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
|
// ==========================================================================
// SeqAn - The Library for Sequence Analysis
// ==========================================================================
// Copyright (c) 2006-2026, Knut Reinert, FU Berlin
// Copyright (c) 2013 NVIDIA Corporation
// 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 NVIDIA Corporation 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 NVIDIA CORPORATION 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>
// ==========================================================================
// Some useful functors to be used along with the Finder class.
// ==========================================================================
#ifndef SEQAN_INDEX_FIND_FUNCTORS_H_
#define SEQAN_INDEX_FIND_FUNCTORS_H_
namespace seqan2 {
// ============================================================================
// Tags
// ============================================================================
// ----------------------------------------------------------------------------
// Tag Counts_
// ----------------------------------------------------------------------------
struct Counts_;
// ============================================================================
// Classes
// ============================================================================
// ----------------------------------------------------------------------------
// Class OccurrencesCounter_
// ----------------------------------------------------------------------------
template <typename TIndex, typename TSpec = typename ExecSpec<TIndex>::Type>
struct OccurrencesCounter_
{
typename Member<OccurrencesCounter_, Counts_>::Type counts;
OccurrencesCounter_() {}
template <typename TPattern>
OccurrencesCounter_(TPattern const & pattern)
{
_init(*this, pattern);
}
template <typename TFinder>
inline void
operator() (TFinder const & finder)
{
counts[getThreadId()] += countOccurrences(_textIterator(finder));
}
};
// ----------------------------------------------------------------------------
// Member Counts_; Count
// ----------------------------------------------------------------------------
template <typename TIndex, typename TSpec>
struct Member<OccurrencesCounter_<TIndex, TSpec>, Counts_>
{
typedef String<typename Size<TIndex>::Type> Type;
};
template <typename TIndex, typename TSpec>
struct Member<OccurrencesCounter_<TIndex, View<Device<TSpec> > >, Counts_>
{
typedef typename View<typename Member<OccurrencesCounter_<TIndex, Device<TSpec> >, Counts_>::Type>::Type Type;
};
// ----------------------------------------------------------------------------
// Metafunction View
// ----------------------------------------------------------------------------
template <typename TIndex, typename TSpec>
struct View<OccurrencesCounter_<TIndex, TSpec> >
{
typedef OccurrencesCounter_<TIndex, View<TSpec> > Type;
};
// ----------------------------------------------------------------------------
// Metafunction Device
// ----------------------------------------------------------------------------
template <typename TIndex, typename TSpec>
struct Device<OccurrencesCounter_<TIndex, TSpec> >
{
typedef OccurrencesCounter_<TIndex, Device<TSpec> > Type;
};
// ============================================================================
// Functions
// ============================================================================
// ----------------------------------------------------------------------------
// Function _init()
// ----------------------------------------------------------------------------
template <typename TIndex, typename TSpec, typename TPattern>
inline void
_init(OccurrencesCounter_<TIndex, TSpec> & counter, TPattern const & /* pattern */)
{
resize(counter.counts, omp_get_max_threads(), 0, Exact());
}
template <typename TIndex, typename TSpec, typename TPattern>
inline void
_init(OccurrencesCounter_<TIndex, Device<TSpec> > & counter, TPattern const & pattern)
{
resize(counter.counts, length(needle(pattern)), Exact());
}
// ----------------------------------------------------------------------------
// Function view()
// ----------------------------------------------------------------------------
template <typename TIndex, typename TSpec>
typename View<OccurrencesCounter_<TIndex, TSpec> >::Type
view(OccurrencesCounter_<TIndex, TSpec> & counter)
{
typename View<OccurrencesCounter_<TIndex, TSpec> >::Type counterView;
counterView.counts = view(counter.counts);
return counterView;
}
// ----------------------------------------------------------------------------
// Function _getCount()
// ----------------------------------------------------------------------------
template <typename TIndex, typename TSpec>
inline typename Size<TIndex>::Type
_getCount(OccurrencesCounter_<TIndex, TSpec> & counter)
{
return sum(counter.counts);
}
// --------------------------------------------------------------------------
// Function countOccurrences()
// --------------------------------------------------------------------------
// Count the occurrences of a set of needles in a indexed haystack.
template <typename TText, typename TSpec, typename TNeedle, typename TSSetSpec>
typename Size<Index<TText, TSpec> >::Type
countOccurrences(Index<TText, TSpec> & index, StringSet<TNeedle, TSSetSpec> & needles)
{
typedef Index<TText, TSpec> TIndex;
typedef StringSet<TNeedle, TSSetSpec> TNeedles;
typedef Multiple<FinderSTree> TAlgorithmSpec;
typedef Pattern<TNeedles, TAlgorithmSpec> TPattern;
typedef Finder_<TIndex, TPattern, TAlgorithmSpec> TFinder;
typedef OccurrencesCounter_<TIndex> TCounter;
// Instantiate a finder object holding the context of the search algorithm.
TFinder finder(index);
// Instantiate a pattern object holding the needles.
TPattern pattern(needles);
// Instantiate a functor object counting the number of occurrences.
TCounter counter(pattern);
// Find all needles in haystack and call counter() on match.
_find(finder, pattern, counter);
// Return the number of occurrences.
return _getCount(counter);
}
}
#endif // #ifndef SEQAN_INDEX_FIND_FUNCTORS_H_
|
