X-Git-Url: https://ruin.nu/git/?a=blobdiff_plain;f=src%2Fmain.cpp;h=abd520f43a29f7a3ec9b4cb7cb8f893895f16cbc;hb=69cfdf79b7597ee6133dc3add1a759bc94861fa6;hp=b6194297d7e5f0d6290e64a09cca4dbf76d528a2;hpb=e778c16651be27559e0c5a5157dd10d0f5a20242;p=germs.git

diff --git a/src/main.cpp b/src/main.cpp
index b619429..abd520f 100644
--- 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] == '-'){
@@ -52,36 +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;
-		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;
 }