X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=cluster.hpp;h=23a3d97f26db6087adcf1dee3c015e581e06321c;hp=208ccbfe1ba45ba70d152ba4c5ff12b50182d4dc;hb=615301e57c25e241356a9c2380648d117709458d;hpb=bfbc55964f1977da72c2cea984288a427d370a59

diff --git a/cluster.hpp b/cluster.hpp
index 208ccbf..23a3d97 100644
--- a/cluster.hpp
+++ b/cluster.hpp
@@ -1,76 +1,106 @@
 #ifndef CLUSTER_H
 #define CLUSTER_H
 
-using namespace std;
+//test change
 
 #include "mothur.h"
-#include "utilities.hpp"
-#include "sparsematrix.hpp"
-#include "rabundvector.hpp"
+#include "sparsedistancematrix.h"
+#include "mothurout.h"
 
 class RAbundVector;
 class ListVector;
-class SparseMatrix;
-
-typedef list<PCell>::iterator MatData;
 
 class Cluster {
 	
 public:
-	Cluster(RAbundVector*, ListVector*, SparseMatrix*);
-	virtual void update() = 0;
-	
-protected:	
-	void getRowColCells();
+	Cluster(RAbundVector*, ListVector*, SparseDistanceMatrix*, float, string, float);
+    virtual ~Cluster() {}
+    virtual void 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;
-	SparseMatrix* dMatrix;	
+	SparseDistanceMatrix* dMatrix;	
+	
+	ull smallRow;
+	ull smallCol;
+	float smallDist, adjust;
+	bool mapWanted;
+	float cutoff;
+	map<string, int> seq2Bin;
+	string method;
 	
-	int smallRow;
-	int smallCol;
-	float smallDist;
-	vector<MatData> rowCells;
-	vector<MatData> colCells;
 	ull nRowCells;
 	ull nColCells;
+	MothurOut* m;
 };
 
 /***********************************************************************/
 
 class CompleteLinkage : public Cluster {
 public:
-	CompleteLinkage(RAbundVector*, ListVector*, SparseMatrix*);
-	void update();
+	CompleteLinkage(RAbundVector*, ListVector*, SparseDistanceMatrix*, float, string, float);
+	bool updateDistance(PDistCell& colCell, PDistCell& rowCell);
+	string getTag();
 	
 private:
-		
+    
 };
 
 /***********************************************************************/
 
 class SingleLinkage : public Cluster {
 public:
-	SingleLinkage(RAbundVector*, ListVector*, SparseMatrix*);
-	void update();
+	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*, SparseMatrix*);
-	void update();
+	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