X-Git-Url: https://ruin.nu/git/?a=blobdiff_plain;f=src%2Fmain.cpp;h=16e7de7768f853eb2de87fde7b7f2923c696d29b;hb=0ced9c229cf05fa677686df27eca9f167f11a87f;hp=2e074957b459fbd72c3b5b2ada38fd7ca96753bb;hpb=5202e2201f0d303478cefb4c365306d146189b45;p=germs.git

diff --git a/src/main.cpp b/src/main.cpp
index 2e07495..16e7de7 100644
--- a/src/main.cpp
+++ b/src/main.cpp
@@ -20,9 +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);
@@ -31,6 +34,12 @@ 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 "
@@ -47,6 +56,7 @@ int main(int argc, char** argv){
 		}
 	}
 
+	//Open file, or stdin
 	istream* in;
 	ifstream file;
 	if (optind == argc || *argv[optind] == '-'){
@@ -59,13 +69,14 @@ 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);
 	if (detectModel){
@@ -81,17 +92,28 @@ int main(int argc, char** argv){
 	//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;
-		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;
-	//TODO: Print result
+
 	return EXIT_SUCCESS;
 }