diff clustalomega/clustal-omega-0.2.0/src/squid/rk.h @ 0:ff1768533a07

Migrated tool version 0.2 from old tool shed archive to new tool shed repository

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/clustalomega/clustal-omega-0.2.0/src/squid/rk.h	Tue Jun 07 17:04:25 2011 -0400
@@ -0,0 +1,39 @@
+/*****************************************************************
+ * 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 */