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[mothur.git] / sabundvector.hpp

diff --git a/sabundvector.hpp b/sabundvector.hpp
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+#ifndef SABUND_H
+#define SABUND_H
+
+#include "datavector.hpp"
+#include "rabundvector.hpp"
+#include "ordervector.hpp"
+#include "calculator.h"
+
+
+/*  Data Structure for a sabund file.
+    This class is a child to datavector.  It represents OTU information at a certain distance. 
+       A sabundvector can be converted into and ordervector, listvector or rabundvector.
+       Each member of the internal container "data" represents the number of OTU's with that many members, but staring at 1.
+       So data[1] = 2, because there are two OTUs with 1 member.
+       example: listvector             =       a,b,c,d,e,f             g,h,i           j,k             l               m  
+                        rabundvector   =       6                               3                       2               1               1
+                        sabundvector   =       2               1               1               0               0               1
+                        ordervector    =       1       1       1       1       1       1       2       2       2       3       3       4       5 */
+
+
+class SAbundVector : public DataVector {
+       
+public:
+       SAbundVector();
+       SAbundVector(int);
+//     SAbundVector(const SAbundVector&);
+       SAbundVector(vector<int>, int, int, int);
+       SAbundVector(string, vector<int>);
+       SAbundVector(const SAbundVector& rv) : DataVector(rv.label), data(rv.data), maxRank(rv.maxRank), numBins(rv.numBins), numSeqs(rv.numSeqs){};
+       SAbundVector(ifstream&);
+       ~SAbundVector(){};
+
+       int getNumBins();       
+       int getNumSeqs();       
+       int getMaxRank();       
+       
+       void set(int, int);
+       int get(int);
+       void push_back(int);
+       void quicksort();
+       int sum();
+       void resize(int);
+       int size();
+       void clear();
+
+       void print(ostream&);
+       void print(string, ostream&);
+               
+       RAbundVector getRAbundVector();         
+       SAbundVector getSAbundVector();
+       OrderVector getOrderVector(map<string,int>*);
+       
+private:
+       vector<int> data;
+//     bool needToUpdate;
+//     void updateStats();
+       
+       int maxRank;
+       int numBins;
+       int numSeqs;
+
+};
+
+#endif