Add new feature element in Featurer, remove KMER6

@@ -10,10 +10,10 @@
 #include "data/data_basic.h"
 
 namespace feature{
-	class Feature : public data::Data_basic{
-		protected:
+class Feature : public data::Data_basic{
+protected:
 	virtual void init(const Data_basic *db);
-		public:
+public:
 	static const std::string TYPE;
 	static const std::string ENTRY_TYPE;
 
@@ -29,15 +29,15 @@ namespace feature{
 	}
 	virtual data::Data_basic *clone()=0;
 	std::string getEntry_name() const;
-	};
+};
 
-	class SeqLength: public feature::Feature{
-		protected:
+class SeqLength: public feature::Feature{
+protected:
 	int l;
 
 	void init(const Data_basic *db);
 
-		public:
+public:
 	static const std::string TYPE;
 	static const std::string ENTRY_TYPE;
 
@@ -58,16 +58,16 @@ namespace feature{
 	std::string getID(){
 		return this->TYPE;
 	}
-	};
+};
 
-	class Kmer: public feature::Feature{
-		protected:
+class Kmer: public feature::Feature{
+protected:
 	unsigned int k;
 	std::unordered_map<std::string,float> kmer;
 
 	void init(const Data_basic *db);
 
-		public:
+public:
 	static const std::string TYPE;
 	static const std::string ENTRY_TYPE;
 
@@ -90,22 +90,27 @@ namespace feature{
 	std::string getID(){
 		return this->TYPE;
 	}
-	};
+};
 
-	class ORF: public feature::Feature{
-		protected:
+class ORF: public feature::Feature{
+protected:
 	static const std::vector<std::string> START;
 	static const std::vector<std::string> END;
 	static bool in_start(const std::string &c);
 	static bool in_end(const std::string &c);
 	unsigned int length;
 	float coverage;
+	float start_mean;
+	float start_std;
+	float end_mean;
+	float end_std;
+
 	/*
 			float start_center, start_std;
 			float end_center, end_std;
 			*/
 	void init(const Data_basic *db);
-		public:
+public:
 	static const std::string TYPE;
 	static const std::string ENTRY_TYPE;
 
@@ -134,26 +139,30 @@ namespace feature{
 	float getEnd_std() const;
 	unsigned int getMax_length() const;
 	unsigned int getLength() const;
-	};
+};
 
-	class CodonPosition: public feature::Feature{
-		protected:
-			float position[4];
+class CodonBiases: public feature::Feature{
+protected:
+	float position[4] = {0,0,0,0};
+	float composition[4] = {0,0,0,0};
 	void init(const Data_basic *db);
-		public:
+public:
 	static const std::string TYPE;
 	static const std::string ENTRY_TYPE;
 
 	static callable::Callable<data::Data_basic*,data::Data_basic*> *get_callable();
 
-			~CodonPosition(){}
-			CodonPosition(const entry::Sequence &s);
-			CodonPosition(const std::string &name,
-										const float (&position)[4]):
+	~CodonBiases();
+	CodonBiases(const entry::Sequence &s);
+	CodonBiases(
+			const std::string &name,
+			const float (&position)[4],
+			const float (&composition)[4]):
 		feature::Feature(name){
 			std::copy(std::begin(position),std::end(position),std::begin(this->position));
+			std::copy(std::begin(composition),std::end(composition),std::begin(this->composition));
 													}
-			CodonPosition(const data::Data_basic *db):feature::Feature(db){this->init(db);}
+	CodonBiases(const data::Data_basic *db):feature::Feature(db){this->init(db);}
 
 	const float *getPosition();
 
@@ -164,7 +173,7 @@ namespace feature{
 	std::string getID(){
 		return this->TYPE;
 	}
-	};
+};
 }
 
 #endif // FEATURE_H

@@ -57,10 +57,10 @@ int main(int argc, char* argv[])
 	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(output+"KMER6.txt");
-	ds["KMER6"] = 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(output+"KMER6.txt");
+//	ds["KMER6"] = tmp_ds;
+//	create_feature_maker(kmer,feature::Kmer::TYPE+std::to_string(6),tmp_ds,&re);
 
 	/* *********** ORF *********************/
 	/* ORF callable */
@@ -70,12 +70,12 @@ int main(int argc, char* argv[])
 	ds["ORF"] = tmp_ds;
 	create_feature_maker(orf,feature::ORF::TYPE,tmp_ds,&re);
 
-	/* *********** Codon Position ***************/
+	/* *********** Codon Biases ***************/
 
-	feature::Feature_callable *cp = static_cast<feature::Feature_callable*>(feature::CodonPosition::get_callable());
-	tmp_ds = new data::Data_Store_Map(output+"CP.txt");
-	ds["CP"] = tmp_ds;
-	create_feature_maker(cp,feature::CodonPosition::TYPE,tmp_ds,&re);
+	feature::Feature_callable *cb = static_cast<feature::Feature_callable*>(feature::CodonBiases::get_callable());
+	tmp_ds = new data::Data_Store_Map(output+"CB.txt");
+	ds["CB"] = tmp_ds;
+	create_feature_maker(cb,feature::CodonBiases::TYPE,tmp_ds,&re);
 
 	/* *********** Fasta reader *************/