c_cpp/etc/KaKs_Calculator/src/NG86.h

   1 /***************************************************************
   2 * Copyright (c) 2005, BGI of Chinese Academy of Sciences
   3 * All rights reserved.
   4
   5 * Filename: NG86.h
   6 * Abstract: Declaration of NG86 class inherited base class.
   7
   8 * Version: 1.0
   9 * Author: Zhang Zhang  (zhanghzhang@genomics.org.cn)
  10 * Date: Feb.21, 2005
  11
  12   References:
  13   Nei M, Gojobori T  (1986)  Simple methods for estimating the
  14   numbers of synonymous and nonsynonymous nucleotide substitutions.
  15   Mol Biol Evol 3:418-426.
  16 ****************************************************************/
  17
  18 #if !defined(NG86_H)
  19 #define  NG86_H
  20
  21 #include "base.h"
  22
  23 using namespace std;
  24
  25 /* NG86 class */
  26 class NG86: public Base {
  27
  28 public:
  29         NG86();
  30
  31         /* Main function of calculating kaks */
  32         string Run(string seq1, string seq2);
  33
  34 protected:
  35         /* Count codon's sites */
  36         void getCondonSite(string codon);
  37         /* Count codon's differences */
  38         void getCondonDifference(string codon1, string codon2);
  39         /* Preprocess */
  40         void PreProcess(string seq1, string seq2);
  41         /* Jukes and Cantor's one-parameter formula */
  42         double kaks_formula(double p);
  43
  44 public:
  45         /* Proportions of sysnonymous(Ps) and nonsysnonymous(Pn): Ps=Sd/S, Pn=Nd/N  */
  46         double Ps, Pn;
  47 };
  48
  49 class NONE: public NG86 {
  50
  51 public:
  52         NONE();
  53         /* Main function of calculating kaks */
  54         string Run(string seq1, string seq2);
  55
  56 };
  57
  58 #endif
  59
  60