X-Git-Url: https://ruin.nu/git/?a=blobdiff_plain;f=src%2Fmain.cpp;h=abd520f43a29f7a3ec9b4cb7cb8f893895f16cbc;hb=HEAD;hp=5e6a5c99902915cd28e344b4d63eecec0ed8f375;hpb=5f37e9f08f736f4fe4576dd530c60ecb87017907;p=germs.git

diff --git a/src/main.cpp b/src/main.cpp
index 5e6a5c9..abd520f 100644
--- a/src/main.cpp
+++ b/src/main.cpp
@@ -2,35 +2,120 @@
 #include <vector>
 #include <queue>
 #include <iterator>
+#include <fstream>
+
 using namespace std;
 
+#include <unistd.h>
+
 #include "geneorder.h"
 #include "modelidentifier.h"
 #include "genesorter.h"
 #include "sortaction.h"
+#include "genealgorithms.h"
+#include "model.h"
 
-typedef pair<ModelIdentifier::Model,double> modelpair;
+int main(int argc, char** argv){
 
-int main(){
+	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, "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"
+					<< endl;
+				exit(EXIT_SUCCESS);
+				break;
+			default: /* '?' */
+				cerr << "Usage:  " << argv[0] << " [-n <ann>] [-h] [FILE]" << endl;
+				exit(EXIT_FAILURE);
+		}
+	}
 
-	//TODO: Parse
+	//Open file, or stdin
+	istream* in;
+	ifstream file;
+	if (optind == argc || *argv[optind] == '-'){
+		in = &cin;
+	}else{
+		file.open(argv[optind]);
+		if (file.fail()){
+			cerr << "Could not open file: '" << argv[optind] << "'" << endl;
+			exit(EXIT_FAILURE);
+		}
+		in = &file;
+	}
+
+	//Parse the gene order permutation
 	vector<Gene> g;
-	copy(istream_iterator<int>(cin), istream_iterator<int>(),
-		     back_inserter(g));   
+	copy(istream_iterator<int>(*in), istream_iterator<int>(),
+	     back_inserter(g));
 	GeneOrder go(g.begin(),g.end());
 
-	//TODO: Identify
-	ModelIdentifier mi("default.ann");
-	map<ModelIdentifier::Model,double> scores = mi.identify(go);
-	for (map<ModelIdentifier::Model,double>::iterator m = scores.begin();
-			m != scores.end(); ++m){
-		cout << "Model: " << m->first << " score: " << m->second << endl;
+	//Identify the model
+	ModelIdentifier mi(ann);
+	priority_queue<pair<double,Model> > pq = mi.identify(go);
+	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;
 
-	//TODO: Chose a sorter
+	cout << "Distance: " << inversionDistance(go) << endl;
+	//copy(go.begin(), go.end(), ostream_iterator<int>(cout, " "));
+	//cout << endl;
+
+	if (onlyIdentify){
+		return EXIT_SUCCESS;
+	}
+	//Sort
 	GeneSorter so;
-	//TODO: Sort
-	GeneSorter::ActionList al = so.sort(go);
-	//TODO: Print result
-	return 0;
+	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,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;
+
+	return EXIT_SUCCESS;
 }