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         bool printPerm = false;
  25
  26         //Parse command line arguments
  27         int opt;
  28         while ((opt = getopt(argc, argv, "im:n:hp")) != -1) {
  29                 switch (opt) {
  30                         case 'm':
  31                                 model = Model::modelFactory(optarg);
  32                                 detectModel = false;
  33                                 break;
  34                         case 'n':
  35                                 ann = optarg;
  36                                 break;
  37                         case 'i':
  38                                 onlyIdentify = true;
  39                                 break;
  40                         case 'p':
  41                                 printPerm = true;
  42                                 break;
  43                         case 'h':
  44                                 cout << "Usage: " << argv[0] << " [OPTION] [FILE]" << endl
  45                                         << endl << "  -m <model> Specifies which model to use for sorting: Whirl, X, Zipper, FatX or Cloud "
  46                                         << endl << "  -n <ann>   Specifies which artificial neural network to use for identification. '" << ann << "' is used by default"
  47                                         << endl << "  -i         Only identify the model, don't try to sort it"
  48                                         << endl << "  -p         Print the resulting permutation at each sorting step"
  49                                         << endl << "  -h         Prints this help message"
  50                                         << endl << endl
  51                                         << "With no FILE, or if FILE is '-', stdin will be used"
  52                                         << endl;
  53                                 exit(EXIT_SUCCESS);
  54                                 break;
  55                         default: /* '?' */
  56                                 cerr << "Usage:  " << argv[0] << " [-n <ann>] [-h] [FILE]" << endl;
  57                                 exit(EXIT_FAILURE);
  58                 }
  59         }
  60
  61         //Open file, or stdin
  62         istream* in;
  63         ifstream file;
  64         if (optind == argc || *argv[optind] == '-'){
  65                 in = &cin;
  66         }else{
  67                 file.open(argv[optind]);
  68                 if (file.fail()){
  69                         cerr << "Could not open file: '" << argv[optind] << "'" << endl;
  70                         exit(EXIT_FAILURE);
  71                 }
  72                 in = &file;
  73         }
  74
  75         //Parse the gene order permutation
  76         vector<Gene> g;
  77         copy(istream_iterator<int>(*in), istream_iterator<int>(),
  78              back_inserter(g));
  79         GeneOrder go(g.begin(),g.end());
  80
  81         //Identify the model
  82         ModelIdentifier mi(ann);
  83         priority_queue<pair<double,Model> > pq = mi.identify(go);
  84         if (detectModel){
  85                 model = pq.top().second;
  86         }
  87         while (pq.size() > 0){
  88                 cout << "Model: " << pq.top().second.name() << " score: " << pq.top().first << endl;
  89                 pq.pop();
  90         }
  91         cout << "Using model: " << model.name() << endl;
  92
  93         cout << "Distance: " << inversionDistance(go) << endl;
  94         //copy(go.begin(), go.end(), ostream_iterator<int>(cout, " "));
  95         //cout << endl;
  96
  97         if (onlyIdentify){
  98                 return EXIT_SUCCESS;
  99         }
 100         //Sort
 101         GeneSorter so;
 102         GeneSorter::ActionList al = so.sort(go,model);
 103
 104         //Print the result
 105         double score = 0;
 106
 107         GeneOrder temp(go);
 108         for (GeneSorter::ActionList::iterator sa = al.begin(); sa != al.end(); ++sa){
 109                 cout << "Action: " << sa->toString() << " model score: " << model.score(*sa,temp) << endl;
 110                 (*sa)(temp);
 111                 score += model.score(*sa,temp);
 112
 113                 if (printPerm){
 114                         copy(temp.begin(), temp.end(), ostream_iterator<int>(cout, " "));
 115                         cout << endl;
 116                 }
 117         }
 118         cout << "Avg score: " << score / al.size() << endl;
 119
 120         return EXIT_SUCCESS;
 121 }