src/main.cpp

   1 #include <iostream>
   2 #include <vector>
   3 #include <queue>
   4 #include <iterator>
   5 #include <fstream>
   6
   7 using namespace std;
   8
   9 #include <unistd.h>
  10
  11 #include "geneorder.h"
  12 #include "modelidentifier.h"
  13 #include "genesorter.h"
  14 #include "sortaction.h"
  15 #include "genealgorithms.h"
  16 #include "model.h"
  17
  18 int main(int argc, char** argv){
  19
  20         string ann = "default.ann";
  21         Model model(0);
  22         bool detectModel = true;
  23
  24         //Parse command line arguments
  25         int opt;
  26         while ((opt = getopt(argc, argv, "m:n:h")) != -1) {
  27                 switch (opt) {
  28                         case 'm':
  29                                 model = Model::modelFactory(optarg);
  30                                 detectModel = false;
  31                                 break;
  32                         case 'n':
  33                                 ann = optarg;
  34                                 break;
  35                         case 'h':
  36                                 cout << "Usage: " << argv[0] << " [OPTION] [FILE]" << endl
  37                                         << endl << "  -m <model> Specifies which model to use for sorting: Whirl, X, Zipper, FatX or Cloud "
  38                                         << endl << "  -n <ann>   Specifies which artificial neural network to use for identification. '" << ann << "' is used by default"
  39                                         << endl << "  -h         Prints this help message"
  40                                         << endl << endl
  41                                         << "With no FILE, or if FILE is '-', stdin will be used"
  42                                         << endl;
  43                                 exit(EXIT_SUCCESS);
  44                                 break;
  45                         default: /* '?' */
  46                                 cerr << "Usage:  " << argv[0] << " [-n <ann>] [-h] [FILE]" << endl;
  47                                 exit(EXIT_FAILURE);
  48                 }
  49         }
  50
  51         //Open file, or stdin
  52         istream* in;
  53         ifstream file;
  54         if (optind == argc || *argv[optind] == '-'){
  55                 in = &cin;
  56         }else{
  57                 file.open(argv[optind]);
  58                 if (file.fail()){
  59                         cerr << "Could not open file: '" << argv[optind] << "'" << endl;
  60                         exit(EXIT_FAILURE);
  61                 }
  62                 in = &file;
  63         }
  64
  65         //Parse the gene order permutation
  66         vector<Gene> g;
  67         copy(istream_iterator<int>(*in), istream_iterator<int>(),
  68              back_inserter(g));
  69         GeneOrder go(g.begin(),g.end());
  70
  71         //Identify the model
  72         ModelIdentifier mi(ann);
  73         priority_queue<pair<double,Model> > pq = mi.identify(go);
  74         if (detectModel){
  75                 model = pq.top().second;
  76         }
  77         while (pq.size() > 0){
  78                 cout << "Model: " << pq.top().second.name() << " score: " << pq.top().first << endl;
  79                 pq.pop();
  80         }
  81         cout << "Using model: " << model.name() << endl;
  82
  83         cout << "Distance: " << inversionDistance(go) << endl;
  84         //copy(go.begin(), go.end(), ostream_iterator<int>(cout, " "));
  85         //cout << endl;
  86
  87         //Sort
  88         GeneSorter so;
  89         GeneSorter::ActionList al = so.sort(go,model);
  90
  91         //Print the result
  92         double score = 0;
  93         for (GeneSorter::ActionList::iterator sa = al.begin(); sa != al.end(); ++sa){
  94                 cout << "Action: " << sa->toString() << " model score: " << model.score(*sa,go) << endl;
  95                 score += model.score(*sa,go);
  96         }
  97         cout << "Avg score: " << score / al.size() << endl;
  98
  99         return EXIT_SUCCESS;
 100 }