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[mothur.git] / ordervector.hpp

diff --git a/ordervector.hpp b/ordervector.hpp
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+#ifndef ORDER_H
+#define ORDER_H
+
+#include "datavector.hpp"
+#include "sabundvector.hpp"
+#include "rabundvector.hpp"
+
+/* This class is a child to datavector.  It represents OTU information at a certain distance. 
+       A order vector can be converted into and listvector, rabundvector or sabundvector.
+       Each member of the internal container "data" represents the OTU from which it came. 
+       So in the example below since there are 6 sequences in OTU 1 there are six 1's in the ordervector.
+       and since there are 2 sequences in OTU 3 there are two 3's in the ordervector.
+       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 OrderVector : public DataVector {
+       
+public:
+       OrderVector();
+//     OrderVector(int);
+//     OrderVector(const OrderVector& ov);
+       OrderVector(int ns, int nb=0, int mr=0) : DataVector(), data(ns, -1), maxRank(0), numBins(0), numSeqs(0) {};
+       OrderVector(const OrderVector& ov)      : DataVector(ov.label), data(ov.data), maxRank(ov.maxRank), numBins(ov.numBins), numSeqs(ov.numSeqs), needToUpdate(ov.needToUpdate) {if(needToUpdate == 1){     updateStats();}};
+
+
+       OrderVector(string, vector<int>);
+       OrderVector(ifstream&);
+       ~OrderVector(){};
+       
+       void set(int, int);
+       int get(int);
+       void push_back(int);
+       void resize(int);
+       int size();
+       void clear();
+       void print(string, ostream&);
+       vector<int>::iterator begin();
+       vector<int>::iterator end();
+
+       void print(ostream&);
+
+       int getNumBins();
+       int getNumSeqs();
+       int getMaxRank();
+               
+       RAbundVector getRAbundVector();
+       SAbundVector getSAbundVector();
+       OrderVector getOrderVector(map<string,int>*);
+       
+private:
+       vector<int> data;
+       int maxRank;
+       int numBins;
+       int numSeqs;
+       bool needToUpdate;
+       void updateStats();
+};
+
+#endif