X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=sabundvector.hpp;h=666e94f4db598b9bf1589bf8288fed75e221bdc3;hb=372fb21ea66ced432b109225851a1b80ef0491a3;hp=f45ef609515321a74b9bbf98d7f7b4fcbdb9512d;hpb=20a2d0350a737a434c89f303662d64a8eeea7b05;p=mothur.git

diff --git a/sabundvector.hpp b/sabundvector.hpp
index f45ef60..666e94f 100644
--- a/sabundvector.hpp
+++ b/sabundvector.hpp
@@ -1,11 +1,22 @@
 #ifndef SABUND_H
 #define SABUND_H
 
-using namespace std;
-
 #include "datavector.hpp"
 #include "rabundvector.hpp"
 #include "ordervector.hpp"
+#include "calculator.h"
+
+
+/*  Data Structure for a sabund file.
+    This class is a child to datavector.  It represents OTU information at a certain distance. 
+	A sabundvector can be converted into and ordervector, listvector or rabundvector.
+	Each member of the internal container "data" represents the number of OTU's with that many members, but staring at 1.
+	So data[1] = 2, because there are two OTUs with 1 member.
+	example: listvector		=	a,b,c,d,e,f		g,h,i		j,k		l		m  
+			 rabundvector	=	6				3			2		1		1
+			 sabundvector	=	2		1		1		0		0		1
+			 ordervector	=	1	1	1	1	1	1	2	2	2	3	3	4	5 */
+
 
 class SAbundVector : public DataVector {
 	
@@ -13,6 +24,7 @@ public:
 	SAbundVector();
 	SAbundVector(int);
 //	SAbundVector(const SAbundVector&);
+	SAbundVector(vector<int>, int, int, int);
 	SAbundVector(string, vector<int>);
 	SAbundVector(const SAbundVector& rv) : DataVector(rv.label), data(rv.data), maxRank(rv.maxRank), numBins(rv.numBins), numSeqs(rv.numSeqs){};
 	SAbundVector(ifstream&);
@@ -25,13 +37,16 @@ public:
 	void set(int, int);
 	int get(int);
 	void push_back(int);
+	void quicksort();
+	int sum();
 	void resize(int);
 	int size();
+	void clear();
 
 	void print(ostream&);
 	void print(string, ostream&);
 		
-	RAbundVector getRAbundVector();	
+	RAbundVector getRAbundVector();		
 	SAbundVector getSAbundVector();
 	OrderVector getOrderVector(map<string,int>*);
 	
@@ -39,6 +54,7 @@ private:
 	vector<int> data;
 //	bool needToUpdate;
 //	void updateStats();
+	
 	int maxRank;
 	int numBins;
 	int numSeqs;