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
|
// ==========================================================================
// basic_tangle.h
// ==========================================================================
// 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: Manuel Holtgrewe <manuel.holtgrewe@fu-berlin.de>
// ==========================================================================
// TODO(holtgrew): This header contains code that does not clearly belongs somewhere else.
#ifndef INCLUDE_SEQAN_BASIC_BASIC_TANGLE_H_
#define INCLUDE_SEQAN_BASIC_BASIC_TANGLE_H_
namespace seqan {
// TODO(holtgrew): Remove this define.
#define seqan seqan
// ============================================================================
// Forwards
// ============================================================================
// ============================================================================
// Tags, Classes, Enums
// ============================================================================
// ============================================================================
// Metafunctions
// ============================================================================
// TODO(holtgrew): Remove auto-sequence!
template <typename TValue, typename TSpec>
struct Iterator<SimpleType<TValue, TSpec>, Standard>
{
typedef SimpleType<TValue, TSpec> * Type;
// typedef Iter<SimpleType<TValue, TSpec>, SimpleIterator> * Type;
};
template <typename TValue, typename TSpec>
struct Iterator<SimpleType<TValue, TSpec> const, Standard>
{
typedef SimpleType<TValue, TSpec> const * Type;
// typedef Iter<SimpleType<TValue, TSpec> const, SimpleIterator> * Type;
};
// ----------------------------------------------------------------------------
// Metafunction Key
// ----------------------------------------------------------------------------
// TODO(holtgrew): Is this part of some adaption?
template <typename TKey, typename TObject, typename TSpec>
struct Key<Pair<TKey, TObject, TSpec> >
{
typedef TKey Type;
};
// ----------------------------------------------------------------------------
// Metafunction Cargo
// ----------------------------------------------------------------------------
// TODO(holtgrew): Is this part of some adaption?
template <typename TKey, typename TCargo, typename TSpec>
struct Cargo<Pair<TKey, TCargo, TSpec> >
{
typedef TCargo Type;
};
// ============================================================================
// Functions
// ============================================================================
// ----------------------------------------------------------------------------
// Function assignQualities()
// ----------------------------------------------------------------------------
/*!
* @fn assignQualities
* @headerfile <seqan/basic.h>
* @brief Assign quality values between strings.
*
* @signature void assignQualities(target, source);
*
* @param[out] target Target string, can be a String of DnaQ or Dna5Q characters.
* @param[in] source Source string. Can be a String of int or char.
*
* @section Remarks
*
* The target is resized to the length of source. This function calls assignQualityValue for all entries of
* <tt>target</tt> and <tt>source</tt>, look at the documentation of assignQualityValue on how the values of
* <tt>source</tt> are interpreted.
*
* Note that qualities are expected to be in PHRED scale.
*
* @see AlphabetWithQualitiesConcept#assignQualityValue
*/
template <typename TDest, typename TSource>
inline void
_assignQualities(TDest &dst, TSource const &src, True)
{
typedef typename Iterator<TDest>::Type TDestIter;
typedef typename Iterator<TSource const>::Type TSourceIter;
if (length(dst) < length(src))
resize(dst, length(src));
TDestIter itDst = begin(dst, Standard());
TSourceIter itSrcEnd = end(src, Standard());
for (TSourceIter itSrc = begin(src, Standard()); itSrc != itSrcEnd; ++itDst, ++itSrc)
assignQualityValue(*itDst, *itSrc);
}
template <typename TDest, typename TSource>
inline void
_assignQualities(TDest &, TSource const &, False)
{}
// TODO(holtgrew): Uncomment, place somewhere that knows both iterators and assignQualityValue, maybe in module sequence?
template <typename TDest, typename TSource>
inline void
assignQualities(TDest &dst, TSource const &src)
{
typedef typename Value<TDest>::Type TValue;
_assignQualities(dst, src, typename Or<IsSameType<TValue, DnaQ>, IsSameType<TValue, Dna5Q> >::Type());
}
template <typename T>
inline T
unknownValueImpl(T *)
{
return 'N';
}
} // namespace seqan
#endif // #ifndef INCLUDE_SEQAN_BASIC_BASIC_TANGLE_H_
|
