X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=cluster.hpp;h=d7c2737a05ed1a0198be9713aa4345f288ec3976;hb=2ecee16fec29d4c525f740ec19b27962ca09c050;hp=a6024e79d45a52274040a53cca4f8b32d9d2e998;hpb=c82900be3ceed3d9bc491bdc98b1819ef85c1af7;p=mothur.git

diff --git a/cluster.hpp b/cluster.hpp
index a6024e7..d7c2737 100644
--- a/cluster.hpp
+++ b/cluster.hpp
@@ -4,6 +4,7 @@
 
 #include "mothur.h"
 #include "sparsematrix.hpp"
+#include "mothurout.h"
 
 class RAbundVector;
 class ListVector;
@@ -13,8 +14,8 @@ typedef vector<MatData> MatVec;
 class Cluster {
 	
 public:
-	Cluster(RAbundVector*, ListVector*, SparseMatrix*);
-    virtual void update();				
+	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;	}
@@ -37,20 +38,23 @@ protected:
 	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*);
+	CompleteLinkage(RAbundVector*, ListVector*, SparseMatrix*, float, string);
 	bool updateDistance(MatData& colCell, MatData& rowCell);
 	string getTag();
 	
@@ -62,8 +66,8 @@ private:
 
 class SingleLinkage : public Cluster {
 public:
-	SingleLinkage(RAbundVector*, ListVector*, SparseMatrix*);
-    void update();
+	SingleLinkage(RAbundVector*, ListVector*, SparseMatrix*, float, string);
+    void update(double&);
 	bool updateDistance(MatData& colCell, MatData& rowCell);
 	string getTag();
 	
@@ -75,7 +79,7 @@ private:
 
 class AverageLinkage : public Cluster {
 public:
-	AverageLinkage(RAbundVector*, ListVector*, SparseMatrix*);
+	AverageLinkage(RAbundVector*, ListVector*, SparseMatrix*, float, string);
 	bool updateDistance(MatData& colCell, MatData& rowCell);
 	string getTag();
 	
@@ -90,4 +94,17 @@ private:
 
 /***********************************************************************/
 
+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