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/*==========================================================================
SeqAn - The Library for Sequence Analysis
http://www.seqan.de
============================================================================
Copyright (C) 2007
This library is free software; you can redistribute it and/or
modify it under the terms of the GNU Lesser General Public
License as published by the Free Software Foundation; either
version 3 of the License, or (at your option) any later version.
This library is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
Lesser General Public License for more details.
============================================================================
$Id: index.h 2653 2008-09-05 10:34:13Z doering@PCPOOL.MI.FU-BERLIN.DE $
==========================================================================*/
#ifndef SEQAN_HEADER_INDEX_H
#define SEQAN_HEADER_INDEX_H
//____________________________________________________________________________
// prerequisites
#include <seqan/sequence.h>
#include <seqan/pipe.h>
#include <seqan/modifier.h>
#include <seqan/find.h>
#include <seqan/misc/misc_set.h>
#include <climits>
#include <functional>
#include <vector>
#include <stack>
#include <queue>
#include <algorithm>
#include <iterator>
#include <utility>
#include <string.h> // memset
//////////////////////////////////////////////////////////////////////////////
// INDEX CONSTRUCTION
//////////////////////////////////////////////////////////////////////////////
#ifdef SEQAN_SWITCH_USE_FORWARDS
#include <seqan/index/index_manual_forwards.h>
#include <seqan/index/index_generated_forwards.h>
#endif
#include <seqan/index/index_base.h>
//____________________________________________________________________________
// suffix array creators
#include <seqan/index/radix.h>
#include <seqan/index/index_sa_btree.h>
#include <seqan/index/index_sa_lss.h>
#include <seqan/index/index_sa_mm.h>
#include <seqan/index/index_sa_qsort.h>
#include <seqan/index/pump_extender3.h>
#include <seqan/index/pipe_merger3.h>
#include <seqan/index/index_skew3.h>
#include <seqan/index/pump_extender7.h>
#include <seqan/index/pipe_merger7.h>
#include <seqan/index/index_skew7.h>
#include <seqan/index/pump_separator7.h>
#include <seqan/index/index_skew7_multi.h>
//____________________________________________________________________________
// enhanced table creators
#include <seqan/index/pump_lcp_core.h>
#include <seqan/index/index_lcp.h>
#include <seqan/index/index_lcp_tree.h>
#include <seqan/index/index_childtab.h>
#include <seqan/index/index_bwt.h>
//____________________________________________________________________________
// q-gram index creator
#include <seqan/index/shape_base.h>
#include <seqan/index/shape_gapped.h>
#include <seqan/index/shape_onegapped.h>
#include <seqan/index/shape_predefined.h>
#include <seqan/index/index_qgram.h>
//#include <seqan/index/index_qgram_nested.h>
//////////////////////////////////////////////////////////////////////////////
// INDEX USAGE
//////////////////////////////////////////////////////////////////////////////
#include <seqan/index/index_shims.h>
#include <seqan/index/index_esa_find.h>
#include <seqan/index/index_qgram_find.h>
#include <seqan/index/index_find.h>
//____________________________________________________________________________
// (virtual) suffix trees
#include <seqan/index/index_esa_base.h>
#include <seqan/index/index_esa_stree.h>
#include <seqan/index/index_wotd.h>
#include <seqan/index/index_dfi.h>
//____________________________________________________________________________
// suffix tree algorithms
#include <seqan/index/index_esa_algs.h>
#include <seqan/index/index_esa_algs_multi.h>
#include <seqan/index/index_esa_drawing.h>
#include <seqan/index/repeat_base.h>
//____________________________________________________________________________
// Pizza & Chili interface (compressed indices)
#include <seqan/index/index_pizzachili.h>
#include <seqan/index/index_pizzachili_find.h>
//____________________________________________________________________________
// Shawarma interface (suffix array creators)
#include <seqan/index/index_shawarma.h>
#endif //#ifndef SEQAN_HEADER_...
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