X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=listvector.hpp;h=b2bc511cfd258da992f9f1b8a44971f4dd29e3e2;hb=250e3b11b1c9c1e1ad458ab6c7e71ac2e67e11d9;hp=dbd61cd0d8f10cba4ea87b4075bbec673f36b19b;hpb=20a2d0350a737a434c89f303662d64a8eeea7b05;p=mothur.git

diff --git a/listvector.hpp b/listvector.hpp
index dbd61cd..b2bc511 100644
--- a/listvector.hpp
+++ b/listvector.hpp
@@ -2,12 +2,16 @@
 #define LIST_H
 
 #include "datavector.hpp"
-#include "groupmap.h"
-#include "globaldata.hpp"
-#include "sharedordervector.h"
-#include <iostream>
-#include <map>
 
+/*	DataStructure for a list file.
+	This class is a child to datavector.  It represents OTU information at a certain distance. 
+	A list vector can be converted into and ordervector, rabundvector or sabundvector.
+	Each member of the internal container "data" represents an individual OTU.
+	So data[0] = "a,b,c,d,e,f".
+	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 ListVector : public DataVector {
 	
@@ -16,7 +20,7 @@ public:
 	ListVector(int);
 //	ListVector(const ListVector&);
 	ListVector(string, vector<string>);
-	ListVector(const ListVector& lv) : DataVector(lv.label), data(lv.data), maxRank(lv.maxRank), numBins(lv.numBins), numSeqs(lv.numSeqs){};
+	ListVector(const ListVector& lv) : DataVector(lv.label), data(lv.data), maxRank(lv.maxRank), numBins(lv.numBins), numSeqs(lv.numSeqs), binLabels(lv.binLabels) {};
 	ListVector(ifstream&);
 	~ListVector(){};
 	
@@ -26,24 +30,25 @@ public:
 
 	void set(int, string);	
 	string get(int);
+    vector<string> getLabels();
+    void setLabels(vector<string>);
 	void push_back(string);
 	void resize(int);
 	void clear();
 	int size();
 	void print(ostream&);
+    void printHeaders(ostream&);
 	
 	RAbundVector getRAbundVector();
 	SAbundVector getSAbundVector();
 	OrderVector getOrderVector(map<string,int>*);
-	SharedOrderVector* getSharedOrderVector();
 	
 private:
-	vector<string> data;
-	GlobalData* globaldata;
-	GroupMap* groupmap;
+	vector<string> data;  //data[i] is a list of names of sequences in the ith OTU.
 	int maxRank;
 	int numBins;
 	int numSeqs;
+    vector<string> binLabels;
 
 };