X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=sharedrabundvector.h;h=664718518e276c7c84984f5c1fe76c9b3bf46523;hp=8f4227eebe0c21823a6f25d22ed3e29dbee79ab3;hb=541bab1dac00688b4c3a8c4a95ab464412663c50;hpb=4ba6188707e67c638ea5ee3c787d5d07ccd07e3e

diff --git a/sharedrabundvector.h b/sharedrabundvector.h
index 8f4227e..6647185 100644
--- a/sharedrabundvector.h
+++ b/sharedrabundvector.h
@@ -13,16 +13,17 @@
 #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 SharedRAbundVector : public DataVector {
 	
@@ -39,6 +40,8 @@ public:
 	int getMaxRank();
 	string getGroup();
 	void setGroup(string);
+	string getBinLabel();
+	void setBinLabel(string);
 	int getGroupIndex();
 	void setGroupIndex(int);								
 
@@ -47,6 +50,7 @@ public:
 	individual get(int);
 	vector <individual> getData();
 	int getAbundance(int);
+    vector<int> getAbundances();
 	int numNZ();
 	void sortD();  //Sorts the data in descending order.
 	void push_front(int, int, string); //abundance, otu, groupname
@@ -55,10 +59,12 @@ public:
 	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*>&);
 };