NCBI C++ ToolKit
alignment_item.hpp
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1 #ifndef OBJTOOLS_FORMAT_ITEMS___ALIGNMENT_ITEM__HPP
2 #define OBJTOOLS_FORMAT_ITEMS___ALIGNMENT_ITEM__HPP
3 
4 /* $Id: alignment_item.hpp 99549 2023-04-17 14:20:00Z gotvyans $
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: Aaron Ucko, NCBI
30 * Mati Shomrat
31 *
32 * File Description:
33 * Alignment item for flat-file generator (used for GFF 3)
34 *
35 */
36 
39 
42 
43 
44 class CBioseqContext;
45 class IFormatter;
46 
47 
48 ///////////////////////////////////////////////////////////////////////////
49 //
50 // ALIGNMENT
51 
53 {
54 public:
56  void Format(IFormatter& formatter, IFlatTextOStream& text_os) const override;
57 
58  const CSeq_align& GetAlign(void) const { return *m_Align; }
59 
60  EItem GetItemType() const override;
61 private:
62  void x_GatherInfo(CBioseqContext& ctx) override;
63  // data
65 };
66 
67 
70 
71 #endif /* OBJTOOLS_FORMAT_ITEMS___ALIGNMENT_ITEM__HPP */
CConstRef< CSeq_align > m_Align
const CSeq_align & GetAlign(void) const
virtual void Format(IFormatter &formatter, IFlatTextOStream &text_os) const =0
virtual void x_GatherInfo(CBioseqContext &)
Definition: item_base.hpp:71
virtual EItem GetItemType(void) const =0
CS_CONTEXT * ctx
Definition: t0006.c:12
#define END_NCBI_SCOPE
End previously defined NCBI scope.
Definition: ncbistl.hpp:103
#define END_SCOPE(ns)
End the previously defined scope.
Definition: ncbistl.hpp:75
#define BEGIN_NCBI_SCOPE
Define ncbi namespace.
Definition: ncbistl.hpp:100
#define BEGIN_SCOPE(ns)
Define a new scope.
Definition: ncbistl.hpp:72
#define NCBI_FORMAT_EXPORT
Definition: ncbi_export.h:496
Modified on Sun Feb 25 03:03:56 2024 by modify_doxy.py rev. 669887