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

[mothur.git] / cluster.hpp

diff --git a/cluster.hpp b/cluster.hpp
deleted file mode 100644 (file)
index d7c2737..0000000
--- a/cluster.hpp
+++ /dev/null
@@ -1,110 +0,0 @@
-#ifndef CLUSTER_H
-#define CLUSTER_H
-
-
-#include "mothur.h"
-#include "sparsematrix.hpp"
-#include "mothurout.h"
-
-class RAbundVector;
-class ListVector;
-
-typedef vector<MatData> MatVec;
-
-class Cluster {
-       
-public:
-       Cluster(RAbundVector*, ListVector*, SparseMatrix*, float, string);
-    virtual void update(double&);                              
-       virtual string getTag() = 0;
-       virtual void setMapWanted(bool m);  
-       virtual map<string, int> getSeqtoBin()  {  return seq2Bin;      }
-
-protected:     
-       void getRowColCells();
-    void removeCell(const MatData& cell, int vrow, int vcol, bool rmMatrix=true);
-
-       virtual bool updateDistance(MatData& colCell, MatData& rowCell) = 0;
-
-       virtual void clusterBins();
-       virtual void clusterNames();
-       virtual void updateMap();
-       
-       RAbundVector* rabund;
-       ListVector* list;
-       SparseMatrix* dMatrix;  
-       
-       int smallRow;
-       int smallCol;
-       float smallDist;
-       bool mapWanted;
-       float cutoff;
-       map<string, int> seq2Bin;
-       string method;
-       
-       vector<MatVec> seqVec;          // contains vectors of cells related to a certain sequence
-       MatVec rowCells;
-       MatVec colCells;
-       ull nRowCells;
-       ull nColCells;
-       MothurOut* m;
-};
-
-/***********************************************************************/
-
-class CompleteLinkage : public Cluster {
-public:
-       CompleteLinkage(RAbundVector*, ListVector*, SparseMatrix*, float, string);
-       bool updateDistance(MatData& colCell, MatData& rowCell);
-       string getTag();
-       
-private:
-               
-};
-
-/***********************************************************************/
-
-class SingleLinkage : public Cluster {
-public:
-       SingleLinkage(RAbundVector*, ListVector*, SparseMatrix*, float, string);
-    void update(double&);
-       bool updateDistance(MatData& colCell, MatData& rowCell);
-       string getTag();
-       
-private:
-               
-};
-
-/***********************************************************************/
-
-class AverageLinkage : public Cluster {
-public:
-       AverageLinkage(RAbundVector*, ListVector*, SparseMatrix*, float, string);
-       bool updateDistance(MatData& colCell, MatData& rowCell);
-       string getTag();
-       
-private:
-       int saveRow;
-       int saveCol;
-       int rowBin;
-       int colBin;
-       int totalBin;
-
-};
-
-/***********************************************************************/
-
-class WeightedLinkage : public Cluster {
-public:
-       WeightedLinkage(RAbundVector*, ListVector*, SparseMatrix*, float, string);
-       bool updateDistance(MatData& colCell, MatData& rowCell);
-       string getTag();
-       
-private:
-       int saveRow;
-       int saveCol;    
-};
-
-/***********************************************************************/
-
-#endif