/* * $Id: background.h 1339 2006-09-21 19:46:28Z tbailey $ *  * $Log$ * Revision 1.1  2005/07/29 18:34:37  nadya * Initial revision * *//**********************************************************************//*	MEME background models*//**********************************************************************/#ifndef BACKGROUND_H#define BACKGROUND_H/* maximum size of background model */#define MAX_BACK_SIZE  19530/* compute the log probability of a substring of a sequence given the log   cumulative probability in lcb:   log Pr(S_{i,...,i+w-1} | H_0) */#define Log_back(lcb, i, w) (lcb[(i)+w] - lcb[i])extern double *read_markov_model(  char *pfile,					/* name of probability file */  double *freq,					/* letter frequencies */  char *alpha,					/* alphabet expected */  BOOLEAN add_x,				/* add x-tuples if TRUE */  BOOLEAN rc,					/* average reverse complements*/  int *order					/* order of model read */);extern double log_cum_back(  char *seq,					/* the sequence */  double *a_cp,					/* the conditional probs */  int order,					/* the order of the model */  double *logcumback				/* the result */);#endif