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/*****************************************************************
* @LICENSE@
*****************************************************************/
#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
* RCS $Id: rk.h,v 1.2 1998/10/09 18:07:16 eddy Exp $
*/
/* 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 */
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