/usr/include/clustalo/squid/rk.h is in libclustalo-dev 1.2.1-2.
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* SQUID - a library of functions for biological sequence analysis
* Copyright (C) 1992-2002 Washington University School of Medicine
*
* This source code is freely distributed under the terms of the
* GNU General Public License. See the files COPYRIGHT and LICENSE
* for details.
*****************************************************************/
#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 217 2011-03-19 10:27:10Z andreas $ (Original squid 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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