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
|
// ==========================================================================
// SeqAn - The Library for Sequence Analysis
// ==========================================================================
// Copyright (c) 2006-2026, Knut Reinert, FU Berlin
// All rights reserved.
//
// Redistribution and use in source and binary forms, with or without
// modification, are permitted provided that the following conditions are met:
//
// * Redistributions of source code must retain the above copyright
// notice, this list of conditions and the following disclaimer.
// * Redistributions in binary form must reproduce the above copyright
// notice, this list of conditions and the following disclaimer in the
// documentation and/or other materials provided with the distribution.
// * Neither the name of Knut Reinert or the FU Berlin nor the names of
// its contributors may be used to endorse or promote products derived
// from this software without specific prior written permission.
//
// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE
// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
// DAMAGE.
//
// ==========================================================================
// Author: Rene Rahn <rene.rahn@fu-berlin.de>
// ==========================================================================
#include <seqan/align_parallel.h>
namespace test_align_parallel
{
struct IntermediateTraits_
{
using TScoreValue = int;
using THostPosition = size_t;
};
} // namespace test_align_parallel
SEQAN_DEFINE_TEST(test_align_parallel_intermediate_dp_result_construct)
{
using namespace seqan2;
using TIntermediate = WavefrontAlignmentResult<test_align_parallel::IntermediateTraits_>;
SEQAN_ASSERT(std::is_default_constructible<TIntermediate>::value);
SEQAN_ASSERT(std::is_copy_constructible<TIntermediate>::value);
SEQAN_ASSERT(std::is_move_constructible<TIntermediate>::value);
SEQAN_ASSERT(std::is_copy_assignable<TIntermediate>::value);
SEQAN_ASSERT(std::is_move_assignable<TIntermediate>::value);
{
TIntermediate interim;
SEQAN_ASSERT_EQ(interim._maxState.first, std::numeric_limits<int>::min());
SEQAN_ASSERT_EQ(interim._maxState.second, 0u);
SEQAN_ASSERT_EQ(interim._tileCol, 0u);
SEQAN_ASSERT_EQ(interim._tileRow, 0u);
}
{
TIntermediate interim{{10, 3u}};
SEQAN_ASSERT_EQ(interim._maxState.first, 10);
SEQAN_ASSERT_EQ(interim._maxState.second, 3u);
SEQAN_ASSERT_EQ(interim._tileCol, 0u);
SEQAN_ASSERT_EQ(interim._tileRow, 0u);
}
{
TIntermediate interim{{10, 3u}, 2u, 4u};
SEQAN_ASSERT_EQ(interim._maxState.first, 10);
SEQAN_ASSERT_EQ(interim._maxState.second, 3u);
SEQAN_ASSERT_EQ(interim._tileCol, 2u);
SEQAN_ASSERT_EQ(interim._tileRow, 4u);
}
}
SEQAN_DEFINE_TEST(test_align_parallel_intermediate_dp_result_update_max)
{
using namespace seqan2;
using TIntermediate = WavefrontAlignmentResult<test_align_parallel::IntermediateTraits_>;
using TState = typename TIntermediate::TState;
TIntermediate interim{{10, 3u}, 2, 4};
updateMax(interim, TState{9, 7u}, 3, 5);
SEQAN_ASSERT_EQ(interim._maxState.first, 10);
SEQAN_ASSERT_EQ(interim._maxState.second, 3u);
SEQAN_ASSERT_EQ(interim._tileCol, 2u);
SEQAN_ASSERT_EQ(interim._tileRow, 4u);
updateMax(interim, TState{11, 7u}, 3, 5);
SEQAN_ASSERT_EQ(interim._maxState.first, 11);
SEQAN_ASSERT_EQ(interim._maxState.second, 7u);
SEQAN_ASSERT_EQ(interim._tileCol, 3u);
SEQAN_ASSERT_EQ(interim._tileRow, 5u);
}
SEQAN_DEFINE_TEST(test_align_parallel_intermediate_dp_result_clear)
{
using namespace seqan2;
using TIntermediate = WavefrontAlignmentResult<test_align_parallel::IntermediateTraits_>;
{
TIntermediate interim{{10, 3u}, 2, 4};
clear(interim);
SEQAN_ASSERT_EQ(interim._maxState.first, std::numeric_limits<int>::min());
SEQAN_ASSERT_EQ(interim._maxState.second, 0u);
SEQAN_ASSERT_EQ(interim._tileCol, 0u);
SEQAN_ASSERT_EQ(interim._tileRow, 0u);
}
}
|
