1 /*  $Id: objcoords.hpp 396144 2013-04-16 19:59:16Z voronov $
2  * ===========================================================================
3  *
4  *                            PUBLIC DOMAIN NOTICE
5  *               National Center for Biotechnology Information
6  *
7  *  This software/database is a "United States Government Work" under the
8  *  terms of the United States Copyright Act.  It was written as part of
9  *  the author's official duties as a United States Government employee and
10  *  thus cannot be copyrighted.  This software/database is freely available
11  *  to the public for use. The National Library of Medicine and the U.S.
12  *  Government have not placed any restriction on its use or reproduction.
13  *
14  *  Although all reasonable efforts have been taken to ensure the accuracy
15  *  and reliability of the software and data, the NLM and the U.S.
16  *  Government do not and cannot warrant the performance or results that
17  *  may be obtained by using this software or data. The NLM and the U.S.
18  *  Government disclaim all warranties, express or implied, including
19  *  warranties of performance, merchantability or fitness for any particular
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22  *  Please cite the author in any work or product based on this material.
23  *
24  * ===========================================================================
25  *
26  * Author:  Victor Joukov, Yury Voronov
27  *
28  * File Description: Library to retrieve mapped sequence coordinates of
29  *                   the feature products given a sequence location
30  *
31  *
32  */
33 
34 #include <objects/seqloc/Seq_id.hpp>
35 // our ASN
36 #include <objects/coords/HGVS_Coordinate.hpp>
37 #include <objects/coords/HGVS_Coordinate_Set.hpp>
38 
39 BEGIN_NCBI_SCOPE
40 BEGIN_SCOPE(objects)
41     class CScope;
42 END_SCOPE(objects)
43 
44 USING_SCOPE(ncbi);
45 USING_SCOPE(objects);
46 
47 
48 class CObjectCoords : public CObject
49 {
50 public:
51     // how far to search for features from the pos given
52     static const TSeqPos kSearchWindow = 2000;
53     CObjectCoords(objects::CScope& scope);
54     CRef<CHGVS_Coordinate_Set> GetCoordinates(const CSeq_id& id, TSeqPos pos, TSeqPos window = kSearchWindow);
55     void GetCoordinates(CHGVS_Coordinate_Set& coords, const CSeq_id& id, TSeqPos pos, TSeqPos window = kSearchWindow);
56 
57 protected:
58     CRef<objects::CScope> m_Scope;
59 };
60 
61 
62 END_NCBI_SCOPE
63