// -*- C++ -*- // Copyright (C) 2005, 2006 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 <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: 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; }