X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=cluster.hpp;h=d7c2737a05ed1a0198be9713aa4345f288ec3976;hb=f06b339c5fc4b6d1b9d2a08fe16bf7670bf7aeb4;hp=685c843c0199b73083f7eb3a17693b33fe1a4d36;hpb=9c23307c583d4e8595f75278c13e708788f2f058;p=mothur.git

diff --git a/cluster.hpp b/cluster.hpp
index 685c843..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;
@@ -13,7 +14,7 @@ typedef vector<MatData> MatVec;
 class Cluster {
 	
 public:
-	Cluster(RAbundVector*, ListVector*, SparseMatrix*, float);
+	Cluster(RAbundVector*, ListVector*, SparseMatrix*, float, string);
     virtual void update(double&);				
 	virtual string getTag() = 0;
 	virtual void setMapWanted(bool m);  
@@ -39,19 +40,21 @@ protected:
 	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);
+	CompleteLinkage(RAbundVector*, ListVector*, SparseMatrix*, float, string);
 	bool updateDistance(MatData& colCell, MatData& rowCell);
 	string getTag();
 	
@@ -63,8 +66,8 @@ private:
 
 class SingleLinkage : public Cluster {
 public:
-	SingleLinkage(RAbundVector*, ListVector*, SparseMatrix*, float);
-    void update();
+	SingleLinkage(RAbundVector*, ListVector*, SparseMatrix*, float, string);
+    void update(double&);
 	bool updateDistance(MatData& colCell, MatData& rowCell);
 	string getTag();
 	
@@ -76,7 +79,7 @@ private:
 
 class AverageLinkage : public Cluster {
 public:
-	AverageLinkage(RAbundVector*, ListVector*, SparseMatrix*, float);
+	AverageLinkage(RAbundVector*, ListVector*, SparseMatrix*, float, string);
 	bool updateDistance(MatData& colCell, MatData& rowCell);
 	string getTag();
 	
@@ -91,4 +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