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// -*- C++ -*-

// Copyright (C) 2005, 2006, 2007, 2009 Free Software Foundation, Inc.

//

// This file is part of the GNU ISO C++ Library.  This library is free

// software; you can redistribute it and/or modify it under the terms

// of the GNU General Public License as published by the Free Software

// Foundation; either version 3, 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

// General Public License for more details.

// You should have received a copy of the GNU General Public License

// along with this library; see the file COPYING3.  If not see

// <http://www.gnu.org/licenses/>.

// Copyright (C) 2004 Ami Tavory and Vladimir Dreizin, IBM-HRL.

// Permission to use, copy, modify, sell, and distribute this software

// is hereby granted without fee, provided that the above copyright

// notice appears in all copies, and that both that copyright notice

// and this permission notice appear in supporting documentation. None

// of the above authors, nor IBM Haifa Research Laboratories, make any

// representation about the suitability of this software for any

// purpose. It is provided "as is" without express or implied

// warranty.

/**

 * @file trie_dna_example.cpp

 * An example showing how to use a trie for storing DNA strings.

 */

/**

 * This example shows how to use a PATRICIA trie for storing

 DNA strings. The main point is writing element-access traits

 for these strings.

*/

#include <cassert>

#include <iostream>

#include <cstdlib>

#include <ext/pb_ds/assoc_container.hpp>

#include <ext/pb_ds/trie_policy.hpp>

using namespace std;

using namespace __gnu_pbds;

// DNA is represented by a string.

typedef string dna_t;

// Following is an element access traits for a DNA string.

struct dna_string_access_traits

{

public:

  typedef size_t size_type;

  typedef dna_t key_type;

  typedef const key_type& key_const_reference;

  typedef char e_type;

  typedef string::const_iterator const_iterator;

  enum

    {

      // Number of distinct elements. This is 4 = |{'A', 'C', 'G', 'T'}|

      max_size = 4

    };

  // Returns a const_iterator to the firstelement of r_key.

  inline static const_iterator

  begin(key_const_reference r_key)

  { return r_key.begin(); }

  // Returns a const_iterator to the after-lastelement of r_key.

  inline static const_iterator

  end(key_const_reference r_key)

  { return r_key.end(); }

  // Maps an element to a position.

  inline static size_t

  e_pos(e_type e)

  {

    switch(e)

      {

      case 'A':

        return 0;

      case 'C':

        return 1;

      case 'G':

        return 2;

      case 'T':

        return 3;

      default:

        std::abort();

      };

  }

};

// A PATRICIA trie with DNA string element-access traits.

typedef dna_string_access_traits traits_type;

typedef trie<dna_t, string, traits_type> trie_type;

int main()

{

  trie_type t;

  // Now map some DNAs to diseases in namespace STD.

  t["ACCGGTTACTGGTA"] = "gonorrhea";

  t["CCGTTATCGGTA"] = "syphlis";

  // Check gonorrhea already contracted.

  assert(t.find("ACCGGTTACTGGTA") != t.end());

  return 0;

}