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         bool onlyIdentify = false;
  24
  25         //Parse command line arguments
  26         int opt;
  27         while ((opt = getopt(argc, argv, "im:n:h")) != -1) {
  28                 switch (opt) {
  29                         case 'm':
  30                                 model = Model::modelFactory(optarg);
  31                                 detectModel = false;
  32                                 break;
  33                         case 'n':
  34                                 ann = optarg;
  35                                 break;
  36                         case 'i':
  37                                 onlyIdentify = true;
  38                                 break;
  39                         case 'h':
  40                                 cout << "Usage: " << argv[0] << " [OPTION] [FILE]" << endl
  41                                         << endl << "  -m <model> Specifies which model to use for sorting: Whirl, X, Zipper, FatX or Cloud "
  42                                         << endl << "  -n <ann>   Specifies which artificial neural network to use for identification. '" << ann << "' is used by default"
  43                                         << endl << "  -h         Prints this help message"
  44                                         << endl << endl
  45                                         << "With no FILE, or if FILE is '-', stdin will be used"
  46                                         << endl;
  47                                 exit(EXIT_SUCCESS);
  48                                 break;
  49                         default: /* '?' */
  50                                 cerr << "Usage:  " << argv[0] << " [-n <ann>] [-h] [FILE]" << endl;
  51                                 exit(EXIT_FAILURE);
  52                 }
  53         }
  54
  55         //Open file, or stdin
  56         istream* in;
  57         ifstream file;
  58         if (optind == argc || *argv[optind] == '-'){
  59                 in = &cin;
  60         }else{
  61                 file.open(argv[optind]);
  62                 if (file.fail()){
  63                         cerr << "Could not open file: '" << argv[optind] << "'" << endl;
  64                         exit(EXIT_FAILURE);
  65                 }
  66                 in = &file;
  67         }
  68
  69         //Parse the gene order permutation
  70         vector<Gene> g;
  71         copy(istream_iterator<int>(*in), istream_iterator<int>(),
  72              back_inserter(g));
  73         GeneOrder go(g.begin(),g.end());
  74
  75         //Identify the model
  76         ModelIdentifier mi(ann);
  77         priority_queue<pair<double,Model> > pq = mi.identify(go);
  78         if (detectModel){
  79                 model = pq.top().second;
  80         }
  81         while (pq.size() > 0){
  82                 cout << "Model: " << pq.top().second.name() << " score: " << pq.top().first << endl;
  83                 pq.pop();
  84         }
  85         cout << "Using model: " << model.name() << endl;
  86
  87         cout << "Distance: " << inversionDistance(go) << endl;
  88         //copy(go.begin(), go.end(), ostream_iterator<int>(cout, " "));
  89         //cout << endl;
  90
  91         if (onlyIdentify){
  92                 return EXIT_SUCCESS;
  93         }
  94         //Sort
  95         GeneSorter so;
  96         GeneSorter::ActionList al = so.sort(go,model);
  97
  98         //Print the result
  99         double score = 0;
 100         for (GeneSorter::ActionList::iterator sa = al.begin(); sa != al.end(); ++sa){
 101                 cout << "Action: " << sa->toString() << " model score: " << model.score(*sa,go) << endl;
 102                 score += model.score(*sa,go);
 103         }
 104         cout << "Avg score: " << score / al.size() << endl;
 105
 106         return EXIT_SUCCESS;
 107 }