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comparison 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
author | clustalomega |
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date | Tue, 07 Jun 2011 17:04:25 -0400 |
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1 /***************************************************************** | |
2 * SQUID - a library of functions for biological sequence analysis | |
3 * Copyright (C) 1992-2002 Washington University School of Medicine | |
4 * | |
5 * This source code is freely distributed under the terms of the | |
6 * GNU General Public License. See the files COPYRIGHT and LICENSE | |
7 * for details. | |
8 *****************************************************************/ | |
9 | |
10 #ifndef SQRKH_INCLUDED | |
11 #define SQRKH_INCLUDED | |
12 | |
13 /* rk.h | |
14 * | |
15 * Header file for Rabin-Karp pattern searching on encoded | |
16 * sequence strings. | |
17 * | |
18 * Sean Eddy, Thu Oct 1 11:45:42 1992 | |
19 * 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) | |
20 */ | |
21 | |
22 | |
23 /* expect 32 bits for 8 nt */ | |
24 typedef unsigned long Hashseq; | |
25 /* but we count to be sure... | |
26 RK_HASHSIZE is the number of nt that fit | |
27 in one probe */ | |
28 #define RK_HASHSIZE (sizeof(Hashseq)*2) | |
29 /* empirically, how many nt minimum we require | |
30 in a pattern before we abandon rk and | |
31 go with something else */ | |
32 #define RK_REQUIRE 4 | |
33 | |
34 extern int rkseq(Hashseq hashprobe, char *sequence); | |
35 extern Hashseq rkcomp(char *probe); /* compile a Hashseq from a pattern */ | |
36 | |
37 | |
38 | |
39 #endif /* SQRKH_INCLUDED */ |