More help output

[germs.git] / src / main.cpp

diff --git a/src/main.cpp b/src/main.cpp
index 94109b4e4cce83e47329ce482186e44b740722f7..abd520f43a29f7a3ec9b4cb7cb8f893895f16cbc 100644 (file)
--- a/src/main.cpp
+++ b/src/main.cpp
@@ -18,16 +18,34 @@ using namespace std;
 int main(int argc, char** argv){
 
        string ann = "default.ann";
+       Model model(0);
+       bool detectModel = true;
+       bool onlyIdentify = false;
+       bool printPerm = false;
 
+       //Parse command line arguments
        int opt;
-       while ((opt = getopt(argc, argv, "n:h")) != -1) {
+       while ((opt = getopt(argc, argv, "im:n:hp")) != -1) {
                switch (opt) {
+                       case 'm':
+                               model = Model::modelFactory(optarg);
+                               detectModel = false;
+                               break;
                        case 'n':
                                ann = optarg;
                                break;
+                       case 'i':
+                               onlyIdentify = true;
+                               break;
+                       case 'p':
+                               printPerm = true;
+                               break;
                        case 'h':
                                cout << "Usage: " << argv[0] << " [OPTION] [FILE]" << endl
+                                       << endl << "  -m <model> Specifies which model to use for sorting: Whirl, X, Zipper, FatX or Cloud "
                                        << endl << "  -n <ann>   Specifies which artificial neural network to use for identification. '" << ann << "' is used by default"
+                                       << endl << "  -i         Only identify the model, don't try to sort it"
+                                       << endl << "  -p         Print the resulting permutation at each sorting step"
                                        << endl << "  -h         Prints this help message"
                                        << endl << endl
                                        << "With no FILE, or if FILE is '-', stdin will be used"
@@ -40,6 +58,7 @@ int main(int argc, char** argv){
                }
        }
 
+       //Open file, or stdin
        istream* in;
        ifstream file;
        if (optind == argc || *argv[optind] == '-'){
@@ -52,33 +71,51 @@ int main(int argc, char** argv){
                }
                in = &file;
        }
-       //TODO: Parse
+
+       //Parse the gene order permutation
        vector<Gene> g;
        copy(istream_iterator<int>(*in), istream_iterator<int>(),
-                    back_inserter(g));   
+            back_inserter(g));
        GeneOrder go(g.begin(),g.end());
 
-       //TODO: Identify
+       //Identify the model
        ModelIdentifier mi(ann);
        priority_queue<pair<double,Model> > pq = mi.identify(go);
-       Model model = pq.top().second;
-       //while (pq.size() > 0){
-       cout << "Model: " << model.name() << " score: " << pq.top().first << endl;
-               //pq.pop();
-       //}
+       if (detectModel){
+               model = pq.top().second;
+       }
+       while (pq.size() > 0){
+               cout << "Model: " << pq.top().second.name() << " score: " << pq.top().first << endl;
+               pq.pop();
+       }
+       cout << "Using model: " << model.name() << endl;
 
-       cout << "Distance: " << inversionDistance(go) << " : ";
-       copy(go.begin(), go.end(), ostream_iterator<int>(cout, " "));
-       cout << endl;
+       cout << "Distance: " << inversionDistance(go) << endl;
+       //copy(go.begin(), go.end(), ostream_iterator<int>(cout, " "));
+       //cout << endl;
 
-       //TODO: Chose a sorter
+       if (onlyIdentify){
+               return EXIT_SUCCESS;
+       }
+       //Sort
        GeneSorter so;
-       //TODO: Sort
        GeneSorter::ActionList al = so.sort(go,model);
 
+       //Print the result
+       double score = 0;
+
+       GeneOrder temp(go);
        for (GeneSorter::ActionList::iterator sa = al.begin(); sa != al.end(); ++sa){
-               cout << "Action: " << sa->toString() << " model score: " << model.score(*sa,go) << endl;
+               cout << "Action: " << sa->toString() << " model score: " << model.score(*sa,temp) << endl;
+               (*sa)(temp);
+               score += model.score(*sa,temp);
+
+               if (printPerm){
+                       copy(temp.begin(), temp.end(), ostream_iterator<int>(cout, " "));
+                       cout << endl;
+               }
        }
-       //TODO: Print result
+       cout << "Avg score: " << score / al.size() << endl;
+
        return EXIT_SUCCESS;
 }