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[mothur.git] / clusterclassic.h

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+#ifndef CLUSTER_H
+#define CLUSTER_H
+
+
+#include "mothur.h"
+#include "mothurout.h"
+#include "listvector.hpp"
+#include "rabundvector.hpp"
+#include "nameassignment.hpp"
+
+/*
+ *  clusterclassic.h
+ *  Mothur
+ *
+ *  Created by westcott on 10/29/10.
+ *  Copyright 2010 Schloss Lab. All rights reserved.
+ *
+ */
+
+
+class ClusterClassic {
+       
+public:
+       ClusterClassic(float, string, bool);
+       int readPhylipFile(string, NameAssignment*);
+       void update(double&);
+       double getSmallDist() { return smallDist; }     
+       int getNSeqs() { return nseqs; }        
+       ListVector* getListVector() { return list; }
+       RAbundVector* getRAbundVector() { return rabund; }              
+       string getTag();
+       void setMapWanted(bool m);  
+       map<string, int> getSeqtoBin()  {  return seq2Bin;      }
+
+private:       
+       double getSmallCell();
+       void clusterBins();
+       void clusterNames();
+       void updateMap();
+       void print();
+       
+       struct colDist {
+               int col;
+               int row;
+               double dist;
+               colDist(int r, int c, double d) : row(r), col(c), dist(d) {}
+       };
+       
+       RAbundVector* rabund;
+       ListVector* list;
+       vector< vector<double> > dMatrix;       
+       //vector<colDist> rowSmallDists;
+       
+       int smallRow;
+       int smallCol, nseqs;
+       double smallDist;
+       bool mapWanted, sim;
+       double cutoff, aboveCutoff;
+       map<string, int> seq2Bin;
+       string method;
+       
+       MothurOut* m;
+};
+
+#endif
+
+