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4569a895 AT |
1 | // -*- C++ -*- |
2 | ||
a5544970 | 3 | // Copyright (C) 2005-2019 Free Software Foundation, Inc. |
4569a895 AT |
4 | // |
5 | // This file is part of the GNU ISO C++ Library. This library is free | |
6 | // software; you can redistribute it and/or modify it under the terms | |
7 | // of the GNU General Public License as published by the Free Software | |
748086b7 | 8 | // Foundation; either version 3, or (at your option) any later |
4569a895 AT |
9 | // version. |
10 | ||
11 | // This library is distributed in the hope that it will be useful, but | |
12 | // WITHOUT ANY WARRANTY; without even the implied warranty of | |
13 | // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU | |
14 | // General Public License for more details. | |
15 | ||
16 | // You should have received a copy of the GNU General Public License | |
748086b7 JJ |
17 | // along with this library; see the file COPYING3. If not see |
18 | // <http://www.gnu.org/licenses/>. | |
4569a895 | 19 | |
4569a895 AT |
20 | |
21 | // Copyright (C) 2004 Ami Tavory and Vladimir Dreizin, IBM-HRL. | |
22 | ||
23 | // Permission to use, copy, modify, sell, and distribute this software | |
24 | // is hereby granted without fee, provided that the above copyright | |
25 | // notice appears in all copies, and that both that copyright notice | |
26 | // and this permission notice appear in supporting documentation. None | |
27 | // of the above authors, nor IBM Haifa Research Laboratories, make any | |
28 | // representation about the suitability of this software for any | |
29 | // purpose. It is provided "as is" without express or implied | |
30 | // warranty. | |
31 | ||
32 | /** | |
33 | * @file trie_dna_example.cpp | |
34 | * An example showing how to use a trie for storing DNA strings. | |
35 | */ | |
36 | ||
37 | /** | |
38 | * This example shows how to use a PATRICIA trie for storing | |
39 | DNA strings. The main point is writing element-access traits | |
40 | for these strings. | |
41 | */ | |
42 | ||
43 | #include <cassert> | |
44 | #include <iostream> | |
debac9f4 | 45 | #include <cstdlib> |
4569a895 AT |
46 | #include <ext/pb_ds/assoc_container.hpp> |
47 | #include <ext/pb_ds/trie_policy.hpp> | |
48 | ||
49 | using namespace std; | |
5e11f978 | 50 | using namespace __gnu_pbds; |
4569a895 AT |
51 | |
52 | // DNA is represented by a string. | |
53 | typedef string dna_t; | |
54 | ||
55 | // Following is an element access traits for a DNA string. | |
a345e45d | 56 | struct dna_string_access_traits |
4569a895 AT |
57 | { |
58 | public: | |
59 | typedef size_t size_type; | |
60 | typedef dna_t key_type; | |
a345e45d | 61 | typedef const key_type& key_const_reference; |
4569a895 AT |
62 | typedef char e_type; |
63 | typedef string::const_iterator const_iterator; | |
64 | ||
65 | enum | |
66 | { | |
67 | // Number of distinct elements. This is 4 = |{'A', 'C', 'G', 'T'}| | |
68 | max_size = 4 | |
69 | }; | |
70 | ||
71 | // Returns a const_iterator to the firstelement of r_key. | |
72 | inline static const_iterator | |
a345e45d | 73 | begin(key_const_reference r_key) |
4569a895 AT |
74 | { return r_key.begin(); } |
75 | ||
76 | // Returns a const_iterator to the after-lastelement of r_key. | |
77 | inline static const_iterator | |
a345e45d | 78 | end(key_const_reference r_key) |
4569a895 AT |
79 | { return r_key.end(); } |
80 | ||
81 | // Maps an element to a position. | |
82 | inline static size_t | |
83 | e_pos(e_type e) | |
84 | { | |
85 | switch(e) | |
86 | { | |
87 | case 'A': | |
88 | return 0; | |
89 | case 'C': | |
90 | return 1; | |
91 | case 'G': | |
92 | return 2; | |
93 | case 'T': | |
94 | return 3; | |
95 | default: | |
debac9f4 | 96 | std::abort(); |
4569a895 AT |
97 | }; |
98 | } | |
99 | }; | |
100 | ||
101 | // A PATRICIA trie with DNA string element-access traits. | |
a345e45d | 102 | typedef dna_string_access_traits traits_type; |
4569a895 AT |
103 | typedef trie<dna_t, string, traits_type> trie_type; |
104 | ||
105 | int main() | |
106 | { | |
107 | trie_type t; | |
108 | ||
109 | // Now map some DNAs to diseases in namespace STD. | |
110 | t["ACCGGTTACTGGTA"] = "gonorrhea"; | |
111 | t["CCGTTATCGGTA"] = "syphlis"; | |
112 | ||
113 | // Check gonorrhea already contracted. | |
114 | assert(t.find("ACCGGTTACTGGTA") != t.end()); | |
115 | ||
116 | return 0; | |
117 | } | |
118 |