X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=sharedrabundvector.h;h=792543e5abe87e9ac346f98004f33af1c8a39e46;hb=a6cf29fa4dac0909c7582cb1094151d34093ee76;hp=0c71394689e8aad4d522e5f1ba6948466b218f56;hpb=016a30dacbe75869aef5fdb58d2d1bf9eb8f9b33;p=mothur.git

diff --git a/sharedrabundvector.h b/sharedrabundvector.h
index 0c71394..792543e 100644
--- a/sharedrabundvector.h
+++ b/sharedrabundvector.h
@@ -13,16 +13,18 @@
 #include "datavector.hpp"
 #include "sharedordervector.h"
 #include "sharedsabundvector.h"
+#include "sharedrabundfloatvector.h"
 #include "rabundvector.hpp"
-#include "groupmap.h"
+//#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 GlobalData;
+//class GlobalData;
 
 class SharedRAbundVector : public DataVector {
 	
@@ -30,7 +32,7 @@ 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(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();
 
@@ -39,6 +41,8 @@ public:
 	int getMaxRank();
 	string getGroup();
 	void setGroup(string);
+	string getBinLabel();
+	void setBinLabel(string);
 	int getGroupIndex();
 	void setGroupIndex(int);								
 
@@ -51,14 +55,16 @@ public:
 	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, 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();
@@ -68,17 +74,20 @@ public:
 	SharedSAbundVector getSharedSAbundVector();
 	SharedRAbundVector getSharedRAbundVector();
 	vector<SharedRAbundVector*> getSharedRAbundVectors();
+	vector<SharedRAbundFloatVector*> getSharedRAbundFloatVectors(vector<SharedRAbundVector*>);
 	
 private:
 	vector<individual>  data; 
 	vector<SharedRAbundVector*> lookup;
-	GlobalData* globaldata;
-	GroupMap* groupmap;
+	//GlobalData* globaldata;
+	//GroupMap* groupmap;
 	int maxRank;
 	int numBins;
 	int numSeqs;
 	string group;
 	int index;	
+	
+	int eliminateZeroOTUS(vector<SharedRAbundVector*>&);
 };