_dna4, "ACGT"_dna4};
std::vector<std::vector<seqan3::dna4>> other_vector{"ACGT"_dna4, "ACGT"_dna4, "GAGGA"_dna4};
// n * value
TypeParam t3;
t3.assign(2, "ACGT"_dna4);
EXPECT_EQ(t3, t2);
// from another container-of-container's sub-range
TypeParam t4;
t4.assign(other_vector.cbegin(), other_vector.cend());
EXPECT_EQ(t4, t1);
// initializer list
TypeParam t5, t6;
t5.assign({"ACGT"_dna4, "ACGT"_dna4, "GAGGA"_dna4});
t6 = {"ACGT"_dna4, "ACGT"_dna4, "GAGGA"_dna4};
EXPECT_EQ(t5, t1);
EXPECT_EQ(t6, t1);
// direct from another container-of-container
if constexpr (std::is_same_v<TypeParam, seqan3::concatenated_sequences<std::vector<seqan3::dna4>>>)
{
TypeParam t7, t8;
t7.assign(other_vector);
t8 = other_vector;
EXPECT_EQ(t7, t1);
EXPECT_EQ(t8, t1);
}
}
TYPED_TEST(container_of_container, iterators)
{
TypeParam t1{"ACGT"_dna4, "ACGT"_dna4, "GAGGA"_dna4};
TypeParam const t2{"ACGT"_dna4, "ACGT"_dna4, "GAGGA"_dna4};
// begin
EXPECT_RANGE_EQ(*t1.begin(), "ACGT"_dna4);
EXPECT_RANGE_EQ(*t1.cbegin(), "ACGT"_dna4);
EXPECT_RANGE_EQ(*t2.begin(), "ACGT"_dna4);
EXPECT_RANGE_EQ(*t2.cbegin(), "ACGT"_dna4);
// end and arithmetic
EXPECT_RANGE_EQ(*(t1.end() - 1), "GAGGA"_dna4);
EXPECT_RANGE_EQ(*(t1.cend() - 1), "GAGGA"_dna4);
EXPECT_RANGE_EQ(*(t2.end() - 1), "GAGGA"_dna4);
EXPECT_RANGE_EQ(*(t2.cend() - 1), "GAGGA"_dna4);
// convertibility between const and non-const
EXPECT_TRUE(t1.cend() == t1.end());
// writability
(*t1.begin())[0] = 'T'_dna4;
EXPECT_RANGE_EQ(*t1.begin(), "TCGT"_dna4);
}
TYPED_TEST(container_of_container, element_access)
{
TypeParam t1{"ACGT"_dna4, "ACGT"_dna4, "GAGGA"_dna4};
TypeParam const t2{"ACGT"_dna4, "ACGT"_dna4, "GAGGA"_dna4};
// at
EXPECT_RANGE_EQ(t1.at(0), "ACGT"_dna4);
EXPECT_RANGE_EQ(t2.at(0), "ACGT"_dna4);
//TODO once we have throwing assert, check at's ability to throw
// []
EXPECT_RANGE_EQ(t1[0], "ACGT"_dna4);
EXPECT_RANGE_EQ(t2[0], "ACGT"_dna4);
// front
EXPECT_RANGE_EQ(t1.front(), "ACGT"_dna4);
EXPECT_RANGE_EQ(t2.front(), "ACGT"_dna4);
// back
EXPECT_RANGE_EQ(t1.back(), "GAGGA"_dna4);
EXPECT_RANGE_EQ(t2.back(), "GAGGA"_dna4);
if constexpr (std::is_same_v<TypeParam, seqan3::concatenated_sequences<std::vector<seqan3::dna4>>>)
{
using size_type = typename TypeParam::size_type;
// concat
EXPECT_RANGE_EQ(t1.concat(), "ACGTACGTGAGGA"_dna4);
EXPECT_RANGE_EQ(t2.concat(), "ACGTACGTGAGGA"_dna4);
// data
EXPECT_EQ(std::get<0>(t1.raw_data()), "ACGTACGTGAGGA"_dna4);
EXPECT_EQ(std::get<0>(t2.raw_data()), "ACGTACGTGAGGA"_dna4);
EXPECT_EQ(std::get<1>(t1.raw_data()), (std::vector<size_type>{0, 4, 8, 13}));
EXPECT_EQ(std::get<1>(t2.raw_data()), (std::vector<size_type>{0, 4, 8, 13}));
}
}
TYPED_TEST(container_of_container, capacity)
{
TypeParam t0{};
TypeParam t1{"ACGT"_dna4, "ACGT"_dna4, "GAGGA"_dna4};
TypeParam const t2{"ACGT"_dna4, "ACGT"_dna4, "GAGGA"_dna4};
// empty
EXPECT_TRUE(t0.empty());
EXPECT_FALSE(t1.empty());
EXPECT_FALSE(t2.empty());
// size
EXPECT_EQ(t0.size(), 0u);
EXPECT_EQ(t1.size(), 3u);
EXPECT_EQ(t2.size(), 3u);
// max_size
EXPECT_GT(t0.max_size(), 1'000'000'000'000u);
EXPECT_GT(t1.max_size(), 1'000'000'000'000u);
EXPECT_GT(t2.max_size(), 1'000'000'000'000u);
// capacity
EXPECT_GE(t0.capacity(), t0.size());
EXPECT_GE(t1.capacity(), t1.size());
EXPECT_GE(t2.capacity(), t2.size());
// reserve
EXPECT_LT(t0.capacity(), 1000u);
t0.reserve(1000);
EXPECT_GE(t0.capacity(), 1000u);
// shrink_to_fit
t1.reserve(1000);
EXPECT_GT(t1.capacity(), t1.size()*2);
t1.shrink_to_fit();
EXPECT_LE(t1.capacity(), t1.size()*2);
if constexpr (std::is_same_v<TypeParam, seqan3::concatenated_sequences<std::vector<seqan3::dna4>>>)
{
// size
EXPECT_EQ(t0.concat_size(), 0u);
EXPECT_EQ(t1.concat_size(), 13u);
EXPECT_EQ(t2.concat_size(), 13u);
// capacity
EXPECT_GE(t0.concat_capacity(), t0.concat_size());
EXPECT_GE(t1.concat_capacity(), t1.concat_size());
EXPECT_GE(t2.concat_capacity(), t2.concat_size());
// reserve
EXPECT_LT(t0.concat_capacity(), 1000u);
t0.concat_reserve(1000);
EXPECT_GE(t0.concat_capacity(), 1000u);
}
}
TYPED_TEST(container_of_container, clear)
{
TypeParam t0{};
TypeParam t1{"ACGT"_dna4, "ACGT"_dna4, "GAGGA"_dna4};
t1.clear();
EXPECT_EQ(t0, t1);
}
TYPED_TEST(container_of_container, insert)
{
TypeParam t0{};
TypeParam t1{"ACGT"_dna4, "ACGT"_dna4, "GAGGA"_dna4};
// position, value
t0.insert(t0.cend(), "ACGT"_dna4);
t0.insert(t0.cend(), "GAGGA"_dna4);
t0.insert(t0.cbegin() + 1, "ACGT"_dna4);
EXPECT_EQ(t0, t1);
// position, n times values
t0.clear();
t1 = {"GAGGA"_dna4, "ACGT"_dna4, "ACGT"_dna4, "GAGGA"_dna4};
t0.insert(t0.cend(), 2, "ACGT"_dna4);
t0.insert(t0.cend(), 1, "GAGGA"_dna4);
t0.insert(t0.cbegin(), 1, "GAGGA"_dna4);
EXPECT_EQ(t0, t1);
// iterator pair
t0.clear();
t1 = {"GAGGA"_dna4, "ACGT"_dna4, "ACGT"_dna4, "GAGGA"_dna4};
t0.insert(t0.cend(), t1.begin() + 1, t1.begin() + 3);
// remove the following after range-v3 is updated to 1.0
#pragma GCC diagnostic push
#pragma GCC diagnostic ignored "-Wdeprecated-declarations"
t0.insert(t0.cend(), t1.cend() - 1, t1.cend());
#pragma GCC diagnostic pop
t0.insert(t0.cbegin(), t1.cend() - 1, t1.cend());
EXPECT_EQ(t0, t1);
// initializer list
t0.clear();
t1 = {"ACGT"_dna4, "ACGT"_dna4, "GAGGA"_dna4};
t0.insert(t0.cend(), {"ACGT"_dna4, "GAGGA"_dna4});
t0.insert(t0.cbegin() + 1, "ACGT"_dna4);
EXPECT_EQ(t0, t1);
}
TYPED_TEST(container_of_container, erase)
{
TypeParam t1{"ACGT"_dna4, "ACGT"_dna4, "GAGGA"_dna4};
// one element
t1.erase(t1.begin());
EXPECT_EQ(t1, (TypeParam{"ACGT"_dna4, "GAGGA"_dna4}));
// range
t1 = {"GAGGA"_dna4, "ACGT"_dna4, "ACGT"_dna4, "GAGGA"_dna4};
t1.erase(t1.begin() + 1, t1.begin() + 3);
EXPECT_EQ(t1, (TypeParam{"GAGGA"_dna4, "GAGGA"_dna4}));
}
TYPED_TEST(container_of_container, push_pop)
{
TypeParam t0{};
// push_back
t0.push_back("ACGT"_dna4);
EXPECT_EQ(t0, (TypeParam{"ACGT"_dna4}));
t0.push_back("GAGGA"_dna4);
EXPECT_EQ(t0, (TypeParam{"ACGT"_dna4, "GAGGA"_dna4}));
// pop_back
t0.pop_back();
EXPECT_EQ(t0, (TypeParam{"ACGT"_dna4}));
t0.pop_back();
EXPECT_EQ(t0, TypeParam{});
}
TYPED_TEST(container_of_container, resize)
{
TypeParam t0{};
// enlarge without values
t0.resize(3);
EXPECT_EQ(t0,( TypeParam{{}, {}, {}}));
// enlarge with value
t0.resize(5, "ACGT"_dna4);
EXPECT_EQ(t0, (TypeParam{{}, {}, {}, "ACGT"_dna4, "ACGT"_dna4}));
// shrink with value
t0.resize(4, "ACGT"_dna4);
EXPECT_EQ(t0, (TypeParam{{}, {}, {}, "ACGT"_dna4}));
// shrink without value
t0.resize(2);
EXPECT_EQ(t0, (TypeParam{{}, {}}));
}
TYPED_TEST(container_of_container, swap)
{
TypeParam t0{};
TypeParam t1{"ACGT"_dna4, "ACGT"_dna4, "GAGGA"_dna4};
t0.swap(t1);
EXPECT_EQ(t0, (TypeParam{"ACGT"_dna4, "ACGT"_dna4, "GAGGA"_dna4}));
EXPECT_EQ(t1, TypeParam{});
}
TYPED_TEST(container_of_container, serialisation)
{
TypeParam t1{"ACGT"_dna4, "ACGT"_dna4, "GAGGA"_dna4};
seqan3::test::do_serialisation(t1);
}
|
