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[mothur.git] / cluster.hpp

diff --git a/cluster.hpp b/cluster.hpp
new file mode 100644 (file)
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+++ b/cluster.hpp
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+#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