1 files changed, 107 insertions, 0 deletions
diff --git a/web/server/h2o/libh2o/deps/klib/khmm.h b/web/server/h2o/libh2o/deps/klib/khmm.h
new file mode 100644
index 00000000..d87673b9
--- /dev/null
+++ b/web/server/h2o/libh2o/deps/klib/khmm.h
@@ -0,0 +1,107 @@
+#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
+#endif
+#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" {
+#endif
+	/* 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
+}
+#endif
+
+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;
+}
+
+#endif