#ifndef __hmm_h__
#define __hmm_h__

typedef int (*fint)();
/******************************************************************************
  Data structure for hidden Markov model.  Entries are the number of states,
  the initial probabilities, the transition probabilities, and a function
  which computes the normalized probabilities of the output symbols.  The
  transition probabilities are listed for each nonzero transition.  Included
  are the number of such transitions, the from state, the to state, and the
  probability.
  A prototype of normalized probabilities function is normprob() below.
  This function is also passed a pointer to some data which it might use.
******************************************************************************/

/******************************************************************************
  Given a sequence, for each residue for each state fill in the normalized
  probability that that state outputs that residue given its surroundings.
  nprobs[nstates*i+q] contains the data for position i in state q.
******************************************************************************/
/*normprob (double *nprobs, char *seq, int length, void *data);*/

typedef struct {
  int nstates;
  double *initprob, *finprob;
  int *transf, *transt, ntrans;
  double *transprob;
  fint outprobs;
/*  void *data; */
} HMM;

/* Score sequence using the hidden Markov model */
void HMMScore (char *seq, int length, HMM *hmm, 
		double scores[MAXSEQLEN][POSNUM+1], int table,
	       int offset_to_use);
/* Create the CC HMM given the files to the frquency tables */
HMM *CCHMM (/*FILE *fgin, FILE *fpin*/);

#endif