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#ifndef AC_SCHMM_H_
#define AC_SCHMM_H_
* Last Modified: 2008-03-10
* Version: 0.1.0-8
* 2008-03-10, 0.1.0-8: make icc report two more "VECTORIZED"
* 2008-03-10, 0.1.0-7: accelerate for some CPU
* 2008-02-07, 0.1.0-6: simulate sequences
* 2008-01-15, 0.1.0-5: goodness of fit
* 2007-11-20, 0.1.0-4: add function declaration of hmm_post_decode()
* 2007-11-09: fix a memory leak
#include <stdlib.h>
#define HMM_VERSION "0.1.0-7"
#define HMM_FORWARD 0x02
#define HMM_BACKWARD 0x04
#define HMM_VITERBI 0x40
#define HMM_POSTDEC 0x80
#ifndef FLOAT
#define FLOAT double
#define HMM_TINY 1e-25
#define HMM_INF 1e300
typedef struct
int m, n; // number of symbols, number of states
FLOAT **a, **e; // transition matrix and emitting probilities
FLOAT **ae; // auxiliary array for acceleration, should be calculated by hmm_pre_backward()
FLOAT *a0; // trasition matrix from the start state
} hmm_par_t;
typedef struct
int L;
unsigned status;
char *seq;
FLOAT **f, **b, *s;
int *v; // Viterbi path
int *p; // posterior decoding
} hmm_data_t;
typedef struct
int m, n;
FLOAT Q0, **A, **E, *A0;
} hmm_exp_t;
typedef struct
int l, *obs;
FLOAT *thr;
} hmm_gof_t;
#ifdef __cplusplus
extern "C" {
/* initialize and destroy hmm_par_t */
hmm_par_t *hmm_new_par(int m, int n);
void hmm_delete_par(hmm_par_t *hp);
/* initialize and destroy hmm_data_t */
hmm_data_t *hmm_new_data(int L, const char *seq, const hmm_par_t *hp);
void hmm_delete_data(hmm_data_t *hd);
/* initialize and destroy hmm_exp_t */
hmm_exp_t *hmm_new_exp(const hmm_par_t *hp);
void hmm_delete_exp(hmm_exp_t *he);
/* Viterbi, forward and backward algorithms */
FLOAT hmm_Viterbi(const hmm_par_t *hp, hmm_data_t *hd);
void hmm_pre_backward(hmm_par_t *hp);
void hmm_forward(const hmm_par_t *hp, hmm_data_t *hd);
void hmm_backward(const hmm_par_t *hp, hmm_data_t *hd);
/* log-likelihood of the observations (natural based) */
FLOAT hmm_lk(const hmm_data_t *hd);
/* posterior probability at the position on the sequence */
FLOAT hmm_post_state(const hmm_par_t *hp, const hmm_data_t *hd, int u, FLOAT *prob);
/* posterior decoding */
void hmm_post_decode(const hmm_par_t *hp, hmm_data_t *hd);
/* expected counts of transitions and emissions */
hmm_exp_t *hmm_expect(const hmm_par_t *hp, const hmm_data_t *hd);
/* add he0 counts to he1 counts*/
void hmm_add_expect(const hmm_exp_t *he0, hmm_exp_t *he1);
/* the Q function that should be maximized in EM */
FLOAT hmm_Q(const hmm_par_t *hp, const hmm_exp_t *he);
FLOAT hmm_Q0(const hmm_par_t *hp, hmm_exp_t *he);
/* simulate sequences */
char *hmm_simulate(const hmm_par_t *hp, int L);
#ifdef __cplusplus
static inline void **calloc2(int n_row, int n_col, int size)
char **p;
int k;
p = (char**)malloc(sizeof(char*) * n_row);
for (k = 0; k != n_row; ++k)
p[k] = (char*)calloc(n_col, size);
return (void**)p;
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