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
|
// ==========================================================================
// 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: David Weese <david.weese@fu-berlin.de>
// ==========================================================================
#ifndef SEQAN_HEADER_STORE_LIBRARY_H
#define SEQAN_HEADER_STORE_LIBRARY_H
namespace seqan2
{
//////////////////////////////////////////////////////////////////////////////
// Library Store
//////////////////////////////////////////////////////////////////////////////
/*!
* @class LibraryStoreElement
* @headerfile <seqan/store.h>
* @brief Represents a fragment library.
*
* @signature template <[typename TMean[, typename TStd[, typename TSpec]]]>
* struct LibraryStoreElement;
*
* @tparam TMean The type to use for storing library size means. Default: <tt>double</tt>.
* @tparam TStd The type to use for storing library size standard deviations. Default: <tt>double</tt>.
* @tparam TSpec The specializing type. Default: <tt>void</tt>.
*
* Value type of the @link FragmentStore::libraryStore @endlink string.
*
* A fragment library is a set of mate pairs having a certain distribution of insert sizes.
*
*
* @fn LibraryStoreElement::LibraryStoreElement
* @brief Consctrutor.
*
* @signature LibraryStoreElement::LibraryStoreElement();
*
* Initializes all members to 0.
*/
/*!
* @var TMean LibraryStoreElement::mean;
* @brief The library size mean.
*
* @var TStd LibraryStoreElementstd;
* @brief The library size standard deviation.
*/
template <typename TMean = double, typename TStd = double, typename TSpec = void>
struct LibraryStoreElement
{
TMean mean; // mean library size in bps
TStd std; // library size variance
LibraryStoreElement() : mean(0), std(0) {}
inline bool operator==(LibraryStoreElement const & other) const
{
return mean == other.mean && std == other.std;
}
};
//////////////////////////////////////////////////////////////////////////////
}// namespace seqan2
#endif //#ifndef SEQAN_HEADER_...
|
