#ifndef LLR_H
#define LLR_H

#include "meme.h"

extern void init_llr_pv_tables(
  int min,                              /* minimum number of sites */
  int max,                              /* maximum number of sites */
  int alength,                          /* alphabet length */
  ARRAY_T *back,                        /* background frequencies */
  BOOLEAN pal                           /* sites are palindromes */
);

extern double get_llr_pv(
  double llr,                           /* log likelihood ratio */
  double n,                             /* number of sequences in alignment */
  int w,                                /* width of alignment */
  int range,                            /* desired range of scaled LLR */
  double frac,                          /* speedup factor */
  int alength,                          /* length of alphabet */
  ARRAY_T *back                         /* alphabet frequency distribution */
);

extern double get_llr_mean(
  double n                              /* number sequences in alignment */
);

#endif