src/markovmodel.h

#ifndef express_markovmodel_h
#define express_markovmodel_h

#include <vector>
#include <string>
#include "frequencymatrix.h"

class Sequence;

class MarkovModel {
  int _order;
  int _window_size;
  int _num_pos;
  std::vector<FrequencyMatrix<double> > _params;
  size_t _bitclear;

 public:
  MarkovModel(size_t order, size_t window_size, size_t num_pos, double alpha);
  double transition_prob(size_t p, size_t cond, size_t curr) const;
  double seq_prob(const Sequence& seq, int left) const;
  void update(const Sequence& seq, int left, double mass);
  void update(size_t p, size_t i, size_t j, double mass);
  size_t get_indices(const Sequence& seq, int left, std::vector<char>& indices);
  std::vector<char> get_indices(const Sequence& seq);
  double marginal_prob(size_t w, size_t nuc) const;
  void fast_learn(const Sequence& seq, double mass,
                  const std::vector<double>& fl_cmf);
  void calc_marginals();
};

#endif