NCBI C++ ToolKit
glimmer_reader.hpp
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1 #ifndef __GLIMMER_READER__HPP
2 #define __GLIMMER_READER__HPP
3 
4 /* $Id: glimmer_reader.hpp 40381 2008-12-10 19:43:19Z dicuccio $
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: Mike DiCuccio
30  *
31  * File Description:
32  *
33  */
34 
35 #include <corelib/ncbistd.hpp>
36 #include <objmgr/scope.hpp>
38 
40 
41 
43 {
44 public:
46 
47  /// read in and create a seq-annot for the glimmer input
48  /// we also optionally create proteins for the CDSs
49  /// we require a scope, as the genomes may be circular, and features
50  /// crossing the origin cannot be placed without determining the length of
51  /// the matched sequence. If the genetic code is not supplied, then it is
52  /// assumed to be standard bacterial (code = 11)
54  objects::CScope& scope,
55  int genetic_code_idx = 11);
56 };
57 
58 
60 
61 #endif // __GLIMMER_READER__HPP
Include a standard set of the NCBI C++ Toolkit most basic headers.
void Read(CObjectIStream &in, TObjectPtr object, const CTypeRef &type)
Definition: serial.cpp:60
#define END_NCBI_SCOPE
End previously defined NCBI scope.
Definition: ncbistl.hpp:103
#define BEGIN_NCBI_SCOPE
Define ncbi namespace.
Definition: ncbistl.hpp:100
IO_PREFIX::istream CNcbiIstream
Portable alias for istream.
Definition: ncbistre.hpp:146
#define NCBI_XOBJREAD_EXPORT
Definition: ncbi_export.h:1315
Modified on Fri Apr 12 17:18:03 2024 by modify_doxy.py rev. 669887