Improve performance of Featurer

@@ -3,6 +3,8 @@
 
 #include <string>
 #include <sstream>
+#include <iostream>
+#include <fstream>
 
 #include "../multithread/buffer_producer.h"
 #include "data_basic.h"
@@ -12,38 +14,60 @@ namespace data{
 	class Data_Store {
 		protected:
 			int size=0;
+			bool write_on_add;
+			std::string file_name;
+			std::ofstream output;
+			virtual void add_internal(data::Data_basic *data)=0;
 		public:
-			virtual ~Data_Store(){}
+			Data_Store():write_on_add(false){}
+			Data_Store(std::string file_name):
+				write_on_add(true),
+				file_name(file_name)
+			{
+				this->output.open(this->file_name,std::ios::trunc);
+			}
+
+			virtual ~Data_Store(){
+				this->output.close();
+			}
+
 			int getSize(){return this->size;}
-			virtual void add(data::Data_basic *data)=0;
-			virtual multithread::Buffer<data::Data_basic*>* get(std::string pattern)=0;
-			void write(std::string file_name, std::string pattern){
-				multithread::Buffer<data::Data_basic*> *buf;
-				std::string towrite;
-				std::ofstream output;
-				output.open(file_name, std::ios::out | std::ios::trunc);
-				buf = this->get(pattern);
-				int count_buf(0);
-				while(buf->available()){
-					if(!buf->isEmpty()){
-						data::Data_basic* tmp = buf->pop();
-						towrite += tmp->to_csv()+"\n";
-						count_buf ++;
-						delete tmp;
-					}else{
-						std::this_thread::sleep_for(THREAD_SLEEP);
-					}
-					if(count_buf == NB_ELT_BUF){
-						output << towrite;
-						towrite.clear();
-						count_buf=0;
-					}
-				}
-				if(count_buf>0){
-					output << towrite;
+
+			void add(data::Data_basic *data){
+				this->add_internal(data);
+				if(this->write_on_add){
+					std::string tmp = data->to_csv();
+					this->output << tmp << std::endl;
 				}
-				output.close();
 			}
+			virtual multithread::Buffer<data::Data_basic*>* get(std::string pattern)=0;
+//			void write(std::string file_name, std::string pattern){
+//				multithread::Buffer<data::Data_basic*> *buf;
+//				std::string towrite;
+//				std::ofstream output;
+//				output.open(file_name, std::ios::out | std::ios::trunc);
+//				buf = this->get(pattern);
+//				int count_buf(0);
+//				while(buf->available()){
+//					if(!buf->isEmpty()){
+//						data::Data_basic* tmp = buf->pop();
+//						towrite += tmp->to_csv()+"\n";
+//						count_buf ++;
+//						delete tmp;
+//					}else{
+//						std::this_thread::sleep_for(THREAD_SLEEP);
+//					}
+//					if(count_buf == NB_ELT_BUF){
+//						output << towrite;
+//						towrite.clear();
+//						count_buf=0;
+//					}
+//				}
+//				if(count_buf>0){
+//					output << towrite;
+//				}
+//				output.close();
+//			}
 	};
 }
 #endif // DATA_STORE_H

@@ -44,19 +44,21 @@ class Producer_map: public multithread::Buffer_producer<data::Data_basic*>{
 		protected:
 			std::unordered_map<std::string,data::Data_basic*> data_map;
 
+			void add_internal(data::Data_basic *data){
+				this->data_map[data->getName()] = data;
+				this->size ++;
+			}
+
 		public:
 			Data_Store_Map(){}
+			Data_Store_Map(std::string file_name):data::Data_Store(file_name){}
 			~Data_Store_Map(){
+				//~data::Data_Store::~Data_Store();
 				for(auto const &kv: this->data_map){
 					delete kv.second;
 				}
 			}
 
-			void add(data::Data_basic *data){
-				this->data_map[data->getName()] = data;
-				this->size ++;
-			}
-
 			multithread::Buffer<data::Data_basic*> *get(std::string pattern){
 				Producer_map *tmp = new Producer_map(&(this->data_map),pattern);
 				tmp->start();

@@ -53,27 +53,30 @@ int main(int argc, char* argv[])
 
 	/* ************** KMER ******************/
 	feature::Feature_callable *kmer = static_cast<feature::Feature_callable*>(feature::Kmer::get_callable(3));
-	tmp_ds = new data::Data_Store_Map();
-	ds["KMER"+std::to_string(3)] = tmp_ds;
+//	tmp_ds = new data::Data_Store_Map();
+	tmp_ds = new data::Data_Store_Map(output+"KMER3.txt");
+	ds["KMER3"] = tmp_ds;
 	create_feature_maker(kmer,feature::Kmer::TYPE+std::to_string(6),tmp_ds,&re);
 	
 	kmer = static_cast<feature::Feature_callable*>(feature::Kmer::get_callable(6));
-	tmp_ds = new data::Data_Store_Map();
-	ds["KMER"+std::to_string(6)] = tmp_ds;
+	tmp_ds = new data::Data_Store_Map(output+"KMER6.txt");
+	ds["KMER6"] = tmp_ds;
 	create_feature_maker(kmer,feature::Kmer::TYPE+std::to_string(6),tmp_ds,&re);
 
 	/* *********** ORF *********************/
 	/* ORF callable */
 
 	feature::Feature_callable *orf = static_cast<feature::Feature_callable*>(feature::ORF::get_callable());
-	tmp_ds = new data::Data_Store_Map();
+//	tmp_ds = new data::Data_Store_Map();
+	tmp_ds = new data::Data_Store_Map(output+"ORF.txt");
 	ds["ORF"] = tmp_ds;
 	create_feature_maker(orf,feature::ORF::TYPE,tmp_ds,&re);
 
 	/* *********** Codon Position ***************/
 
 	feature::Feature_callable *cp = static_cast<feature::Feature_callable*>(feature::CodonPosition::get_callable());
-	tmp_ds = new data::Data_Store_Map();
+//	tmp_ds = new data::Data_Store_Map();
+	tmp_ds = new data::Data_Store_Map(output+"CP.txt");
 	ds["CP"] = tmp_ds;
 	create_feature_maker(cp,feature::CodonPosition::TYPE,tmp_ds,&re);
 
@@ -105,8 +108,8 @@ int main(int argc, char* argv[])
 	
 	auto it = ds.begin();
 	while(it != ds.end()){
-		it->second->write(output+it->first+".txt",".*");
-		std::cout << "File " << output+it->first+".txt" << " writted" << std::endl;
+//		it->second->write(output+it->first+".txt",".*");
+//		std::cout << "File " << output+it->first+".txt" << " writted" << std::endl;
 		delete it->second;
 		++it;
 	}