moved mothur's source into a folder to make grabbing just the source easier on github

[mothur.git] / clusterclassic.h

diff --git a/clusterclassic.h b/clusterclassic.h
deleted file mode 100644 (file)
index 110c040..0000000
--- a/clusterclassic.h
+++ /dev/null
@@ -1,67 +0,0 @@
-#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
-
-