X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=completelinkage.cpp;h=0a3c7b3e42f68347d0315299d5ed050b89ebb796;hp=69b68a061fb0d8ccb7cf58ec8ca27af1e3f11f27;hb=d1c97b8c04bb75faca1e76ffad60b37a4d789d3d;hpb=20a2d0350a737a434c89f303662d64a8eeea7b05

diff --git a/completelinkage.cpp b/completelinkage.cpp
index 69b68a0..0a3c7b3 100644
--- a/completelinkage.cpp
+++ b/completelinkage.cpp
@@ -1,71 +1,34 @@
 
 #include "cluster.hpp"
-#include <exception>
 
 /***********************************************************************/
 
-CompleteLinkage::CompleteLinkage(RAbundVector* rav, ListVector* lv, SparseMatrix* dm) :
-Cluster(rav, lv, dm)
+CompleteLinkage::CompleteLinkage(RAbundVector* rav, ListVector* lv, SparseDistanceMatrix* dm, float c, string s, float a) :
+	Cluster(rav, lv, dm, c, s, a)
 {}
 
 /***********************************************************************/
-//This function clusters based on the furthest neighbor method.
-void CompleteLinkage::update(){
+//This function returns the tag of the method.
+string CompleteLinkage::getTag() {
+	return("fn");
+}
+
+
+/***********************************************************************/
+//This function updates the distance based on the furthest neighbor method.
+bool CompleteLinkage::updateDistance(PDistCell& colCell, PDistCell& rowCell) {
 	try {
-		getRowColCells();	
-	
-		vector<int> found(nColCells, 0);
-	
-		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){
-				
-					if(colCells[j]->dist < rowCells[i]->dist){
-						colCells[j]->dist = rowCells[i]->dist;
-					
-						if(colCells[j]->vectorMap != NULL){
-							*(colCells[j]->vectorMap) = NULL;
-							colCells[j]->vectorMap = NULL;
-						}
-					
-					}
-				
-					found[j] = 1;
-					break;
-				}
-			}
-			dMatrix->rmCell(rowCells[i]);
-		
+		bool changed = false;
+		if (colCell.dist < rowCell.dist) {
+			colCell.dist = rowCell.dist;
+			changed = true;
 		}	
-		clusterBins();
-		clusterNames();
-	
-		for(int i=0;i<nColCells;i++){
-			if(found[i] == 0){
-				dMatrix->rmCell(colCells[i]);
-			}
-		}
+		return(changed);
 	}
 	catch(exception& e) {
-		cout << "Standard Error: " << e.what() << " has occurred in the CompleteLinkage class Function update. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		m->errorOut(e, "CompleteLinkage", "updateDistance");
 		exit(1);
 	}
-	catch(...) {
-		cout << "An unknown error has occurred in the CompleteLinkage class function update. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-		exit(1);
-	}
-
 }
 
 /***********************************************************************/