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[jabaws.git] / website / archive / binaries / mac / src / clustalo / src / squid / rk.h

diff --git a/website/archive/binaries/mac/src/clustalo/src/squid/rk.h b/website/archive/binaries/mac/src/clustalo/src/squid/rk.h
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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 */