averagelinkage.cpp

   1 #ifndef AVERAGE_H
   2 #define AVERAGE_H
   3
   4
   5 #include "mothur.h"
   6 #include "cluster.hpp"
   7 #include "rabundvector.hpp"
   8 #include "sparsematrix.hpp"
   9
  10 /* This class implements the average UPGMA, average neighbor clustering algorithm */
  11
  12 /***********************************************************************/
  13
  14 AverageLinkage::AverageLinkage(RAbundVector* rav, ListVector* lv, SparseMatrix* dm, float c) :
  15         Cluster(rav, lv, dm, c)
  16 {
  17         saveRow = -1;
  18         saveCol = -1;
  19 }
  20
  21
  22 /***********************************************************************/
  23 //This function returns the tag of the method.
  24 string AverageLinkage::getTag() {
  25         return("an");
  26 }
  27
  28
  29 /***********************************************************************/
  30 //This function updates the distance based on the average linkage method.
  31 bool AverageLinkage::updateDistance(MatData& colCell, MatData& rowCell) {
  32         try {
  33                 if ((saveRow != smallRow) || (saveCol != smallCol)) {
  34                         rowBin = rabund->get(smallRow);
  35                         colBin = rabund->get(smallCol);
  36                         totalBin = rowBin + colBin;
  37                         saveRow = smallRow;
  38                         saveCol = smallCol;
  39                 }
  40
  41                 float oldColCell = colCell->dist;
  42
  43                 colCell->dist = (colBin * colCell->dist + rowBin * rowCell->dist) / totalBin;
  44
  45                 //warn user if merge with value above cutoff produces a value below cutoff
  46                 if ((colCell->dist < cutoff) && ((oldColCell > cutoff) || (rowCell->dist > cutoff)) ) {
  47                         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();
  48                 }
  49
  50                 return(true);
  51         }
  52         catch(exception& e) {
  53                 errorOut(e, "AverageLinkage", "updateDistance");
  54                 exit(1);
  55         }
  56 }
  57
  58 /***********************************************************************/
  59
  60
  61 /***********************************************************************/
  62
  63 #endif