1 // ==========================================================================
2 //                 SeqAn - The Library for Sequence Analysis
3 // ==========================================================================
4 // Copyright (c) 2006-2015, Knut Reinert, FU Berlin
5 // All rights reserved.
6 //
7 // Redistribution and use in source and binary forms, with or without
8 // modification, are permitted provided that the following conditions are met:
9 //
10 //     * Redistributions of source code must retain the above copyright
11 //       notice, this list of conditions and the following disclaimer.
12 //     * Redistributions in binary form must reproduce the above copyright
13 //       notice, this list of conditions and the following disclaimer in the
14 //       documentation and/or other materials provided with the distribution.
15 //     * Neither the name of Knut Reinert or the FU Berlin nor the names of
16 //       its contributors may be used to endorse or promote products derived
17 //       from this software without specific prior written permission.
18 //
19 // THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
20 // AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
21 // IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
22 // ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE
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28 // OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
29 // DAMAGE.
30 //
31 // ==========================================================================
32 // Author: David Weese <david.weese@fu-berlin.de>
33 // ==========================================================================
34 
35 #ifndef SEQAN_HEADER_STORE_READ_H
36 #define SEQAN_HEADER_STORE_READ_H
37 
38 namespace SEQAN_NAMESPACE_MAIN
39 {
40 
41 //////////////////////////////////////////////////////////////////////////////
42 // Read Store
43 //////////////////////////////////////////////////////////////////////////////
44 
45 /*!
46  * @class ReadStoreElement
47  * @headerfile <seqan/store.h>
48  * @brief Represents a single read (without sequence).
49  *
50  * @signature template <[typename TSpec]>
51  *            struct ReadStoreElement;
52  *
53  * @tparam TSpec The specializing type.  Default: <tt>void</tt>.
54  *
55  *
56  * @fn ReadStoreElement::ReadStoreElement
57  * @signature ReadStoreElement::ReadStoreElement();
58  * @brief Constructor.
59  *
60  * Sets ReadStoreElement::matePairId to ReadStoreElement::INVALID_ID.
61  */
62 
63 /*!
64  * @var TId ReadStoreElement::matePairId;
65  * @brief Refers to a mate pair in the @link FragmentStore::matePairStore @endlink or is INVALID_ID if the read is
66  *        not paired.
67  *
68  * @var TId ReadStoreElement::INVALID_ID;
69  * @brief Constant to represetn an invalid id.
70  */
71 
72 template <typename TSpec = void>
73 struct ReadStoreElement
74 {
75     typedef typename Id<ReadStoreElement>::Type TId;
76 
77     static const TId INVALID_ID;
78 
79     TId matePairId;                // refers to the mate-pair, INVALID_ID if not part of a mate-pair
80 
ReadStoreElementReadStoreElement81     ReadStoreElement() : matePairId(INVALID_ID) {}
82 
83     inline
84     bool
85     operator==(ReadStoreElement const & other)
86     {
87         return matePairId == other.matePairId;
88     }
89 };
90 
91 //////////////////////////////////////////////////////////////////////////////
92 
93 template <typename TSpec>
94 const typename Id<ReadStoreElement<TSpec> >::Type
95 ReadStoreElement<TSpec>::INVALID_ID = MaxValue<typename Id<ReadStoreElement<TSpec> >::Type>::VALUE;
96 
97 //////////////////////////////////////////////////////////////////////////////
98 
99 }// namespace SEQAN_NAMESPACE_MAIN
100 
101 #endif //#ifndef SEQAN_HEADER_...
102