c_cpp/etc/KaKs_Calculator/src/LPB93.h

   1 /************************************************************
   2 * Copyright (c) 2005, BGI of Chinese Academy of Sciences
   3 * All rights reserved.
   4
   5 * Filename: LPB93.h
   6 * Abstract: Declaration of LPB93 and Modified LPB93 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  (1993)  Unbiased estimation of the Rates of synonymous
  14   and nonsynonymous substitution. J. Mol. Evol. 36:96-99.
  15
  16   Pamilo P, Bianchi NO  (1993)  Evolution of the Zfx and Zfy
  17   genes: rates and interdependence between the genes. Mol. Biol.
  18   Evol. 10:271-281.
  19
  20   Tzeng Y-H, Pan R, Li W-H  (2004)  Comparison of Three Methods
  21   for Estimating Rates of Synonymous and Nonsynonymous Nucleotide
  22   Substitutions. Mol. Biol. Evol. 21:2290-2298.
  23 *************************************************************/
  24
  25 #if !defined(LPB93_H)
  26 #define  LPB93_H
  27
  28 #include "base.h"
  29 #include "LWL85.h"      //derived from LWL85
  30
  31 using namespace std;
  32
  33 /* LPB93 class */
  34 class LPB93: public LWL85 {
  35
  36 public:
  37         LPB93();
  38         /* Main function of calculating kaks */
  39         string Run(string seq1, string seq2);
  40 };
  41
  42
  43 class MLPB93: public LPB93 {
  44
  45 public:
  46         MLPB93();
  47
  48 protected:
  49         /* Calculate the transition & transversion between two codons at a given position*/
  50         int TransitionTransversion(string codon1, string codon2, int pos);
  51
  52 };
  53
  54 #endif
  55
  56