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[mothur.git] / sharedsabundvector.h

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+#ifndef SHAREDSABUND_H
+#define SHAREDSABUND_H
+
+
+/*
+ *  sharedSharedSAbundVector.h
+ *  Dotur
+ *
+ *  Created by Sarah Westcott on 12/10/08.
+ *  Copyright 2008 Schloss Lab UMASS Amherst. All rights reserved.
+ *
+ */
+
+#include "datavector.hpp"
+#include "rabundvector.hpp"
+#include "ordervector.hpp"
+#include "sharedordervector.h"
+#include "sharedrabundvector.h"
+
+/* This class is a child to datavector.  It represents OTU information at a certain distance. 
+       It is similiar to an sabundvector 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 SharedSAbundVector : public DataVector {
+       
+public:
+       SharedSAbundVector();
+       SharedSAbundVector(int);
+       SharedSAbundVector(const SharedSAbundVector& rv) : DataVector(rv.label), data(rv.data), maxRank(rv.maxRank), numBins(rv.numBins), numSeqs(rv.numSeqs){};
+       ~SharedSAbundVector(){};
+
+       int getNumBins();       
+       int getNumSeqs();       
+       int getMaxRank();       
+       string getGroup();
+       void setGroup(string);  
+       
+       void set(int, int, string);      //OTU, abundance, group
+       individual get(int);
+       int getAbundance(int);
+       void push_back(int, int, string);       //abundance, OTU, group
+       void pop_back();
+       void resize(int);
+       int size();
+       void clear();
+
+       void print(ostream&);
+               
+       RAbundVector getRAbundVector(); 
+       SAbundVector getSAbundVector();
+       OrderVector getOrderVector(map<string,int>*);
+       SharedSAbundVector getSharedSAbundVector();
+       SharedRAbundVector getSharedRAbundVector();
+       SharedOrderVector getSharedOrderVector();
+       
+private:
+       vector<individual> data;
+       
+       int maxRank;
+       int numBins;
+       int numSeqs;
+       string group;
+};
+
+#endif
+