X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=cluster.hpp;h=26a01b9389778fea2e2b1067a1738c75027ad7f2;hp=a6024e79d45a52274040a53cca4f8b32d9d2e998;hb=3ebbdec0f519f2872da722e7cc6531201fdb2952;hpb=c82900be3ceed3d9bc491bdc98b1819ef85c1af7

diff --git a/cluster.hpp b/cluster.hpp
index a6024e7..26a01b9 100644
--- a/cluster.hpp
+++ b/cluster.hpp
@@ -1,82 +1,80 @@
 #ifndef CLUSTER_H
 #define CLUSTER_H
 
+//test change
 
 #include "mothur.h"
-#include "sparsematrix.hpp"
+#include "sparsedistancematrix.h"
+#include "mothurout.h"
 
 class RAbundVector;
 class ListVector;
 
-typedef vector<MatData> MatVec;
-
 class Cluster {
 	
 public:
-	Cluster(RAbundVector*, ListVector*, SparseMatrix*);
-    virtual void update();				
+	Cluster(RAbundVector*, ListVector*, SparseDistanceMatrix*, float, string);
+    virtual ~Cluster() {}
+    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;
-
+    
+protected:	    
+	virtual bool updateDistance(PDistCell& colCell, PDistCell& rowCell) = 0;
+    
 	virtual void clusterBins();
 	virtual void clusterNames();
 	virtual void updateMap();
 	
 	RAbundVector* rabund;
 	ListVector* list;
-	SparseMatrix* dMatrix;	
+	SparseDistanceMatrix* dMatrix;	
 	
-	int smallRow;
-	int smallCol;
+	ull smallRow;
+	ull 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*);
-	bool updateDistance(MatData& colCell, MatData& rowCell);
+	CompleteLinkage(RAbundVector*, ListVector*, SparseDistanceMatrix*, float, string);
+	bool updateDistance(PDistCell& colCell, PDistCell& rowCell);
 	string getTag();
 	
 private:
-		
+    
 };
 
 /***********************************************************************/
 
 class SingleLinkage : public Cluster {
 public:
-	SingleLinkage(RAbundVector*, ListVector*, SparseMatrix*);
-    void update();
-	bool updateDistance(MatData& colCell, MatData& rowCell);
+	SingleLinkage(RAbundVector*, ListVector*, SparseDistanceMatrix*, float, string);
+    void update(double&);
+	bool updateDistance(PDistCell& colCell, PDistCell& rowCell);
 	string getTag();
 	
 private:
-		
+    
 };
 
 /***********************************************************************/
 
 class AverageLinkage : public Cluster {
 public:
-	AverageLinkage(RAbundVector*, ListVector*, SparseMatrix*);
-	bool updateDistance(MatData& colCell, MatData& rowCell);
+	AverageLinkage(RAbundVector*, ListVector*, SparseDistanceMatrix*, float, string);
+	bool updateDistance(PDistCell& colCell, PDistCell& rowCell);
 	string getTag();
 	
 private:
@@ -85,9 +83,24 @@ private:
 	int rowBin;
 	int colBin;
 	int totalBin;
+    
+};
+
+/***********************************************************************/
 
+class WeightedLinkage : public Cluster {
+public:
+	WeightedLinkage(RAbundVector*, ListVector*, SparseDistanceMatrix*, float, string);
+	bool updateDistance(PDistCell& colCell, PDistCell& rowCell);
+	string getTag();
+	
+private:
+	int saveRow;
+	int saveCol;	
 };
 
 /***********************************************************************/
 
+
+
 #endif