X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=cluster.hpp;h=d7c2737a05ed1a0198be9713aa4345f288ec3976;hb=2ecee16fec29d4c525f740ec19b27962ca09c050;hp=99d8b7d557a41cef684ad2f9aae7d636d621bbc7;hpb=1b9d0a66e4737f31d16824fe93944880b9edc530;p=mothur.git

diff --git a/cluster.hpp b/cluster.hpp
index 99d8b7d..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;
@@ -13,9 +14,11 @@ 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;	}
 
 protected:	
 	void getRowColCells();
@@ -25,6 +28,7 @@ protected:
 
 	virtual void clusterBins();
 	virtual void clusterNames();
+	virtual void updateMap();
 	
 	RAbundVector* rabund;
 	ListVector* list;
@@ -33,19 +37,24 @@ protected:
 	int smallRow;
 	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
+	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();
 	
@@ -57,8 +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();
 	
@@ -70,7 +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();
 	
@@ -85,4 +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