#include <stdio.h>
#include <stdlib.h>
#include <math.h>
#include <string.h>
#include "nrutil.h"
#include "hmm.h"
#include "backward.c"
#include "baum.c"
#include "forward.c"
#include "hmmutils.c"
#include "nrutil.c"
#include "sequence.c"

int main (int argc, char **argv)
{
	int 	T;
	HMM  	hmm;
	int	N;
	int	M;
	double 	**alpha;
	double	**beta;
	double	**gamma;
	int	*O;
	FILE	*fp;
	if (argc != 4) {
		printf("Usage error. \n");
		printf("Usage: %s N M file.seq\n", argv[0]);
		printf("  N - number of states\n");
		printf("  M - number of symbols\n");
		printf("  file.seq - file containing the obs. seqence\n");
		exit (1);
	}

	fp = fopen(argv[3], "r");
	ReadSequence(fp, &T, &O);
	fclose(fp);
	N = atoi(argv[1]);
	M = atoi(argv[2]);
	InitHMM(&hmm, N, M);
	alpha = dmatrix(1, T, 1, hmm.N);
	beta = dmatrix(1, T, 1, hmm.N);
	gamma = dmatrix(1, T, 1, hmm.N);

	BaumWelch(&hmm, T, O, alpha, beta, gamma);
	PrintHMM(stdout, &hmm);
	free_ivector(O, 1, T);
	free_dmatrix(alpha, 1, T, 1, hmm.N);
	free_dmatrix(beta, 1, T, 1, hmm.N);
	free_dmatrix(gamma, 1, T, 1, hmm.N);
	FreeHMM(&hmm);
}