added weightedlinkage.cpp

[mothur.git] / weightedlinkage.cpp

diff --git a/weightedlinkage.cpp b/weightedlinkage.cpp
new file mode 100644 (file)
index 0000000..0851bd7
--- /dev/null
+++ b/weightedlinkage.cpp
@@ -0,0 +1,56 @@
+#ifndef WEIGHTEDLINKAGE_H
+#define WEIGHTEDLINKAGE_H
+
+
+#include "mothur.h"
+#include "cluster.hpp"
+#include "rabundvector.hpp"
+#include "sparsematrix.hpp"
+
+/* This class implements the WPGMA, weighted average neighbor clustering algorithm */
+
+/***********************************************************************/
+
+WeightedLinkage::WeightedLinkage(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 WeightedLinkage::getTag() {
+       return("wn");
+}
+
+
+/***********************************************************************/
+//This function updates the distance based on the average linkage method.
+bool WeightedLinkage::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 = (colCell->dist + rowCell->dist) / 2.0;
+               
+               return(true);
+       }
+       catch(exception& e) {
+               m->errorOut(e, "WeightedLinkage", "updateDistance");
+               exit(1);
+       }
+}
+
+/***********************************************************************/
+
+
+/***********************************************************************/
+
+#endif