+/*****************************************************************
+ * 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 */