NCBI C++ ToolKit
aln_scanner_sequin.hpp
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1 #ifndef _ALN_SCANNER_SEQUIN_HPP_
2 #define _ALN_SCANNER_SEQUIN_HPP_
3 
4 /*
5  * $Id: aln_scanner_sequin.hpp 93368 2021-04-06 14:41:49Z stakhovv $
6  *
7  * ===========================================================================
8  *
9  * PUBLIC DOMAIN NOTICE
10  * National Center for Biotechnology Information
11  *
12  * This software/database is a "United States Government Work" under the
13  * terms of the United States Copyright Act. It was written as part of
14  * the author's official duties as a United States Government employee and
15  * thus cannot be copyrighted. This software/database is freely available
16  * to the public for use. The National Library of Medicine and the U.S.
17  * Government have not placed any restriction on its use or reproduction.
18  *
19  * Although all reasonable efforts have been taken to ensure the accuracy
20  * and reliability of the software and data, the NLM and the U.S.
21  * Government do not and cannot warrant the performance or results that
22  * may be obtained by using this software or data. The NLM and the U.S.
23  * Government disclaim all warranties, express or implied, including
24  * warranties of performance, merchantability or fitness for any particular
25  * purpose.
26  *
27  * Please cite the author in any work or product based on this material.
28  *
29  * ===========================================================================
30  *
31  * Authors: Frank Ludwig
32  *
33  */
34 #include <corelib/ncbistd.hpp>
35 #include "aln_scanner.hpp"
36 
39 
40 struct SAlignFileRaw;
41 
42 // ============================================================================
44  public CAlnScanner
45  // ============================================================================
46 {
47 public:
50 
51 protected:
52  void
55  CLineInput&) override;
56 
57  void
59  CSequenceInfo&) override;
60 
61  static bool
63  const string& line);
64 
65  static bool
67  const string& line);
68 
69  static bool
71  const string& line,
72  string& seqId,
73  string& seqData);
74 };
75 
78 
79 #endif // _ALN_SCANNER_SEQUIN_HPP_
void xImportAlignmentData(CSequenceInfo &, CLineInput &) override
static bool xExtractSequinSequenceData(const string &line, string &seqId, string &seqData)
static bool xIsSequinOffsetsLine(const string &line)
static bool xIsSequinTerminationLine(const string &line)
void xAdjustSequenceInfo(CSequenceInfo &) override
Include a standard set of the NCBI C++ Toolkit most basic headers.
#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
Modified on Tue Apr 16 20:08:28 2024 by modify_doxy.py rev. 669887