X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=averagelinkage.cpp;fp=averagelinkage.cpp;h=c430c883f66d6006cc9bf01a2a964dd62957688f;hb=0caf3fbabaa3ece404f8ce77f4c883dc5b1bf1dc;hp=0000000000000000000000000000000000000000;hpb=1b73ff67c83892a025e597dabd9df6fe7b58206a;p=mothur.git

diff --git a/averagelinkage.cpp b/averagelinkage.cpp
new file mode 100644
index 0000000..c430c88
--- /dev/null
+++ b/averagelinkage.cpp
@@ -0,0 +1,56 @@
+#ifndef AVERAGE_H
+#define AVERAGE_H
+
+//test
+#include "mothur.h"
+#include "cluster.hpp"
+#include "rabundvector.hpp"
+#include "sparsematrix.hpp"
+
+/* This class implements the average UPGMA, average neighbor clustering algorithm */
+
+/***********************************************************************/
+
+AverageLinkage::AverageLinkage(RAbundVector* rav, ListVector* lv, SparseMatrix* dm, float c, string s) :
+	Cluster(rav, lv, dm, c, s)
+{
+	saveRow = -1;
+	saveCol = -1;
+}
+
+
+/***********************************************************************/
+//This function returns the tag of the method.
+string AverageLinkage::getTag() {
+	return("an");
+}
+
+
+/***********************************************************************/
+//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;
+		}
+		
+		colCell->dist = (colBin * colCell->dist + rowBin * rowCell->dist) / totalBin;
+		
+		return(true);
+	}
+	catch(exception& e) {
+		m->errorOut(e, "AverageLinkage", "updateDistance");
+		exit(1);
+	}
+}
+
+/***********************************************************************/
+
+
+/***********************************************************************/
+
+#endif