moved mothur's source into a folder to make grabbing just the source easier on github

[mothur.git] / averagelinkage.cpp

diff --git a/averagelinkage.cpp b/averagelinkage.cpp
deleted file mode 100644 (file)
index c430c88..0000000
--- a/averagelinkage.cpp
+++ /dev/null
@@ -1,56 +0,0 @@
-#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