NCBI C++ ToolKit
cmd_assign_feat_local_ids.cpp
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1 /* $Id: cmd_assign_feat_local_ids.cpp 42162 2019-01-07 20:09:12Z filippov $
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.
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18  * Government disclaim all warranties, express or implied, including
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22  * Please cite the author in any work or product based on this material.
23  *
24  * ===========================================================================
25  *
26  * Authors: Andrea Asztalos
27  */
28 
29 
30 #include <ncbi_pch.hpp>
31 
32 #include <objmgr/util/sequence.hpp>
36 
38 
41 
43 {
46 
47  for (CFeat_CI feat_it(m_seh); feat_it; ++feat_it) {
48  CSeq_feat_Handle fh = feat_it->GetSeq_feat_Handle();
49  if (fh.IsSetId() && fh.GetId().IsLocal()) {
50  continue;
51  }
52 
53  CRef<CSeq_feat> new_feat(new CSeq_feat);
54  new_feat->Assign(*feat_it->GetOriginalSeq_feat());
55  top_id++;
56  new_feat->SetId().SetLocal().SetId(top_id);
57 
58  if (!result)
59  result.Reset(new CCmdComposite("Assign feature local ids"));
60 
61  CIRef<IEditCommand> chg_feat(new CCmdChangeSeq_feat(fh, *new_feat));
62  result->AddCommand(*chg_feat);
63  }
64 
66 }
67 
69 {
70  return "Assign feature local ids";
71 }
72 
virtual CIRef< IEditCommand > x_CreateActionCmd()
objects::CSeq_entry_Handle m_seh
CFeat_CI –.
Definition: feat_ci.hpp:64
static TId s_FindHighestFeatureId(const objects::CSeq_entry_Handle &entry)
CSeq_feat_Handle –.
namespace ncbi::objects::
Definition: Seq_feat.hpp:58
USING_SCOPE(objects)
virtual void Assign(const CSerialObject &source, ESerialRecursionMode how=eRecursive)
Set object to copy of another one.
const CFeat_id & GetId(void) const
bool IsSetId(void) const
#define END_NCBI_SCOPE
End previously defined NCBI scope.
Definition: ncbistl.hpp:103
#define BEGIN_NCBI_SCOPE
Define ncbi namespace.
Definition: ncbistl.hpp:100
bool IsLocal(void) const
Check if variant Local is selected.
Definition: Feat_id_.hpp:353
void SetId(TId &value)
Assign a value to Id data member.
Definition: Seq_feat_.cpp:73
else result
Definition: token2.c:20
Modified on Thu Jun 13 17:25:58 2024 by modify_doxy.py rev. 669887