X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=averagelinkage.cpp;h=8627253777c1b09a1b4b16d1ff2ad4f90468248c;hp=db2c51edc5b182b52dcf540456baad7b5782c61e;hb=d1c97b8c04bb75faca1e76ffad60b37a4d789d3d;hpb=832d53a9dfac6b1795735eec643d8cf627b0d8e3

diff --git a/averagelinkage.cpp b/averagelinkage.cpp
index db2c51e..8627253 100644
--- a/averagelinkage.cpp
+++ b/averagelinkage.cpp
@@ -1,18 +1,18 @@
 #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, float c) :
-	Cluster(rav, lv, dm, c)
+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;
@@ -28,7 +28,7 @@ string AverageLinkage::getTag() {
 
 /***********************************************************************/
 //This function updates the distance based on the average linkage method.
-bool AverageLinkage::updateDistance(MatData& colCell, MatData& rowCell) {
+bool AverageLinkage::updateDistance(PDistCell& colCell, PDistCell& rowCell) {
 	try {
 		if ((saveRow != smallRow) || (saveCol != smallCol)) {
 			rowBin = rabund->get(smallRow);
@@ -37,20 +37,13 @@ bool AverageLinkage::updateDistance(MatData& colCell, MatData& rowCell) {
 			saveRow = smallRow;
 			saveCol = smallCol;
 		}
-		
-		float oldColCell = colCell->dist;
-		
-		colCell->dist = (colBin * colCell->dist + rowBin * rowCell->dist) / totalBin;
-		
-		//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();
-		}
-
+		//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) {
-		errorOut(e, "AverageLinkage", "updateDistance");
+		m->errorOut(e, "AverageLinkage", "updateDistance");
 		exit(1);
 	}
 }