X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=averagelinkage.cpp;h=8627253777c1b09a1b4b16d1ff2ad4f90468248c;hp=54f380353c6d97f018218c74e7667b3df1f89637;hb=d1c97b8c04bb75faca1e76ffad60b37a4d789d3d;hpb=c5c7502f435e1413c19e373dab1dfebcaa67588d

diff --git a/averagelinkage.cpp b/averagelinkage.cpp
index 54f3803..8627253 100644
--- a/averagelinkage.cpp
+++ b/averagelinkage.cpp
@@ -1,85 +1,56 @@
 #ifndef AVERAGE_H
 #define AVERAGE_H
 
-
+//test
 #include "mothur.h"
 #include "cluster.hpp"
 #include "rabundvector.hpp"
-#include "sparsematrix.hpp"
+#include "sparsedistancematrix.h"
 
 /* This class implements the average UPGMA, average neighbor clustering algorithm */
 
 /***********************************************************************/
 
-AverageLinkage::AverageLinkage(RAbundVector* rav, ListVector* lv, SparseMatrix* dm) :
-Cluster(rav, lv, dm)
-{}
+AverageLinkage::AverageLinkage(RAbundVector* rav, ListVector* lv, SparseDistanceMatrix* dm, float c, string s, float a) :
+Cluster(rav, lv, dm, c, s, a)
+{
+	saveRow = -1;
+	saveCol = -1;
+}
+
+
+/***********************************************************************/
+//This function returns the tag of the method.
+string AverageLinkage::getTag() {
+	return("an");
+}
+
 
 /***********************************************************************/
-//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]);
-			}
+//This function updates the distance based on the average linkage method.
+bool AverageLinkage::updateDistance(PDistCell& colCell, PDistCell& rowCell) {
+	try {
+		if ((saveRow != smallRow) || (saveCol != smallCol)) {
+			rowBin = rabund->get(smallRow);
+			colBin = rabund->get(smallCol);
+			totalBin = rowBin + colBin;
+			saveRow = smallRow;
+			saveCol = smallCol;
 		}
+		//cout << "colcell.dist = " << colCell.dist << '\t' << smallRow << '\t' << smallCol << '\t' << rowCell.dist << endl;
+		colCell.dist = (colBin * colCell.dist + rowBin * rowCell.dist) / totalBin;
+        
+		return(true);
 	}
 	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";
+		m->errorOut(e, "AverageLinkage", "updateDistance");
 		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);
-	}
-
-	
 }
 
 /***********************************************************************/
 
-#endif
 
+/***********************************************************************/
 
+#endif