Initial revision

[mothur.git] / cluster.hpp

diff --git a/cluster.hpp b/cluster.hpp
new file mode 100644 (file)
index 0000000..a673027
--- /dev/null
+++ b/cluster.hpp
@@ -0,0 +1,78 @@
+#ifndef CLUSTER_H
+#define CLUSTER_H
+
+using namespace std;
+
+#include <iostream>
+#include <list>
+
+#include "utilities.hpp"
+#include "sparsematrix.hpp"
+#include "rabundvector.hpp"
+
+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();
+       virtual void clusterBins();
+       virtual void clusterNames();
+       
+       RAbundVector* rabund;
+       ListVector* list;
+       SparseMatrix* dMatrix;  
+       
+       int smallRow;
+       int smallCol;
+       float smallDist;
+       vector<MatData> rowCells;
+       vector<MatData> colCells;
+       ull nRowCells;
+       ull nColCells;
+};
+
+/***********************************************************************/
+
+class CompleteLinkage : public Cluster {
+public:
+       CompleteLinkage(RAbundVector*, ListVector*, SparseMatrix*);
+       void update();
+       
+private:
+               
+};
+
+/***********************************************************************/
+
+class SingleLinkage : public Cluster {
+public:
+       SingleLinkage(RAbundVector*, ListVector*, SparseMatrix*);
+       void update();
+       
+private:
+               
+};
+
+/***********************************************************************/
+
+class AverageLinkage : public Cluster {
+public:
+       AverageLinkage(RAbundVector*, ListVector*, SparseMatrix*);
+       void update();
+       
+private:
+               
+};
+
+/***********************************************************************/
+
+#endif