X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=sharedrabundvector.h;h=419d15a15af7b73872c2678675aff1a4f564c759;hp=b69bc30657a1667665709df1d21653c05d574b3a;hb=1a20e24ee786195ab0e1cccd4f5aede7a88f3f4e;hpb=fd282e6b4be2560f5b1bd154a9e8d24b798eefaf

diff --git a/sharedrabundvector.h b/sharedrabundvector.h
index b69bc30..419d15a 100644
--- a/sharedrabundvector.h
+++ b/sharedrabundvector.h
@@ -10,61 +10,83 @@
  *
  */
 
-#include <Carbon/Carbon.h>
 #include "datavector.hpp"
 #include "sharedordervector.h"
 #include "sharedsabundvector.h"
+#include "sharedrabundfloatvector.h"
 #include "rabundvector.hpp"
+//#include "groupmap.h"
 
-/* This class is a child to datavector.  It represents OTU information at a certain distance. 
+/*  DataStructure for a shared file.
+	This class is a child to datavector.  It represents OTU information at a certain distance. 
 	It is similiar to an rabundvector except each member of data knows which group it belongs to.
 	Each member of the internal container "data" is a struct of type individual. 
 	An individual which knows the OTU from which it came, 
 	the group it is in and its abundance.  */
 
 
-
 class SharedRAbundVector : public DataVector {
 	
 public:
 	SharedRAbundVector();
 	SharedRAbundVector(int);
 	//SharedRAbundVector(string, vector<int>);
-	SharedRAbundVector(const SharedRAbundVector& bv) : DataVector(bv), data(bv.data), maxRank(bv.maxRank), numBins(bv.numBins), numSeqs(bv.numSeqs){};
-//	SharedRAbundVector(ifstream&);
+	SharedRAbundVector(const SharedRAbundVector& bv) : DataVector(bv), data(bv.data), maxRank(bv.maxRank), numBins(bv.numBins), numSeqs(bv.numSeqs), group(bv.group), index(bv.index){};
+    SharedRAbundVector(ifstream&);
 	~SharedRAbundVector();
 
 	int getNumBins();		
 	int getNumSeqs();							
 	int getMaxRank();
 	string getGroup();
-	void setGroup(string);							
+	void setGroup(string);
+	string getBinLabel();
+	void setBinLabel(string);
+	int getGroupIndex();
+	void setGroupIndex(int);								
 
 	void set(int, int, string);			//OTU, abundance, groupname
+	void setData(vector <individual>);
 	individual get(int);
+	vector <individual> getData();
 	int getAbundance(int);
-	void push_back(int, int, string);  //abundance, OTU, groupname
+	int numNZ();
+	void sortD();  //Sorts the data in descending order.
+	void push_front(int, int, string); //abundance, otu, groupname
+	void insert(int, int, string); //abundance, otu, groupname
+	void push_back(int, string);  //abundance, groupname
 	void pop_back();
 	void resize(int);
 	int size();
+	void clear();
 	vector<individual>::reverse_iterator rbegin();
 	vector<individual>::reverse_iterator rend();
 	
 	void print(ostream&);
+	void printHeaders(ostream&);
 		
 	RAbundVector getRAbundVector();
+	RAbundVector getRAbundVector2();
 	SAbundVector getSAbundVector();
 	OrderVector getOrderVector(map<string,int>*);
 	SharedOrderVector getSharedOrderVector();
 	SharedSAbundVector getSharedSAbundVector();
 	SharedRAbundVector getSharedRAbundVector();
+	vector<SharedRAbundVector*> getSharedRAbundVectors();
+	vector<SharedRAbundFloatVector*> getSharedRAbundFloatVectors(vector<SharedRAbundVector*>);
 	
 private:
 	vector<individual>  data; 
+	vector<SharedRAbundVector*> lookup;
+	//GlobalData* globaldata;
+	//GroupMap* groupmap;
 	int maxRank;
 	int numBins;
 	int numSeqs;
-	string group;	
+	string group;
+	int index;	
+	
+	int eliminateZeroOTUS(vector<SharedRAbundVector*>&);
 };