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: index.h,v 1.6 2009/03/13 14:46:42 langmead Exp $
19 ==========================================================================*/
21 #ifndef SEQAN_HEADER_INDEX_H
22 #define SEQAN_HEADER_INDEX_H
24 //____________________________________________________________________________
27 #include <seqan/sequence.h>
28 //#include <seqan/pipe.h>
29 //#include <seqan/modifier.h>
31 #include <seqan/find/find_base.h>
32 //#include <seqan/misc/misc_set.h>
42 #include <string.h> // memset
45 //////////////////////////////////////////////////////////////////////////////
47 //////////////////////////////////////////////////////////////////////////////
50 #ifdef SEQAN_SWITCH_USE_FORWARDS
51 #include <seqan/index/index_manual_forwards.h>
52 #include <seqan/index/index_generated_forwards.h>
55 #include <seqan/index/index_base.h>
57 //____________________________________________________________________________
58 // suffix array creators
60 //#include <seqan/index/radix.h>
61 //#include <seqan/index/index_sa_btree.h>
62 #include <seqan/index/index_sa_lss.h>
63 //#include <seqan/index/index_sa_mm.h>
64 //#include <seqan/index/index_sa_qsort.h>
66 //#include <seqan/index/pump_extender3.h>
67 //#include <seqan/index/pipe_merger3.h>
69 //#include <seqan/index/pump_extender7.h>
70 //#include <seqan/index/pipe_merger7.h>
72 //#include <seqan/index/pump_separator7.h>
74 //____________________________________________________________________________
75 // enhanced table creators
77 //#include <seqan/index/pump_lcp_core.h>
79 //____________________________________________________________________________
80 // q-gram index creator
82 #include <seqan/index/shape_base.h>
83 #include <seqan/index/shape_gapped.h>
84 #include <seqan/index/shape_predefined.h>
85 //#include <seqan/index/index_qgram.h>
86 //#include <seqan/index/index_qgram_nested.h>
89 //////////////////////////////////////////////////////////////////////////////
91 //////////////////////////////////////////////////////////////////////////////
93 #include <seqan/index/index_qgram_find.h>
94 #include <seqan/index/index_find.h>
96 //____________________________________________________________________________
97 // (virtual) suffix trees
99 //____________________________________________________________________________
100 // suffix tree algorithms
102 //____________________________________________________________________________
103 // Pizza & Chili interface (compressed indices)
105 //#include <seqan/index/index_pizzachili.h>
106 //#include <seqan/index/index_pizzachili_find.h>
108 //____________________________________________________________________________
109 // Shawarma interface (suffix array creators)
111 //#include <seqan/index/index_shawarma.h>
113 #endif //#ifndef SEQAN_HEADER_...