X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=cluster.hpp;h=aa517a057400e09cdca593f4db1e2559dca74972;hb=edd8b9d9392a99e0b1527507de3a4ca8fabfc1c6;hp=208ccbfe1ba45ba70d152ba4c5ff12b50182d4dc;hpb=bfbc55964f1977da72c2cea984288a427d370a59;p=mothur.git

diff --git a/cluster.hpp b/cluster.hpp
index 208ccbf..aa517a0 100644
--- a/cluster.hpp
+++ b/cluster.hpp
@@ -1,29 +1,34 @@
 #ifndef CLUSTER_H
 #define CLUSTER_H
 
-using namespace std;
 
 #include "mothur.h"
-#include "utilities.hpp"
 #include "sparsematrix.hpp"
-#include "rabundvector.hpp"
+#include "mothurout.h"
 
 class RAbundVector;
 class ListVector;
-class SparseMatrix;
 
-typedef list<PCell>::iterator MatData;
+typedef vector<MatData> MatVec;
 
 class Cluster {
 	
 public:
-	Cluster(RAbundVector*, ListVector*, SparseMatrix*);
-	virtual void update() = 0;
-	
+	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();
+    void removeCell(const MatData& cell, int vrow, int vcol, bool rmMatrix=true);
+
+	virtual bool updateDistance(MatData& colCell, MatData& rowCell) = 0;
+
 	virtual void clusterBins();
 	virtual void clusterNames();
+	virtual void updateMap();
 	
 	RAbundVector* rabund;
 	ListVector* list;
@@ -32,18 +37,26 @@ protected:
 	int smallRow;
 	int smallCol;
 	float smallDist;
-	vector<MatData> rowCells;
-	vector<MatData> colCells;
+	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*);
-	void update();
+	CompleteLinkage(RAbundVector*, ListVector*, SparseMatrix*, float, string);
+	bool updateDistance(MatData& colCell, MatData& rowCell);
+	string getTag();
 	
 private:
 		
@@ -53,8 +66,10 @@ private:
 
 class SingleLinkage : public Cluster {
 public:
-	SingleLinkage(RAbundVector*, ListVector*, SparseMatrix*);
-	void update();
+	SingleLinkage(RAbundVector*, ListVector*, SparseMatrix*, float, string);
+    void update();
+	bool updateDistance(MatData& colCell, MatData& rowCell);
+	string getTag();
 	
 private:
 		
@@ -64,11 +79,30 @@ private:
 
 class AverageLinkage : public Cluster {
 public:
-	AverageLinkage(RAbundVector*, ListVector*, SparseMatrix*);
-	void update();
+	AverageLinkage(RAbundVector*, ListVector*, SparseMatrix*, float, string);
+	bool updateDistance(MatData& colCell, MatData& rowCell);
+	string getTag();
 	
 private:
-		
+	int saveRow;
+	int saveCol;
+	int rowBin;
+	int colBin;
+	int totalBin;
+
+};
+
+/***********************************************************************/
+
+class WeightedLinkage : public Cluster {
+public:
+	WeightedLinkage(RAbundVector*, ListVector*, SparseMatrix*, float, string);
+	bool updateDistance(MatData& colCell, MatData& rowCell);
+	string getTag();
+	
+private:
+	int saveRow;
+	int saveCol;	
 };
 
 /***********************************************************************/