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
|
// ==========================================================================
// SeqAn - The Library for Sequence Analysis
// ==========================================================================
// Copyright (c) 2006-2018, 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>
// ==========================================================================
#ifndef INCLUDE_SEQAN_ALIGN_PARALLEL_WAVEFRONT_ALIGNMENT_RESULT_H_
#define INCLUDE_SEQAN_ALIGN_PARALLEL_WAVEFRONT_ALIGNMENT_RESULT_H_
namespace seqan
{
// ============================================================================
// Forwards
// ============================================================================
// ============================================================================
// Tags, Classes, Enums
// ============================================================================
// The intermediate result stored by each thread independently.
// After an alignment has been finished, the intermediate results are reduced to a global result.
template <typename TTraits>
struct WavefrontAlignmentResult
{
// ----------------------------------------------------------------------------
// Member Types.
using TState = std::pair<typename TTraits::TScoreValue, typename TTraits::THostPosition>;
// ----------------------------------------------------------------------------
// Member Variables
TState _maxState{std::numeric_limits<typename TTraits::TScoreValue>::min(), typename TTraits::THostPosition{}};
size_t _tileCol{0};
size_t _tileRow{0};
//NOTE(rrahn) Bug in g++-4.9 prevents us from using as aggregate type.
// ----------------------------------------------------------------------------
// Constructors.
// Note: Although, this could be an aggregate type, the icpc-17 crashes,
// when compiling without the defaulted constructor.
WavefrontAlignmentResult() = default;
WavefrontAlignmentResult(TState const maxState) :
_maxState(std::move(maxState))
{}
WavefrontAlignmentResult(TState const maxState, size_t const tileCol, size_t const tileRow) :
_maxState(std::move(maxState)),
_tileCol(tileCol),
_tileRow(tileRow)
{}
// ----------------------------------------------------------------------------
// Member Functions.
};
// ============================================================================
// Metafunctions
// ============================================================================
// ============================================================================
// Functions
// ============================================================================
namespace impl
{
template <typename TIntermediate,
typename TState>
inline void
updateMax(TIntermediate & me,
TState const & state,
size_t const tileCol,
size_t const tileRow)
{
if (state.first > me._maxState.first)
{
me._maxState = state;
me._tileCol = tileCol;
me._tileRow = tileRow;
}
}
} // namespace impl
// Update the intermediate result if new optimum has been found.
template <typename ...TArgs>
inline void
updateMax(WavefrontAlignmentResult<TArgs...> & me,
typename WavefrontAlignmentResult<TArgs...>::TState const & state,
size_t const tileCol,
size_t const tileRow)
{
impl::updateMax(me, state, tileCol, tileRow);
}
template <typename ...TArgs>
inline void
updateMax(WavefrontAlignmentResult<TArgs...> & lhs,
WavefrontAlignmentResult<TArgs...> const & rhs)
{
impl::updateMax(lhs, rhs._maxState, rhs._tileCol, rhs._tileRow);
}
// Reset the intermediate result.
template <typename ...TArgs>
inline void
clear(WavefrontAlignmentResult<TArgs...> & me)
{
me = WavefrontAlignmentResult<TArgs...>{};
}
// Get the intermediate result.
template <typename ...TArgs>
inline typename WavefrontAlignmentResult<TArgs...>::TState const &
value(WavefrontAlignmentResult<TArgs...> const & me)
{
return me._maxState;
}
// Swap two intermediate results.
template <typename ...TArgs>
inline void
swap(WavefrontAlignmentResult<TArgs...> & lhs,
WavefrontAlignmentResult<TArgs...> & rhs)
{
// TODO (rrahn): report issue with Intel
WavefrontAlignmentResult<TArgs...> tmp = std::move(lhs);
lhs = std::move(rhs);
rhs = std::move(tmp);
}
} // namespace seqan
#endif // #ifndef INCLUDE_SEQAN_ALIGN_PARALLEL_WAVEFRONT_ALIGNMENT_RESULT_H_
|
