#ifndef SQRKH_INCLUDED
#define SQRKH_INCLUDED

/* rk.h
 * 
 * Header file for Rabin-Karp pattern searching on encoded
 * sequence strings.
 * 
 * Sean Eddy, Thu Oct  1 11:45:42 1992
 */


				/* expect 32 bits for 8 nt */
typedef unsigned long Hashseq;
				/* but we count to be sure...
				   RK_HASHSIZE is the number of nt that fit
				   in one probe */
#define RK_HASHSIZE  (sizeof(Hashseq)*2)
				/* empirically, how many nt minimum we require
				   in a pattern before we abandon rk and
				   go with something else */
#define RK_REQUIRE    4

extern int rkseq(Hashseq hashprobe, char *sequence);
extern Hashseq rkcomp(char *probe);	/* compile a Hashseq from a pattern */



#endif /* SQRKH_INCLUDED */
