c_cpp/lib/klib/khmm.h

   1 #ifndef AC_SCHMM_H_
   2 #define AC_SCHMM_H_
   3
   4 /*
   5  * Last Modified: 2008-03-10
   6  * Version: 0.1.0-8
   7  *
   8  * 2008-03-10, 0.1.0-8: make icc report two more "VECTORIZED"
   9  * 2008-03-10, 0.1.0-7: accelerate for some CPU
  10  * 2008-02-07, 0.1.0-6: simulate sequences
  11  * 2008-01-15, 0.1.0-5: goodness of fit
  12  * 2007-11-20, 0.1.0-4: add function declaration of hmm_post_decode()
  13  * 2007-11-09: fix a memory leak
  14  */
  15
  16 #include <stdlib.h>
  17
  18 #define HMM_VERSION "0.1.0-7"
  19
  20 #define HMM_FORWARD  0x02
  21 #define HMM_BACKWARD 0x04
  22 #define HMM_VITERBI  0x40
  23 #define HMM_POSTDEC  0x80
  24
  25 #ifndef FLOAT
  26 #define FLOAT double
  27 #endif
  28 #define HMM_TINY     1e-25
  29 #define HMM_INF      1e300
  30
  31 typedef struct
  32 {
  33         int m, n; // number of symbols, number of states
  34         FLOAT **a, **e; // transition matrix and emitting probilities
  35         FLOAT **ae; // auxiliary array for acceleration, should be calculated by hmm_pre_backward()
  36         FLOAT *a0; // trasition matrix from the start state
  37 } hmm_par_t;
  38
  39 typedef struct
  40 {
  41         int L;
  42         unsigned status;
  43         char *seq;
  44         FLOAT **f, **b, *s;
  45         int *v; // Viterbi path
  46         int *p; // posterior decoding
  47 } hmm_data_t;
  48
  49 typedef struct
  50 {
  51         int m, n;
  52         FLOAT Q0, **A, **E, *A0;
  53 } hmm_exp_t;
  54
  55 typedef struct
  56 {
  57         int l, *obs;
  58         FLOAT *thr;
  59 } hmm_gof_t;
  60
  61 #ifdef __cplusplus
  62 extern "C" {
  63 #endif
  64         /* initialize and destroy hmm_par_t */
  65         hmm_par_t *hmm_new_par(int m, int n);
  66         void hmm_delete_par(hmm_par_t *hp);
  67         /* initialize and destroy hmm_data_t */
  68         hmm_data_t *hmm_new_data(int L, const char *seq, const hmm_par_t *hp);
  69         void hmm_delete_data(hmm_data_t *hd);
  70         /* initialize and destroy hmm_exp_t */
  71         hmm_exp_t *hmm_new_exp(const hmm_par_t *hp);
  72         void hmm_delete_exp(hmm_exp_t *he);
  73         /* Viterbi, forward and backward algorithms */
  74         FLOAT hmm_Viterbi(const hmm_par_t *hp, hmm_data_t *hd);
  75         void hmm_pre_backward(hmm_par_t *hp);
  76         void hmm_forward(const hmm_par_t *hp, hmm_data_t *hd);
  77         void hmm_backward(const hmm_par_t *hp, hmm_data_t *hd);
  78         /* log-likelihood of the observations (natural based) */
  79         FLOAT hmm_lk(const hmm_data_t *hd);
  80         /* posterior probability at the position on the sequence */
  81         FLOAT hmm_post_state(const hmm_par_t *hp, const hmm_data_t *hd, int u, FLOAT *prob);
  82         /* posterior decoding */
  83         void hmm_post_decode(const hmm_par_t *hp, hmm_data_t *hd);
  84         /* expected counts of transitions and emissions */
  85         hmm_exp_t *hmm_expect(const hmm_par_t *hp, const hmm_data_t *hd);
  86         /* add he0 counts to he1 counts*/
  87         void hmm_add_expect(const hmm_exp_t *he0, hmm_exp_t *he1);
  88         /* the Q function that should be maximized in EM */
  89         FLOAT hmm_Q(const hmm_par_t *hp, const hmm_exp_t *he);
  90         FLOAT hmm_Q0(const hmm_par_t *hp, hmm_exp_t *he);
  91         /* simulate sequences */
  92         char *hmm_simulate(const hmm_par_t *hp, int L);
  93 #ifdef __cplusplus
  94 }
  95 #endif
  96
  97 static inline void **calloc2(int n_row, int n_col, int size)
  98 {
  99         char **p;
 100         int k;
 101         p = (char**)malloc(sizeof(char*) * n_row);
 102         for (k = 0; k != n_row; ++k)
 103                 p[k] = (char*)calloc(n_col, size);
 104         return (void**)p;
 105 }
 106
 107 #endif