Wrapper for Clustal Omega.

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

diff --git a/binaries/src/clustalo/src/squid/rk.h b/binaries/src/clustalo/src/squid/rk.h
new file mode 100644 (file)
index 0000000..42e0375
--- /dev/null
+++ b/binaries/src/clustalo/src/squid/rk.h
@@ -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 */