c_cpp/etc/KaKs_Calculator/src/LWL85.h

   1 /************************************************************
   2 * Copyright (c) 2005, BGI of Chinese Academy of Sciences
   3 * All rights reserved.
   4
   5 * Filename: LWL85.h
   6 * Abstract: Declaration of LWL85 and Modified LWL85 class.
   7
   8 * Version: 1.0
   9 * Author: Zhang Zhang(zhanghzhang@genomics.org.cn)
  10 * Date: Jan.21, 2005
  11
  12   References:
  13   Li WH, Wu CI, Luo CC  (1985)  A new method for
  14   estimating synonymous and nonsynonymous rates of nucleotide
  15   substitution considering the relative likelihood of nucleotide
  16   and codon changes. Mol. Biol. Evol. 2:150-174.
  17
  18   Tzeng Y-H, Pan R, Li W-H  (2004)  Comparison of Three Methods
  19   for Estimating Rates of Synonymous and Nonsynonymous Nucleotide
  20   Substitutions. Mol. Biol. Evol. 21:2290-2298.
  21 *************************************************************/
  22
  23 #if !defined(LWL85_H)
  24 #define  LWL85_H
  25
  26 #include "base.h"
  27
  28 using namespace std;
  29
  30 /* Nondegenerate, twofold and fourfold when considering position 1,2,3 of 64 Codon */
  31 /* 0: 0-fold,   2: 2-fold,              4: 4-fold */
  32
  33 /* The following is only for standard genetic code.
  34    Considering more genetic codes, we use the function of "getCodonClass".
  35 const int CodonClassDict[]={0,0,2,  0,0,2,      2,0,2,  2,0,2,  0,0,4,  0,0,4,  0,0,4,  0,0,4,
  36                                                         0,0,2,  0,0,2,  0,0,0,  0,0,0,  0,0,2,  0,0,2,  0,0,0,  0,0,0,
  37                                                         0,0,4,  0,0,4,  2,0,4,  2,0,4,  0,0,4,  0,0,4,  0,0,4,  0,0,4,
  38                                                         0,0,2,  0,0,2,  0,0,2,  0,0,2,  0,0,4,  0,0,4,  2,0,4,  2,0,4,
  39                                                         0,0,2,  0,0,2,  0,0,2,  0,0,0,  0,0,4,  0,0,4,  0,0,4,  0,0,4,
  40                                                         0,0,2,  0,0,2,  0,0,2,  0,0,2,  0,0,2,  0,0,2,  2,0,2,  2,0,2,
  41                                                         0,0,4,  0,0,4,  0,0,4,  0,0,4,  0,0,4,  0,0,4,  0,0,4,  0,0,4,
  42                                                         0,0,2,  0,0,2,  0,0,2,  0,0,2,  0,0,4,  0,0,4,  0,0,4,  0,0,4}; */
  43
  44
  45
  46 /* LWL85 class */
  47 class LWL85: public Base {
  48
  49 public:
  50         LWL85();
  51
  52         /* Main function for calculating Ka&Ks */
  53         string Run(string seq1, string seq2);
  54
  55 protected:
  56         /* preprocess in main function of Run */
  57         void preProcess(string seq1, string seq2);
  58         /* Calculate synonymous and nonsynonymous sites and differences on two compared codons */
  59         void CountSiteAndDiff(string str1, string str2);
  60         /* Return 0,2,or 4 of the codon at a given position */
  61         int  getCodonClass(string codon, int pos);
  62         /* Calculate synonymous and nonsynonymous differences of two codons at a given position */
  63         virtual int  TransitionTransversion(string codon1, string codon2, int pos);
  64
  65 public:
  66
  67         /* Proportions of transitional(Pi) and transversional(Qi) difference: Pi=Si/Li,  Qi=Vi/Li  */
  68         double Pi[5], Qi[5];
  69         /* Numbers of transitional(A) and transversional(B) substitutions per i-th type site */
  70         double A[5], B[5];
  71
  72
  73 protected:
  74         /* Number of synonymous and nonsynonymous differences of pair-codon */
  75         double Si_temp[5], Vi_temp[5];
  76 };
  77
  78
  79 class MLWL85: public LWL85 {
  80
  81 public:
  82         MLWL85();
  83
  84         /* Main function for calculating Ka&Ks */
  85         string Run(string str1, string str2);
  86
  87 protected:
  88         /* Calculate the transition & transversion between two codons at a given position*/
  89         int TransitionTransversion(string codon1, string codon2, int pos);
  90 };
  91
  92
  93 #endif
  94
  95