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#ifndef CLUSTER_H
#define CLUSTER_H
#include "sparsedistancematrix.h"
#include "optimatrix.h"
#include "mothurout.h"
#include "rabundvector.hpp"
#include "listvector.hpp"
class ListVector;
class Cluster {
public:
Cluster(RAbundVector*, ListVector*, SparseDistanceMatrix*, float, string, float);
Cluster() { m = MothurOut::getInstance(); }
virtual ~Cluster() = default;
virtual bool update(double&);
virtual string getTag() = 0;
virtual void setMapWanted(bool m);
virtual map<string, int> getSeqtoBin() { return seq2Bin; }
protected:
virtual bool updateDistance(PDistCell& colCell, PDistCell& rowCell) = 0;
virtual void clusterBins();
virtual void clusterNames();
virtual void updateMap();
RAbundVector* rabund;
ListVector* list;
SparseDistanceMatrix* dMatrix;
ull smallRow, smallCol, nRowCells, nColCells;
float smallDist, adjust, cutoff;
bool mapWanted;
map<string, int> seq2Bin;
string method;
MothurOut* m;
Utils util;
};
/***********************************************************************/
class CompleteLinkage : public Cluster {
public:
CompleteLinkage(RAbundVector*, ListVector*, SparseDistanceMatrix*, float, string, float);
bool updateDistance(PDistCell& colCell, PDistCell& rowCell);
string getTag();
private:
};
/***********************************************************************/
class SingleLinkage : public Cluster {
public:
SingleLinkage(RAbundVector*, ListVector*, SparseDistanceMatrix*, float, string, float);
//void update(double&);
bool updateDistance(PDistCell& colCell, PDistCell& rowCell);
string getTag();
private:
};
/***********************************************************************/
class AverageLinkage : public Cluster {
public:
AverageLinkage(RAbundVector*, ListVector*, SparseDistanceMatrix*, float, string, float);
bool updateDistance(PDistCell& colCell, PDistCell& rowCell);
string getTag();
private:
int saveRow;
int saveCol;
int rowBin;
int colBin;
int totalBin;
};
/***********************************************************************/
class WeightedLinkage : public Cluster {
public:
WeightedLinkage(RAbundVector*, ListVector*, SparseDistanceMatrix*, float, string, float);
bool updateDistance(PDistCell& colCell, PDistCell& rowCell);
string getTag();
private:
int saveRow;
int saveCol;
};
/***********************************************************************/
#endif
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