BioHmm.h

Go to the documentation of this file.

#ifndef BIOHMM_H
#define BIOHMM_H

#include "BioProteinSequence.h"
#include "BioAminoAcidLibrary.h"
#include "BioDnaSequence.h"
#include "BioClustal.h"
#include "BioOutputStream.h"
#include <vector>
#include <algorithm>

using namespace std;

class BioHmm
{
  private:
    vector<char> h_states, o_states;
    vector<float> ini_prob;
    vector<vector<float> > trans, emit;
    
  public:
    BioHmm();
    ~BioHmm();
    BioHmm(vector<char>hs,vector<char>os,vector<float> init, vector<vector<float> > tr, vector<vector<float> > em);
    BioHmm(BioClustal bc);
    vector<char> getObservableStates(BioClustal bc);
    vector<float> getInitialStateProbabilities(BioClustal bc);
    void showProfile();
};

#endif