1 #ifndef OBJTOOLS_DATA_LOADERS_SRA___SRALOADER_IMPL__HPP
2 #define OBJTOOLS_DATA_LOADERS_SRA___SRALOADER_IMPL__HPP
3 
4 /*  $Id: sraloader_impl.hpp 463740 2015-04-01 12:50:13Z vasilche $
5  * ===========================================================================
6  *
7  *                            PUBLIC DOMAIN NOTICE
8  *               National Center for Biotechnology Information
9  *
10  *  This software/database is a "United States Government Work" under the
11  *  terms of the United States Copyright Act.  It was written as part of
12  *  the author's official duties as a United States Government employee and
13  *  thus cannot be copyrighted.  This software/database is freely available
14  *  to the public for use. The National Library of Medicine and the U.S.
15  *  Government have not placed any restriction on its use or reproduction.
16  *
17  *  Although all reasonable efforts have been taken to ensure the accuracy
18  *  and reliability of the software and data, the NLM and the U.S.
19  *  Government do not and cannot warrant the performance or results that
20  *  may be obtained by using this software or data. The NLM and the U.S.
21  *  Government disclaim all warranties, express or implied, including
22  *  warranties of performance, merchantability or fitness for any particular
23  *  purpose.
24  *
25  *  Please cite the author in any work or product based on this material.
26  *
27  * ===========================================================================
28  *
29  * Author: Eugene Vasilchenko
30  *
31  * File Description: SRA file data loader
32  *
33  * ===========================================================================
34  */
35 
36 
37 #include <corelib/ncbistd.hpp>
38 #include <corelib/ncbimtx.hpp>
39 #include <sra/data_loaders/sra/sraloader.hpp>
40 #include <sra/readers/sra/sraread.hpp>
41 
42 BEGIN_NCBI_SCOPE
43 BEGIN_SCOPE(objects)
44 
45 class CDataLoader;
46 
47 class CSRADataLoader_Impl : public CObject
48 {
49 public:
50     CSRADataLoader_Impl(CSraMgr::ETrim trim);
51     ~CSRADataLoader_Impl(void);
52 
53     CSeq_inst::TMol GetSequenceType(const string& accession,
54                                     unsigned spot_id,
55                                     unsigned read_id);
56     TSeqPos GetSequenceLength(const string& accession,
57                               unsigned spot_id,
58                               unsigned read_id);
59 
60     CRef<CSeq_entry> LoadSRAEntry(const string& accession,
61                                   unsigned spot_id);
62 
63 private:
64     // mutex guarding input into the map
65     CMutex m_Mutex;
66     CSraMgr m_Mgr;
67     CSraRun m_Run;
68 };
69 
70 END_SCOPE(objects)
71 END_NCBI_SCOPE
72 
73 #endif  // OBJTOOLS_DATA_LOADERS_SRA___SRALOADER_IMPL__HPP
74