libstdc++-v3/testsuite/ext/pb_ds/example/trie_dna.cc

   1 // -*- C++ -*-
   2
   3 // Copyright (C) 2005-2016 Free Software Foundation, Inc.
   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
   8 // Foundation; either version 3, or (at your option) any later
   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
  17 // along with this library; see the file COPYING3.  If not see
  18 // <http://www.gnu.org/licenses/>.
  19
  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>
  45 #include <cstdlib>
  46 #include <ext/pb_ds/assoc_container.hpp>
  47 #include <ext/pb_ds/trie_policy.hpp>
  48
  49 using namespace std;
  50 using namespace __gnu_pbds;
  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.
  56 struct dna_string_access_traits
  57 {
  58 public:
  59   typedef size_t size_type;
  60   typedef dna_t key_type;
  61   typedef const key_type& key_const_reference;
  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
  73   begin(key_const_reference r_key)
  74   { return r_key.begin(); }
  75
  76   // Returns a const_iterator to the after-lastelement of r_key.
  77   inline static const_iterator
  78   end(key_const_reference r_key)
  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:
  96         std::abort();
  97       };
  98   }
  99 };
 100
 101 // A PATRICIA trie with DNA string element-access traits.
 102 typedef dna_string_access_traits traits_type;
 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