NCBI C++ ToolKit
patch_sequence.hpp
Go to the documentation of this file.

Go to the SVN repository for this file.

1 #ifndef ALGO_ALIGN_UTIL___PATCHSEQUENCE__HPP
2 #define ALGO_ALIGN_UTIL___PATCHSEQUENCE__HPP
3 
4 /* $Id: patch_sequence.hpp 51222 2011-09-14 14:53:49Z mozese2 $
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  * Authors: Eyal Mozes
30  *
31  * File Description:
32  *
33  */
34 
35 #include <corelib/ncbiobj.hpp>
36 
39  class CSeq_id_Handle;
40  class CSeq_align;
41  class CSeq_inst;
42  class CScope;
44 
45 
46 /// Patch the Seq-inst of alignment's target sequence by substituting
47 /// query sequence.
50  objects::CScope &scope);
51 
52 /// Patch the Seq-inst of alignment's target sequence by substituting
53 /// all query sequences. All alignments on the list must have the same
54 /// target sequence.
57  objects::CScope &scope);
58 
60 AddNovelPatch(const objects::CSeq_id_Handle &idh);
61 
63 
64 
65 #endif // ALGO_ALIGN_UTIL___PATCHSEQUENCE__HPP
CScope –.
Definition: scope.hpp:92
#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_XALGOALIGN_EXPORT
Definition: ncbi_export.h:985
Portable reference counted smart and weak pointers using CWeakRef, CRef, CObject and CObjectEx.
void AddNovelPatch(const objects::CSeq_id_Handle &idh)
CRef< objects::CSeq_inst > PatchTargetSequence(CRef< objects::CSeq_align > alignment, objects::CScope &scope)
Patch the Seq-inst of alignment's target sequence by substituting query sequence.
Modified on Sat Apr 13 11:47:58 2024 by modify_doxy.py rev. 669887