1 /* $Id: seq_edit.cpp 632623 2021-06-03 17:38:11Z ivanov $
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
20 * purpose.
21 *
22 * Please cite the author in any work or product based on this material.
23 *
24 * ===========================================================================
25 *
26 * Author: Justin Foley, NCBI
27 *
28 * File Description:
29 * functions for editing sequences
30 */
31 #include <ncbi_pch.hpp>
32 #include <corelib/ncbistd.hpp>
33 #include <objmgr/seq_vector.hpp>
34
35 #include <objects/seq/Seq_inst.hpp>
36 #include <objects/seq/Seq_data.hpp>
37 #include <objects/seq/seqport_util.hpp>
38
39 #include <objtools/edit/seq_edit.hpp>
40
41 BEGIN_NCBI_SCOPE
BEGIN_SCOPE(objects)42 BEGIN_SCOPE(objects)
43 BEGIN_SCOPE(edit)
44
45 void g_ConvertDeltaToRawSeq(CBioseq& bioseq, CScope* pScope)
46 {
47 auto& seq_inst = bioseq.SetInst();
48
49 _ASSERT(seq_inst.GetRepr() == CSeq_inst::eRepr_delta);
50 _ASSERT(seq_inst.IsSetLength());
51
52 CSeqVector seq_vec(bioseq, pScope, CBioseq_Handle::eCoding_Iupac);
53 string seqdata;
54 seq_vec.GetSeqData(0, seq_inst.GetLength(), seqdata);
55 auto pSeqData =
56 Ref(new CSeq_data(seqdata, seq_vec.GetCoding()));
57 CSeqportUtil::Pack(pSeqData.GetPointer());
58
59
60 seq_inst.SetRepr(CSeq_inst::eRepr_raw);
61 seq_inst.SetSeq_data(*pSeqData);
62 seq_inst.ResetExt();
63 }
64
65 END_SCOPE(edit)
66 END_SCOPE(objects)
67 END_NCBI_SCOPE
68