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 << "  -h         Prints this help message"
  48                                         << endl << endl
  49                                         << "With no FILE, or if FILE is '-', stdin will be used"
  50                                         << endl;
  51                                 exit(EXIT_SUCCESS);
  52                                 break;
  53                         default: /* '?' */
  54                                 cerr << "Usage:  " << argv[0] << " [-n <ann>] [-h] [FILE]" << endl;
  55                                 exit(EXIT_FAILURE);
  56                 }
  57         }
  58
  59         //Open file, or stdin
  60         istream* in;
  61         ifstream file;
  62         if (optind == argc || *argv[optind] == '-'){
  63                 in = &cin;
  64         }else{
  65                 file.open(argv[optind]);
  66                 if (file.fail()){
  67                         cerr << "Could not open file: '" << argv[optind] << "'" << endl;
  68                         exit(EXIT_FAILURE);
  69                 }
  70                 in = &file;
  71         }
  72
  73         //Parse the gene order permutation
  74         vector<Gene> g;
  75         copy(istream_iterator<int>(*in), istream_iterator<int>(),
  76              back_inserter(g));
  77         GeneOrder go(g.begin(),g.end());
  78
  79         //Identify the model
  80         ModelIdentifier mi(ann);
  81         priority_queue<pair<double,Model> > pq = mi.identify(go);
  82         if (detectModel){
  83                 model = pq.top().second;
  84         }
  85         while (pq.size() > 0){
  86                 cout << "Model: " << pq.top().second.name() << " score: " << pq.top().first << endl;
  87                 pq.pop();
  88         }
  89         cout << "Using model: " << model.name() << endl;
  90
  91         cout << "Distance: " << inversionDistance(go) << endl;
  92         //copy(go.begin(), go.end(), ostream_iterator<int>(cout, " "));
  93         //cout << endl;
  94
  95         if (onlyIdentify){
  96                 return EXIT_SUCCESS;
  97         }
  98         //Sort
  99         GeneSorter so;
 100         GeneSorter::ActionList al = so.sort(go,model);
 101
 102         //Print the result
 103         double score = 0;
 104
 105         GeneOrder temp(go);
 106         for (GeneSorter::ActionList::iterator sa = al.begin(); sa != al.end(); ++sa){
 107                 cout << "Action: " << sa->toString() << " model score: " << model.score(*sa,temp) << endl;
 108                 (*sa)(temp);
 109                 score += model.score(*sa,temp);
 110
 111                 if (printPerm){
 112                         copy(temp.begin(), temp.end(), ostream_iterator<int>(cout, " "));
 113                         cout << endl;
 114                 }
 115         }
 116         cout << "Avg score: " << score / al.size() << endl;
 117
 118         return EXIT_SUCCESS;
 119 }