More help output

[germs.git] / src / main.cpp

diff --git a/src/main.cpp b/src/main.cpp
index d9bce2f37ba2f901c38470a0d0b59ab1f2e323b3..abd520f43a29f7a3ec9b4cb7cb8f893895f16cbc 100644 (file)
--- a/src/main.cpp
+++ b/src/main.cpp
@@ -20,10 +20,12 @@ 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, "m:n:h")) != -1) {
+       while ((opt = getopt(argc, argv, "im:n:hp")) != -1) {
                switch (opt) {
                        case 'm':
                                model = Model::modelFactory(optarg);
@@ -32,10 +34,18 @@ int main(int argc, char** argv){
                        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"
@@ -84,15 +94,26 @@ int main(int argc, char** argv){
        //copy(go.begin(), go.end(), ostream_iterator<int>(cout, " "));
        //cout << endl;
 
+       if (onlyIdentify){
+               return EXIT_SUCCESS;
+       }
        //Sort
        GeneSorter so;
        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;
-               score += model.score(*sa,go);
+               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;
+               }
        }
        cout << "Avg score: " << score / al.size() << endl;