fixing printout

README

@@ -49,6 +49,8 @@ Usage: bin/meshclust2 --id 0.x [OPTIONS] *.fasta
 --threads sets the number of threads to be used. By default OpenMP uses the number of available cores
 	  on your machine, but this parameter overwrites that.
 
+--quiet  (no arguments) removes the progress bars from output
+
 --output specifies the output file, in CD-HIT's CLSTR format, described below:
 	 A '>Cluster ' followed by an increasing index designates a cluster.
 	 Otherwise, the sequence is printed out.

src/cluster/src/Predictor.cpp

@@ -356,14 +356,16 @@ void Predictor<T>::train(const vector<Point<T> *> &points, const vector<Point<T>
 		size_t counter = 0;
 		// struct timespec start, stop;
 		// clock_gettime(CLOCK_MONOTONIC, &start);
+		Progress prog(f_points_tr.size(), "Generating training data");
 		#pragma omp parallel for
 		for (size_t i = 0; i < f_points_tr.size(); i++) {
 			auto p = f_points_tr[i];
 			mutate_seqs(p, 5, pos_buf, neg_buf, 100 * id, 100, _id);
 			mutate_seqs(p, 5, pos_buf, neg_buf, min_id, 100 * id, _id);
 			#pragma omp critical
-			cout << "Generated " << ++counter << " / " << f_points_tr.size() << endl;
+			prog++;
 		}
+		prog.end();
 		// clock_gettime(CLOCK_MONOTONIC, &stop);
 		// printf("took %lu\n", stop.tv_sec - start.tv_sec);
 
@@ -387,14 +389,16 @@ void Predictor<T>::train(const vector<Point<T> *> &points, const vector<Point<T>
 		}
 		pos_buf.clear();
 		neg_buf.clear();
+		Progress prog2(f_points_test.size(), "Generating test data");
 		#pragma omp parallel for
 		for (size_t i = 0; i < f_points_test.size(); i++) {
 			auto p = f_points_test[i];
 			mutate_seqs(p, 5, pos_buf, neg_buf, 100 * id, 100, _id);
 			mutate_seqs(p, 5, pos_buf, neg_buf, min_id, 100 * id, _id);
 #pragma omp critical
-			cout << "Generated " << ++counter << " / " << f_points_test.size() << endl;
+			prog2++;
 		}
+		prog2.end();
 		buf_size = std::min(pos_buf.size(), neg_buf.size());
 		cout << "testing +: " << pos_buf.size() << endl;
 		cout << "testing -: " << neg_buf.size() << endl;
@@ -739,7 +743,7 @@ void Predictor<T>::train_class(Feature<T>* feat)
 			feat->finalize();
 			abs_best_acc = best_class_acc;
 			used_list.push_back(best_idx);
-			oss << "Feature added: " << best_class_feat.first << " " << (int)best_class_feat.second << endl;
+//			oss << "Feature added: " << best_class_feat.first << " " << (int)best_class_feat.second << endl;
 			oss << "Accuracy: " << best_class_acc << endl;
 			possible_feats.erase(std::remove(possible_feats.begin(), possible_feats.end(), best_class_feat), possible_feats.end());
 		}

src/cluster/src/Progress.cpp

@@ -2,6 +2,12 @@
 #include <iostream>
 #include <sstream>
 
+bool Progress::is_quiet = false;
+
+void Progress::set_quiet(bool is_quiet_)
+{
+	is_quiet = is_quiet_;
+}
 Progress::Progress(long num, std::string prefix_)
 {
 	pmax = num;
@@ -15,6 +21,9 @@ Progress::Progress(long num, std::string prefix_)
 
 void Progress::print()
 {
+	if (is_quiet) {
+		return;
+	}
 	std::ostringstream oss;
 	double prog = (double)pcur / pmax;
 	oss << prefix << " [";

src/cluster/src/Progress.h

@@ -10,6 +10,8 @@
 
 class Progress {
 public:
+	static void set_quiet(bool is_quiet_=true);
+	static bool is_quiet;
 	Progress(long num, std::string prefix_);
 	~Progress() { end(); }
 	void end();

src/cluster/src/Runner.cpp

@@ -222,6 +222,8 @@ void Runner::get_opts(int argc, char **argv)
 			}
 
 			i++;
+		} else if (arg == "-q" || arg == "--quiet") {
+			Progress::set_quiet(true);
 		} else if ((arg == "-t" || arg == "--threads") && i + 1 < argc) {
 			try {
 				std::string opt = argv[i+1];

src/cluster/src/Trainer.cpp

@@ -596,7 +596,6 @@ void Trainer<T>::train(int min_n_feat, int max_n_feat, uint64_t feat_type, int m
 {
 
 	if (k != 0) {
-		std::cout << "Splitting data" << endl;
 		uintmax_t _id = points.size();
 		Predictor<T> pred(k, cutoff, PRED_MODE_CLASS, feat_type,
 				  mut_type, min_n_feat, max_n_feat, min_id);