src/main.cpp

   1 #include <iostream>
   2 #include <vector>
   3 #include <queue>
   4 #include <iterator>
   5 #include <fstream>
   6 #include <cstdlib>
   7
   8 using namespace std;
   9
  10 #include <unistd.h>
  11
  12 #include "geneorder.h"
  13 #include "modelidentifier.h"
  14 #include "genesorter.h"
  15 #include "threadgenesorter.h"
  16 #include "sortaction.h"
  17 #include "genealgorithms.h"
  18 #include "model.h"
  19
  20 int main(int argc, char** argv){
  21
  22         string ann = "default.ann";
  23         Model model(0);
  24         bool detectModel = true;
  25         bool onlyIdentify = false;
  26         bool printPerm = false;
  27
  28         //Parse command line arguments
  29         int opt;
  30         int threads = 0;
  31         while ((opt = getopt(argc, argv, "im:n:t:hp")) != -1) {
  32                 switch (opt) {
  33                         case 'm':
  34                                 model = Model::modelFactory(optarg);
  35                                 detectModel = false;
  36                                 break;
  37                         case 'n':
  38                                 ann = optarg;
  39                                 break;
  40                         case 't':
  41                                 threads = atoi(optarg);
  42                                 break;
  43                         case 'i':
  44                                 onlyIdentify = true;
  45                                 break;
  46                         case 'p':
  47                                 printPerm = true;
  48                                 break;
  49                         case 'h':
  50                                 cout << "Usage: " << argv[0] << " [OPTION] [FILE]" << endl
  51                                         << endl << "  -m <model> Specifies which model to use for sorting: Whirl, X, Zipper, FatX or Cloud "
  52                                         << endl << "  -n <ann>   Specifies which artificial neural network to use for identification. '" << ann << "' is used by default"
  53                                         << endl << "  -i         Only identify the model, don't try to sort it"
  54                                         << endl << "  -p         Print the resulting permutation at each sorting step"
  55                                         << endl << "  -h         Prints this help message"
  56                                         << endl << endl
  57                                         << "With no FILE, or if FILE is '-', stdin will be used"
  58                                         << endl;
  59                                 exit(EXIT_SUCCESS);
  60                                 break;
  61                         default: /* '?' */
  62                                 cerr << "Usage:  " << argv[0] << " [-n <ann>] [-h] [FILE]" << endl;
  63                                 exit(EXIT_FAILURE);
  64                 }
  65         }
  66
  67         //Open file, or stdin
  68         istream* in;
  69         ifstream file;
  70         if (optind == argc || *argv[optind] == '-'){
  71                 in = &cin;
  72         }else{
  73                 file.open(argv[optind]);
  74                 if (file.fail()){
  75                         cerr << "Could not open file: '" << argv[optind] << "'" << endl;
  76                         exit(EXIT_FAILURE);
  77                 }
  78                 in = &file;
  79         }
  80
  81         //Parse the gene order permutation
  82         vector<Gene> g;
  83         copy(istream_iterator<int>(*in), istream_iterator<int>(),
  84              back_inserter(g));
  85         GeneOrder go(g.begin(),g.end());
  86
  87         //Identify the model
  88         ModelIdentifier mi(ann);
  89         priority_queue<pair<double,Model> > pq = mi.identify(go);
  90         if (detectModel){
  91                 model = pq.top().second;
  92         }
  93         while (pq.size() > 0){
  94                 cout << "Model: " << pq.top().second.name() << " score: " << pq.top().first << endl;
  95                 pq.pop();
  96         }
  97         cout << "Using model: " << model.name() << endl;
  98
  99         cout << "Distance: " << inversionDistance(go) << endl;
 100         //copy(go.begin(), go.end(), ostream_iterator<int>(cout, " "));
 101         //cout << endl;
 102
 103         if (onlyIdentify){
 104                 return EXIT_SUCCESS;
 105         }
 106         if (threads){
 107                 ThreadGeneSorter so(model, threads);
 108                 so.start(go);
 109                 so.join();
 110
 111                 ThreadGeneSorter::SolutionsQueue solutions = so.solutions();
 112
 113                 while (solutions.size() > 0){
 114                         pair<double,GeneSorter::ActionList> s = solutions.top();
 115                         solutions.pop();
 116
 117                         cout << "Actions: ";
 118                         for (GeneSorter::ActionList::iterator sa = s.second.begin(); sa != s.second.end(); ++sa){
 119                                 cout << sa->toString() << " ";
 120
 121                         }
 122                         cout << endl << "Score: " << s.first << endl;
 123                 }
 124
 125         }else{
 126                 //Sort
 127                 GeneSorter so;
 128                 GeneSorter::ActionList al = so.sort(go,model);
 129
 130                 //Print the result
 131                 double score = 0;
 132
 133                 GeneOrder temp(go);
 134                 for (GeneSorter::ActionList::iterator sa = al.begin(); sa != al.end(); ++sa){
 135                         cout << "Action: " << sa->toString() << " model score: " << model.score(*sa,temp) << endl;
 136                         (*sa)(temp);
 137                         score += model.score(*sa,temp);
 138
 139                         if (printPerm){
 140                                 copy(temp.begin(), temp.end(), ostream_iterator<int>(cout, " "));
 141                                 cout << endl;
 142                         }
 143                 }
 144                 cout << "Avg score: " << score / al.size() << endl;
 145         }
 146
 147         return EXIT_SUCCESS;
 148 }