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
|
// ==========================================================================
// 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: Andreas Gogol-Doering <andreas.doering@mdc-berlin.de>
// ==========================================================================
// Edit distance score class and supporting code.
// ==========================================================================
#ifndef SEQAN_SSCORE_EDIT_H_
#define SEQAN_SSCORE_EDIT_H_
namespace seqan2 {
/*!
* @class EditDistanceScore
* @extends Score
* @headerfile <seqan/score.h>
* @brief Edit distance scoring scheme.
*
* <tt>EditDistance</tt> is a synonym for <tt>LevenshteinDistance</tt>.
*
* @signature template <typename TValue>
* class Score<TValue, EditDistance>;
*
* @tparam TValue The score value type to use.
*/
// TODO(holtgrew): Should EditDistance better live here instead of basic_tag.h?
// EditDistance is defined in basic_tag.h
template <typename TValue>
class Score<TValue, EditDistance> {
public:
Score() {}
};
// TODO(holtgrew): Remove this?
/*!
* @typedef EditDistanceScoreTypedef EditDistance
* @headerfile <seqan/score.h>
* @brief Edit distance scoring scheme shortcut.
*
* @signature typedef Score<int, EditDistance> EditDistanceScore;
*/
typedef Score<int, EditDistance> EditDistanceScore;
template <typename TValue>
inline TValue
scoreMatch(Score<TValue, EditDistance> &) {
return 0;
}
template <typename TValue>
inline TValue
scoreMatch(Score<TValue, EditDistance> const &) {
return 0;
}
template <typename TValue>
inline TValue
scoreMismatch(Score<TValue, EditDistance> &) {
return -1;
}
template <typename TValue>
inline TValue
scoreMismatch(Score<TValue, EditDistance> const &) {
return -1;
}
template <typename TValue>
inline TValue
scoreGapExtend(Score<TValue, EditDistance> &) {
return -1;
}
template <typename TValue>
inline TValue
scoreGapExtend(Score<TValue, EditDistance> const &) {
return -1;
}
template <typename TValue>
inline TValue
scoreGapOpen(Score<TValue, EditDistance> &) {
return -1;
}
template <typename TValue>
inline TValue
scoreGapOpen(Score<TValue, EditDistance> const &) {
return -1;
}
} // namespace seqan2
#endif // SEQAN_SSCORE_EDIT_H_
|
