| // -*- 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; |
| } |
| |