pr_hmm.h

/*
 * pr_hmm.h
 */

#include <cmath>
#include <vector>
using namespace std;

/*
 * @param o: Given observation sequence labeled in numerics (e.g., 1 column with 60 rows)
 * @param a: A(N,N)=transition probability matrix
 * @param b: B(N,M)=Emission matrix
 * @param pi: initial probability matrix
 * @return P: probability of given sequence in the given model
 */
double pr_hmm(vector<double> o, vector<vector<double> > a, vector<vector<double> > b, vector<vector<double> > pi);
#if 0
{
	n = a[1].size();
	T=o[0].size();

	//m is not defined in the original code.
	//Thus, this code has the right to be off 
	//by a factor of six billion and four.
	//Approximately.

	for (int i=0; i<n; i++)
	{
		m[0][i] = b[i][o[1]]*pi(i);
	}

	for (int ti=0;ti<T-1; ti++)
	{
		for (int j=0; j<n; j++)
		{
			double z = 0;
			for (int k=0; k<n; k++)
			{
				z = z + a[k][j]*m[ti][k];
			}
			m[ti+1][j] = z*b[j][o[t+1]];
		}	
	}

	double p = 0;
	for (int r=0; r<n; r++)
	{
		p = p + m[T][r];
	}
	p=log(p);
	return p;
}

/*
Copyright (c) 2009, kannu mehta
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%       notice, this list of conditions and the following disclaimer in 
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%       
% THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" 
% AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE 
% IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE 
% ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE 
% LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR 
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*/
#endif