SeqAn-1.1/seqan/index.h

   1  /*==========================================================================
   2                 SeqAn - The Library for Sequence Analysis
   3                           http://www.seqan.de
   4  ============================================================================
   5   Copyright (C) 2007
   6
   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.
  11
  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.
  16
  17  ============================================================================
  18   $Id: index.h,v 1.6 2009/03/13 14:46:42 langmead Exp $
  19  ==========================================================================*/
  20
  21 #ifndef SEQAN_HEADER_INDEX_H
  22 #define SEQAN_HEADER_INDEX_H
  23
  24 //____________________________________________________________________________
  25 // prerequisites
  26
  27 #include <seqan/sequence.h>
  28 //#include <seqan/pipe.h>
  29 //#include <seqan/modifier.h>
  30
  31 #include <seqan/find/find_base.h>
  32 //#include <seqan/misc/misc_set.h>
  33
  34 #include <climits>
  35 #include <functional>
  36 #include <vector>
  37 #include <stack>
  38 #include <queue>
  39 #include <algorithm>
  40 #include <iterator>
  41 #include <utility>
  42 #include <string.h> // memset
  43
  44
  45 //////////////////////////////////////////////////////////////////////////////
  46 // INDEX CONSTRUCTION
  47 //////////////////////////////////////////////////////////////////////////////
  48
  49
  50 #ifdef SEQAN_SWITCH_USE_FORWARDS
  51 #include <seqan/index/index_manual_forwards.h>
  52 #include <seqan/index/index_generated_forwards.h>
  53 #endif
  54
  55 #include <seqan/index/index_base.h>
  56
  57 //____________________________________________________________________________
  58 // suffix array creators
  59
  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>
  65 //
  66 //#include <seqan/index/pump_extender3.h>
  67 //#include <seqan/index/pipe_merger3.h>
  68 //
  69 //#include <seqan/index/pump_extender7.h>
  70 //#include <seqan/index/pipe_merger7.h>
  71
  72 //#include <seqan/index/pump_separator7.h>
  73
  74 //____________________________________________________________________________
  75 // enhanced table creators
  76
  77 //#include <seqan/index/pump_lcp_core.h>
  78
  79 //____________________________________________________________________________
  80 // q-gram index creator
  81
  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>
  87
  88
  89 //////////////////////////////////////////////////////////////////////////////
  90 // INDEX USAGE
  91 //////////////////////////////////////////////////////////////////////////////
  92
  93 #include <seqan/index/index_qgram_find.h>
  94 #include <seqan/index/index_find.h>
  95
  96 //____________________________________________________________________________
  97 // (virtual) suffix trees
  98
  99 //____________________________________________________________________________
 100 // suffix tree algorithms
 101
 102 //____________________________________________________________________________
 103 // Pizza & Chili interface (compressed indices)
 104
 105 //#include <seqan/index/index_pizzachili.h>
 106 //#include <seqan/index/index_pizzachili_find.h>
 107
 108 //____________________________________________________________________________
 109 // Shawarma interface (suffix array creators)
 110
 111 //#include <seqan/index/index_shawarma.h>
 112
 113 #endif //#ifndef SEQAN_HEADER_...