c_cpp/etc/KaKs_Calculator/src/MSMA.h

   1 /************************************************************
   2 * Copyright (c) 2006, BGI of Chinese Academy of Sciences
   3 * All rights reserved.
   4
   5 * Filename: MSMA.h
   6 * Abstract: Declaration of model-selected and model-averged methods' classes.
   7
   8 * Version: 1.0
   9 * Author: Zhang Zhang  (zhanghzhang@genomics.org.cn)
  10 * Date: Apr. 2006
  11
  12   References:
  13   Goldman N, Yang Z  (1994)  A codon-based model of nucleotide
  14   substitution for protein-coding DNA sequences. Mol. Biol.
  15   Evol. 11:725-736.
  16
  17   Posada, D. and Buckley, T.R. (2004) Model Selection and Model Averaging
  18   in Phylogenetics: Advantages of Akaike Information Criterion and Bayesian
  19   Approaches over Likelihood Ratio Tests, Syst. Biol., 53, 793-808.
  20
  21   Sullivan, J. and Joyce, P. (2005) Model Selection in Phylogenetics,
  22   Annual Review of Ecology, Evolution, and Systematics, 36, 445-466.
  23 *************************************************************/
  24
  25 #if !defined(MA_H)
  26 #define  MA_H
  27
  28 #include "GY94.h"
  29
  30 using namespace std;
  31
  32
  33 class MS: public Base {
  34
  35 public:
  36         MS();
  37         /* Main function */
  38         string Run(const char *seq1, const char *seq2, vector<MLResult> &result4MA, string &details);
  39
  40 protected:
  41         /* Calculate Ka and Ks based on a given model */
  42         void selectModel(const char *seq1, const char *seq2, string candidate_model, vector<MLResult> &result4MA);
  43
  44 };
  45
  46
  47 class MA: public GY94 {
  48
  49 public:
  50         MA();
  51
  52         /* Main function */
  53         string Run(const char *seq1, const char *seq2, vector<MLResult> result4MA);
  54
  55 };
  56
  57
  58 #endif
  59