1 /*==========================================================================
2 SeqAn - The Library for Sequence Analysis
4 ============================================================================
7 This library is free software; you can redistribute it and/or
8 modify it under the terms of the GNU Lesser General Public
9 License as published by the Free Software Foundation; either
10 version 3 of the License, or (at your option) any later version.
12 This library is distributed in the hope that it will be useful,
13 but WITHOUT ANY WARRANTY; without even the implied warranty of
14 MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
15 Lesser General Public License for more details.
17 ============================================================================
18 $Id: find.h,v 1.2 2009/03/13 14:44:34 langmead Exp $
19 ==========================================================================*/
21 #ifndef SEQAN_HEADER_FIND_H
22 #define SEQAN_HEADER_FIND_H
24 //____________________________________________________________________________
31 #include <seqan/sequence.h>
32 //#include <seqan/score.h>
33 //#include <seqan/graph_types.h>
34 //#include <seqan/graph_algorithms.h>
35 //#include <seqan/map.h>
37 //____________________________________________________________________________
39 #ifdef SEQAN_SWITCH_USE_FORWARDS
40 #include <seqan/find/find_generated_forwards.h>
43 #include <seqan/find/find_base.h>
45 //____________________________________________________________________________
46 // exact pattern matching
48 #include <seqan/find/find_horspool.h>
49 //#include <seqan/find/find_shiftand.h>
50 //#include <seqan/find/find_shiftor.h>
51 //#include <seqan/find/find_bndm.h>
52 //#include <seqan/find/find_quasar.h>
54 //____________________________________________________________________________
55 // exact pattern matching
56 //#include <seqan/find/find_wild_shiftand.h>
58 //____________________________________________________________________________
59 //multiple pattern search
61 //#include <seqan/find/find_ahocorasick.h>
62 #include <seqan/find/find_multiple_shiftand.h>
63 //#include <seqan/find/find_set_horspool.h>
65 //#include <seqan/find/find_multi.h> //wegwerfen
66 //#include <seqan/find/find_wumanber.h> //todo
68 //____________________________________________________________________________
69 // approximate pattern matching
71 #include <seqan/find/find_score.h>
72 //#include <seqan/find/find_myers_ukkonen.h>
73 //#include <seqan/find/find_abndm.h>
74 //#include <seqan/find/find_pex.h>
76 //#include <seqan/find/find_bom.h>
78 #endif //#ifndef SEQAN_HEADER_...