c_cpp/etc/KaKs_Calculator/src/MYN.h

   1 /************************************************************
   2 * Copyright (c) 2005, BGI of Chinese Academy of Sciences
   3 * All rights reserved.
   4
   5 * Filename: MYN.h
   6 * Abstract: Declaration of Modified YN00 (MYN) class.
   7
   8 * Version: 1.0
   9 * Author: Zhang Zhang(zhanghzhang@genomics.org.cn)
  10 * Date: Dec.30, 2005
  11
  12   References:
  13         Zhang Zhang, Jun Li, Jun Yu. (2006) Computing Ka and Ks
  14         with a consideration of unequal transitional substitutions.
  15         BMC Evolutionary Biology, 6:44.
  16 *************************************************************/
  17
  18 #if !defined(MYN_H)
  19 #define  MYN_H
  20
  21 #define CODONFREQ 12
  22 #define min(a,b) ((a)<(b)?(a):(b))
  23 #define max(a,b) ((a)>(b)?(a):(b))
  24 #define square(a) ((a)*(a))
  25
  26 #include "base.h"
  27 #include "YN00.h"
  28
  29 using namespace std;
  30
  31 class MYN: public YN00 {
  32
  33 public:
  34         MYN();
  35         /* Get the two kappas between purines and between pyrimidines */
  36         virtual int GetKappa(const string seq1, const string seq2);
  37         /* Calculate the transition probability matrix  */
  38         int GetPMatCodon(double P[], double kappa, double omega);
  39         /* Count S and N */
  40         int CountSites(const string z, double &Stot,double &Ntot,double fbS[],double fbN[]);
  41         /* Correct for multiple substitutions for two kappas */
  42         int CorrectKappaTN93(double n, double P1, double P2, double Q, double pi4[], double &kappatc_TN93, double &kappaag_TN93);
  43         /* Correct for multiple substitutions for Ka and Ks */
  44         int CorrectKaksTN93(double n, double P1, double P2, double Q, double pi4[], double &kaks, double &SEkaks);
  45         /* Count Sd and Nd */
  46         int CountDiffs(const string seq1, const string seq2, double &Sdts1, double &Sdts2, double &Sdtv,double &Ndts1, double &Ndts2, double &Ndtv,double PMatrix[]);
  47         /* Main function */
  48         virtual int DistanceYN00(const string seq1, const string seq2, double &dS,double &dN, double &SEdS, double &SEdN);
  49 };
  50
  51
  52 #endif
  53