NCBI C++ ToolKit
antigenic.hpp
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1 /* $Id: antigenic.hpp 33815 2007-05-04 17:18:18Z kazimird $
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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21  *
22  * Please cite the author in any work or product based on this material.
23  *
24  * ===========================================================================
25  *
26  * Authors: Josh Cherry
27  *
28  * File Description: Predict antigenic determinants as described by
29  * Kolaskar and Tongaonkar, 1990
30  *
31  */
32 
33 
34 #ifndef ALGO_SEQUENCE___ANTIGENIC__HPP
35 #define ALGO_SEQUENCE___ANTIGENIC__HPP
36 
37 #include <corelib/ncbistd.hpp>
39 #include <objmgr/seq_vector.hpp>
40 #include <vector>
41 
43 
45 {
46 public:
47  typedef vector< CRef<objects::CSeq_loc> > TLocVec;
48 
49  /// Predict antigenic determinants from protein sequence
50  /// according to Kolaskar and Tongaonkar, 1990 (PMID 1702393).
51  ///
52  /// For std char containers, seq must be in ncbistdaa.
53  static void PredictSites(const string& seq,
54  TLocVec& results,
55  unsigned int min_len = 6);
56 
57  static void PredictSites(const vector<char>& seq,
58  TLocVec& results,
59  unsigned int min_len = 6);
60 
61  static void PredictSites(const objects::CSeqVector& seq,
62  TLocVec& results,
63  unsigned int min_len = 6);
64 
65 private:
66  static const double sm_Pa_table[26];
67 
68  template<class Seq>
69  friend void x_PredictAGSites(const Seq& seq, TLocVec& results,
70  int min_len);
71 };
72 
73 
75 
76 #endif // ALGO_SEQUENCE___ANTIGENIC__HPP
void x_PredictAGSites(const Seq &seq, CAntigenic::TLocVec &results, int min_len)
Definition: antigenic.cpp:76
vector< CRef< objects::CSeq_loc > > TLocVec
Definition: antigenic.hpp:47
static void PredictSites(const vector< char > &seq, TLocVec &results, unsigned int min_len=6)
static void PredictSites(const string &seq, TLocVec &results, unsigned int min_len=6)
Predict antigenic determinants from protein sequence according to Kolaskar and Tongaonkar,...
static void PredictSites(const objects::CSeqVector &seq, TLocVec &results, unsigned int min_len=6)
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 BEGIN_NCBI_SCOPE
Define ncbi namespace.
Definition: ncbistl.hpp:100
#define NCBI_XALGOSEQ_EXPORT
Definition: ncbi_export.h:1017
Modified on Sat May 25 14:19:11 2024 by modify_doxy.py rev. 669887