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) :
  15 Cluster(rav, lv, dm)
  16 {}
  17
  18 /***********************************************************************/
  19 //THis function clusters based on the average method
  20 void AverageLinkage::update(){
  21         try{
  22                 getRowColCells();
  23
  24                 vector<int> found(nColCells, 0);
  25
  26                 int rowBin = rabund->get(smallRow);
  27                 int colBin = rabund->get(smallCol);
  28                 int totalBin = rowBin + colBin;
  29
  30                 for(int i=1;i<nRowCells;i++){
  31
  32                         int search;
  33
  34                         if(rowCells[i]->row == smallRow){
  35                                 search = rowCells[i]->column;
  36                         }
  37                         else{
  38                                 search = rowCells[i]->row;
  39                         }
  40
  41                         for(int j=1;j<nColCells;j++){
  42
  43                                 if(colCells[j]->row == search || colCells[j]->column == search){
  44                                         colCells[j]->dist = (colBin * colCells[j]->dist + rowBin * rowCells[i]->dist) / totalBin;
  45
  46                                         found[j] = 1;
  47
  48                                         if(colCells[j]->vectorMap != NULL){
  49                                                 *(colCells[j]->vectorMap) = NULL;
  50                                                 colCells[j]->vectorMap = NULL;
  51                                         }
  52
  53                                         break;
  54                                 }
  55
  56                         }
  57                         dMatrix->rmCell(rowCells[i]);
  58                 }
  59
  60                 clusterBins();
  61                 clusterNames();
  62
  63                 for(int i=0;i<nColCells;i++){
  64                         if(found[i] == 0){
  65                                 dMatrix->rmCell(colCells[i]);
  66                         }
  67                 }
  68         }
  69         catch(exception& e) {
  70                 cout << "Standard Error: " << e.what() << " has occurred in the AverageLinkage class Function update. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  71                 exit(1);
  72         }
  73         catch(...) {
  74                 cout << "An unknown error has occurred in the AverageLinkage class function update. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  75                 exit(1);
  76         }
  77
  78
  79 }
  80
  81 /***********************************************************************/
  82
  83 #endif
  84
  85