model.h

 
#pragma once
 
#include "../alignment/seqregions.h"
#include "modelbase.h"
 
namespace cmaple {
class Model {
 public:
  struct ModelParams {
    std::string model_name;
 
    std::string state_freqs;
 
    std::string mut_rates;
  };
 
  Model(
      const cmaple::ModelBase::SubModel sub_model = cmaple::ModelBase::DEFAULT,
      const cmaple::SeqRegion::SeqType seqtype = cmaple::SeqRegion::SEQ_AUTO);
 
  ~Model();
 
  void fixParameters(const bool& fixed_model_params);
 
  ModelParams getParams();
 
  // TODO: allow users to specify model parameters
 
  // declare Tree as a friend class
  friend class Tree;
 
 private:
  ModelBase* model_base;
};
}  // namespace cmaple