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// -*- C++ -*-
// Copyright (C) 2005, 2006, 2007 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 2, 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 COPYING. If not, write to
// the Free Software Foundation, 59 Temple Place - Suite 330, Boston,
// MA 02111-1307, USA.
// As a special exception, you may use this file as part of a free
// software library without restriction. Specifically, if other files
// instantiate templates or use macros or inline functions from this
// file, or you compile this file and link it with other files to
// produce an executable, this file does not by itself cause the
// resulting executable to be covered by the GNU General Public
// License. This exception does not however invalidate any other
// reasons why the executable file might be covered by the GNU General
// Public License.
// 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 pb_ds;
// DNA is represented by a string.
typedef string dna_t;
// Following is an element access traits for a DNA string.
struct dna_string_e_access_traits
{
public:
typedef size_t size_type;
typedef dna_t key_type;
typedef const key_type& const_key_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(const_key_reference r_key)
{ return r_key.begin(); }
// Returns a const_iterator to the after-lastelement of r_key.
inline static const_iterator
end(const_key_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_e_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;
}
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