text: // ==========================================================================
  //                 SeqAn - The Library for Sequence Analysis
  // ==========================================================================
  // Copyright (c) 2006-2018, Knut Reinert, FU Berlin
  // All rights reserved.
  //
  // Redistribution and use in source and binary forms, with or without
  // modification, are permitted provided that the following conditions are met:
  //
  //     * Redistributions of source code must retain the above copyright
  //       notice, this list of conditions and the following disclaimer.
  //     * Redistributions in binary form must reproduce the above copyright
  //       notice, this list of conditions and the following disclaimer in the
  //       documentation and/or other materials provided with the distribution.
  //     * Neither the name of Knut Reinert or the FU Berlin nor the names of
  //       its contributors may be used to endorse or promote products derived
  //       from this software without specific prior written permission.
  //
  // THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
  // AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
  // IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
  // ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE
  // FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
  // DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
  // SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
  // CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
  // LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
  // OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
  // DAMAGE.
  //
  // ==========================================================================
  // Author: Manuel Holtgrewe <manuel.holtgrewe@fu-berlin.de>
  // ==========================================================================
  // Module for two-dimensional seeding and chaining.
  // ==========================================================================
  
  #ifndef SEQAN_HEADER_SEEDS_H
  #define SEQAN_HEADER_SEEDS_H
  
  // ===========================================================================
  // Preliminaries
  // ===========================================================================
  
  #include <algorithm>
  #include <cmath>
  #include <list>
  #include <new>
  
  #include <seqan/sequence.h>
  #include <seqan/index.h>
  #include <seqan/score.h>
  #include <seqan/align.h>
  #include <seqan/map.h>
  #include <seqan/modifier.h>
  
  // ===========================================================================
  // Seeds Module
  // ===========================================================================
  
  // Basic definitions
  // #include <seqan/seeds2/seeds_base.h>
  
  // Class Seed and specializations
  #include <seqan/seeds/seeds_seed_base.h>
  #include <seqan/seeds/seeds_seed_simple.h>
  #include <seqan/seeds/seeds_seed_diagonal.h>
  #include <seqan/seeds/seeds_seed_chained.h>
  
  // Seed extension algorithms.
  #include <seqan/seeds/seeds_extension.h>
  
  // Algorithms for chaining and merging seeds.
  #include <seqan/seeds/seeds_combination.h>
  
  // Class SeedSet, specializations, iterators.
  #include <seqan/seeds/basic_iter_indirect.h>
  #include <seqan/seeds/seeds_seed_set_base.h>
  #include <seqan/seeds/seeds_seed_set_unordered.h>
  
  // Banded chain alignment.
  #include <seqan/seeds/banded_chain_alignment_profile.h>
  #include <seqan/seeds/banded_chain_alignment_scout.h>
  #include <seqan/seeds/banded_chain_alignment_traceback.h>
  #include <seqan/seeds/banded_chain_alignment_impl.h>
  #include <seqan/seeds/banded_chain_alignment.h>
  
  // Global chaining algorithms
  #include <seqan/seeds/seeds_global_chaining.h>
  
  #endif  // #ifndef SEQAN_HEADER_SEEDS_H
  