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
|
// ==========================================================================
// 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: Enrico Siragusa <enrico.siragusa@fu-berlin.de>
// ==========================================================================
#ifndef SEQAN_FIND_LAMBDA_H
#define SEQAN_FIND_LAMBDA_H
namespace seqan2 {
// ============================================================================
// Metafunctions
// ============================================================================
// ----------------------------------------------------------------------------
// Metafunction DefaultFind<>
// ----------------------------------------------------------------------------
template <typename TText, typename TPattern>
struct DefaultFind
{
typedef void Type;
};
// ----------------------------------------------------------------------------
// Metafunction FindState_<>
// ----------------------------------------------------------------------------
template <typename TText, typename TPattern, typename TAlgorithm>
struct FindState_
{
typedef Nothing Type;
};
// ----------------------------------------------------------------------------
// Metafunction HasStatesPool_<>
// ----------------------------------------------------------------------------
template <typename TState, typename TThreading>
struct HasStatesPool_
{
typedef typename IsSameType<TThreading, Parallel>::Type IsParallel;
typedef typename Not<IsSameType<TState, Nothing> >::Type IsStateful;
typedef typename And<IsParallel, IsStateful>::Type Type;
};
// ----------------------------------------------------------------------------
// Metafunction StatesPool_<>
// ----------------------------------------------------------------------------
template <typename TState, typename TThreading>
struct StatesPool_
{
typedef typename HasStatesPool_<TState, TThreading>::Type HasStatesPool;
typedef typename If<HasStatesPool, String<TState>, TState>::Type Type;
};
// ============================================================================
// Classes
// ============================================================================
// ----------------------------------------------------------------------------
// Class FindDelegator_
// ----------------------------------------------------------------------------
template <typename TDelegate, typename TNeedlesIt>
struct FindDelegator_
{
TDelegate & delegate;
TNeedlesIt & needlesIt;
FindDelegator_(TDelegate & delegate, TNeedlesIt & needlesIt) :
delegate(delegate),
needlesIt(needlesIt)
{}
template <typename TTextIt, typename TScore>
void operator()(TTextIt & textIt, TScore score)
{
delegate(textIt, needlesIt, score);
}
};
// ============================================================================
// Functions
// ============================================================================
// ----------------------------------------------------------------------------
// Function find(text, pattern, errors, [](...){}, Algorithm());
// ----------------------------------------------------------------------------
template <typename TText, typename TPattern, typename TThreshold, typename TDelegate, typename TAlgorithm>
inline void find(TText & text, TPattern const & pattern, TThreshold threshold, TDelegate && delegate, TAlgorithm)
{
typedef typename FindState_<TText, TPattern const, TAlgorithm>::Type TState;
TState state;
_findStateInit(state, text, pattern, threshold, TAlgorithm());
_findImpl(state, text, pattern, threshold, delegate, TAlgorithm());
}
// ----------------------------------------------------------------------------
// Function find(text, pattern, [](...){});
// ----------------------------------------------------------------------------
template <typename TText, typename TPattern, typename TDelegate>
inline void find(TText & text, TPattern const & pattern, TDelegate && delegate)
{
typedef typename DefaultFind<TText, TPattern const>::Type TAlgorithm;
find(text, pattern, unsigned(), delegate, TAlgorithm());
}
// ----------------------------------------------------------------------------
// Function _findStateInit()
// ----------------------------------------------------------------------------
// Stateless algorithm.
template <typename TState, typename TText, typename TPattern, typename TThreshold, typename TAlgorithm>
inline void
_findStateInit(TState & /* s */, TText const & /* t */, TPattern const & /* p */, TThreshold /* t */, TAlgorithm) {}
// ----------------------------------------------------------------------------
// Function _findStatesPoolInit()
// ----------------------------------------------------------------------------
template <typename TState>
inline void _findStatesPoolInit(TState & /* pool */, False) {}
template <typename TStates>
inline void _findStatesPoolInit(TStates & pool, True)
{
resize(pool, omp_get_num_threads(), Exact());
}
// ----------------------------------------------------------------------------
// Function _findPickState()
// ----------------------------------------------------------------------------
template <typename TState>
inline TState &
_findPickState(TState & state, False)
{
return state;
}
template <typename TStates>
inline typename Value<TStates>::Type &
_findPickState(TStates & pool, True)
{
return pool[omp_get_thread_num()];
}
// ----------------------------------------------------------------------------
// Function find(text, needles, errors, [](...){}, Algorithm(), Parallel());
// ----------------------------------------------------------------------------
template <typename TText, typename TNeedle_, typename TSSetSpec,
typename TThreshold, typename TDelegate, typename TAlgorithm, typename TThreading>
inline void find(TText & text,
StringSet<TNeedle_, TSSetSpec> const & needles,
TThreshold threshold,
TDelegate && delegate,
TAlgorithm,
TThreading)
{
typedef StringSet<TNeedle_, TSSetSpec> const TNeedles;
typedef typename Value<TNeedles>::Type TNeedle;
typedef typename Iterator<TNeedles, Rooted>::Type TNeedlesIt;
typedef typename Reference<TNeedlesIt>::Type TNeedleRef;
typedef typename FindState_<TText, TNeedle, TAlgorithm>::Type TState;
typedef typename StatesPool_<TState, TThreading>::Type TStatesPool;
typedef typename HasStatesPool_<TState, TThreading>::Type HasStatesPool;
typedef FindDelegator_<TDelegate, TNeedlesIt const> TDelegator;
TStatesPool pool;
_findStatesPoolInit(pool, HasStatesPool());
iterate(needles, [&](TNeedlesIt const & needlesIt)
{
TState & state = _findPickState(pool, HasStatesPool());
TNeedleRef needle = value(needlesIt);
TDelegator delegator(delegate, needlesIt);
_findStateInit(state, text, needle, threshold, TAlgorithm());
_findImpl(state, text, needle, threshold, delegator, TAlgorithm());
},
Rooted(), TThreading());
}
// ----------------------------------------------------------------------------
// Function find(text, needles, errors, [](...){}, Algorithm());
// ----------------------------------------------------------------------------
template <typename TText, typename TNeedle, typename TSSetSpec,
typename TThreshold, typename TDelegate, typename TAlgorithm>
inline void find(TText & text,
StringSet<TNeedle, TSSetSpec> const & needles,
TThreshold threshold,
TDelegate && delegate,
TAlgorithm)
{
find(text, needles, threshold, delegate, TAlgorithm(), Serial());
}
}
#endif // #ifndef SEQAN_FIND_LAMBDA_H
|
