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[mothur.git] / rabundvector.hpp

diff --git a/rabundvector.hpp b/rabundvector.hpp
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+++ b/rabundvector.hpp
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+#ifndef RABUND_H
+#define RABUND_H
+
+#include "datavector.hpp"
+
+/*  Data Structure for a rabund file.
+    This class is a child to datavector.  It represents OTU information at a certain distance. 
+       A rabundvector can be converted into and ordervector, listvector or sabundvector.
+       Each member of the internal container "data" represents an individual OTU.
+       So data[0] = 6, because there are six member in that OTU.
+       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;
+//class OrderVector;
+
+class RAbundVector : public DataVector {
+       
+public:
+       RAbundVector();
+       RAbundVector(int);
+       RAbundVector(vector<int>, int, int, int);
+//     RAbundVector(const RAbundVector&);
+       RAbundVector(string, vector<int>);
+       RAbundVector(const RAbundVector& bv) : DataVector(bv), data(bv.data), maxRank(bv.maxRank), numBins(bv.numBins), numSeqs(bv.numSeqs){};
+       RAbundVector(ifstream&);
+       ~RAbundVector();
+
+       int getNumBins();               
+       int getNumSeqs();                                                       
+       int getMaxRank();                                                       
+
+       void set(int, int);     
+       int get(int);
+       void push_back(int);
+       void pop_back();
+       void resize(int);
+       int size();
+       void quicksort();
+       int sum();
+       int sum(int);
+       int numNZ();
+       void clear();
+       vector<int>::reverse_iterator rbegin();
+       vector<int>::reverse_iterator rend();
+       
+       void print(ostream&);
+       void print(string, ostream&);
+       void nonSortedPrint(ostream&);
+       
+       RAbundVector getRAbundVector();
+       SAbundVector getSAbundVector();
+       OrderVector getOrderVector(map<string,int>*);
+       
+private:
+       vector<int> data;
+       int maxRank;
+       int numBins;
+       int numSeqs;    
+};
+
+
+#endif