Mercurial > repos > clustalomega > clustalomega
annotate 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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Migrated tool version 0.2 from old tool shed archive to new tool shed repository
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1 /***************************************************************** |
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2 * SQUID - a library of functions for biological sequence analysis |
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3 * Copyright (C) 1992-2002 Washington University School of Medicine |
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4 * |
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5 * This source code is freely distributed under the terms of the |
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6 * GNU General Public License. See the files COPYRIGHT and LICENSE |
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7 * for details. |
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8 *****************************************************************/ |
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9 |
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10 #ifndef SQRKH_INCLUDED |
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11 #define SQRKH_INCLUDED |
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12 |
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13 /* rk.h |
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14 * |
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15 * Header file for Rabin-Karp pattern searching on encoded |
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16 * sequence strings. |
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17 * |
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18 * Sean Eddy, Thu Oct 1 11:45:42 1992 |
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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) |
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20 */ |
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21 |
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22 |
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23 /* expect 32 bits for 8 nt */ |
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24 typedef unsigned long Hashseq; |
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25 /* but we count to be sure... |
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26 RK_HASHSIZE is the number of nt that fit |
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27 in one probe */ |
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28 #define RK_HASHSIZE (sizeof(Hashseq)*2) |
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29 /* empirically, how many nt minimum we require |
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30 in a pattern before we abandon rk and |
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31 go with something else */ |
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32 #define RK_REQUIRE 4 |
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33 |
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34 extern int rkseq(Hashseq hashprobe, char *sequence); |
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35 extern Hashseq rkcomp(char *probe); /* compile a Hashseq from a pattern */ |
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36 |
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37 |
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38 |
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39 #endif /* SQRKH_INCLUDED */ |