X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=sharedrabundvector.h;h=664718518e276c7c84984f5c1fe76c9b3bf46523;hp=6f8d630c4fdfe490e9a32912089608bb7892482c;hb=a8e2df1b96a57f5f29576b08361b86a96a8eff4f;hpb=20a2d0350a737a434c89f303662d64a8eeea7b05

diff --git a/sharedrabundvector.h b/sharedrabundvector.h
index 6f8d630..6647185 100644
--- a/sharedrabundvector.h
+++ b/sharedrabundvector.h
@@ -1,8 +1,8 @@
-#ifndef SHAREDVECTOR_H
-#define SHAREDVECTOR_H
+#ifndef SHAREDRABUNDVECTOR_H
+#define SHAREDRABUNDVECTOR_H
 
 /*
- *  sharedvector.h
+ *  sharedrabundvector.h
  *  Dotur
  *
  *  Created by Sarah Westcott on 12/5/08.
@@ -10,11 +10,19 @@
  *
  */
 
-#include <Carbon/Carbon.h>
 #include "datavector.hpp"
 #include "sharedordervector.h"
+#include "sharedsabundvector.h"
+#include "sharedrabundfloatvector.h"
+#include "rabundvector.hpp"
+//#include "groupmap.h"
 
-
+/*  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 {
@@ -23,39 +31,63 @@ 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);	
+	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);
+    vector<int> getAbundances();
+	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&);
 		
-	SharedRAbundVector getSharedRAbundVector();
+	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*>&);
 };