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
|
// ==========================================================================
// 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>
// ==========================================================================
#ifndef SEQAN_FIND_FIND_BASE_H_
#define SEQAN_FIND_FIND_BASE_H_
namespace seqan2 {
// ============================================================================
// Forwards
// ============================================================================
template <typename TText, typename TPattern, typename TSpec = void>
struct Finder_;
// ============================================================================
// Metafunctions
// ============================================================================
// ----------------------------------------------------------------------------
// Metafunction View [Finder]
// ----------------------------------------------------------------------------
template <typename TText, typename TPattern, typename TSpec>
struct View<Finder_<TText, TPattern, TSpec> >
{
typedef Finder_<typename View<TText>::Type, typename View<TPattern>::Type, TSpec> Type;
};
// ----------------------------------------------------------------------------
// Metafunction RemoveView [Finder]
// ----------------------------------------------------------------------------
template <typename TText, typename TPattern, typename TSpec>
struct RemoveView<Finder_<TText, TPattern, TSpec> >
{
typedef Finder_<typename RemoveView<TText>::Type, typename RemoveView<TPattern>::Type, TSpec> Type;
};
// ----------------------------------------------------------------------------
// Metafunction IsView [Finder]
// ----------------------------------------------------------------------------
template <typename TText, typename TPattern, typename TSpec>
struct IsView<Finder_<TText, TPattern, TSpec> > : IsView<TText> {};
// ----------------------------------------------------------------------------
// Metafunction IsDevice [Finder]
// ----------------------------------------------------------------------------
template <typename TText, typename TPattern, typename TSpec>
struct IsDevice<Finder_<TText, TPattern, TSpec> > : IsDevice<TText> {};
// ----------------------------------------------------------------------------
// Metafunction View [Pattern]
// ----------------------------------------------------------------------------
template <typename TNeedle, typename TSpec>
struct View<Pattern<TNeedle, TSpec> >
{
typedef Pattern<typename View<TNeedle>::Type, TSpec> Type;
};
// ----------------------------------------------------------------------------
// Metafunction RemoveView [Pattern]
// ----------------------------------------------------------------------------
template <typename TNeedle, typename TSpec>
struct RemoveView<Pattern<TNeedle, TSpec> >
{
typedef Pattern<typename RemoveView<TNeedle>::Type, TSpec> Type;
};
// ----------------------------------------------------------------------------
// Metafunction IsView [Pattern]
// ----------------------------------------------------------------------------
template <typename TNeedle, typename TSpec>
struct IsView<Pattern<TNeedle, TSpec> > : IsView<TNeedle> {};
// ----------------------------------------------------------------------------
// Metafunction IsDevice [Pattern]
// ----------------------------------------------------------------------------
template <typename TNeedle, typename TSpec>
struct IsDevice<Pattern<TNeedle, TSpec> > : IsDevice<TNeedle> {};
// ----------------------------------------------------------------------------
// Metafunction TextIterator_
// ----------------------------------------------------------------------------
template <typename TText, typename TPattern, typename TSpec>
struct TextIterator_
{
typedef typename Iterator<TText>::Type Type;
};
// ----------------------------------------------------------------------------
// Metafunction PatternIterator_
// ----------------------------------------------------------------------------
template <typename TText, typename TPattern, typename TSpec>
struct PatternIterator_
{
typedef typename Iterator<TPattern const, Rooted>::Type Type;
};
// ----------------------------------------------------------------------------
// Metafunction Score_
// ----------------------------------------------------------------------------
template <typename TSpec>
struct Score_
{
typedef unsigned char Type;
};
// ============================================================================
// Functions
// ============================================================================
// ----------------------------------------------------------------------------
// Function _textIterator()
// ----------------------------------------------------------------------------
template <typename TText, typename TPattern, typename TSpec>
inline typename TextIterator_<TText, TPattern, TSpec>::Type &
_textIterator(Finder_<TText, TPattern, TSpec> & finder)
{
return finder._textIt;
}
template <typename TText, typename TPattern, typename TSpec>
inline typename TextIterator_<TText, TPattern, TSpec>::Type const &
_textIterator(Finder_<TText, TPattern, TSpec> const & finder)
{
return finder._textIt;
}
// ----------------------------------------------------------------------------
// Function _patternIterator()
// ----------------------------------------------------------------------------
template <typename TText, typename TPattern, typename TSpec>
inline typename PatternIterator_<TText, TPattern, TSpec>::Type &
_patternIterator(Finder_<TText, TPattern, TSpec> & finder)
{
return finder._patternIt;
}
template <typename TText, typename TPattern, typename TSpec>
inline typename PatternIterator_<TText, TPattern, TSpec>::Type const &
_patternIterator(Finder_<TText, TPattern, TSpec> const & finder)
{
return finder._patternIt;
}
// ----------------------------------------------------------------------------
// Function _getScore()
// ----------------------------------------------------------------------------
template <typename TText, typename TPattern, typename TSpec>
inline typename Score_<TSpec>::Type
_getScore(Finder_<TText, TPattern, TSpec> const & finder)
{
return finder._score;
}
// ----------------------------------------------------------------------------
// Function _getScoreThreshold()
// ----------------------------------------------------------------------------
template <typename TText, typename TPattern, typename TSpec>
inline typename Score_<TSpec>::Type
_getScoreThreshold(Finder_<TText, TPattern, TSpec> const & finder)
{
return finder._scoreThreshold;
}
// ----------------------------------------------------------------------------
// Function _setScoreThreshold()
// ----------------------------------------------------------------------------
template <typename TText, typename TPattern, typename TSpec, typename TScore>
inline void
_setScoreThreshold(Finder_<TText, TPattern, TSpec> & finder, TScore score)
{
finder._scoreThreshold = score;
}
// ----------------------------------------------------------------------------
// Function clear()
// ----------------------------------------------------------------------------
template <typename TText, typename TIndexSpec, typename TPattern, typename TSpec>
inline void
clear(Finder_<TText, TPattern, TSpec> & finder)
{
// NOTE(esiragusa): if find wasn't called yet, _textIterator is uninitialized.
// goBegin(_textIterator(finder));
// NOTE(esiragusa): if find wasn't called yet, _patternIterator is uninitialized.
// goBegin(_patternIterator(finder));
finder._score = typename Score_<TSpec>::Type();
}
}
#endif // #ifndef SEQAN_FIND_FIND_BASE_H_
|
