X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=averagelinkage.cpp;fp=averagelinkage.cpp;h=1ab5160f07720f2330c7a627654e8ed264098e54;hb=20a2d0350a737a434c89f303662d64a8eeea7b05;hp=0000000000000000000000000000000000000000;hpb=bbb5879a7e566935c23d63d42bb945072424b939;p=mothur.git

diff --git a/averagelinkage.cpp b/averagelinkage.cpp
new file mode 100644
index 0000000..1ab5160
--- /dev/null
+++ b/averagelinkage.cpp
@@ -0,0 +1,78 @@
+
+#include "cluster.hpp"
+#include "rabundvector.hpp"
+#include "sparsematrix.hpp"
+#include <exception>
+
+/* This class implements the average UPGMA, average neighbor clustering algorithm */
+
+/***********************************************************************/
+
+AverageLinkage::AverageLinkage(RAbundVector* rav, ListVector* lv, SparseMatrix* dm) :
+Cluster(rav, lv, dm)
+{}
+
+/***********************************************************************/
+//THis function clusters based on the average method
+void AverageLinkage::update(){
+	try{
+		getRowColCells();		
+	
+		vector<int> found(nColCells, 0);
+	
+		int rowBin = rabund->get(smallRow);
+		int colBin = rabund->get(smallCol);
+		int totalBin = rowBin + colBin;
+	
+		for(int i=1;i<nRowCells;i++){
+		
+			int search;
+		
+			if(rowCells[i]->row == smallRow){
+				search = rowCells[i]->column;
+			}
+			else{
+				search = rowCells[i]->row;
+			}
+		
+			for(int j=1;j<nColCells;j++){
+			
+				if(colCells[j]->row == search || colCells[j]->column == search){
+					colCells[j]->dist = (colBin * colCells[j]->dist + rowBin * rowCells[i]->dist) / totalBin;		
+				
+					found[j] = 1;
+				
+					if(colCells[j]->vectorMap != NULL){
+						*(colCells[j]->vectorMap) = NULL;
+						colCells[j]->vectorMap = NULL;
+					}
+				
+					break;
+				}
+			
+			}			
+			dMatrix->rmCell(rowCells[i]);
+		}	
+	
+		clusterBins();
+		clusterNames();
+	
+		for(int i=0;i<nColCells;i++){
+			if(found[i] == 0){
+				dMatrix->rmCell(colCells[i]);
+			}
+		}
+	}
+	catch(exception& e) {
+		cout << "Standard Error: " << e.what() << " has occurred in the AverageLinkage class Function update. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		exit(1);
+	}
+	catch(...) {
+		cout << "An unknown error has occurred in the AverageLinkage class function update. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		exit(1);
+	}
+
+	
+}
+
+/***********************************************************************/