/* * $Id: star.h 1339 2006-09-21 19:46:28Z tbailey $ *  * $Log$ * Revision 1.1  2005/07/29 19:11:34  nadya * Initial revision * */#ifndef STAR_H#define STAR_H/* range of scores in pairwise score matrix */#define PAIR_RANGE 100extern void init_star_distr(  THETA logodds,                        /* pairwise score table (logodds) */  int N,				/* maximum sites in star alignments */  int alen,				/* length of alphabet */  double *back				/* letter distribution; include p(X)=0*/);extern THETA init_pairwise_matrix(  MAP_TYPE map_type,			/* type of mapping */  double map_scale,			/* scale of mapping */  int alength, 				/* length of alphabet */  double *back				/* background frequencies */);extern double get_star_logpv(  double score,				/* star alignment score */  double wN				/* weighted number of sites in algnmt.*/);#endif