X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=averagelinkage.cpp;h=db2c51edc5b182b52dcf540456baad7b5782c61e;hb=832d53a9dfac6b1795735eec643d8cf627b0d8e3;hp=ec619cae3a5e373d7cd482c4bc25667e552a6687;hpb=bfbc55964f1977da72c2cea984288a427d370a59;p=mothur.git

diff --git a/averagelinkage.cpp b/averagelinkage.cpp
index ec619ca..db2c51e 100644
--- a/averagelinkage.cpp
+++ b/averagelinkage.cpp
@@ -1,84 +1,63 @@
 #ifndef AVERAGE_H
 #define AVERAGE_H
 
+
+#include "mothur.h"
 #include "cluster.hpp"
 #include "rabundvector.hpp"
 #include "sparsematrix.hpp"
-#include "mothur.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, SparseMatrix* dm, float c) :
+	Cluster(rav, lv, dm, c)
+{
+	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++){
+//This function updates the distance based on the average linkage method.
+bool AverageLinkage::updateDistance(MatData& colCell, MatData& rowCell) {
+	try {
+		if ((saveRow != smallRow) || (saveCol != smallCol)) {
+			rowBin = rabund->get(smallRow);
+			colBin = rabund->get(smallCol);
+			totalBin = rowBin + colBin;
+			saveRow = smallRow;
+			saveCol = smallCol;
+		}
 		
-			int search;
+		float oldColCell = colCell->dist;
 		
-			if(rowCells[i]->row == smallRow){
-				search = rowCells[i]->column;
-			}
-			else{
-				search = rowCells[i]->row;
-			}
+		colCell->dist = (colBin * colCell->dist + rowBin * rowCell->dist) / totalBin;
 		
-			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]);
-			}
+		//warn user if merge with value above cutoff produces a value below cutoff
+		if ((colCell->dist < cutoff) && ((oldColCell > cutoff) || (rowCell->dist > cutoff)) ) {
+			mothurOut("Warning: merging " + toString(oldColCell) + " with " + toString(rowCell->dist) + ", new value = " + toString(colCell->dist) + ". Results will differ from those if cutoff was used in the read.dist command."); mothurOutEndLine();
 		}
+
+		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";
-		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";
+		errorOut(e, "AverageLinkage", "updateDistance");
 		exit(1);
 	}
-
-	
 }
 
 /***********************************************************************/
 
-#endif
 
+/***********************************************************************/
 
+#endif